Howard Hershey's Challenge of Sean Pitman's Assumptions
Seanpit
> Here is Sean's description of the calculation of "average gap
> size"
*****
> "Well, first we have to calculate the likely gap size. Using an
> average between the calculations of Yockey and Sauer, the ratio of
> potential beneficial vs. non-beneficial for 100aa systems is about
> 1e-40. This creates a ratio for a 1,000aa system of about
> 1e-40^(1000/100) = 1e-400. So, the average gap size between
> potentially beneficial sequences at this level would be about 308
> residue differences - i.e., 20^308 = 1e400."
*****
> I have often accused Sean of numerology, or essentially of pulling
> numbers out of his arse and claiming that they represent things that
> they, in fact, do not represent. Take a look at the above calculation
> which is the mathematical basis of just about all his sequence
> arguments. You might think, unless you *actually* do some thinking,
> that Sean is performing some hard-nosed mathematical analysis here
> rather than merely manipulating numbers and assigning "scientific-
> sounding" names to them. Thus, unless you actually look at what the
> numbers mean, you might be fooled into thinking that Sean actually is
> calculating "likely gap size" or "average gap size" by doing the above
> mathematical manipulations of numbers, which are assumed to be based
> on hard evidence, and that he is accurately telling us what the
> numbers mean. Nothing could be further from the truth. In fact, I
> think that the first person Sean 'fooled' by his mathematical
> manipulations was Sean himself. He was fooled because he did not
> actually think about what he was doing and let the fact that the
> numbers he got seemed to "prove his point" cloud his thinking to the
> point that he actually does think that the ratio he calculated was
> "potential beneficial vs. non-beneficial", that there is his
> exponential relationship between length and the above ratio, and that
> he has calculated the "average gap size". Sean probably does think
> that his numerology is a "mathematical proof" of the impossibility of
> evolution.
>
> Let me summarize the problems I see with the above calculation:
>
> 1) The calculations of Yockey and Sauer do NOT give us the ratio of
> "potential beneficial vs. non-benecial" sequences for 100aa systems.
> They give us an estimate of the number of sequences that have
> cytochrome c function and related sequence divided by the total number
> of sequences at 100 aa level.
Yockey's estimate is in fact dealing specifically with CytoC
functionality. I've noted this several times on my website myself.
Sauer and Olsen are dealing with lambda repressor functionality, not
CytoC. What these and other similar estimates indicate is that a
certain degree of required sequence specificity produces a certain
ratio of sequences in sequence space that could produce some useful
degree of functionality of the type in question.
Obviously, this doesn't tell us how many potentially beneficial
sequences of all kinds exist in 100aa sequence space. But, what it
does do is illustrate a pattern of an exponentially declining ratio of
beneficial vs. non-beneficial with increasing size and/or specificity
requirements. In order to avoid this exponential increase, one would
have to hypothesize that the number of different potentially
beneficial sequences/structures increases at pretty much the same rate
as the size of sequence/structure space increases with each increase
in minimum structural threshold requirements. That notion simply
isn't tenable to anyone who approaches this problem with a remotely
candid mind. It isn't true in any language/information system that we
know of and it isn't true for genetically based information systems
either.
That's the point. There is a clear pattern of exponentially
increasing non-beneficial sequences relative to each increase in
potentially beneficial sequences with each increase in minimum
structural threshold requirements. This point should be so obvious as
to be beyond argument.
> Mathematically, if we call the
> estimated number of sequences that have cytochrome c function C, and T
> is the totality of sequence space for 100 aa long peptides, then the
> equation that Sean is claiming represents as "potential beneficial vs.
> non-beneficial" ratio is actually C/T. T can be mathematically
> estimated as 20^le, where le is the length of the sequence, since
> there are 20 possible amino acids at each position. Converting to
> base 10, this would be 10^le^log20. Log 20 is about 1.3. So the
> ratio, R(100), of what Sean calls "potential beneficial vs. non-
> beneficial" sequences is really the equation:
>
> R(le) = C/10^le^1.3 = 10^40 when le = 100.
>
> Moreover, this relationship (the ratio of sequences with cytochrome c
> function and sequence to all possible 100 aa long sequences) has ONLY
> been determined (well, estimated) for the case where le = 100.
That's because 100aa is fairly close to the minimum structural
threshold requirement needed for CytoC. You can't produce a
beneficial degree of CytoC functionality with just 50aa - no matter
how they are arranged relative to each other.
> 2) Problems with calling the numerator "potential beneficial
> sequences". It should, in fact, be obvious to anyone that C, the
> number of sequences that have cytochrome c-like function and sequence,
> is NOT all possible "potential beneficial sequences". I think even
> Sean sees that.
Of course it's not. But, statistically, this point is pretty much
irrelevant to the main issue. Again, given that one is looking for
targets that require a minimum of at least 100aa with an equivalent
degree of specificity as that required by CytoC functionality, the
actual ratio of beneficial vs. non-beneficial is not going to be
significantly different from the ratio of CytoC to non-CytoC in
sequence/structure space.
I've tried to explain this concept to you before, but I'll try again.
Either you say that there is absolutely no way to get any idea at all
as to the likely ratio of total targets to non-targets (which removes
the scientific basis for your proposed mechanism by the way) or you
try to use the available evidence to get as best as an idea as you
can.
One approach to determining the most likely number of potentially
beneficial targets at a given threshold level is to consider how many
total novel beneficial systems are in existence today in all living
things at a given level. This number can be roughly known and it is
not more than a trillion for the 100aa level. Even if it was 10
trillion, it wouldn't make any significant difference. The reason for
this is that 10 trillion uniquely different 100aa systems with the
minimum degree of specificity of CytoC would take up no more than 1 in
1e27 sequences in sequence space. That is still a very tiny fraction
of the available space of just over 1e130 sequences. The potential
targets are still vastly outnumbered by non-beneficial sequences.
This ratio only gets exponentially worse with increasing minimums.
Keep the specificity requirement the same and raise the number of
amino acid residues, the ratio drops exponentially. Keep the number
of residues the same and raise the specificity, the ratio drops
exponentially. That's the whole point.
> But is it even *possible* to calculate the number of "potential
> beneficial sequences"? The answer is 'sort of', but only in a squishy
> soft way that allows one to say that "potential beneficial sequences"
> are a heck of a lot more frequent than cytochrome c-like sequences.
There might appear to be a "heck of a lot more" beneficial targets
than CytoC targets - - at first approximation. But, when you compare
this "heck of a lot" to the total size of sequence space, it is a tiny
little spec of dust in the bottom of the bucket. It isn't remotely
close, relative to the vast horde of non-beneficial sequences, to
being a "heck of a lot".
You have to starting thinking in relative terms here.
> First we have the problem that "beneficial" is not an inherent feature
> of a sequence, but a conditional one. Even the cytochrome c sequence
> is not 'beneficial' in every situation or organism (think anaerobes).
> And "potential" is important, since we cannot assume that a sequence
> is useless until or unless we have a context to put it in.
The context is any living thing in any particular environment. Take
your pick. Whatever context you choose will have the same problem.
The ratios are not going to be significantly different regardless of
context. Bringing up the context is therefore irrelevant - a red
herring.
> But, if you understand how proteins actually work to produce
> 'function' in organisms, we can think about this problem in a more
> reasoned way than Sean has (i.e., by not assuming that the number of
> cytochrome c-like sequences is a good stand-in for all "potential
> beneficial sequences"). Proteins 'function' by providing surfaces
> with affinity for biologically relevant structures or parts of
> biologically relevant structures. Enzymes work because proteins bind
> the substrates and products of the reaction less well than the
> stressed intermediate. [Which is also why compounds related to
> substrates or products but with equal or higher affinity for the
> protein surface can be toxins or antibiotics.] Proteins also form
> multimers and complex structures because of the affinity of small
> patches of aa's on each protein for each other. Which biological
> structure an amino acid sequence has affinity for determines its
> 'function'. Moreover, because most biologically relevant structures
> are small, the number of aa's involved in any particular binding
> feature is also small. That is, the 'function' of proteins is a
> consequence of the binding of epitopes by a small number of aa's.
> That, of course, is the reason we can say, for example, that the
> sequence of FliG involved in binding to FliF is a particular small
> stretch of aa's within FliG, not the entire protein. That is, most
> functional proteins have more than one functional surface and, often,
> these surfaces can be modified without affecting the binding
> properties of other parts of the protein. That is, a functional
> protein can typically be thought of as a conglomerate of smaller
> sequences that each has a binding surface. Change in one aa often
> does not radically change the affinities of other parts of the protein
> (or even the one it is involved in).
Again, this is completely irrelevant to the fact that different types
of systems have different minimum structural threshold requirements.
This is true of all language/information systems. For example, it is
true of the English language that a change of most single characters,
taken one at a time, will most likely not completely destroy the
particular intended functionality or meaning of the paragraph
completely.
The same thing is true of biosystems. However, there is a limit
beyond which change or removal of characters will completely destroy
the functionality in question. This limit is what I call the
structural threshold. Every type of functional system has such a
limit and this limit is different for different types of systems.
Some systems have greater limits while others have lower limits.
Those systems that require greater limitations are exponentially rarer
in sequence/structure space.
This concept is actually quite simple and downright intuitive. It
really isn't some great mystery.
> Now, if we recognize that the 'function' of any stretch of aa's in a
> protein is binding an epitope that has the potential to be
> biologically relevant, we can ask if there are proteins in which there
> is a reason to have a stretch of aa's that bind radically different,
> but biologically relevant, epitopes. The obvious place to look is the
> immunoglobins (but self-sterility alleles might be a good second).
> [Actually, because the stretch of aa's in the variable region is long
> and we can only detect binding that binds quite tightly, recognizing a
> binding requires an even tighter affinity between protein surface and
> epitope and typically requires a larger than average epitope.] There
> is a stretch of aa's in immunoglobins that vary by mutation and or
> other chance mechanisms. The question then is, what fraction of these
> randomly generated variable sequences within the immunoglobin molecule
> produce completely functionless immunoglobins that cannot bind any
> biologically relevant structure? Actually, that cannot be answered,
> per se, since most of the *actual* randomly generated immunoglobins
> will be functionally useless in any individual's lifetime because the
> individual will not come in contact with the epitope recognized by
> that variant. But we *can* ask if there are any biologically relevant
> epitopes of sufficient size (other than those for self, which actually
> do form, but, in general are eliminated) that the immunoglobin system
> *cannot* recognize. The answer appears to be "Not many." Antibody
> binding even occurs to structures that have never been produced in
> nature.
I can't believe you are using the example of immune system evolution.
That's just classic.
While immune system evolution is a real example of evolution in
action, it isn't an example of evolution of higher-level systems where
more than sequence matching to some pre-formed template. The immune
system works in a very similar way to Dawkins's famous "Methinks it is
like a weasel" evolution algorithm. Along comes a foreign antigen
epitope that is typically about 20 residues in size. So, the total
number of possible antigen epitopes is about 20^20 or
104,857,600,000,000,000,000,000,000 or ~100 trillion trillion. Since
there are trillions of different possible antigen epitopes, how does
one's immune system cope with such a variety of potential enemies?
Well, there are many immune cells produced by the body. In humans, in
particular, about 10^12 lymphocytes are present at any given time. Not
all the T-cells have different Y-shaped receptors, but many of them
do. Chances are that if enough non-self enemies get into the body at
least one of the immune cells will recognize the non-self marker
sequences or "antigens" located on this invader as "foreign" to at
least some useful degree. The odds that a single T-cell will
recognize a random epitope to at least some useful degree is about 1
in 10^12. So, does this mean it would take a trillion different T-
cells to cover all possible invaders? Well, no. The reason is
because an average cell or foreign invader "bug" has about 10^12
different antigen epitopes. So, on average, a single T-cell will
recognize at least one of the potential antigen epitopes of a foreign
invader.
That's why the immune system is actually likely to recognize all
foreign invaders to at least some degree of usefulness - even at
initial exposure. After this point, improved immune system
recognition and defense is simply a matter of random mutations and
improved character matching from one generation of immune cells to the
next. This process is not at all different from what Richard Dawkins
did with his evolution algorithm where each single additional
character match provides the individual with improved reproductive
advantage. This means that that gap between what currently exists as a
starting point and the next closest potentially beneficial sequence is
always only one character change away. Immune system evolution is
therefore predictably rapid and efficient. No big surprise
http://www.detectingdesign.com/immunesystem.html
The problems come when one is trying to demonstrate how novel systems
of function evolve where template matching can't be used - like in the
evolution of high-level systems like flagellar motility. There are no
templates upon which to build such systems where each and ever single
character change will be recognized as more beneficial than the last.
That's why such systems end up having to cross vast gaps that can only
be traversed by dozens of non-beneficial character changes.
> Would that be possible if Sean's calculation of the ratio of
> "beneficial to non-beneficial sequences" were a good estimate? No way
> in hell. A ratio of one "potentially beneficial" sequence to 10^40
> "non-beneficial sequences" at the 100 aa level (which is a little
> longer than the two variable regions, H and L, together) would mean
> that to generate a single *potentially beneficial* immunoglobin that
> binds a potential biologically relevant epitope, you would have to
> produce 10^40 different mutations in 10^40 different cells. That,
> however, is significantly more than the number of cells in your body
> (which is about 10^14). In fact, that is most likely more than the
> number of cells in all the humans that ever existed. And that,
> according to Sean, is what would be needed to generate a *single*
> potentially beneficial sequence by random mutation of the variable
> region sequence of immunoglobins.
You are confusing different types of functions here that do not have
the same minimum structural threshold requirements. Simply antigen
binding isn't a very complex function. Simple binding to at least a
useful degree does not require more than 20 or so very loosely
specified amino acid residue positions. The immune system function
and overall antibody functionality requires a greater minimum than
this, but the basic binding function is very simple. In the same way,
basic binding of a protein to a lactose sugar molecule is also very
simple and does not require many residues nor does it require high
sequence specificity. However, if the function in question requires
more than mere binding, as in the lactase function, a great deal more
size and specificity is needed - i.e., at least 380 fairly
specifically arranged residues.
Again, you are trying to compare apples to oranges here. Different
types of functions have different minimum structural requirements.
> In fact, once you understand the basis behind protein 'function', it
> may well be that the ratio of "*potential* beneficial" to "total
> sequence space" would be close to one.
Now that is wishful thinking if I ever saw it. Again, we are talking
specifically about systems that have certain MINIMUM size and
specificity requirements. You are trying to compare systems with
different minimum thresholds to each other when the ratio in question
only concerns systems with the same minimum requirements. Systems
with higher minimum requirements will be linearly farther away from
other systems within the same level as well as from potentially
beneficial targets within the level just above and just below.
> Each new protein sequence
> resulting from the change of a single aa would still have a structure
> that would typically (in the parts that weren't changed) still bind to
> particular biologically useful structures. And we know for a fact
> that in some cases loss of binding a particular substrate *is* what
> causes a change to be *actually* 'beneficial'.
A function gained by loss of pre-existing binding is very easy to
evolve. This is the basis for most forms of antibiotic resistance.
Such evolution happens very commonly and rapidly.
> The number of *actual*
> beneficial sequences, however, is clearly much smaller than the number
> of *potentially* beneficial sequences, but the benefit of a sequence
> is highly dependent on *actual* conditions. Again, 'beneficial' is a
> conditional state involving the interaction of sequence and
> environment, not an inherent state dependent solely on sequence.
Although true, this concept is essentially irrelevant to the problem
at hand - as noted above.
> Something clearly does not compute here. Of course, once you
> recognize that Sean's ratio does not mean what he claims it means,
> "the ratio of potentially beneficial vrs non-beneficial sequences",
> you can recognize a major flaw in his argument. The number he uses in
> the numerator is irrelevant to the claim that he is making for that
> number.
Once you start comparing apples to apples you will see that your
argument doesn't hold water. You can't compare systems that have
different size or specificity requirements to each other to obtain the
"ratio". The ratio of interest involves comparing systems with the
same minimum requirements to sequence space at that level.
> In short, the numerator value, as an estimate of the number of
> "potentially beneficial sequences", is actually a number (an estimate
> of the number of sequences 100 aa long that have cytochrome c activity
> and sequence similarity) that doesn't have any clear relationship to
> the claim. Ergo, GIGO.
The notion that the number of targets vs. the total number of
sequences being 1:1 is what is absolute GIGO.
> 2) Problems with the denominator.
>
> Although the denominator that Sean is using is *actually* the number
> of sequences of length le in total sequence space and Sean claims it
> is the number of non-beneficial sequences of that length, the
> difference between the two numbers is irrelevant numerically so long
> as you assume (as Sean clearly does) that the number of "potentially
> beneficial" sequences is a very small fraction of total sequence
> space. That is total sequence space is approximately the same as
> total sequence space - "potentially beneficial sequences", but only if
> "the number of cytochrome c-like sequences" is a good estimate of
> "potentially beneficial sequences". The problem with claiming that
> the denominator is the number of non-beneficial sequences rather than
> total sequence space for sequences of that size is more a matter of
> principle than anything else.
You can say that again. That's because there is no practical value to
this point whatsoever.
> If you are going to present a number
> that you are going to use in a mathematical claim, you should define
> it accurately. If you want to say that "total sequence space" is a
> reasonable estimate of "number of non-cytochrome c-like sequences"
> because subtraction of that value is insignificantly different, do so.
The total sequence space size for 100aa is 1e130. That's the total
size. Of this, the number of CytoCs is about 1e90. Now, I ask you,
what is the total number of non-CytoC sequences in sequence space
given these numbers? Is it not roughly 1e130 - 1e90 = ~1e130?
What's your point here with this quibble? What relevance does your
"matter of principle" really have to the problem at hand?
> 3) Problems with the extension of the equation to larger sequence
> sizes.
>
> Even if you *accurately* describe what Sean's equation *really*
> measures: Namely, the ratio of cytochrome c-like sequences divided by
> total sequence space or the mathematically similar ratio of cytochrome
> c-like sequences per non-cytochrome c-like sequences, this ratio ONLY
> holds for the length of 100 aa's. That is because that is the only
> data point we have been given.
Not if you define the levels you are considering as having an
equivalent degree of specificity. Again, it doesn't matter what
degree of specificity you choose. If you keep that degree of minimum
specificity the same, and increase the minimum number of required
residues, the ratio of targets vs. non-targets will drop
exponentially.
> Sean, however, *claims* (apparently out of thin air) that this ratio
> decreases exponentially with increases in total length.
It does if you keep the specificity requirement constant.
> More
> importantly, he *claims* that the exponential decrease in the ratio
> exactly matches the increase in total sequence space.
I never said the match was exact. It is indeed close at higher
levels, but not exact.
> That is, for
> every ten-fold increase in total sequence space, the ratio of number
> of cytochrome-like sequences per total sequence space (or non-
> cytochrome c-like sequences) decreases ten-fold.
You don't seem to understand that we are only talking about the
minimum structural threshold requirements for a system. CytoC has a
minimum of about 100aa (more like 80, but that's beside the point).
Other systems with equivalent specificity requirements that ALSO have
greater minimum size requirements, like a few hundred, will be
exponentially rarer than CytoC in their own sequence spaces.
> Essentially, this
> amounts to a claim that C, the number of cytochrome c-like sequences
> that Sean claims represents ALL "potentially beneficial sequences"
> doesn't change at ALL with an increase in protein length!
What? I'm not talking about CytoC functionality at higher levels
because CytoC functionality doesn't have a higher minimum than 100aa.
Higher level systems are NOT CytoC systems because CytoC is not a
higher-level system. CytoC is a fairly low-level system that actually
requires a minimum structural threshold of less than 100 fairly
specified residues.
> When asked about this, Sean merely claims that this particular
> exponential relationship between the ratio of "potentially beneficial
> vrs. non-beneficial sequences [sic]" is "obvious" and anyone who
> questions it is brain-dead or a liar. Well, it may be "obvious" to
> him. But it sure ain't obvious to me. Especially since no data at
> all are presented that demonstrates that this particular exponential
> relationship *is* the relationship. Rather than, say, even a
> relationship in which the number of cytochrome c-like sequences
> increases in lockstep with the increase in length, producing a
> constant *ratio* of "potentially beneficial to non-beneficial"
> sequences as size increases.
>
> So, basically, in asserting a specific exponential relationship for
> which Sean has presented no evidence whatsoever, he generates numbers
> that, to say the least, are of questionable validity. Ergo, GIGO.
You don't seem to grasp the concept of the minimum structural
threshold requirement. The question is, how many potentially
beneficial target functions require at least 100 amino acid residues
with a degree of specificity of 1e-40? What is the answer to that
question? Now, compare this to the question of how many potentially
beneficial target functions require at least 200 amino acid residues
with the same degree of specificity? The answer to this second
question will be exponentially lower than the answer to the first
question. CytoC does not qualify as an answer to the second question
because it's threshold limit is at 100aa, not 200aa. Do you grasp
that concept?
Until you do, there is no point dealing with the rest of your "points"
- because they are all related to this basic misunderstanding of yours
regarding minimum structural threshold requirements. You just don't
seem to understand this concept.
Sean Pitman
www.DetectingDesign.com
> 4) What does his "average gap size" *really* mean?
>
> Let us *assume*, purely for the sake of argument only, that Sean's
> numbers actually measure what he claims and assume also, purely for
> the sake of argument, that Sean is correct in his "exponential*
> increase. I think that I have demonstrated that this is hardly likely
> to be true, but let's go deeper into the land of unreality and
> mathematical mumbo-jumbo. Let's assume that what Sean has generated
> is indeed a ratio not too far from the actual values of "beneficial to
> non-beneficial sequences". That means that the reciprocal of that
> ratio tells you how many non-beneficial sequences exist per single
> beneficial sequence. Sean then takes the twentieth root of this
> number and claims, ta-da, that the result is the "average gap size"
> between beneficial sequences. But is it, really? I think not. What
> Sean has is a new population size (the number of sequences of a given
> size that do not have beneficial function per sequence that does).
> This population size is, of course, smaller than the total sequence
> space for a protein of length le. So what the 20th root of that
> population size *really* means is that, *if we had a total sequence
> space of that size* and were to reverse the calculation of total
> sequence space, 20^le, we could find out how many le for a sequence
> would produce a total sequence space of that size. Sean *claims* that
> this number (the number of aa's needed to produce a total sequence
> space of the size determined by the number of non-functional sequences
> per functional ones) is "average gap size". Am I missing something?
> I see no reason at all to think that such a number represents "average
> gap size". Ergo, GIGO.
>
> So to summarize, Sean has calculated a number he calls "average gap
> size" by calling a ratio something it isn't, that makes unlikely
> assertions about the relationship of this ratio to changes in length,
> and then comes up with a number that doesn't seem to be "average gap
> size" at all. IOW, a GIGO ratio with an assumed GIGO relationship
> with increasing length which is used to produce a GIGO number.
> <sarcasm on>This, of course, represents the very best of creation
> science. That is because the numbers produced are the ones that a
> creationist wants. It doesn't matter how these numbers are derived
> nor what they mean. <sarcasm off>
Ron O
SNIP:
Seans usual obfuscation scam.
Hey Sean what about telling us the science of ID that you said that
you could teach to school kids?
What about that alternative to common descent and the evidence for it
that you claimed was just as good as what science had?
You made the claims, so why can't you make good on them? Why all this
bull pucky about proteins if you don't have any science worth talking
about, and you don't have an alternative worth jack?
Why do you always run from your own claims? You don't even bother to
deny that you made the claims, you just run and pretend. Does that
make what you do any more honest?
Ron Okimoto
hersheyh
Then why did you claim that *these* ratios represented "the ratio of
potential beneficial vs. non-beneficial for 100aa systems" [see your
statement above to determine if I am out-of-context]?
> What these and other similar estimates indicate is that a
> certain degree of required sequence specificity produces a certain
> ratio of sequences in sequence space that could produce some useful
> degree of functionality of the type in question.
That is NOT what your claim was. Your claim was that this ratio
represented the ratio of *all* "potentially beneficial" sequences to
non-beneficial sequence space. Don't you read what you wrote? You
did not say that this ratio represents all 100 aa sequences that have
all the properties needed to provide the function of cytochrome c in a
modern context. You did not say that this ratio represents all 100 aa
sequences that have all the properties needed to act as a lambda
repressor against a modern lamda gene site. For a simple example, if
you change a particular aa in cytochrome c, that may change the energy
level of electron that the heme takes up (the heme is the actual
electron-transporting element), thus eliminating the "cytochrome c
function" without changing the ability of the protein to bind to heme
significantly. Is a protein that binds heme, but doesn't function as a
cytochrome c "beneficial"? Only context can say.
No. Each of these ratios is an estimate of the ratio of sequences that
produce *a specific* modern function in a particular modern context to
total sequence space. Surely you can see that there is a difference
between saying "some useful degree of functionality *of the type in
question*" and "all potentially beneficial sequences". Note that your
description in your statement makes no reference at all to "useful
degree of functionality of the type in question". I am not a mind-
reader. You CLAIMED that your ratio represented "potential beneficial
vs non-beneficial" sequences. Even you know that isn't the case.
That alone means that the rest of your calculation is GIGO. I don't
have to go any further. But I did and will again. Because it is so
much fun to point out that, wrt making a meaningful calculation, you
performed three mathematical steps and whiffed with each swing. You
are batting 0 for 3.
> Obviously, this doesn't tell us how many potentially beneficial
> sequences of all kinds exist in 100aa sequence space. But, what it
> does do is illustrate a pattern of an exponentially declining ratio of
> beneficial vs. non-beneficial with increasing size and/or specificity
> requirements.
Then you agree with me that the ratio you presented is NOT the ratio
you claim to have presented when you said that the ratio was of
"potential beneficial vs. non-beneficial sequences". You, I presume,
will go back and correct your appendix to accurately state that you
have no idea what the ratio of "beneficial sequences vs non-beneficial
sequences" is and the ratio you are presenting makes no claim to
represent such a number. [Again, you don't have to say
"Acknowledgement goes to H. Hershey and his many clones for preventing
me from foolishly claiming that this ratio actually was the ratio of
"beneficial vs. non-beneficial sequences" when you correct this
obvious mistake.] Thus any calculation that derives from this ratio
does not, even if the rest of the calculation were correct, calculate
the "average gap size" since the number you do need is, indeed, an
estimate of potentially beneficial to total sequences, from which you
can calculate the ratio of "potential beneficial to non-beneficial
sequences".
> In order to avoid this exponential increase, one would
> have to hypothesize that the number of different potentially
> beneficial sequences/structures increases at pretty much the same rate
> as the size of sequence/structure space increases with each increase
> in minimum structural threshold requirements. That notion simply
> isn't tenable to anyone who approaches this problem with a remotely
> candid mind. It isn't true in any language/information system that we
> know of and it isn't true for genetically based information systems
> either.
And, to point out the obvious, this demonstrates that you are merely
asserting the *particular* (and highly unlikely) exponential ratio you
use because you do not ACTUALLY have any evidence about what the real
relationship is.
If the number of "potential beneficial" sequences were to grow two-
fold for a ten-fold increase in total sequence space, that would also
result in an "exponential" decrease in the ratio of "potential
beneficial to total" sequences. But it would be much slower than the
ratio you used. You, apparently out of thin air, assume that there is
absolutely NO increase in the number of beneficial sequences with
increases in length. Why you didn't choose to arbitrarily declare
that the number of "potential beneficial" sequences *decreased* with
increasing length I don't know. Why you claim that it is impossible
for the number of "potential beneficial" sequences to increase in a
linear relationship I don't know. I don't know because you have
presented precisely zero evidence to support your particular
exponential math that declares that the there is zero increase in the
number of "potential beneficial sequences" as total length increases.
Zero. Nada. Not a shred.
> That's the point. There is a clear pattern of exponentially
> increasing non-beneficial sequences relative to each increase in
> potentially beneficial sequences with each increase in minimum
> structural threshold requirements. This point should be so obvious as
> to be beyond argument.
Sorry. Your mathematical claim is quite a bit more specific. Your
claim is that the ratio is exponential *and* that the number of
sequences that have your *specified function* (which we can agree is
NOT "potential beneficial sequences) does not change with increases
(or decreases?) in length.
> > Mathematically, if we call the
> > estimated number of sequences that have cytochrome c function C, and T
> > is the totality of sequence space for 100 aa long peptides, then the
> > equation that Sean is claiming represents as "potential beneficial vs.
> > non-beneficial" ratio is actually C/T. T can be mathematically
> > estimated as 20^le, where le is the length of the sequence, since
> > there are 20 possible amino acids at each position. Converting to
> > base 10, this would be 10^le^log20. Log 20 is about 1.3. So the
> > ratio, R(100), of what Sean calls "potential beneficial vs. non-
> > beneficial" sequences is really the equation:
>
> > R(le) = C/10^le^1.3 = 10^40 when le = 100.
>
> > Moreover, this relationship (the ratio of sequences with cytochrome c
> > function and sequence to all possible 100 aa long sequences) has ONLY
> > been determined (well, estimated) for the case where le = 100.
>
> That's because 100aa is fairly close to the minimum structural
> threshold requirement needed for CytoC. You can't produce a
> beneficial degree of CytoC functionality with just 50aa - no matter
> how they are arranged relative to each other.
Irrelevant. That is not the point. I wouldn't care if it were 90 or
70 or whatever. The point is that you only have data (such that it
is) for this one point. You cannot determine what the relationship is
between this ratio and increasing length when you only have one data
point. You need at least two data points to decide if the
relationship is linear, or exponential, or something else.
> > 2) Problems with calling the numerator "potential beneficial
> > sequences". It should, in fact, be obvious to anyone that C, the
> > number of sequences that have cytochrome c-like function and sequence,
> > is NOT all possible "potential beneficial sequences". I think even
> > Sean sees that.
>
> Of course it's not. But, statistically, this point is pretty much
> irrelevant to the main issue.
The ratio you present is most certainly NOT irrelevant if you are
going to use this *ratio* to claim that a number derived from this
ratio represents "average gap size" between beneficial sequences.
> Again, given that one is looking for
> targets that require a minimum of at least 100aa with an equivalent
> degree of specificity as that required by CytoC functionality, the
> actual ratio of beneficial vs. non-beneficial is not going to be
> significantly different from the ratio of CytoC to non-CytoC in
> sequence/structure space.
No, Sean. You are looking for the ratio of "potentially beneficial"
sequences to total potential sequences. The ratio of sequences that
perform all the functions involved in what a modern cytochrome c does
in a modern context as a fraction of total sequence space cannot
possibly give you the ratio you need.
>
> I've tried to explain this concept to you before, but I'll try again.
> Either you say that there is absolutely no way to get any idea at all
> as to the likely ratio of total targets to non-targets (which removes
> the scientific basis for your proposed mechanism by the way) or you
> try to use the available evidence to get as best as an idea as you
> can.
Actually, *my* mechanism says that the ratio of beneficial targets to
non-targets is irrelevant, because what counts is the "minimum actual
gap size" or even the "minimum possible gap size" in some cases. And
that number is idiosyncratic and dependent upon precise local
conditions and genomes. *My* mechanism says that your numerology is
irrelevant. But that is also what your math says, since the numbers
you generate have no relationship to what you claim they represent.
> One approach to determining the most likely number of potentially
> beneficial targets at a given threshold level is to consider how many
> total novel beneficial systems are in existence today in all living
> things at a given level.
If you knew that the ratio you presented was bogus, why didn't you
present your "correction", such as it is, right from the get go? I
find more likely a scenario that you are so clueless about what you
are calculating that you actually believed that this ratio was the
ratio of "potential beneficial vs non-beneficial sequences".
> This number can be roughly known and it is
> not more than a trillion for the 100aa level. Even if it was 10
> trillion, it wouldn't make any significant difference. The reason for
> this is that 10 trillion uniquely different 100aa systems with the
> minimum degree of specificity of CytoC would take up no more than 1 in
> 1e27 sequences in sequence space. That is still a very tiny fraction
> of the available space of just over 1e130 sequences. The potential
> targets are still vastly outnumbered by non-beneficial sequences.
My counterpoint would be that *almost* any aa sequence that forms a
(or perhaps a couple) of thermodynamically preferred structures has
the capacity to bind to one or more biologically relevant epitopes.
The benefit or lack thereof of such binding is conditionally
determined and not an inherent feature that is invariant. The problem
with proteins that don't form a stable structure is not that they bind
to or interact with too few biological structures, but that they bind
to too many. And my further point is that most proteins do indeed form
a few thermodynamic minimum structures rather than be completely
structureless.
The context is all the living things that have ever existed in all the
environments that have ever existed. We are talking about "total
sequence space", so we have to talk about "total possible benefit
space". And a 300 aa protein that binds heme using only 100 of its
300 aa's would be just as likely to be 'beneficial' as one with only
100 aa's. And, in some contexts, one that binds far more weakly than
modern heme binding proteins do would be 'beneficial' whereas in any
modern cell it would not be. What is 'beneficial' in the context of
natural selection depends on what the competition has (or lacks).
Will you f**king forget about false analogies with English! Deal with
proteins. And the word "system" has no meaning here. What you seem
to mean is "some enzyme activity that exists in and has co-evolved in
some organism". Unlike English words, proteins do not cease to be
proteins because they change. And the parts of proteins that did not
change often do not lose *all* function, even if the protein no longer
has the original function.
>
> The same thing is true of biosystems. However, there is a limit
> beyond which change or removal of characters will completely destroy
> the functionality in question. This limit is what I call the
> structural threshold. Every type of functional system has such a
> limit and this limit is different for different types of systems.
> Some systems have greater limits while others have lower limits.
> Those systems that require greater limitations are exponentially rarer
> in sequence/structure space.
But this knowledge does not tell us how far away a protein with a
related function or with functions that include, say, the heme binding
but not the electron transport functions of cytochrome c is.
> This concept is actually quite simple and downright intuitive. It
> really isn't some great mystery.
Even if it is "quite simple" and "downright intuitive", that is not
your claim in the quoted mathematics. The claim I am disecting is
whether you can use the ratio of cytochrome c or lamda repressor
sequences that retain sufficient activity in a modern system (which
you misleadingly claim represents "potential beneficial sequences") to
total sequence space in order to calculate "average gap distance". I
am pointing out 1) that the ratio is not what you claim it is. 2)
That the relationship of that ratio to length of the aa sequence is
unevidenced and merely assumed. And 3) that the number you call
"average gap size" isn't. Focus, Sean. More to the point, you have
already admitted that the ratio you presented in mathematical analysis
is not what you claimed it was. That means you need to change what
you claim.
And how big is lactose?
> So, the total
> number of possible antigen epitopes is about 20^20 or
> 104,857,600,000,000,000,000,000,000 or ~100 trillion trillion. Since
> there are trillions of different possible antigen epitopes, how does
> one's immune system cope with such a variety of potential enemies?
> Well, there are many immune cells produced by the body. In humans, in
> particular, about 10^12 lymphocytes are present at any given time.
And fewer than that that have different sequences.
> Not
> all the T-cells have different Y-shaped receptors, but many of them
> do. Chances are that if enough non-self enemies get into the body at
> least one of the immune cells will recognize the non-self marker
> sequences or "antigens" located on this invader as "foreign" to at
> least some useful degree.
Yep. Do note that it is not the entire antibody that binds an
'epitope', but only a relatively short sequence. It is the
distinction between 'epitopes' bound that represents the "functional"
difference between these sequences. And "at least to some useful
degree" is *all* that is needed whether the binding is 'just' binding
or is 'binding' that leads to a catalytic speeding up of a reaction or
represents interaction of subunits in a multimer. Evolution does not
require that one land on an optimal sequence immediately.
> The odds that a single T-cell will
> recognize a random epitope to at least some useful degree is about 1
> in 10^12. So, does this mean it would take a trillion different T-
> cells to cover all possible invaders? Well, no. The reason is
> because an average cell or foreign invader "bug" has about 10^12
> different antigen epitopes. So, on average, a single T-cell will
> recognize at least one of the potential antigen epitopes of a foreign
> invader.
>
> That's why the immune system is actually likely to recognize all
> foreign invaders to at least some degree of usefulness - even at
> initial exposure.
The point is that a very, very, very wide range of biologically
relevant epitopes can be recognized and bound to a "useful", but not
necessarily "optimal", degree by a limited number of sequences about
100 aa in length. That is all that evolution needs to do as well.
Like the immune system, after you have the "some degree of
usefulness", generating optimization is simple.
> After this point, improved immune system
> recognition and defense is simply a matter of random mutations and
> improved character matching from one generation of immune cells to the
> next. This process is not at all different from what Richard Dawkins
> did with his evolution algorithm where each single additional
> character match provides the individual with improved reproductive
> advantage. This means that that gap between what currently exists as a
> starting point and the next closest potentially beneficial sequence is
> always only one character change away. Immune system evolution is
> therefore predictably rapid and efficient. No big surprise
>
> http://www.detectingdesign.com/immunesystem.html
>
> The problems come when one is trying to demonstrate how novel systems
> of function evolve where template matching can't be used - like in the
> evolution of high-level systems like flagellar motility.
Flagellar motility is due to epitope binding that is every bit as much
a matter of 'template matching' as the binding of an immunoglobin to a
foreign epitope.
> There are no
> templates upon which to build such systems where each and ever single
> character change will be recognized as more beneficial than the last.
That is merely unsupported assertion.
> That's why such systems end up having to cross vast gaps that can only
> be traversed by dozens of non-beneficial character changes.
That is unsupported assertion.
>
> > Would that be possible if Sean's calculation of the ratio of
> > "beneficial to non-beneficial sequences" were a good estimate? No way
> > in hell. A ratio of one "potentially beneficial" sequence to 10^40
> > "non-beneficial sequences" at the 100 aa level (which is a little
> > longer than the two variable regions, H and L, together) would mean
> > that to generate a single *potentially beneficial* immunoglobin that
> > binds a potential biologically relevant epitope, you would have to
> > produce 10^40 different mutations in 10^40 different cells. That,
> > however, is significantly more than the number of cells in your body
> > (which is about 10^14). In fact, that is most likely more than the
> > number of cells in all the humans that ever existed. And that,
> > according to Sean, is what would be needed to generate a *single*
> > potentially beneficial sequence by random mutation of the variable
> > region sequence of immunoglobins.
>
> You are confusing different types of functions here that do not have
> the same minimum structural threshold requirements. Simply antigen
> binding isn't a very complex function.
ALL protein functions involve a protein providing a surface (or
several different surfaces) that interact with some biologically
relevant structure. I see no difference between an antigen binding to
an antigen and a FliG binding to FliF. In fact, the binding of FliG
to FliF involves *fewer* aa residues. Can you name a single protein
that does not accomplish its 'functions' (and the plural is
intentional) by providing a surface (or several, generally independent
surfaces in some cases) that interacts with some biologically relevant
structure?
> Simple binding to at least a
> useful degree does not require more than 20 or so very loosely
> specified amino acid residue positions. The immune system function
> and overall antibody functionality requires a greater minimum than
> this, but the basic binding function is very simple. In the same way,
> basic binding of a protein to a lactose sugar molecule is also very
> simple and does not require many residues nor does it require high
> sequence specificity. However, if the function in question requires
> more than mere binding, as in the lactase function, a great deal more
> size and specificity is needed - i.e., at least 380 fairly
> specifically arranged residues.
>
> Again, you are trying to compare apples to oranges here. Different
> types of functions have different minimum structural requirements.
So you assert. But the comparison with the immune system is not the
main point here, even if I were wrong about my ideas about the *real*
ratio of "potential beneficial vs non-beneficial" sequences. The main
point is that you have made a calculation of "average gap size" that
involves taking a ratio that you assert means something even you admit
that is not what it means. And then assuming, in the absence of
evidence, a specific (and unlikely) relationship between that ratio
and length of the sequence. And then taking a 20th root and simply
calling it "average gap size".
>
> > In fact, once you understand the basis behind protein 'function', it
> > may well be that the ratio of "*potential* beneficial" to "total
> > sequence space" would be close to one.
>
> Now that is wishful thinking if I ever saw it.
Not at all. If every protein that has a particular sequence also has
a preferred thermodynamic minimum structure (or even a few), that
means that every protein forms specific surfaces that have the
*potential* to bind to *some* biologically relevant molecule. In many
cases, binding a biologically relevant molecule *is* beneficial in and
of itself.
> Again, we are talking
> specifically about systems that have certain MINIMUM size and
> specificity requirements.
I think you are claiming that there is only one "function" in any
enzyme rather than that different parts of a protein have different
subfunctions that, together, generate what you call *the* or
teleological function. You seem to be assuming that function is
something vaguely distributed over the entire structure rather than a
consequence of subfunctions due to specific sites that can be useful
either independently or in fewer combinations. But again, whether or
not I am right or wrong in estimating a much different ratio of
"potential beneficial sequences" to total sequence space, you are
still wrong. Your calculation of "average gap size" is still GIGO.
Just from the fact that the ratio you present is not what you claim it
is. Even before we look at the rest of the calculation.
Whether I am right or wrong here is irrelevant. My being wrong would
not make your calculation anything other than GIGO. This is not a
dichotomy. We can both be wrong. In your case, that is a certainty,
since we already know that you are calling the ratio you use something
it isn't.
> You can't compare systems that have
> different size or specificity requirements to each other to obtain the
> "ratio". The ratio of interest involves comparing systems with the
> same minimum requirements to sequence space at that level.
>
> > In short, the numerator value, as an estimate of the number of
> > "potentially beneficial sequences", is actually a number (an estimate
> > of the number of sequences 100 aa long that have cytochrome c activity
> > and sequence similarity) that doesn't have any clear relationship to
> > the claim. Ergo, GIGO.
>
> The notion that the number of targets vs. the total number of
> sequences being 1:1 is what is absolute GIGO.
So any protein that forms a specific (or even several) structure lacks
what property, do you think, that would allow it to interact (as a
surface) with some biologically relevant structure? My claim is that
all that is needed for a protein to have "potential benefit" is for
that protein to interact with some biologically relevant structure
(actually it should also include interact with structures that are not
currently relevant but might be in the future or have been so in the
past). For a protein to have "actual benefit", of course, it must
interact with some biologically relevant structure in the right
context. But if the ratio you want and claim you need to calculate
"average gap size" is the ratio of "potentially beneficial sequences"
to total sequences, then you have to include any and all proteins that
can form a surface that interacts with some biologically relevant
structure.
But, like I said, it really doesn't matter if I am wrong on this. My
being wrong would not make your ratio right.
> > 2) Problems with the denominator.
[snip mostly because we both agree that the numbers *if* you are right
about the relative ratio would not differ significantly]
The fact remains that that is what you have done. I didn't say that
the sequences are cytochrome c. I said that the math claims that
however you calculated the ratio, when the length of the protein is
increased, your math declares that the number (that is number in the
numerator) that you called "potential beneficial sequences" (which
actually are indistinguishable from the number of cytochrome c-like
species in your ratio) doesn't change at all.
> > When asked about this, Sean merely claims that this particular
> > exponential relationship between the ratio of "potentially beneficial
> > vrs. non-beneficial sequences [sic]" is "obvious" and anyone who
> > questions it is brain-dead or a liar. Well, it may be "obvious" to
> > him. But it sure ain't obvious to me. Especially since no data at
> > all are presented that demonstrates that this particular exponential
> > relationship *is* the relationship. Rather than, say, even a
> > relationship in which the number of cytochrome c-like sequences
> > increases in lockstep with the increase in length, producing a
> > constant *ratio* of "potentially beneficial to non-beneficial"
> > sequences as size increases.
>
> > So, basically, in asserting a specific exponential relationship for
> > which Sean has presented no evidence whatsoever, he generates numbers
> > that, to say the least, are of questionable validity. Ergo, GIGO.
>
> You don't seem to grasp the concept of the minimum structural
> threshold requirement.
It doesn't f**king matter. You are saying, by using the particular
exponential relationship you do, that if the denominator (total
sequence space or the numerically similar non-beneficial sequences)
increases 10-fold, the *ratio* decreases approximately 10-fold. That
requires that the numerator remains unchanged. Mathematically. That
is essentially saying that the number of "potential beneficial
sequences" is fixed and independent of the size of total sequence
space. Mathematically.
You could have said that the number of beneficial sequences only
increases 5-fold for every 10-fold increase in total sequence space.
That would have resulted in an exponential decrease in the ratio, but
a slower one. You could have said that the number of beneficial
sequences decreased 2-fold for every 10-fold increase in total
sequence space (which is a function of length). You could even have
said that the number of beneficial sequences increases 10-fold for
every 10-fold increase in total sequence space (i.e., that the
relationship is actually linear). The fact is that there has been NO
EVIDENCE presented to favor ANY of these relationships. All we have
is your assertion that the particular ratio you chose is the correct
one. And the one you chose mathematically declares that the number of
beneficial sequences does not change with changes in total sequence
space.
> The question is, how many potentially
> beneficial target functions require at least 100 amino acid residues
> with a degree of specificity of 1e-40? What is the answer to that
> question? Now, compare this to the question of how many potentially
> beneficial target functions require at least 200 amino acid residues
> with the same degree of specificity? The answer to this second
> question will be exponentially lower than the answer to the first
> question. CytoC does not qualify as an answer to the second question
> because it's threshold limit is at 100aa, not 200aa. Do you grasp
> that concept?
I give a flying f**k whether you think the numerator of the ratio you
determined represents the number of cytochrome c sequences (which, of
course, even you admit that it does), the number of lambda repressor
sequences, or the number of potentially beneficial sequences. The
mathematical relationship you describe when you do your exponential
increase is one which mathematically says that whatever you called the
numerator in your original ratio, that number remains constant
regardless of the increase in the denominator. That is, if for every
ten fold increase in the size of the denominator, the ratio decreases
ten-fold, the only way that can happen is if the numerator, regardless
of what you call it, remains unchanged.
>
> Until you do, there is no point dealing with the rest of your "points"
Just one more point. Namely that your determination of "average gap
size" is no such thing.
> - because they are all related to this basic misunderstanding of yours
> regarding minimum structural threshold requirements. You just don't
> seem to understand this concept.
And you don't seem to understand how math works in science. Namely
little details like not calling a ratio the ratio of "potential
beneficial vs. non-beneficial sequences" when you have no way of
measuring or even estimating that ratio. Little things like not
knowing the mathematical consequence of claiming a very specific
exponential relationship with increasing length and the need for
supporting evidence to make that claim.
Your calculation of "average gap size" is bullshit numerology, Sean.
It was bull shit numerology the moment that you said that the ratio
you declared was the ratio of "potential beneficial vs non-beneficial
sequences" was not really that at all. The fact that the next two
steps are also bullshit is merely adding to the stink adhering to the
bottom lines of these calculations.
Personally, I think you know you cannot answer the last comment
either.
>
> Sean Pitmanwww.DetectingDesign.com
Seanpit
The same old pjoratives without any real argument - the only thing one
can expect from Ron O.
> Ron Okimoto
Sean Pitman
www.DetectingDesign.com
richardal...@googlemail.com
I'm sorry, Sean.
I must have missed the part where you wrote up your "theories" in the
form of a scientific paper and submitted them for publication.
Or perhaps I missed the post in which you told us *who* has the
intellectual capacity to understand your "theories".
Surely you are not setting out once again to verify my hypothesis
about your behaviour? I don't need any more verification. Try for
falsification.
RF
hersheyh
> On Dec 13, 2:36 pm, Seanpit <seanpitnos...@naturalselection.
>
>
>
> 0catch.com> wrote:
> > On Dec 11, 10:18 am, hersheyh <hershe...@yahoo.com> wrote:
>
> > > Here is Sean's description of the calculation of "average gap
> > > size"
>
> > *****
>
> > > "Well, first we have to calculate the likely gap size. Using an
> > > average between the calculations of Yockey and Sauer, the ratio of
> > > potential beneficial vs. non-beneficial for 100aa systems is about
> > > 1e-40. This creates a ratio for a 1,000aa system of about
> > > 1e-40^(1000/100) = 1e-400. So, the average gap size between
> > > potentially beneficial sequences at this level would be about 308
> > > residue differences - i.e., 20^308 = 1e400."
>
> > *****
I will simplify my challenge, since Sean seems to have this capacity
to wander aimlessly spouting meaningless verbiage. First, of course,
Sean would have to admit that the above method of determining "average
gap size" is exactly how he has claimed, in writing, to be calculating
"average gap size". That is these words were not forced out of Sean
at gunpoint and I am not "quote-mining" these words out of context.
The above math used to calculate "average gap size" for a 1000 aa
sequence rests on three individual steps. All three steps have to be
meaningful and do what Sean says they do in order for the end number,
"average gap size", to be a meaningful number rather than GIGO
numerology.
1) The determination of what you call the "ratio of potential
beneficial vs non-beneficial for 100 aa systems" doesn't do so. We
both agree that, despite the very explicit claim above, the ratio you
are presenting is NOT the "ratio of potential beneficial vs non-
beneficial for 100 aa systems". It is a different ratio (the ratio of
sequences 100 aa long that have a specific defined actual amount of a
modern function in a specific modern context to total sequence
space). I have given my reasons why I think this ratio is far from
being correct, but whether I am correct in my discussion doesn't
matter. My being wrong doesn't make Sean right. And Sean already
admits that the ratio he has *actually* generated is NOT the ratio he
claims to have generated. Poetic license of this sort is not allowed
in math or science. Strike one.
2) The math of extension of this ratio to sequences of longer
lengths. Your claim is that there is a *specific* exponential
relationship in which you take the ratio calculated in step one to the
power of the increase in length relative to 100 aa. That is, you take
the ratio of C/T, where C is whatever number of sequences at 100 aa
length that you call "potential beneficial" sequences and T is what
you call "non-beneficial" sequences [we both agree that T is not
significantly different from 20^le where le is the total size of the
sequence].
But Sean's math is NOT saying that there is some vague sort of
exponential relationship whereby the number of sequences that are
"potential beneficial" increases proportionately more slowly than
total sequence space. For example, there is nothing in Sean's
argument which makes it impossible for the number of "potential
beneficial" sequences, C, to increase 5-fold for each 10-fold increase
in T. That would also produce an exponential decrease in the ratio of
the two; but a slower one. But the *specific* exponential
relationship that Sean is claiming is NOT any of these other quite
possible exponential relationships. Sean claims, specifically, that
for every 10-fold increase in T, there is a 10-fold decrease in the
ratio. What that means, mathematically, is that *whatever* one calls
the numerator, C, in the ratio of C/T, it must remain unchanged as T
increases 10-fold. IOW, his choice of this particular exponential
relationship amounts to the claim that C, the number of "potential
beneficial" sequences in *his* terminology, MUST be invariant and not
change significantly with changes in T.
My point, however, is NOT that it is impossible for this to be the
relationship, although I think it highly unlikely that there would be
NO significant increase in C, which Sean calls "potential beneficial"
sequences, with an increase in length. It is that Sean has presented
NO evidence whatsoever to support his particular equation. He still
has not. To do so would require ACTUAL evidence from *at least* one
other data point, of significantly different length, of the ratio he
claims to have only for the 100 aa level: the ratio of "potential
beneficial" vs "non-beneficial" sequences. Only then can you hope to
produce the correct equation, whether that be a linear relationship
(in which case, the ratio would be unchanged with increases in T), an
exponentially decaying one, or even an exponentially increasing one.
So the problem with this step in calculating "average gap size" is
simply that Sean appears to be merely asserting "a" particular
exponential relationship between the ratio he calculated and sequence
length in the absence of any supporting evidence. To say the least,
the scientific value of such an arbitrary calculation not based on any
evidence whatsoever is questionable. That he has chosen, in the
absence of actual evidence, an exponential ratio that assumes that the
number of "potential beneficial" sequences is a constant seems, to say
the least, odd. One possible explanation is that Sean is simply
unaware that other exponential relationships are possible. Strike
two.
3) The third step in this calculation of "average gap size" involves
taking the 20th root of the inverse of the ratio he has determined as
the "ratio of potential beneficial vs non-beneficial" sequences. The
inverse of Sean's ratio represents the number of non-beneficial
sequences per single beneficial sequence. That is, it produces a
*population* of sequences. The 20th root of that "population
size" (which is, obviously, smaller than T) is what Sean calls
"average gap size". The problem is, that is not, as far as I can
tell, what the number means. The only meaning I can extract from this
number is that it represents the number of aa's one would have to
assemble by chance alone (via the "747 in a tornado" strawman) in
order to get a total sequence space equal to the (necessarily smaller)
population that Sean has calculated. Strike three.
Yer out! Three mathematical steps. Not one of them based on anything
other than Sean's need to get some number at the end that he can
pretend represents "average gap size" and that that number be large.
Bullshit numerology. GIGO. Call it what you will.
When and if Sean can produce a meaningful number for "average gap
size", we can continue.
Seanpit
>
> > Yockey's estimate is in fact dealing specifically with CytoC
> > functionality. I've noted this several times on my website myself.
> > Sauer and Olsen are dealing with lambda repressor functionality, not
> > CytoC.
>
> Then why did you claim that *these* ratios represented "the ratio of
> potential beneficial vs. non-beneficial for 100aa systems" [see your
> statement above to determine if I am out-of-context]?
What I claim is that these ratios give a rough idea as to the nature
of sequence space given a certain level of minimum structural
threshold requirements. Not all 100aa systems are at the same
threshold level you know. Some 100aa systems are at much higher
levels than are other 100aa systems. CytoC is pretty high up there
for 100aa systems.
> > What these and other similar estimates indicate is that a
> > certain degree of required sequence specificity produces a certain
> > ratio of sequences in sequence space that could produce some useful
> > degree of functionality of the type in question.
>
> That is NOT what your claim was. Your claim was that this ratio
> represented the ratio of *all* "potentially beneficial" sequences to
> non-beneficial sequence space.
I never said that.
> Don't you read what you wrote? You
> did not say that this ratio represents all 100 aa sequences that have
> all the properties needed to provide the function of cytochrome c in a
> modern context.
That's exactly what I've said both in this forum (many times) and on
my website (several places). I even have the links to the papers by
Sauer and Olsen and the CytoC specificity data listed on my website
for those who care to look.
> You did not say that this ratio represents all 100 aa
> sequences that have all the properties needed to act as a lambda
> repressor against a modern lamda gene site.
Yes, I did.
> For a simple example, if
> you change a particular aa in cytochrome c, that may change the energy
> level of electron that the heme takes up (the heme is the actual
> electron-transporting element), thus eliminating the "cytochrome c
> function" without changing the ability of the protein to bind to heme
> significantly. Is a protein that binds heme, but doesn't function as a
> cytochrome c "beneficial"? Only context can say.
That's right. However, this doesn't remove the fact that CytoC still
has a certain minimum structural threshold requirement to work as a
CytoC system.
> No. Each of these ratios is an estimate of the ratio of sequences that
> produce *a specific* modern function in a particular modern context to
> total sequence space. Surely you can see that there is a difference
> between saying "some useful degree of functionality *of the type in
> question*" and "all potentially beneficial sequences".
I never said that the CytoC or lambda repressor data represented all
potentially beneficial sequences. What I said was that it can given a
rough idea as to the likely number of all potentially beneficial
sequences at a particular level of size AND specificity requirements.
While this idea is admittedly a rough approximation, the overall ratio
and pattern can be suggested to a degree useful enough to make the
pattern of exponentially declining ratios between beneficial targets
and non-targets quite obvious.
> Note that your
> description in your statement makes no reference at all to "useful
> degree of functionality of the type in question". I am not a mind-
> reader. You CLAIMED that your ratio represented "potential beneficial
> vs non-beneficial" sequences.
That is certainly your strawman version of what I actually said. You
simply assumed what I meant to say and so you are the one that put
these words in my mouth. I never said what you claim I said.
> Even you know that isn't the case.
> That alone means that the rest of your calculation is GIGO. I don't
> have to go any further. But I did and will again. Because it is so
> much fun to point out that, wrt making a meaningful calculation, you
> performed three mathematical steps and whiffed with each swing. You
> are batting 0 for 3.
Rather, it is your notion that beneficial vs. all of sequence/
structure space is at a ratio of 1:1 regardless of size or specificity
requirements. That's what really amazing about your thinking on this
issue. How you can come up with such ludicrous baseless numbers is
way beyond me. But, at least you are trying to use some real numbers
now. Which is much more than I can say for most evolutionists.
< snip >
> > In order to avoid this exponential increase, one would
> > have to hypothesize that the number of different potentially
> > beneficial sequences/structures increases at pretty much the same rate
> > as the size of sequence/structure space increases with each increase
> > in minimum structural threshold requirements. That notion simply
> > isn't tenable to anyone who approaches this problem with a remotely
> > candid mind. It isn't true in any language/information system that we
> > know of and it isn't true for genetically based information systems
> > either.
>
> And, to point out the obvious, this demonstrates that you are merely
> asserting the *particular* (and highly unlikely) exponential ratio you
> use because you do not ACTUALLY have any evidence about what the real
> relationship is.
There is a lot of evidence about what the real evidence is. It just
isn't exact. It is a very rough estimate.
You, on the other hand, are basing your notions on a complete lack of
any attempt to make any estimation as to the likely ratios and how
they might change at various threshold levels. You whole theory is
based on absolutely nothing - not even a rough estimate.
> If the number of "potential beneficial" sequences were to grow two-
> fold for a ten-fold increase in total sequence space, that would also
> result in an "exponential" decrease in the ratio of "potential
> beneficial to total" sequences. But it would be much slower than the
> ratio you used.
The degree of ratio change depends on both size and specificity
requirements. If you reduce the specificity requirements for an
increase in size requirement, you will reduce the change in ratio
accordingly. However, if you consider the specificity requirements
for the average protein in a larger multiprotein system like a
flagellar motility system, the ratio change involved isn't going to be
remotely represented by a 2-fold extrapolation (a 10-fold
extrapolation maybe). But, even if your 2-fold suggestion was
representative of such a system, it would be devastating to the ToE.
> You, apparently out of thin air, assume that there is
> absolutely NO increase in the number of beneficial sequences with
> increases in length. Why you didn't choose to arbitrarily declare
> that the number of "potential beneficial" sequences *decreased* with
> increasing length I don't know.
Oh come on now. You yourself admit that Dawkins is correct in saying
that however many ways there are to make something alive there are
vastly more ways that it could be dead. The reason for this is
because there are so many more ways to mess up a system compared to
the number of ways there are for it to be in working order. And, the
more parts that are needed for a system, the exponentially more ways
there are to mess it up without producing any other useful system at
an equivalent degree of complexity. This should be self-evident to
you. It is a fact in every known language system. It can be fairly
well quantitated, directly, in many language/information systems -
like the English language or computer code. It is a very easy
extrapolation to see that the very same thing is true of genetic
information systems.
If you think otherwise, please do provide at least some evidence for
what you think the real ratio might be. Otherwise, your entire theory
on how your proposed mechanism actually works is based on a complete
lack of evidence. You are basically left with the conclusion that you
have no idea how your mechanism works. The only thing that you know
is that it would have to work in a space were the gaps were small.
But, as far as determining the likelihood that the gaps are indeed as
small as they would need to be for your theory to work, you have no
basis in any evidence, not even rough estimates, whatsoever.
> Why you claim that it is impossible
> for the number of "potential beneficial" sequences to increase in a
> linear relationship I don't know. I don't know because you have
> presented precisely zero evidence to support your particular
> exponential math that declares that the there is zero increase in the
> number of "potential beneficial sequences" as total length increases.
> Zero. Nada. Not a shred.
Actually, I've presented quite a number of evidences and reasons for
why I think the ratio changes in an exponential manner. In
comparison, you have presented absolutely no evidence to suggest that
your notion that the gaps sizes are in fact always small between
existing sequences or existing and past sequences. You know that this
would have to be the case for your theories to work, but you have no
evidential basis for determining the likelihood that your notions are
in fact correct. You present no estimates at all for the likely
ratios at various threshold requirements - none at all. Nada. Not a
shred. You simply hide behind the statement that, "I don't know" and
your notion that such things "Cannot be known" to any useful degree.
Well, Howard, that's not really science then is it?
> > That's because 100aa is fairly close to the minimum structural
> > threshold requirement needed for CytoC. You can't produce a
> > beneficial degree of CytoC functionality with just 50aa - no matter
> > how they are arranged relative to each other.
>
> Irrelevant. That is not the point. I wouldn't care if it were 90 or
> 70 or whatever. The point is that you only have data (such that it
> is) for this one point. You cannot determine what the relationship is
> between this ratio and increasing length when you only have one data
> point. You need at least two data points to decide if the
> relationship is linear, or exponential, or something else.
If you have no idea in this regard, you have no scientific basis
behind your notions of evolutionary mechanism.
The exponential relationship is based on a lot of data, to include
extrapolations from other language/information systems and
experimental data that shows a clear stalling out effect of evolution
at higher levels that is exponential.
< snip >
> > Again, given that one is looking for
> > targets that require a minimum of at least 100aa with an equivalent
> > degree of specificity as that required by CytoC functionality, the
> > actual ratio of beneficial vs. non-beneficial is not going to be
> > significantly different from the ratio of CytoC to non-CytoC in
> > sequence/structure space.
>
> No, Sean. You are looking for the ratio of "potentially beneficial"
> sequences to total potential sequences. The ratio of sequences that
> perform all the functions involved in what a modern cytochrome c does
> in a modern context as a fraction of total sequence space cannot
> possibly give you the ratio you need.
You don't seem to grasp the concept of specificity. Sequences that do
not have the same degree of specificity are not at the same level of
complexity. They do not have the same structural threshold
requirements.
> > I've tried to explain this concept to you before, but I'll try again.
> > Either you say that there is absolutely no way to get any idea at all
> > as to the likely ratio of total targets to non-targets (which removes
> > the scientific basis for your proposed mechanism by the way) or you
> > try to use the available evidence to get as best as an idea as you
> > can.
>
> Actually, *my* mechanism says that the ratio of beneficial targets to
> non-targets is irrelevant, because what counts is the "minimum actual
> gap size" or even the "minimum possible gap size" in some cases.
And what do you think the actual gap size is based on? The likelihood
that the actual gap size is as small as you need it to be (often
suggested by you as being very close or equivalent to the minimum
possible gap size), is based on the average gap size, which in turn is
based on the ratio of targets to non-targets.
If you knew anything about statistics and the way known information
systems actually work, you'd understand this concept.
> And
> that number is idiosyncratic and dependent upon precise local
> conditions and genomes.
The ratio is not significantly affected by local conditions and/or
genomes. That means that the overall average distances aren't
affected. That means that the minimum likely distance isn't affected.
That means that the odds of existing starting points being close to
any potential targets at a given threshold level are not affected. If
the odds suggest a likely minimum distance to the closest target of
100 residue changes from anything in the current gene pool, that
distance isn't *likely* to change with a change in environment or
genome - even over the course of trillions of years.
< snip >
> > This number can be roughly known and it is
> > not more than a trillion for the 100aa level. Even if it was 10
> > trillion, it wouldn't make any significant difference. The reason for
> > this is that 10 trillion uniquely different 100aa systems with the
> > minimum degree of specificity of CytoC would take up no more than 1 in
> > 1e27 sequences in sequence space. That is still a very tiny fraction
> > of the available space of just over 1e130 sequences. The potential
> > targets are still vastly outnumbered by non-beneficial sequences.
>
> My counterpoint would be that *almost* any aa sequence that forms a
> (or perhaps a couple) of thermodynamically preferred structures has
> the capacity to bind to one or more biologically relevant epitopes.
That's an irrelevant counterpoint because simple binding is simple.
It doesn't have a very high specificity or size threshold
requirement. Therefore, it is on a much lower level than a system
that does in fact have a high minimum structural threshold
requirement. You are comparing apples and oranges again.
> The benefit or lack thereof of such binding is conditionally
> determined and not an inherent feature that is invariant. The problem
> with proteins that don't form a stable structure is not that they bind
> to or interact with too few biological structures, but that they bind
> to too many. And my further point is that most proteins do indeed form
> a few thermodynamic minimum structures rather than be completely
> structureless.
That is a problem that is caused by the very low threshold
requirements needed to produce the simple "binding" function.
> > > First we have the problem that "beneficial" is not an inherent feature
> > > of a sequence, but a conditional one. Even the cytochrome c sequence
> > > is not 'beneficial' in every situation or organism (think anaerobes).
> > > And "potential" is important, since we cannot assume that a sequence
> > > is useless until or unless we have a context to put it in.
>
> > The context is any living thing in any particular environment. Take
> > your pick. Whatever context you choose will have the same problem.
> > The ratios are not going to be significantly different regardless of
> > context. Bringing up the context is therefore irrelevant - a red
> > herring.
>
> The context is all the living things that have ever existed in all the
> environments that have ever existed. We are talking about "total
> sequence space", so we have to talk about "total possible benefit
> space". And a 300 aa protein that binds heme using only 100 of its
> 300 aa's would be just as likely to be 'beneficial' as one with only
> 100 aa's. And, in some contexts, one that binds far more weakly than
> modern heme binding proteins do would be 'beneficial' whereas in any
> modern cell it would not be. What is 'beneficial' in the context of
> natural selection depends on what the competition has (or lacks).
What works now gives us a decent idea about what could have worked in
the past. Your notion of some special situation that might could work
in the past is just wishful thinking. Very unlikely environments or
situations or sequences existing in the same gene pool are just that -
very unlikely (even given trillions of years of time when it comes to
higher-levels systems).
> > Again, this is completely irrelevant to the fact that different types
> > of systems have different minimum structural threshold requirements.
> > This is true of all language/information systems. For example, it is
> > true of the English language that a change of most single characters,
> > taken one at a time, will most likely not completely destroy the
> > particular intended functionality or meaning of the paragraph
> > completely.
>
> Will you f**king forget about false analogies with English! Deal with
> proteins. And the word "system" has no meaning here. What you seem
> to mean is "some enzyme activity that exists in and has co-evolved in
> some organism". Unlike English words, proteins do not cease to be
> proteins because they change. And the parts of proteins that did not
> change often do not lose *all* function, even if the protein no longer
> has the original function.
The same is true of English words or phrases or sentences. Change a
single letter in this paragraph. Any one. Will the paragraph loose
all of its intended meaning or function? No. The same thing is true
with most English words. Most words can suffer one or two character
changes without a complete loss of their intended meaning. There is a
very close comparison between all language/information systems in this
regard.
> > The same thing is true of biosystems. However, there is a limit
> > beyond which change or removal of characters will completely destroy
> > the functionality in question. This limit is what I call the
> > structural threshold. Every type of functional system has such a
> > limit and this limit is different for different types of systems.
> > Some systems have greater limits while others have lower limits.
> > Those systems that require greater limitations are exponentially rarer
> > in sequence/structure space.
>
> But this knowledge does not tell us how far away a protein with a
> related function or with functions that include, say, the heme binding
> but not the electron transport functions of cytochrome c is.
Yes, it does. It gives us a statistical basis upon which to make
estimates about how far away the next closest beneficial system is
likely to be. Your notion that the next closest system is always
close enough is based on absolutely nothing but your need for this
notion to be true. It isn't based on anything that can be tested and
potentially falsified.
> > This concept is actually quite simple and downright intuitive. It
> > really isn't some great mystery.
>
> Even if it is "quite simple" and "downright intuitive", that is not
> your claim in the quoted mathematics.
Yes, it is. You just misinterpret is all.
> The claim I am disecting is
> whether you can use the ratio of cytochrome c or lamda repressor
> sequences that retain sufficient activity in a modern system (which
> you misleadingly claim represents "potential beneficial sequences")
< snip repetitive >
> > I can't believe you are using the example of immune system evolution.
> > That's just classic.
>
> > While immune system evolution is a real example of evolution in
> > action, it isn't an example of evolution of higher-level systems where
> > more than sequence matching to some pre-formed template. The immune
> > system works in a very similar way to Dawkins's famous "Methinks it is
> > like a weasel" evolution algorithm. Along comes a foreign antigen
> > epitope that is typically about 20 residues in size.
>
> And how big is lactose?
It doesn't matter how big lactose is. Antigens are not significantly
bigger than 20aa. Foreign material is broken down you know, and
presented by antigen presenting cells in "bite sized" pieces.
> > So, the total
> > number of possible antigen epitopes is about 20^20 or
> > 104,857,600,000,000,000,000,000,000 or ~100 trillion trillion. Since
> > there are trillions of different possible antigen epitopes, how does
> > one's immune system cope with such a variety of potential enemies?
> > Well, there are many immune cells produced by the body. In humans, in
> > particular, about 10^12 lymphocytes are present at any given time.
>
> And fewer than that that have different sequences.
>
> > Not
> > all the T-cells have different Y-shaped receptors, but many of them
> > do. Chances are that if enough non-self enemies get into the body at
> > least one of the immune cells will recognize the non-self marker
> > sequences or "antigens" located on this invader as "foreign" to at
> > least some useful degree.
>
> Yep. Do note that it is not the entire antibody that binds an
> 'epitope', but only a relatively short sequence. It is the
> distinction between 'epitopes' bound that represents the "functional"
> difference between these sequences. And "at least to some useful
> degree" is *all* that is needed whether the binding is 'just' binding
> or is 'binding' that leads to a catalytic speeding up of a reaction or
> represents interaction of subunits in a multimer. Evolution does not
> require that one land on an optimal sequence immediately.
Directed non-random evolution requires that the new sequence/structure
be detectably more beneficial than what came before. At higher
levels, this is harder to do because more changes are required, on
average. Simple binding functions are simple because they are not
very complex.
> > The odds that a single T-cell will
> > recognize a random epitope to at least some useful degree is about 1
> > in 10^12. So, does this mean it would take a trillion different T-
> > cells to cover all possible invaders? Well, no. The reason is
> > because an average cell or foreign invader "bug" has about 10^12
> > different antigen epitopes. So, on average, a single T-cell will
> > recognize at least one of the potential antigen epitopes of a foreign
> > invader.
>
> > That's why the immune system is actually likely to recognize all
> > foreign invaders to at least some degree of usefulness - even at
> > initial exposure.
>
> The point is that a very, very, very wide range of biologically
> relevant epitopes can be recognized and bound to a "useful", but not
> necessarily "optimal", degree by a limited number of sequences about
> 100 aa in length. That is all that evolution needs to do as well.
> Like the immune system, after you have the "some degree of
> usefulness", generating optimization is simple.
The useful function in this case is extremely simple and low-level.
It only requires 20aa in loose specificity in a particular location
for the binding function. That is about as low of a level of
complexity as you can get. Other functional properties of the antibody
are what require the additional antibody size and complexity. The
finding function, however, is very simple. Apples and oranges again.
> > After this point, improved immune system
> > recognition and defense is simply a matter of random mutations and
> > improved character matching from one generation of immune cells to the
> > next. This process is not at all different from what Richard Dawkins
> > did with his evolution algorithm where each single additional
> > character match provides the individual with improved reproductive
> > advantage. This means that that gap between what currently exists as a
> > starting point and the next closest potentially beneficial sequence is
> > always only one character change away. Immune system evolution is
> > therefore predictably rapid and efficient. No big surprise
>
> >http://www.detectingdesign.com/immunesystem.html
>
> > The problems come when one is trying to demonstrate how novel systems
> > of function evolve where template matching can't be used - like in the
> > evolution of high-level systems like flagellar motility.
>
> Flagellar motility is due to epitope binding that is every bit as much
> a matter of 'template matching' as the binding of an immunoglobin to a
> foreign epitope.
Nope. A flagellar system cannot be built by template matching where
each individual residue change results in improved flagellar motility
- or even a novel higher-level beneficial system of any kind.
Antibody binding and the resulting immune system function can be
improved by single residue changes along every step of the way. Each
beneficial change can be realized by just one residue change in the
immune system. This is NOT the case for the steppingstones of
flagellar motility. These steppingstones are NOT separated by just
one residue difference. The simple binding of one of the systems to
another in just any old fashion isn't going to get you to the next
beneficial steppingstone. Very specific binding to very specific
lactations in a very specific way for very specific pre-existing
systems is what it takes to build a flagellum. Getting such link-ups
by random mutations are going to involve far more trials and errors
than that required to match up one more residue position on an
antibody to an antigen template.
> > There are no
> > templates upon which to build such systems where each and every single
> > character change will be recognized as more beneficial than the last.
>
> That is merely unsupported assertion.
Rather, it is your assertion to the contrary that has absolutely no
support - either by the structural/sequence data available or the
experimental data that shows a complete lack of evolution at such
levels. There are no examples whatsoever in literature. That should
tell you that this type of function is not at all comparible to the
simple template-binding function of antibody epitopes.
> > That's why such systems end up having to cross vast gaps that can only
> > be traversed by dozens of non-beneficial character changes.
>
> That is unsupported assertion.
Again, it is this comment of yours that is unsupported. All of the
available evidence that we currently have says that your notion of
small gaps, equivalent to gaps between improved antibody binding, is
simply untenable.
< snip rest >
Sean Pitman
www.DetectingDesign.com
Lee Oswald Ving
127a-4f20-942...@i29g2000prf.googlegroups.com:
Well, yes - Mr. Okimoto is asking that you make good instead. Can you not?
<snip "same old pjorative">
hersheyh
Re-including what Sean said in the appendix where he "calculates"
average gap size. Sean seems to have inadvertently deleted it. But
it is important because Sean seems to be claiming that I am
misrepresenting what he says this series of calculations does. Sean
also tries to throw the issue back to me by asking me for the
equations I would use. The question here, however, is not whether I
or anyone else can calculate what Sean wants calculated. It is
whether or not the numbers that Sean calculates are 1) meaningful and
2) give him what he claims they do.
*****here is how Sean says he generates his numbers and what he says
they mean*****
"Well, first we have to calculate the likely gap size. Using an
average between the calculations of Yockey and Sauer, the ratio of
potential beneficial vs. non-beneficial for 100aa systems is about
1e-40. This creates a ratio for a 1,000aa system of about
1e-40^(1000/100) = 1e-400. So, the average gap size between
potentially beneficial sequences at this level would be about 308
residue differences - i.e., 20^308 = 1e400."
******
> > > Yockey's estimate is in fact dealing specifically with CytoC
> > > functionality. I've noted this several times on my website myself.
> > > Sauer and Olsen are dealing with lambda repressor functionality, not
> > > CytoC.
***** The relevant mathematical claim that Sean makes in his
calculation*****
Using an average between the calculations of Yockey and Sauer, the
ratio of potential beneficial vs. non-beneficial for 100aa systems is
about 1e-40."
*********
Note that none of the qualifications that Sean is saying he makes
elsewhere are present in the actual calculation described above. Sean
is saying, quite specifically, that the calculations of Yockey and
Sauer produces a ratio which IS "potential beneficial vs. non-
beneficial for 100 aa systems." Even if he *knows* and *admits*
elsewhere that the ratios provided by these sources does not represent
"the ratio of potential beneficial vs. non-beneficial sequences for
100aa systems", that is not reflected in the words he is using here.
Here he is explicitly claiming that the estimates of Yockey and Sauer
ARE "potential beneficial vs. non-beneficial for 100 aa systems." If
he were to change this to more accurately reflect what he thinks the
ratio of Yockey and Sauer do mean, he would have said something like
the following: "The ratio of potential beneficial vs. non-beneficial
sequences for 100 aa systems is unknown, but if one assumes that the
number of potential beneficial systems is accurately estimated by
counting the number of sequences that have x level of cytochrome c
function in the context of modern systems by looking at how mutation
affects that particular function, then....." That would, then,
clearly indicate the assumptions that went into his belief that the
Yockey and Sauer ratio has some relationship with "potential
beneficial" sequences. But that is not what Sean has actually done.
What he has done is say: "Using an average between the calculations
of Yockey and Sauer, the ratio of potential beneficial vs. non-
beneficial for 100aa systems is about 1e-40."
> > Then why did you claim that *these* ratios represented "the ratio of
> > potential beneficial vs. non-beneficial for 100aa systems" [see your
> > statement above to determine if I am out-of-context]?
>
> What I claim is that these ratios give a rough idea as to the nature
> of sequence space given a certain level of minimum structural
> threshold requirements. Not all 100aa systems are at the same
> threshold level you know. Some 100aa systems are at much higher
> levels than are other 100aa systems. CytoC is pretty high up there
> for 100aa systems.
Irrelevant. The fact remains that you are *claiming* that the ratio
you ACTUALLY use to calculate "average gap size" represents "potential
beneficial vs non-beneficial" sequences when, as you agree above, it
does not. Instead it is "a rough idea". It is dependent on
"threshold level". Cyto C is "high threshold". If you think you need
the ratio of "potential beneficial vs non-beneficial for a 100aa
system" to calculate "average gap size" you have to convince us that
the ratio you used actually does equal or (at least) come close to
equaling "potential beneficial vs non-beneficial for a 100aa system".
Simply asserting that a number that even you admit is NOT "potential
beneficial" sequences represents "potential beneficial" sequences will
not do.
>
> > > What these and other similar estimates indicate is that a
> > > certain degree of required sequence specificity produces a certain
> > > ratio of sequences in sequence space that could produce some useful
> > > degree of functionality of the type in question.
>
> > That is NOT what your claim was. Your claim was that this ratio
> > represented the ratio of *all* "potentially beneficial" sequences to
> > non-beneficial sequence space.
>
> I never said that.
***** Reality check*****
Using an average between the calculations of Yockey and Sauer, the
ratio of potential beneficial vs. non-beneficial for 100aa systems is
about 1e-40."
*******
Note that you do NOT say "the ratio of one potentially beneficial
function" or "sequence". You said that the number you are using
represented "the ratio of potential beneficial vs. non-beneficial for
100aa systems". That means ALL potential beneficial, not just one.
Again, if you want to clarify what this ratio *actually* measures, do
so. Change what you have written. Include what your working
assumptions are. Just don't claim that you have not said exactly what
I am claiming.
> > Don't you read what you wrote? You
> > did not say that this ratio represents all 100 aa sequences that have
> > all the properties needed to provide the function of cytochrome c in a
> > modern context.
>
> That's exactly what I've said both in this forum (many times) and on
> my website (several places). I even have the links to the papers by
> Sauer and Olsen and the CytoC specificity data listed on my website
> for those who care to look.
Then change what you say below to more accurately reflect what you say
you mean. Do NOT continue to claim that the ratio you are using is
"potential beneficial vs. non-beneficial" sequences.
********* a reminder of what Sean's actual claim was
Using an average between the calculations of Yockey and Sauer, the
ratio of potential beneficial vs. non-beneficial for 100aa systems is
about 1e-40."
*******
>
> > You did not say that this ratio represents all 100 aa
> > sequences that have all the properties needed to act as a lambda
> > repressor against a modern lamda gene site.
>
> Yes, I did.
********* a reminder of what Sean's actual claim was
Using an average between the calculations of Yockey and Sauer, the
ratio of potential beneficial vs. non-beneficial for 100aa systems is
about 1e-40."
*******
That is, Sean is either *actually* or *apparently* claiming that there
is no difference between the ratio of sequences that can act as a
lambda repressor in a modern system to total sequence space and the
ratio of "potential beneficial vs. non-beneficial" sequences. A
simple, "Oooops. I misspoke and should have said....Thank you for
pointing out the inadvertant sloppiness in my wording." would do so
long as it is followed by a correction that points out what this ratio
*really* is.
>
> I never said that the CytoC or lambda repressor data represented all
> potentially beneficial sequences. What I said was that it can give a
> rough idea as to the likely number of all potentially beneficial
> sequences at a particular level of size AND specificity requirements.
Sean, why do you claim that this is what you said when I can easily
point out what you really said: "Using an average between the
calculations of Yockey and Sauer, the ratio of potential beneficial
vs. non-beneficial for 100aa systems is about 1e-40." This is a claim
that the ratio you presented here represents (is a good estimate of)
ALL "potential beneficial vs. non-beneficial" sequences and is not
simply the ratio of "all sequences that have the specific beneficial
function of being able to replace w.t. cytochrome c activity in the
context of a modern mitochondrion" or (and importantly not 'and') the
ratio of "all sequences that have the specific beneficial function of
being able to replace w.t. lambda repressor in the context of a modern
bacterial cell".
> While this idea is admittedly a rough approximation, the overall ratio
> and pattern can be suggested to a degree useful enough to make the
> pattern of exponentially declining ratios between beneficial targets
> and non-targets quite obvious.
That's the second point. And, naturally, I didn't see you mention how
"rough" an "approximation" the ratio you present is. Nor even a hint
that it was an approximation of the number you claim it represents
("the ratio of potential beneficial vs. non-beneficial" sequences) by
using a quite different ratio.
> > Note that your
> > description in your statement makes no reference at all to "useful
> > degree of functionality of the type in question". I am not a mind-
> > reader. You CLAIMED that your ratio represented "potential beneficial
> > vs non-beneficial" sequences.
>
> That is certainly your strawman version of what I actually said.
No. It is, in fact, what you *actually* said in the appendix where
you tell us how you calculated "average gap size". Do I have to put
what you *actually* said and the ratio you *actually* used out here
again? If you want to claim that you were simply being sloppy in your
description, fine. But then you will have to go back and actually
correct your sloppy language. Like I said, I won't even expect
acknowledgements for pointing this out to you.
> You
> simply assumed what I meant to say and so you are the one that put
> these words in my mouth. I never said what you claim I said.
********* a reminder of what Sean actually said:
Using an average between the calculations of Yockey and Sauer, the
ratio of potential beneficial vs. non-beneficial for 100aa systems is
about 1e-40."
*******
That sure seems to me that you are claiming that the ratios the stated
authors presented in their respective papers are "the ratio of [there
is an implied 'all' at this point by virtue of the absence of
qualifiers] potential beneficial vs. non-beneficial [sequences] for
100aa systems". And the fact remains that you are using these
author's ratios in your subsequent steps as if it were the ratio of
"[all] potential beneficial vs. non-beneficial" sequences at the 100aa
threshold level.
> > Even you know that isn't the case.
> > That alone means that the rest of your calculation is GIGO. I don't
> > have to go any further. But I did and will again. Because it is so
> > much fun to point out that, wrt making a meaningful calculation, you
> > performed three mathematical steps and whiffed with each swing. You
> > are batting 0 for 3.
>
[snip]
>
> > And, to point out the obvious, this demonstrates that you are merely
> > asserting the *particular* (and highly unlikely) exponential ratio you
> > use because you do not ACTUALLY have any evidence about what the real
> > relationship is.
>
> There is a lot of evidence about what the real evidence is. It just
> isn't exact. It is a very rough estimate.
Then how can you present a very specific exponential relationship of
the ratio of "potential beneficial vs. non-beneficial" to sequence
length rather than a range of possible exponential relationships.
What evidence makes you think that the number of beneficial sequences
remains unchanged regardless of changes (at least increases) in
length? Where do you make any attempt to actually present this
evidence for real proteins?
[snip stuff that even if true would not make Sean's calculation more
meaningful. If I am wrong, that doesn't make Sean right.]
> > If the number of "potential beneficial" sequences were to grow two-
> > fold for a ten-fold increase in total sequence space, that would also
> > result in an "exponential" decrease in the ratio of "potential
> > beneficial to total" sequences. But it would be much slower than the
> > ratio you used.
>
> The degree of ratio change depends on both size and specificity
> requirements. If you reduce the specificity requirements for an
> increase in size requirement, you will reduce the change in ratio
> accordingly.
Another point not mentioned in your calculation of "average gap
size". I presume you have some evidence to indicate that the
specificity of cytc and lambda repressor are about average. But I was
assuming constant specificity. Thus the only thing that changes is
the length of the sequence. I presume that is also what you were
assuming. But you surely should make a point that the actual
relationship of the ratio that you call "potential beneficial vs. non-
beneficial" to increases in length is affected by specificity
requirements.
> However, if you consider the specificity requirements
> for the average protein in a larger multiprotein system like a
> flagellar motility system, the ratio change involved isn't going to be
> remotely represented by a 2-fold extrapolation (a 10-fold
> extrapolation maybe).
How do you know that?
> But, even if your 2-fold suggestion was
> representative of such a system, it would be devastating to the ToE.
>
> > You, apparently out of thin air, assume that there is
> > absolutely NO increase in the number of beneficial sequences with
> > increases in length. Why you didn't choose to arbitrarily declare
> > that the number of "potential beneficial" sequences *decreased* with
> > increasing length I don't know.
>
> Oh come on now. You yourself admit that Dawkins is correct in saying
> that however many ways there are to make something alive there are
> vastly more ways that it could be dead. The reason for this is
> because there are so many more ways to mess up a system compared to
> the number of ways there are for it to be in working order. And, the
> more parts that are needed for a system, the exponentially more ways
> there are to mess it up without producing any other useful system at
> an equivalent degree of complexity. This should be self-evident to
> you. It is a fact in every known language system. It can be fairly
> well quantitated, directly, in many language/information systems -
> like the English language or computer code. It is a very easy
> extrapolation to see that the very same thing is true of genetic
> information systems.
Where is the evidence that *specifically* says that there is no change
in the number of "potential beneficial" English words or computer
codes as the length of the word or code is increased? I thought your
argument using English was about the consequences of mutation of
already present English words or code rather than a description of a
mechanism of their construction. Where is the evidence that
increasing genetic information systems (for example, by slightly
modifying different homeobox genes so that they have overlapping, but
slightly different functions and can partially substitute for each
other -- a definitely more complex system than having a single
homeobox gene) makes the system *more* fragile. Seems to me that
redundancy and partial redundancy makes a genetic information system
more robust rather than more fragile. Besides, we are talking about
your apparently arbitrary choice of a very specific exponential
relationship for proteins as length gets larger. One where,
*mathematically*, the numerator is independent of the denominator and
does not change. The numerator is what you call "[all] potential
beneficial" sequences.
> If you think otherwise, please do provide at least some evidence for
> what you think the real ratio might be. Otherwise, your entire theory
> on how your proposed mechanism actually works is based on a complete
> lack of evidence. You are basically left with the conclusion that you
> have no idea how your mechanism works.
I know how the mechanism of evolution works. This ratio is irrelevant
to that mechanism. Average gap size (even if you could calculate it)
would be irrelevant. But even if I am wrong about that, that doesn't
make your assumption that the ratio of what you call "potential
beneficial vs. non-beneficial" sequence ratio [sic, we both agree that
that is not what the ratio really is] changes exponentially with
sequence length at just the rate which would mean that the number of
"potential beneficial" sequences does not change at all with
increasing size [for a given level of specificity].
> The only thing that you know
> is that it would have to work in a space were the gaps were small.
Which, as I point out is *why* so much evolution involves duplication
and divergence.
> But, as far as determining the likelihood that the gaps are indeed as
> small as they would need to be for your theory to work, you have no
> basis in any evidence, not even rough estimates, whatsoever.
Average gap size is irrelevant. Minimum possible or minimum actual
gap sizes are not. They are not a function of 'average gap size'.
But again, focus. We are focusing on whether *your* so-called
calculation of the value of 'average gap size' involves calling
numbers something they aren't and doing manipulations of numbers that
have no basis or ability to produce the numbers you want. So far, you
have had to admit that you are claiming that the ratio you used in
your calculation as the ratio of "potential beneficial vs. non-
beneficial" sequences doesn't *really* mean that.
> > Why you claim that it is impossible
> > for the number of "potential beneficial" sequences to increase in a
> > linear relationship I don't know. I don't know because you have
> > presented precisely zero evidence to support your particular
> > exponential math that declares that the there is zero increase in the
> > number of "potential beneficial sequences" as total length increases.
> > Zero. Nada. Not a shred.
>
> Actually, I've presented quite a number of evidences and reasons for
> why I think the ratio changes in an exponential manner.
Sean, you are doing far, far more than saying that the ratio changes
in an exponential manner. You are presenting a *specific*
mathematical exponential relationship. One that mathematically
requires that the absolute number of "potential beneficial sequences"
does not change at all as length of sequence increases. And all I
have done is ask you what *evidence* do you have that explicitly
points to this particular exponential relationship. Merely asserting
that you have it is not answering the question. Compound interest
involves an exponential relationship. But it matters if that
relationship involves a growth rate of 3% or 30% or 300% per year.
Me, I would prefer the 300% annual growth rate if it doesn't involve a
Ponzi scheme.
> In
> comparison, you have presented absolutely no evidence to suggest that
> your notion that the gaps sizes are in fact always small between
> existing sequences or existing and past sequences.
Again, even if I couldn't, that wouldn't make your claim that the
relationship is one where the absolute number of "potential
beneficial" sequences doesn't change at all correct. But I have
presented evidence. I said that, for recently diverged functions,
there will be many sequence similarities (many in sites that are
selectively neutral) between the currently existing sequences that
derived from that ancestral source. And as examples, I have given the
evolution of beta globin from alpha globin, the evolution of the
embryonic, fetal, and adult forms of beta globin, and even (though it
is a more distant relationship) the relationship between myoglobin and
hemoglobin. I have also mentioned aldosterone and cortisol
receptors. In fact, I have made the claim that there will be many
clearly historically branching trees or 'families' of functional
proteins in life as a consequence of a mechanism that does not
randomly search total sequence space but searches local sequence space
for novel and locally beneficial sequences that reside in that space.
In such a model, average gap size based on total sequence space is
irrelevant. *That* is a testable prediction from a model of evolution
that involves new functions (usually, nylonase is an exception that
show that even randomly generated proteins have "potential beneficial"
surfaces) arising from modification of old structures that also have
functions. Your turn. What testable prediction arises from a model
of "creation" that involves a superanatural agent somehow poofing
every sequence we see into existence by magic? Or, focus, focus,
focus: Tell us how you determined that the particular exponential
relationship you claim exists, the one in which there is no increase
in the absolute number of "potential beneficial" sequences with
increasing length of the protein, was determined.
[snip]
> The exponential relationship is based on a lot of data, to include
> extrapolations from other language/information systems and
> experimental data that shows a clear stalling out effect of evolution
> at higher levels that is exponential.
Sean, we both agree that as the minimum actual gap size is increased
(say, by eliminating ebg from E. coli genome) that evolving a new
function that *must* cross a bigger gap becomes more difficult. That
happens whatever you calculate as the "average gap size", which is a
value that would not change by eliminating ebg or having it present.
My argument is that when evolution happens, it is far more likely to
be in the particular situation where the actual minimum gap size is
small (i.e., when an ebg is present) than when the actual minimum gap
size is large (i.e., when an ebg is absent). And, of course, that the
resulting lactase will have extensive sequence similarity to the gene
from which this new function is derived. But, again, whether my model
is right or wrong does not determine whether or not your calculation
is based on misinterpreting what numbers mean and inventing specific
(and self-serving) mathematical relationships.
> < snip >
>
> > > Again, given that one is looking for
> > > targets that require a minimum of at least 100aa with an equivalent
> > > degree of specificity as that required by CytoC functionality, the
> > > actual ratio of beneficial vs. non-beneficial is not going to be
> > > significantly different from the ratio of CytoC to non-CytoC in
> > > sequence/structure space.
>
> > No, Sean. You are looking for the ratio of "potentially beneficial"
> > sequences to total potential sequences. The ratio of sequences that
> > perform all the functions involved in what a modern cytochrome c does
> > in a modern context as a fraction of total sequence space cannot
> > possibly give you the ratio you need.
>
> You don't seem to grasp the concept of specificity. Sequences that do
> not have the same degree of specificity are not at the same level of
> complexity. They do not have the same structural threshold
> requirements.
Sean, what I said was that the numerator of the ratio is, in fact,
much more specific and narrow than what you called that numerator
( which was [all] "potential beneficial" sequences). That is
equivalent to calling a "tiger" (a very specific cat) a "carnivore"
and claiming that tiger means the same thing as carnivore. It seems
to me that it is you who has a problem with grasping the concept of
specificity.
[snip]
>
> > Actually, *my* mechanism says that the ratio of beneficial targets to
> > non-targets is irrelevant, because what counts is the "minimum actual
> > gap size" or even the "minimum possible gap size" in some cases.
>
> And what do you think the actual gap size is based on?
That was "minimum actual gap size". It is based on the specifics of
context and existing sequences.
> The likelihood
> that the actual gap size is as small as you need it to be (often
> suggested by you as being very close or equivalent to the minimum
> possible gap size), is based on the average gap size, which in turn is
> based on the ratio of targets to non-targets.
Sean, the minimum possible gap size is NOT based on "average gap
size". Neither is "minimum actual gap size". The minimum actual gap
size for the generation of a lactase in E. coli depends not on some
number that I determine to be "average gap size". It is a function of
the presence or absence of ebg. The specifics of context and existing
sequences.
> If you knew anything about statistics and the way known information
> systems actually work, you'd understand this concept.
>
> > And
> > that number is idiosyncratic and dependent upon precise local
> > conditions and genomes.
>
> The ratio is not significantly affected by local conditions and/or
> genomes. That means that the overall average distances aren't
> affected. That means that the minimum likely distance isn't affected.
> That means that the odds of existing starting points being close to
> any potential targets at a given threshold level are not affected. If
> the odds suggest a likely minimum distance to the closest target of
> 100 residue changes from anything in the current gene pool, that
> distance isn't *likely* to change with a change in environment or
> genome - even over the course of trillions of years.
>
[snip]
> > My counterpoint would be that *almost* any aa sequence that forms a
> > (or perhaps a couple) of thermodynamically preferred structures has
> > the capacity to bind to one or more biologically relevant epitopes.
>
> That's an irrelevant counterpoint because simple binding is simple.
Complex binding is simple binding varied and repeated. But, focus,
whether I am right or wrong is not the question. The validity of your
calculation of "average gap size" is.
[snip discussion where Sean engages more bullshit numerology involving
antibodies. I would be happy to discuss why my view that most
sequence stretches in a protein can, in fact, provide a surface that
can interact with some biologically relevent molecule, and that this
is the only way to 'measure' "potential beneficial", but right now I
want to focus Sean's mind to defend his claim that he can actually
calculate a meaningful number for "average gap size".]
>
> < snip rest >
Especially the part that points out that the last step of your
calculation does not, in fact, produce a number that has any
relationship that I can see with "average gap size".
>
> Sean Pitmanwww.DetectingDesign.com
Ron O
>
The same old dishonesty. I guess that I can't expect more, can I?
Why run away and pretend? Do you ever, just once want to do something
decent and honest? Why obfuscate the issue if you know that you don't
have an alternative worth beans? What does it do for you? Why call
your web site DetectingDesign when you know that the ID scam artists
pulled a fast one on you? If they didn't, where is that ID science
that you claimed that you had?
Trying to make it look like someone else doesn't have an argument is
pretty stupid as well as dishonest. Why not just put up or shut up?
Make good on your claims. Why would that be hard to do for someone
that really had an argument and that wasn't a dishonest blowhard?
Talk about someone that doesn't have a real argument, just look in the
mirror. Really, how many years has it been that you have been running
from what you can't do? You made the claims, you didn't even try to
deny it in your pathetic post above. It is as if you think that if
you don't come out and actually tell the lie that it isn't a lie. How
bogus can you get?
Face it you are lying. If you aren't what are you doing?
Ron Okimoto
Seanpit
> Seanpit <seanpitnos...@naturalselection.0catch.com> wrote in news:f4b38f7a-
> 127a-4f20-942d-91cdde55f...@i29g2000prf.googlegroups.com:
>
>
>
>
>
> > On Dec 13, 7:15 pm, Ron O <rokim...@cox.net> wrote:
> >> On Dec 13, 1:36 pm, Seanpit <seanpitnos...@naturalselection.
>
> >> 0catch.com> wrote:
> >> > On Dec 11, 10:18 am, hersheyh <hershe...@yahoo.com> wrote:
>
> >> SNIP:
>
> >> Seans usual obfuscation scam.
>
> >> you could teach to school kids?
>
> >> What about that alternative to common descent and the evidence for it
> >> that you claimed was just as good as what science had?
>
> >> You made the claims, so why can't you make good on them? Why all this
> >> bull pucky about proteins if you don't have any science worth talking
> >> about, and you don't have an alternative worth jack?
>
> >> Why do you always run from your own claims? You don't even bother to
> >> deny that you made the claims, you just run and pretend. Does that
> >> make what you do any more honest?
>
> > The same old pjoratives without any real argument
>
> Well, yes - Mr. Okimoto is asking that you make good instead. Can you not?
Ron Okimoto makes these same sorts of comments without even reading
the argument presented. He doesn't make any substantive counter
arguments at all. Only pjorative comments. That's really all he's
good for. And, on those rare moments when he does try to come up with
a counter, he cannot defend his position without again resorting to
nothing more substantive than his endless string of pjoratives.
Sean Pitman
www.DetectingDesign.com
Seanpit
> On Dec 14, 9:26 am, Seanpit <seanpitnos...@naturalselection.
>
>
>
>
>
> 0catch.com> wrote:
> > On Dec 13, 7:15 pm, Ron O <rokim...@cox.net> wrote:
>
> > > On Dec 13, 1:36 pm, Seanpit <seanpitnos...@naturalselection.
>
> > > 0catch.com> wrote:
> > > > On Dec 11, 10:18 am, hersheyh <hershe...@yahoo.com> wrote:
>
> > > SNIP:
>
> > > Seans usual obfuscation scam.
>
> > > you could teach to school kids?
>
> > > What about that alternative to common descent and the evidence for it
> > > that you claimed was just as good as what science had?
>
> > > You made the claims, so why can't you make good on them? Why all this
> > > bull pucky about proteins if you don't have any science worth talking
> > > about, and you don't have an alternative worth jack?
>
> > > Why do you always run from your own claims? You don't even bother to
> > > deny that you made the claims, you just run and pretend. Does that
> > > make what you do any more honest?
>
> > The same old pjoratives without any real argument - the only thing one
> > can expect from Ron O.
>
> > > Ron Okimoto
>
>
> The same old dishonesty. I guess that I can't expect more, can I?
> Why run away and pretend? Do you ever, just once want to do something
> decent and honest? Why obfuscate the issue if you know that you don't
> have an alternative worth beans? What does it do for you? Why call
> your web site DetectingDesign when you know that the ID scam artists
> pulled a fast one on you? If they didn't, where is that ID science
> that you claimed that you had?
>
> Trying to make it look like someone else doesn't have an argument is
> pretty stupid as well as dishonest. Why not just put up or shut up?
> Make good on your claims. Why would that be hard to do for someone
> that really had an argument and that wasn't a dishonest blowhard?
>
> Talk about someone that doesn't have a real argument, just look in the
> mirror. Really, how many years has it been that you have been running
> from what you can't do? You made the claims, you didn't even try to
> deny it in your pathetic post above. It is as if you think that if
> you don't come out and actually tell the lie that it isn't a lie. How
> bogus can you get?
>
> Face it you are lying. If you aren't what are you doing?
Did you even read the arguments I presented in the original post of
this thread? Where are your specific counter arguments to the
arguments I presented Ron? Do you have anything other than these
endless pjoratives? What does this sort of mud-slinging do for you or
anyone else?
wf3h
0catch.com> wrote:
>
He doesn't make any substantive counter
> arguments at all. Only pjorative comments. That's really all he's
> good for. And, on those rare moments when he does try to come up with
> a counter, he cannot defend his position without again resorting to
> nothing more substantive than his endless string of pjoratives.
>
>
it staggers the imagination to think that sean thinks 'god did it' is
an answer to the origin and development of life. he insists that, by
observing nature, we can learn that natural processes have
supernatural causes.
the fact that we've never SEEN a supernatural cause doesn't phase him.
nor does the fact that EVERY natural event has been observed to have a
natural cause. nor does the fact that EVERY 'supernatural' cause has
failed. supernaturalism has a 100% track of failure. it's the most
perfect failure in human history.
he has a contradiction: he asserts that natural laws do not apply to
life. and he says he can prove this by observing that 'intelligence'
always uses natural laws. always. without fail.
he's never shown us an incident when intelligence was allowed to
violate a natural law. in fact, the ONLY intelligences we are aware of
in our world ALWAYS obey natural law.
sean's idea is cafeteria science. he wants to pick and choose which
laws of nature, and which observations, he's allowed to use to
demonstrate his ideas.
that's not science...it's religion.
and that's what sean believes.
John Vreeland
0catch.com> wrote:
> On Dec 14, 4:00 pm, Ron O <rokim...@cox.net> wrote:
>
>
>
> > On Dec 14, 9:26 am, Seanpit <seanpitnos...@naturalselection.
>
> > 0catch.com> wrote:
> > > On Dec 13, 7:15 pm, Ron O <rokim...@cox.net> wrote:
>
> > > > On Dec 13, 1:36 pm, Seanpit <seanpitnos...@naturalselection.
>
> > > > 0catch.com> wrote:
> > > > > On Dec 11, 10:18 am, hersheyh <hershe...@yahoo.com> wrote:
>
> > > > SNIP:
>
> > > > Seans usual obfuscation scam.
>
> > > > HeySeanwhat about telling us the science of ID that you said that
> > > > you could teach to school kids?
>
> > > > What about that alternative to common descent and the evidence for it
> > > > that you claimed was just as good as what science had?
>
> > > > You made the claims, so why can't you make good on them? Why all this
> > > > bull pucky about proteins if you don't have any science worth talking
> > > > about, and you don't have an alternative worth jack?
>
> > > > Why do you always run from your own claims? You don't even bother to
> > > > deny that you made the claims, you just run and pretend. Does that
> > > > make what you do any more honest?
>
> > > The same old pjoratives without any real argument - the only thing one
> > > can expect from Ron O.
>
> > > > Ron Okimoto
>
>
> > The same old dishonesty. I guess that I can't expect more, can I?
> > Why run away and pretend? Do you ever, just once want to do something
> > decent and honest? Why obfuscate the issue if you know that you don't
> > have an alternative worth beans? What does it do for you? Why call
> > your web site DetectingDesign when you know that the ID scam artists
> > pulled a fast one on you? If they didn't, where is that ID science
> > that you claimed that you had?
>
> > Trying to make it look like someone else doesn't have an argument is
> > pretty stupid as well as dishonest. Why not just put up or shut up?
> > Make good on your claims. Why would that be hard to do for someone
> > that really had an argument and that wasn't a dishonest blowhard?
>
> > Talk about someone that doesn't have a real argument, just look in the
> > mirror. Really, how many years has it been that you have been running
> > from what you can't do? You made the claims, you didn't even try to
> > deny it in your pathetic post above. It is as if you think that if
> > you don't come out and actually tell the lie that it isn't a lie. How
> > bogus can you get?
>
> > Face it you are lying. If you aren't what are you doing?
>
> Did you even read the arguments I presented in the original post of
> this thread? Where are your specific counter arguments to the
> arguments I presented Ron? Do you have anything other than these
> endless pjoratives? What does this sort of mud-slinging do for you or
> anyone else?
He may be slinging it, but it's your mud and it sticks.
hersheyh
0catch.com> wrote:
> On Dec 13, 9:17 pm, hersheyh <hershe...@yahoo.com> wrote:
>
>
>
> > > Yockey's estimate is in fact dealing specifically with CytoC
> > > functionality. I've noted this several times on my website myself.
> > > Sauer and Olsen are dealing with lambda repressor functionality, not
> > > CytoC.
>
> > Then why did you claim that *these* ratios represented "the ratio of
> > potential beneficial vs. non-beneficial for 100aa systems" [see your
> > statement above to determine if I am out-of-context]?
>
> What I claim is that these ratios give a rough idea as to the nature
> of sequence space given a certain level of minimum structural
> threshold requirements. Not all 100aa systems are at the same
> threshold level you know. Some 100aa systems are at much higher
> levels than are other 100aa systems. CytoC is pretty high up there
> for 100aa systems.
Sean, you are introducing a new variable here: "level of minimum
structural threshold requirements". But that is an intentional
biasing and confounding the calculation of "average gap size". It
also makes the use of total sequence space as the denominator absurd
and makes your claim that the ratio you present is the ratio of
"potential beneficial vs non--beneficial" sequences utter nonsense.
At minimum, you should say that the ratio is the ratio of all 100 aa
sequences that have high specificity and (necessarily, if one is
talking about the protein being assembled completely at random rather
than by evolutionary mechanisms that involve functional intermediates)
thus, will have an equally high "average gap size". IOW, if "average
gap size" is not really a function of the size of the protein, but a
function of the "level of minimum structural threshold requirements",
the entire calculation you did falls apart and your argument becomes
circular.
*If* you are using total sequence space as the denominator, you *must*
include, in the numerator, *all* potential beneficial sequences
regardless of whether that function is due to a particular set of 100
of the 100 aa's or due to 1 or 2 specific aa's in a protein of 100 in
which all of the rest of the sequence can vary by neutral drift.
Otherwise you are intentionally biasing your ratio and will not get
the "average gap size" for proteins of 100aa in length. You will get
the average gap size of proteins with a large number of invariant or
nearly invariant aa's, assuming they were assembled by the strawman
"747 in a tornado" mechanism that assumes no intermediate can be
functional -- except that the calculation you perform would not work
even for that.
Your calculation is GIGO numerology no matter how furiously you wave
your hands and try to qualify or justify it.
If you applied the same logic and, instead of looking at the function
of cytochrome c or lambda repressor (small proteins with many points
of contact with a substrate), looked at, say, the sequence of
fibrinogen peptide, you would get a quite different ratio.
Ron O
0catch.com> wrote:
> On Dec 14, 4:00 pm, Ron O <rokim...@cox.net> wrote:
>
>
>
>
>
> > On Dec 14, 9:26 am, Seanpit <seanpitnos...@naturalselection.
>
> > 0catch.com> wrote:
> > > On Dec 13, 7:15 pm, Ron O <rokim...@cox.net> wrote:
>
> > > > On Dec 13, 1:36 pm, Seanpit <seanpitnos...@naturalselection.
>
> > > > 0catch.com> wrote:
> > > > > On Dec 11, 10:18 am, hersheyh <hershe...@yahoo.com> wrote:
>
> > > > SNIP:
>
> > > > Seans usual obfuscation scam.
>
> > > > HeySeanwhat about telling us the science of ID that you said that
> > > > you could teach to school kids?
>
> > > > What about that alternative to common descent and the evidence for it
> > > > that you claimed was just as good as what science had?
>
> > > > You made the claims, so why can't you make good on them? Why all this
> > > > bull pucky about proteins if you don't have any science worth talking
> > > > about, and you don't have an alternative worth jack?
>
> > > > Why do you always run from your own claims? You don't even bother to
> > > > deny that you made the claims, you just run and pretend. Does that
> > > > make what you do any more honest?
>
> > > The same old pjoratives without any real argument - the only thing one
> > > can expect from Ron O.
>
> > > > Ron Okimoto
>
>
> > The same old dishonesty. I guess that I can't expect more, can I?
> > Why run away and pretend? Do you ever, just once want to do something
> > decent and honest? Why obfuscate the issue if you know that you don't
> > have an alternative worth beans? What does it do for you? Why call
> > your web site DetectingDesign when you know that the ID scam artists
> > pulled a fast one on you? If they didn't, where is that ID science
> > that you claimed that you had?
>
> > Trying to make it look like someone else doesn't have an argument is
> > pretty stupid as well as dishonest. Why not just put up or shut up?
> > Make good on your claims. Why would that be hard to do for someone
> > that really had an argument and that wasn't a dishonest blowhard?
>
> > Talk about someone that doesn't have a real argument, just look in the
> > mirror. Really, how many years has it been that you have been running
> > from what you can't do? You made the claims, you didn't even try to
> > deny it in your pathetic post above. It is as if you think that if
> > you don't come out and actually tell the lie that it isn't a lie. How
> > bogus can you get?
>
> > Face it you are lying. If you aren't what are you doing?
>
> Did you even read the arguments I presented in the original post of
> this thread? Where are your specific counter arguments to the
> arguments I presented Ron? Do you have anything other than these
> endless pjoratives? What does this sort of mud-slinging do for you or
> anyone else?
>
> > Ron Okimoto
>
>
Let's see.... No admission that what I claim is all true. Just
claiming that the other guy has the problem and not Sean. Oh and
running away without addressing the issue. Gee, how predictable can
you get? How dishonest can you get? In the response to Lee above he
even lies about the rare moments. I would contend that Sean would
have to run through a whole lot of posts just to find some rare
instance where I didn't demonstrate that Sean was full of gas.
Sean do that, bring up the references, show that they are rare. You
should show that they are rare when I bothered to take you seriously.
That would be, what? More than 5 years ago? Just randomly take 50 of
my posts where I addressed the issues that you brought up and count up
the times that I didn't set you on your can. You might find one such
post where you may have had some point, and probably not even that if
you only searched 50.
More than 5 years of you running a bogus obfuscation smoke screen,
when you know for a fact that you don't have jack to back it up.
What alternative do you have? What is the great evidence to back it
up? What science would you have taught about intelligent design? Why
bother to keep calling your slock web site Detecting design when you
know it isn't detecting anything except the next creationist scam?
The ID perps lied to you, didn't they? You know that for a fact or
you would have some science to put forward that supported the ID
claptrap.
No one has to counter your junk. It has all been done years ago.
Just look at this thread, you are still going on about proteins. How
stupid is that? What happened to Hall? You ran recently without
acknowledging that you goofed again. It wasn't that long ago that you
tried to counter the claim that Hall got his trick to work in other
species of bacteria. Didn't I put up a ref where not only was another
species involved by another protein had been found that could evolve
beta gal activity. You probably already knew that years ago because I
found it out arguing with you about it, but you tried to run a fast
one to get out of this very thing that you are still running from. It
took you years to try and pull that scam. You never tried to weasel
out of that point for years. What did you expect, that I'd forget how
do do a PubMed search? How dishonest is that?
What does the actual data tell you about your bogus notions of protein
sequence space? Two species of bacteria with only 2000 proteins in
their genomes to mutate and they can evolve beta gal activity. How is
that possible if what you claim about sequence space is at all true?
What is your alternative and the evidence to back it up? Doesn't
science have a verified means of getting what it needs for biological
evolution? What is your alternative? How does it match up with what
we can actually observe happening? How many species do you think Hall
tested and how related were they? Let's say that Hall tested 100
(unlikely). That would be just 200,000 protein sequences scored to
see if he could evolve beta gal activity and select for it. And it
worked, not just once, but at least twice. What is the probability
that, that would happen if your bogus claims were correct about
protein sequence space and the number of viable sequences?
You keep denying the antibody example, claiming that it isn't high
enough about something or other to satisfy you, but you have no
alternative do you? A maximum of 10E12 sequences are tested at any
time and the system works nearly all the time. Such a tiny fraction
of the sequence space has to be sampled to get funtional antibodies
that it makes your claims out to be a joke. You've known for years
that not only can they get antibody activity, but Abzymes demonstrate
that enzymatic function can evolve using the same system.
You know all this, but you keep blowing smoke. Not only that, but you
try to make it look like it is the other guys problem. That is just
sad.
Why not just put up or shut up? You don't deny that you made the
claims, so make good on them. It isn't my problem that you keep
running, it is your problem. You are doing the running and blowing
the smoke.
Ron Okimoto
Seanpit
> On Dec 14, 11:37 am, Seanpit <seanpitnos...@naturalselection.
>
> 0catch.com> wrote:
> > On Dec 13, 9:17 pm, hersheyh <hershe...@yahoo.com> wrote:
>
> Re-including what Sean said in the appendix where he "calculates"
> average gap size. Sean seems to have inadvertently deleted it.
The appendix calculation has not been deleted. It's still there. I
even added a link to this thread.
> But
> it is important because Sean seems to be claiming that I am
> misrepresenting what he says this series of calculations does. Sean
> also tries to throw the issue back to me by asking me for the
> equations I would use. The question here, however, is not whether I
> or anyone else can calculate what Sean wants calculated. It is
> whether or not the numbers that Sean calculates are 1) meaningful and
> 2) give him what he claims they do.
Ah, so you can simply assume that the gaps are small, without
evidence, while anyone who suggests that the gaps are in fact enormous
must provide some evidence? That's most interesting. You are right
by default? I see how it is . . .
I've made it very clear in the referenced essay and in numerous posts
in this forum and elsewhere in numerous places on my website, that the
degree of specificity is important for defining minimum structural
threshold requirements. The minimum size threshold is not the only
criterion. Yet, when presenting my position, you present it this
way. This is a strawman mischaracterization.
For those systems that require at least 100aa with a fair degree of
specificity, equivalent to at least the degree of specificity for
unique systems of function, like lambda repression or CytoC, the
estimates of Sauer, Olsen, and Yockey are quite relevant. Note this
second part of the equation which you always leave out of your
strawman misrepresentation.
> If
> he were to change this to more accurately reflect what he thinks the
> ratio of Yockey and Sauer do mean, he would have said something like
> the following: "The ratio of potential beneficial vs. non-beneficial
> sequences for 100 aa systems is unknown, but if one assumes that the
> number of potential beneficial systems is accurately estimated by
> counting the number of sequences that have x level of cytochrome c
> function in the context of modern systems by looking at how mutation
> affects that particular function, then....." That would, then,
> clearly indicate the assumptions that went into his belief that the
> Yockey and Sauer ratio has some relationship with "potential
> beneficial" sequences. But that is not what Sean has actually done.
> What he has done is say: "Using an average between the calculations
> of Yockey and Sauer, the ratio of potential beneficial vs. non-
> beneficial for 100aa systems is about 1e-40."
You forget that threshold limitation presented here has not only a
minimum of 100aa but a fair degree of specificity. You don't seem to
have grasped the relevance of this second part of the equation because
you continually attempt to compare low-level systems with higher level
systems. For example, you present antibody binding functions, which
are very low-level, with much higher-level systems as if they were
somehow on the same level. You forget, or didn't know, that antibody
binding, by itself, does not require more than 20 or so very loosely
specified residue positions. There simply is no comparison.
> > > Then why did you claim that *these* ratios represented "the ratio of
> > > potential beneficial vs. non-beneficial for 100aa systems" [see your
> > > statement above to determine if I am out-of-context]?
>
> > What I claim is that these ratios give a rough idea as to the nature
> > of sequence space given a certain level of minimum structural
> > threshold requirements. Not all 100aa systems are at the same
> > threshold level you know. Some 100aa systems are at much higher
> > levels than are other 100aa systems. CytoC is pretty high up there
> > for 100aa systems.
>
> Irrelevant.
This single word comment nicely illustrates the confusion of yours
I've been talking about here. The degree of sequence specificity is
not irrelevant to the problem at all. It is a main part of the
equation that defines levels of minimum structural threshold
requirements.
> The fact remains that you are *claiming* that the ratio
> you ACTUALLY use to calculate "average gap size" represents "potential
> beneficial vs non-beneficial" sequences
I'm specifically talking about beneficial vs. non-beneficial at a
given threshold level of minimum structural requirements - not just
any and all levels.
> when, as you agree above, it
> does not. Instead it is "a rough idea".
I've always said it is a rough estimate. We simply don't have enough
information to be exact. This doesn't mean that it is impossible to
have any idea at all as to the likely ratio that exists at a given
threshold level. I mean, if it was impossible, your own theory as to
how random mutation and function-based selection actually did the job
would be baseless as well. The lack of evidence works both ways
here. Your theory is just as much affected by the lack of evidence as
is mine.
> It is dependent on
> "threshold level". Cyto C is "high threshold". If you think you need
> the ratio of "potential beneficial vs non-beneficial for a 100aa
> system" to calculate "average gap size" you have to convince us that
> the ratio you used actually does equal or (at least) come close to
> equaling "potential beneficial vs non-beneficial for a 100aa system".
> Simply asserting that a number that even you admit is NOT "potential
> beneficial" sequences represents "potential beneficial" sequences will
> not do.
I explain the reason why using such calculations does in fact give a
pretty good idea as to the total number of beneficial targets that
likely exist at a given threshold level.
< snip repetitive >
> > > You did not say that this ratio represents all 100 aa
> > > sequences that have all the properties needed to act as a lambda
> > > repressor against a modern lamda gene site.
>
> > Yes, I did.
>
> ********* a reminder of what Sean's actual claim was
> Using an average between the calculations of Yockey and Sauer, the
> ratio of potential beneficial vs. non-beneficial for 100aa systems is
> about 1e-40."
> *******
>
> That is, Sean is either *actually* or *apparently* claiming that there
> is no difference between the ratio of sequences that can act as a
> lambda repressor in a modern system to total sequence space and the
> ratio of "potential beneficial vs. non-beneficial" sequences.
It is a claim that there is no essential difference *at this level* of
minimum structural threshold requirements. I also explain what I mean
by "no essential difference" as well in my website and in this forum
many times.
> A
> simple, "Oooops. I misspoke and should have said....Thank you for
> pointing out the inadvertant sloppiness in my wording." would do so
> long as it is followed by a correction that points out what this ratio
> *really* is.
You just don't understand that these ratios are in fact roughly
representative of the total at a given level.
> > I never said that the CytoC or lambda repressor data represented all
> > potentially beneficial sequences. What I said was that it can give a
> > rough idea as to the likely number of all potentially beneficial
> > sequences at a particular level of size AND specificity requirements.
>
> Sean, why do you claim that this is what you said when I can easily
> point out what you really said: "Using an average between the
> calculations of Yockey and Sauer, the ratio of potential beneficial
> vs. non-beneficial for 100aa systems is about 1e-40." This is a claim
> that the ratio you presented here represents (is a good estimate of)
> ALL "potential beneficial vs. non-beneficial" sequences and is not
> simply the ratio of "all sequences that have the specific beneficial
> function of being able to replace w.t. cytochrome c activity in the
> context of a modern mitochondrion" or (and importantly not 'and') the
> ratio of "all sequences that have the specific beneficial function of
> being able to replace w.t. lambda repressor in the context of a modern
> bacterial cell".
Nope. I mean all beneficial sequences from the perspective of any
population of living things that currently exists or is likely to have
ever existed - - at a given level of structural threshold
requirement. Again, minimum threshold requirements are determined by
both size AND specificity minimums.
> > While this idea is admittedly a rough approximation, the overall ratio
> > and pattern can be suggested to a degree useful enough to make the
> > pattern of exponentially declining ratios between beneficial targets
> > and non-targets quite obvious.
>
> That's the second point. And, naturally, I didn't see you mention how
> "rough" an "approximation" the ratio you present is. Nor even a hint
> that it was an approximation of the number you claim it represents
> ("the ratio of potential beneficial vs. non-beneficial" sequences) by
> using a quite different ratio.
I've mentioned the roughness of the approximation many times in this
forum and elsewhere on my website. And, to make this even more clear,
I've added this explanation to the passage in question, as well as a
link to this thread.
< snip repetitive >
> > However, if you consider the specificity requirements
> > for the average protein in a larger multiprotein system like a
> > flagellar motility system, the ratio change involved isn't going to be
> > remotely represented by a 2-fold extrapolation (a 10-fold
> > extrapolation maybe).
>
> How do you know that?
Because, the average size of a protein in a flagellar system is about
300aa. Of these 300aa, a two-fold extrapolation would mean that all
the residue positions could be replaced by any of 19 different amino
acids at the same time without a complete loss if its function as part
of the flagellar motility system. That notion isn't true. What is
true is that many of the positions could be replaced, one at a time,
by perhaps 8 or 9 different amino acids, generally with the same basic
chemical nature (i.e., acidic, basic, polar non-polar, etc). This
degree of specificity would result is more than a 10-fold
extrapolation.
> > But, even if your 2-fold suggestion was
> > representative of such a system, it would be devastating to the ToE.
Which is also a key point.
> > > You, apparently out of thin air, assume that there is
> > > absolutely NO increase in the number of beneficial sequences with
> > > increases in length. Why you didn't choose to arbitrarily declare
> > > that the number of "potential beneficial" sequences *decreased* with
> > > increasing length I don't know.
>
> > Oh come on now. You yourself admit that Dawkins is correct in saying
> > that however many ways there are to make something alive there are
> > vastly more ways that it could be dead. The reason for this is
> > because there are so many more ways to mess up a system compared to
> > the number of ways there are for it to be in working order. And, the
> > more parts that are needed for a system, the exponentially more ways
> > there are to mess it up without producing any other useful system at
> > an equivalent degree of complexity. This should be self-evident to
> > you. It is a fact in every known language system. It can be fairly
> > well quantitated, directly, in many language/information systems -
> > like the English language or computer code. It is a very easy
> > extrapolation to see that the very same thing is true of genetic
> > information systems.
>
> Where is the evidence that *specifically* says that there is no change
> in the number of "potential beneficial" English words or computer
> codes as the length of the word or code is increased?
What do you mean? There most certainly is a change in the number of
potentially beneficial English words or computer codes as length
increases (from a given system or perspective in a given environment -
of course). This number increases significantly. The problem is that
the number of non-beneficial sequences increases even more
significantly with increasing length - exponentially more.
> I thought your
> argument using English was about the consequences of mutation of
> already present English words or code rather than a description of a
> mechanism of their construction.
It is a description of overall sequence space at a given threshold
level - how many targets vs. non-targets are there?
> Where is the evidence that
> increasing genetic information systems (for example, by slightly
> modifying different homeobox genes so that they have overlapping, but
> slightly different functions and can partially substitute for each
> other -- a definitely more complex system than having a single
> homeobox gene) makes the system *more* fragile. Seems to me that
> redundancy and partial redundancy makes a genetic information system
> more robust rather than more fragile. Besides, we are talking about
> your apparently arbitrary choice of a very specific exponential
> relationship for proteins as length gets larger. One where,
> *mathematically*, the numerator is independent of the denominator and
> does not change. The numerator is what you call "[all] potential
> beneficial" sequences.
The denominator does change. The denominator represents the size of
sequence space itself at different levels. As the minimum length
requirement increases, the denominator increases exponentially. For
example, what is the denominator for 100aa sequences? It is 20^100.
What about for 500aa sequences? It is 20^500. Now, what about the
numerator? That's the question here. Does the numerator increase,
yes. But, does it increase at nearly the same rate as the
denominator? No. Therein lies the reason why the ratio between
targets and non-targets decreases exponentially with increasing
minimum threshold requirements.
> > If you think otherwise, please do provide at least some evidence for
> > what you think the real ratio might be. Otherwise, your entire theory
> > on how your proposed mechanism actually works is based on a complete
> > lack of evidence. You are basically left with the conclusion that you
> > have no idea how your mechanism works.
>
> I know how the mechanism of evolution works. This ratio is irrelevant
> to that mechanism.
You mean you simply assume that the ratio is irrelevant because you
think that regardless of what the true ratio is, the gap distance
could be small therefore you assume that it was small. That's not
evidence Howard. That's blind faith.
> Average gap size (even if you could calculate it)
> would be irrelevant.
Not remotely true. This statement goes completely counter to
statistics and the observed evidence of the location of systems within
sequence/structure space. What is the minimum likely distance?
That's the question. The answer to this question is based entirely on
the average distance. Your assumption that the minimum possible
distance of one is at all relevant to answering this question is
nonsense - it is completely against the statistics of averages and
therefore against science.
> But even if I am wrong about that, that doesn't
> make your assumption that the ratio of what you call "potential
> beneficial vs. non-beneficial" sequence ratio [sic, we both agree that
> that is not what the ratio really is] changes exponentially with
> sequence length at just the rate which would mean that the number of
> "potential beneficial" sequences does not change at all with
> increasing size [for a given level of specificity].
I've always said that the number of potentially beneficial sequences
increases with increasing size. It is just that this increase is
exponentially less than the increase in non-beneficial sequences for
higher and higher threshold levels. That difference in increase
(because the absolute number of targets and non-targets both increase)
is what produces the exponential decline in the ratio between targets
and non-targets in sequence/structure space.
> > The only thing that you know
> > is that it would have to work in a space were the gaps were small.
>
> Which, as I point out is *why* so much evolution involves duplication
> and divergence.
Duplication just produces more of the same starting point. It doesn't
search out sequence/structure space. Divergence is simply random walk
from that starting point. There is no significant improvement of the
odds of success here. If the gaps are small, success will be rapid.
However, if the gaps are larger in a linear degree, success will be
exponentially reduced. No form of random search is going to change
that fact.
And, don't come back again with the argument that the mechanism of
search isn't random because of natural selection. Again, as a pre-
emptive counter, natural selection doesn't come into play until the
next target is actually found. Until this point, natural selection is
powerless as a guiding force and is not involved in the search for
targets - a search that is entirely random.
> > But, as far as determining the likelihood that the gaps are indeed as
> > small as they would need to be for your theory to work, you have no
> > basis in any evidence, not even rough estimates, whatsoever.
>
> Average gap size is irrelevant. Minimum possible or minimum actual
> gap sizes are not. They are not a function of 'average gap size'.
The minimum possible size is not a function of the average gap size
because the minimum possible gap size is always one. Your notion that
this is somehow important to this issue is quite amazing. Don't you
see that the minimum possible gap distance says absolutely nothing
about the minimum likely distance? It is the likely minimum that is
important here, not the minimum possible distance. This minimum
possible distance is completely irrelevant outside of your hope that
it might be the actual minimum. This hope of yours is based on
nothing but blind faith my friend. The minimum likely distance is
what is at issue here. This distance is very much related to the
average distance.
< snip repetitive >
> > The exponential relationship is based on a lot of data, to include
> > extrapolations from other language/information systems and
> > experimental data that shows a clear stalling out effect of evolution
> > at higher levels that is exponential.
>
> Sean, we both agree that as the minimum actual gap size is increased
> (say, by eliminating ebg from E. coli genome) that evolving a new
> function that *must* cross a bigger gap becomes more difficult. That
> happens whatever you calculate as the "average gap size", which is a
> value that would not change by eliminating ebg or having it present.
> My argument is that when evolution happens, it is far more likely to
> be in the particular situation where the actual minimum gap size is
> small (i.e., when an ebg is present) than when the actual minimum gap
> size is large (i.e., when an ebg is absent). And, of course, that the
> resulting lactase will have extensive sequence similarity to the gene
> from which this new function is derived. But, again, whether my model
> is right or wrong does not determine whether or not your calculation
> is based on misinterpreting what numbers mean and inventing specific
> (and self-serving) mathematical relationships.
Of course evolution is more likely to happen with the gap size is
small than when it is large - exponentially more likely. The question
is, how likely is it that the gap size will be small enough to cross
in a reasonable amount of time? You don't even think about these odds
because of your faith that what we see was the result of small gap
sizes. You don't even consider the odds of what you are saying. You
just accept on blind faith that the gap size must have been small or
else evolution couldn't have happened. Since you know, somehow, that
evolution did happen, you therefore conclude that he gap sizes crossed
where small - regardless of threshold levels.
None of these assumptions of yours are based on any sort of evidence
Howard. You have no direct evidence that the gap sizes were small or
likely to have been small. Your use of ebg as an example is nonsense
because lactase is a low-level function - requiring a minimum of no
more than a three or four hundred fairly specified residues at most.
The odds that a target would be fairly close at this low level are
pretty good actually. The odds are exponentially worse at higher
levels. That is why single protein evolution at such low levels has
been observed quite a number of times, while higher level evolution,
beyond the 1000aa threshold, has never been observed even once.
> > > Actually, *my* mechanism says that the ratio of beneficial targets to
> > > non-targets is irrelevant, because what counts is the "minimum actual
> > > gap size" or even the "minimum possible gap size" in some cases.
>
> > And what do you think the actual gap size is based on?
>
> That was "minimum actual gap size". It is based on the specifics of
> context and existing sequences.
Exactly - and what is the basis of your notion that the context and
existing sequences will be just right so that the next closely target
will always be pretty close to the minimum possible distance of one?
- regardless of the level of threshold requirements in question? Hmmm?
> > The likelihood
> > that the actual gap size is as small as you need it to be (often
> > suggested by you as being very close or equivalent to the minimum
> > possible gap size), is based on the average gap size, which in turn is
> > based on the ratio of targets to non-targets.
>
> Sean, the minimum possible gap size is NOT based on "average gap
> size".
That's completely irrelevant.
> Neither is "minimum actual gap size".
That's statistically mistaken. Minimum likely distances are indeed
based on average distances. That is what the Poisson distribution is
all about.
> The minimum actual gap
> size for the generation of a lactase in E. coli depends not on some
> number that I determine to be "average gap size". It is a function of
> the presence or absence of ebg. The specifics of context and existing
> sequences.
The presence or absence of a close sequence, like ebg, is indeed a
function of the average gap distance. And, at this relatively low
threshold level of about 400aa, this actual minimum gap distance of
one is not that unlikely - statistically and in observed reality for a
large population. However, the existence of such a small minimum
approximating the smallest possible minimum is exponentially less
likely at higher thresholds - both statistically and in observed
reality (i.e., it has yet to be seen in reality beyond the 1000aa
threshold).
< snip rest >
Sean Pitman
www.detectingDesign.com
Seanpit
< snip pointless pejoratives >
Finally - some actual arguments.
> What does the actual data tell you about your bogus notions of protein
> sequence space? Two species of bacteria with only 2000 proteins in
> their genomes to mutate and they can evolve beta gal activity. How is
> that possible if what you claim about sequence space is at all true?
The odds are actually pretty good because the lactase function is at a
pretty low level of minimum structural threshold requirements - i.e.,
less than 400 fairly specified residues. The ratio of lactases vs.
non-lactases at this level is actually pretty high. The same thing is
true of other biosystems that are based on equivalently small single
proteins. Such evolution actually happens fairly often at this
level. But, it doesn't happen at all at higher levels - i.e., beyond
the 1000aa threshold. That's what's most interesting about the gap
problem. It is demonstrably exponential in nature.
> What is your alternative and the evidence to back it up? Doesn't
> science have a verified means of getting what it needs for biological
> evolution?
Yes, it does. But, only at very low levels of minimum structural
threshold requirements (i.e., well below the 1000aa threshold).
> What is your alternative? How does it match up with what
> we can actually observe happening? How many species do you think Hall
> tested and how related were they?
Hall only tested one species - E. coli. But, the same thing is likely
to happen in other species occasionally at this level of functional
complexity.
> Let's say that Hall tested 100
> (unlikely). That would be just 200,000 protein sequences scored to
> see if he could evolve beta gal activity and select for it. And it
> worked, not just once, but at least twice.
Actually, it only worked once. Hall did try to evolve Beta gal
activity without the ebg sequence, but it didn't work. After about
40,000 generations of trying, Hall gave up and said that his double
mutant colony had, "Limited evolutionary potential". This goes to
show that even at the 400aa level evolution isn't always easy - even
for a large population. The stalling out effect is starting to become
clear at this level.
> What is the probability
> that, that would happen if your bogus claims were correct about
> protein sequence space and the number of viable sequences?
Pretty good. Evolution happens quite often at this level actually.
What you never seem to consider, however, is why evolution doesn't
happen at higher levels?
> You keep denying the antibody example, claiming that it isn't high
> enough about something or other to satisfy you, but you have no
> alternative do you? A maximum of 10E12 sequences are tested at any
> time and the system works nearly all the time. Such a tiny fraction
> of the sequence space has to be sampled to get funtional antibodies
> that it makes your claims out to be a joke. You've known for years
> that not only can they get antibody activity, but Abzymes demonstrate
> that enzymatic function can evolve using the same system.
Actually, the sequence space involved with antibody binding is quite
small - only about 20^20 sequences. This sequence space can be
exhaustively searched by a relatively small population of immune
cells. Not a problem at this very low level.
You see, all of your examples that you have ever presented are very
low-level examples - every one. None of them comes remotely close to
the 1000aa threshold where sequence space is the size of 20^1000.
I've pointed this out to you many many times, but you act as if
nothing was ever said. You don't even try to address this point, but
act like it is completely irrelevant to the issue and go on presenting
your low-level examples like they somehow explain away the problem.
> You know all this, but you keep blowing smoke. Not only that, but you
> try to make it look like it is the other guys problem. That is just
> sad.
Just answer the question Ron. It isn't just smoke. It is a valid
simple question. Why does evolution not produce any novel beneficial
functional systems that require a minimum of more than 1000 fairly
specified residues? Hmmmmm? Care to take a crack at answering that
question?
> Why not just put up or shut up? You don't deny that you made the
> claims, so make good on them. It isn't my problem that you keep
> running, it is your problem. You are doing the running and blowing
> the smoke.
This paragraph doesn't even make sense. I've presented some simple
questions. Who is the one trying to avoid answering them? I've
answered yours, why not at least try to answer mine? Instead, you
continually present your usual low-level examples and an endless
string of pejoratives? How is that helpful to me or anyone else who
might also like to hear what you have to say regarding this question?
Seanpit
> On Dec 14, 11:37 am, Seanpit <seanpitnos...@naturalselection.
>
>
>
>
>
> 0catch.com> wrote:
> > On Dec 13, 9:17 pm, hersheyh <hershe...@yahoo.com> wrote:
>
> > > > Yockey's estimate is in fact dealing specifically with CytoC
> > > > functionality. I've noted this several times on my website myself.
> > > > Sauer and Olsen are dealing with lambda repressor functionality, not
> > > > CytoC.
>
> > > Then why did you claim that *these* ratios represented "the ratio of
> > > potential beneficial vs. non-beneficial for 100aa systems" [see your
> > > statement above to determine if I am out-of-context]?
>
> > What I claim is that these ratios give a rough idea as to the nature
> > of sequence space given a certain level of minimum structural
> > threshold requirements. Not all 100aa systems are at the same
> > threshold level you know. Some 100aa systems are at much higher
> > levels than are other 100aa systems. CytoC is pretty high up there
> > for 100aa systems.
>
> Sean, you are introducing a new variable here: "level of minimum
> structural threshold requirements".
This isn't a new variable. It has been the basis of my whole position
since the beginning. I don't know how many times I've used this very
same phrase for you directly in many many posts in the past? It has
to be over a 50 times. How can you not remember?
> But that is an intentional
> biasing and confounding the calculation of "average gap size".
Not at all. The minimum structural threshold requirements are what
form the basis of the ratio of targets vs. non-targets - - and hence
the "average gap size" between targets in sequence/structure space.
This average in turn is then used to determine the most likely minimum
gap distance between a given starting point and the next closest
target.
_Arthur
some scientists, Yockey and Sauer, observed that the cytochrome
proteins of many species differed significantly (albeit with the same
basic structure), for the same overall functionality, and so their
genes differed.
Sean Pitt took that "1000 aa" divergence, and promulgated that *ANY*
sequence giving a biologically useful protein would be separated by
at least a 300 point mutations "gap" from *ANY* other protein of any
different function/usefulness.
Now the Pitt Man concedes that his 1000 number was a "rough estimate*,
which should make is 300 gap even rougher.
Of course, Pitts steadfastly refuses to correct his website, despite
the great many biological, mathematical, and logical absurdities
pointed to him, some of which he even very, very, very grudgingly half-
admitted, after years of handwaving, thread-pounding and
grandstanding.
Did I get any of it right ? Roughly ?
Seanpit
Not even close. The differences in sequences that have a given
function, like CytoC functionality, forms the degree of specificity
that this function requires to work within a certain minimum size
requirement. This specificity flexibility does not represent the gap
distance. The gap distance is the distance between any sequence that
can produce a beneficial function, like CytoC, and the next closest
beneficial sequence that can produce a novel beneficial function that
has the same or greater minimum structural threshold requirements.
You equate a gap of 300 residue differences with specificity
flexibility. That is a fundamental error. The gap distance is the
distance between the edge of one beneficial island cluster of
sequences and the next closest edge of beneficial island sequences in
sequence/structure space.
Do you see the distinction? - Because it is fundamentally important to
understanding the problem of expanding gaps with increasing minimum
threshold requirements.
Sean Pitman
www.DetectingDesign.com
Lee Oswald Ving
news:d3f0b76b-1131-445c...@d27g2000prf.googlegroups.com:
You could have simply admitted you could not. Would that have really been
so hard?
I wonder just how long you've been running from these particular
question?
> He doesn't make any substantive counter
> arguments at all.
"What about that alternative to common descent and the evidence for
it that you claimed was just as good as what science had?"
> Only pjorative comments.
You're operating on a different definition of "pjorative" than everyone
else so far.
> That's really all he's
> good for. And, on those rare moments when he does try to come up with
> a counter, he cannot defend his position without again resorting to
> nothing more substantive than his endless string of pjoratives.
I don't find projection very convincing, Pitman, nor have I ever met
anyone who does. Perhaps you like to try some...oh, substantive instead?
_Arthur
No, I don't "see" your distinction. I see word soup and handwaving.
As expected.
_Arthur
0catch.com> wrote:
> You equate a gap of 300 residue differences with specificity
> flexibility. That is a fundamental error. The gap distance is the
> distance between the edge of one beneficial island cluster of
> sequences and the next closest edge of beneficial island sequences in
> sequence/structure space.
> Sean Pitmanwww.DetectingDesign.com
So, Sean, If I was to provide any protein which is used by any
organism for 2 completely unrelated purposes, your 300aa PittMan Gap
Theory would be falsified, would it not ?
We would have a 0-gap, but each of the 2 functions would be the
starting point of a new "cluster" of functional/useful proteins. The
clusters would possibly diverge as measured in numbers of aa from the
common single protein starting point. And at any time, one slightly
different protein of either cluster could show an enzyme or binding
property absent in the cluster, and branch off as a new cluster. We
would now have 3 families of proteins, from a single "starting point".
So, are you confident I cannot find a brain neurotransmitter protein
with an analog used in the gut for digestion ? Or another
neurotransmitter used as a polymer in spider silk ?
Do you agree that the existence of any such protein would entirely
destroy the Pittman Neuttral Gap theory ?
I don't expect you to.
R. Baldwin
news:bcb599e0-c4cf-47ad...@i29g2000prf.googlegroups.com...
> On Dec 15, 8:04 am, hersheyh <hershe...@yahoo.com> wrote:
>> On Dec 14, 11:37 am, Seanpit <seanpitnos...@naturalselection.
>>
>>
>>
>>
>>
>> 0catch.com> wrote:
>> > On Dec 13, 9:17 pm, hersheyh <hershe...@yahoo.com> wrote:
>>
>> > > > Yockey's estimate is in fact dealing specifically with CytoC
>> > > > functionality. I've noted this several times on my website myself.
>> > > > Sauer and Olsen are dealing with lambda repressor functionality,
>> > > > not
>> > > > CytoC.
>>
>> > > Then why did you claim that *these* ratios represented "the ratio of
>> > > potential beneficial vs. non-beneficial for 100aa systems" [see your
>> > > statement above to determine if I am out-of-context]?
>>
>> > What I claim is that these ratios give a rough idea as to the nature
>> > of sequence space given a certain level of minimum structural
>> > threshold requirements. Not all 100aa systems are at the same
>> > threshold level you know. Some 100aa systems are at much higher
>> > levels than are other 100aa systems. CytoC is pretty high up there
>> > for 100aa systems.
>>
>> Sean, you are introducing a new variable here: "level of minimum
>> structural threshold requirements".
>
> This isn't a new variable. It has been the basis of my whole position
> since the beginning. I don't know how many times I've used this very
> same phrase for you directly in many many posts in the past? It has
> to be over a 50 times. How can you not remember?
Google is your friend. 4 hits on the phrase, all within the past week.
[snip]
hersheyh
0catch.com> wrote:
> On Dec 14, 1:23 pm, hersheyh <hershe...@yahoo.com> wrote:
>
> > On Dec 14, 11:37 am, Seanpit <seanpitnos...@naturalselection.
>
> > 0catch.com> wrote:
> > > On Dec 13, 9:17 pm, hersheyh <hershe...@yahoo.com> wrote:
>
> > Re-including what Sean said in the appendix where he "calculates"
> > average gap size. Sean seems to have inadvertently deleted it.
>
> The appendix calculation has not been deleted. It's still there. I
> even added a link to this thread.
>
> > But
> > it is important because Sean seems to be claiming that I am
> > misrepresenting what he says this series of calculations does. Sean
> > also tries to throw the issue back to me by asking me for the
> > equations I would use. The question here, however, is not whether I
> > or anyone else can calculate what Sean wants calculated. It is
> > whether or not the numbers that Sean calculates are 1) meaningful and
> > 2) give him what he claims they do.
>
> Ah, so you can simply assume that the gaps are small, without
> evidence,
As I pointed out, *if* evolution works by finding the places where
small gaps work, where new proteins are a consequence of duplication
and modification or chimeric duplication formation, one consequence
will be that there will be a historical pattern of similarities. That
is "trees of protein families". That is both a specific prediction of
the methodology and an observation of empirical reality.
> while anyone who suggests that the gaps are in fact enormous
> must provide some evidence? That's most interesting. You are right
> by default? I see how it is . . .
Bullshit. I am not *assuming* that gaps are small. I have pointed
out examples of proteins for which there is evidence or a reasonable
way that they could have evolved via a small series of steps. All you
have presented is what is demonstrably GIGO numerology to support
*your* hypothesis that the average gap size is large.
Then your entire argument becomes circular and based on the assumption
that the *only* way the function you name could arise is by random
assembly of amino acids. Yet you claim that your calculation does not
do this.
>
> For those systems that require at least 100aa with a fair degree of
> specificity, equivalent to at least the degree of specificity for
> unique systems of function, like lambda repression or CytoC, the
> estimates of Sauer, Olsen, and Yockey are quite relevant. Note this
> second part of the equation which you always leave out of your
> strawman misrepresentation.
>
> > If
> > he were to change this to more accurately reflect what he thinks the
> > ratio of Yockey and Sauer do mean, he would have said something like
> > the following: "The ratio of potential beneficial vs. non-beneficial
> > sequences for 100 aa systems is unknown, but if one assumes that the
> > number of potential beneficial systems is accurately estimated by
> > counting the number of sequences that have x level of cytochrome c
> > function in the context of modern systems by looking at how mutation
> > affects that particular function, then....." That would, then,
> > clearly indicate the assumptions that went into his belief that the
> > Yockey and Sauer ratio has some relationship with "potential
> > beneficial" sequences. But that is not what Sean has actually done.
> > What he has done is say: "Using an average between the calculations
> > of Yockey and Sauer, the ratio of potential beneficial vs. non-
> > beneficial for 100aa systems is about 1e-40."
>
> You forget that threshold limitation presented here has not only a
> minimum of 100aa but a fair degree of specificity.
The denominator you use to calculate your *ratio*, however, is not
limited to 100 aa sequences of a "fair degree of specificity". That
means that you are NOT calculating the "ratio of potential beneficial
vs. non-beneficial for 100aa systems" and you have absolutely no idea
about the "beneficialness" of sequences that lack your specified
threshold. There could be many, many, many, many, many 100aa
sequences that are "beneficial", both potentially and actually, that
are not included.
> You don't seem to
> have grasped the relevance of this second part of the equation
Oh. I understand. It is your attempt to "cook the books" so that you
can continue to pretend that the number of cytochrome c sequences is
the same as saying "potential beneficial" sequences.
> because
> you continually attempt to compare low-level systems with higher level
> systems. For example, you present antibody binding functions, which
> are very low-level, with much higher-level systems as if they were
> somehow on the same level.
That is hand-waving bullshit. The "level of the system" seems to be
nothing but a bull shitting maneuver that you use whenever reality
interferes with your fantasy. "Level of system" seems to be nothing
but a "codeword" for "must have a small/large gap". All that *any*
functional protein does is provide a surface that interacts with a
biologically relevant molecule. Antibodies manage to bind to (and
later optimize that binding) essentially *any* biologically relevant
molecule using fewer than 100 aa's by randomly changing some of these
aa's. Changing the aa's changes the epitope they bind, thus changing
the specific function of that antibody. That you can generate
antibodies in your own body during your own lifetime that can bind to
(and later optimize that binding) with far fewer than the number of
randomly generated sequences that your math would claim are needed to
generate even one "functional" antibody is what is called
"falsification" of the hypothesis.
> You forget, or didn't know, that antibody
> binding, by itself, does not require more than 20 or so very loosely
> specified residue positions. There simply is no comparison.
So what is the difference between "level of specificity" and "average
gap size"? If they are basically the same thing or the determination
of one requires the other, your argument becomes circular: The average
gap size is large, but only when the specificity is high (when the gap
size is large)? What you will find in such 'high specificity'
proteins is that much of the 'specificity' likely arose *after* some
ancestral protein was produced that had *minimal* function. That is,
most of the specificity is a consequence of quantitative
'optimization' that *starts* with a protein that has 'function' at
each step.
> > > > Then why did you claim that *these* ratios represented "the ratio of
> > > > potential beneficial vs. non-beneficial for 100aa systems" [see your
> > > > statement above to determine if I am out-of-context]?
>
> > > What I claim is that these ratios give a rough idea as to the nature
> > > of sequence space given a certain level of minimum structural
> > > threshold requirements. Not all 100aa systems are at the same
> > > threshold level you know. Some 100aa systems are at much higher
> > > levels than are other 100aa systems. CytoC is pretty high up there
> > > for 100aa systems.
>
> > Irrelevant.
>
> This single word comment nicely illustrates the confusion of yours
> I've been talking about here. The degree of sequence specificity is
> not irrelevant to the problem at all. It is a main part of the
> equation that defines levels of minimum structural threshold
> requirements.
It is NOT a part of the equation at all, Sean. What you claim is that
the ratio is "potential beneficial vs non-beneficial" sequences.
Nowhere in what you claim is there any accomodation or even mention of
"but only for those proteins I consider high-level".
> > The fact remains that you are *claiming* that the ratio
> > you ACTUALLY use to calculate "average gap size" represents "potential
> > beneficial vs non-beneficial" sequences
>
> I'm specifically talking about beneficial vs. non-beneficial at a
> given threshold level of minimum structural requirements - not just
> any and all levels.
Then I hope you will correct what is in your appendix to reflect that
you are not talking about ALL "potential beneficial" sequences per
total sequence space for a 100 aa sequence, but only those "potential
beneficial" sequences that meet your criteria of being "high-level"
function. And that you will then produce a description of what you
mean by high-level function such that the ratio is not simply "I get
to choose only those proteins that I think required assembly by the
"747 in a tornado" methodology and that required what I consider to be
many specific aa's at specific sites. And then I will use this
bullshit ratio to use a bullshit exponetial expansion to produce a
bullshit number that I will call "average gap size". Remember, Sean,
*even if* you can produce a meaningful number at this point, that
doesn't make your exponential equation non-bullshit and doesn't make
the 20th root of a smaller population "average gap size".
> > when, as you agree above, it
> > does not. Instead it is "a rough idea".
>
> I've always said it is a rough estimate. We simply don't have enough
> information to be exact.
But hand-waving bullshit ratios that you call "potential beneficial
vs. non-beneficial" doesn't help to get information. Since the ratio
you give is the ratio that assumes the "747 in a tornado" mechanism of
evolution *and* restricts the ratio to a *specific* single function
which is not even an average, but a high, level of "function" [I don't
know how you measure 'level of function', since 'function' simply
either exists or it doesn't.]
> This doesn't mean that it is impossible to
> have any idea at all as to the likely ratio that exists at a given
> threshold level.
It does mean that you cannot call the ratio you produced "potential
beneficial vs. non-beneficial".
> I mean, if it was impossible, your own theory as to
> how random mutation and function-based selection actually did the job
> would be baseless as well.
The mechanism of random mutation and function-based selection is based
on "modification" of pre-existing structure, not random assembly from
some pool of aa residues. Thus the *real* mechanism of random
mutation and function based selection is a function of finding the
"minimum actual gap" in some specified context (both genetic and
environmental), and is not a function of the "average gap size". Any
calculation of "average gap size" is irrelevant to the real mechanism
of mutation of pre-existing sequence/structure and selection for
function because it assumes the mechanism must start from some average
or random starting site. But since your calculation of "average gap
size" is GIGO numerology, the point is moot in any case.
> The lack of evidence works both ways
> here. Your theory is just as much affected by the lack of evidence as
> is mine.
>
> > It is dependent on
> > "threshold level". Cyto C is "high threshold". If you think you need
> > the ratio of "potential beneficial vs non-beneficial for a 100aa
> > system" to calculate "average gap size" you have to convince us that
> > the ratio you used actually does equal or (at least) come close to
> > equaling "potential beneficial vs non-beneficial for a 100aa system".
> > Simply asserting that a number that even you admit is NOT "potential
> > beneficial" sequences represents "potential beneficial" sequences will
> > not do.
>
> I explain the reason why using such calculations does in fact give a
> pretty good idea as to the total number of beneficial targets that
> likely exist at a given threshold level.
That is not what you claim for your ratio, Sean. No mention is given
of "a given threshold level", nor, even if you did add it now, have
you told us how you determine the threshold level of a "function". If
it your threshold level amounts to nothing more than that you only
want to talk about those "potential beneficial" functions that
*already* exist and involve many of the aa residues of that length,
say so. At least admit that you are not interested in the "average
gap size" for a particular length. That you are only interested in
"average gap size" for a particular length and a function that arises
from many different aa's interacting with the substrate. [Since any
protein of any length can only interact with *part* of a biologically
relevant substrate, that necessarily means that, even if a mutation
eliminates 'the' [teleologic] function that Sean assigns to it, it
could still have other functions, since that mutation will typically
not eliminate the overall structure (and hence binding surfaces).
That is not counting the fact that such mutation may only be
quantitative in nature and only eliminate a level of function that is
useful in a modern context.]
But, again, all I am asking is that you be accurate in your appendix
on this point and not try to claim that you have calculated "potential
beneficial vs non-beneficial" ratio. If you are going to introduce
the criteria of "threshold level", then you need to define and tell us
how to quantitate that term such that it is not, in itself, simply a
circular reflection of "average gap size"
>
> < snip repetitive >
>
>
>
> > > > You did not say that this ratio represents all 100 aa
> > > > sequences that have all the properties needed to act as a lambda
> > > > repressor against a modern lamda gene site.
>
> > > Yes, I did.
>
> > ********* a reminder of what Sean's actual claim was
> > Using an average between the calculations of Yockey and Sauer, the
> > ratio of potential beneficial vs. non-beneficial for 100aa systems is
> > about 1e-40."
> > *******
>
> > That is, Sean is either *actually* or *apparently* claiming that there
> > is no difference between the ratio of sequences that can act as a
> > lambda repressor in a modern system to total sequence space and the
> > ratio of "potential beneficial vs. non-beneficial" sequences.
>
> It is a claim that there is no essential difference *at this level* of
> minimum structural threshold requirements. I also explain what I mean
> by "no essential difference" as well in my website and in this forum
> many times.
That, again, is not what your appendix says. Your appendix makes no
mention of "level of minimum structural threshold requirements" nor
any way to take that into account in the calculation of "average gap
size". Although your "average gap size" calculation is still
nonsense, if you could actually calculate it, what you would have
calculated is "average gap size for x aa long proteins for which the
modern protein has y degree of aa requirements for "level of minimum
structural threshold requirements". What is missing here is any
discussion about the "functionality" that related pre-existing
sequences can have. Instead, your assumption is that the starting
point is some protein that differs at nearly all the aa sites you
assume are part of its "structural threshold level".
>
> > A
> > simple, "Oooops. I misspoke and should have said....Thank you for
> > pointing out the inadvertant sloppiness in my wording." would do so
> > long as it is followed by a correction that points out what this ratio
> > *really* is.
>
> You just don't understand that these ratios are in fact roughly
> representative of the total at a given level.
Then f**king *use* the words "at a given level" in your appendix.
That *still* would not make the ratio meaningful, but at least it
would be honest. And include a description of how anyone other than
you can determine the "level of function".
> > > I never said that the CytoC or lambda repressor data represented all
> > > potentially beneficial sequences. What I said was that it can give a
> > > rough idea as to the likely number of all potentially beneficial
> > > sequences at a particular level of size AND specificity requirements.
>
> > Sean, why do you claim that this is what you said when I can easily
> > point out what you really said: "Using an average between the
> > calculations of Yockey and Sauer, the ratio of potential beneficial
> > vs. non-beneficial for 100aa systems is about 1e-40." This is a claim
> > that the ratio you presented here represents (is a good estimate of)
> > ALL "potential beneficial vs. non-beneficial" sequences and is not
> > simply the ratio of "all sequences that have the specific beneficial
> > function of being able to replace w.t. cytochrome c activity in the
> > context of a modern mitochondrion" or (and importantly not 'and') the
> > ratio of "all sequences that have the specific beneficial function of
> > being able to replace w.t. lambda repressor in the
[snip]
hersheyh
Exactly. ;-)
R. Baldwin
> On Dec 14, 1:23 pm, hersheyh <hershe...@yahoo.com> wrote:
>> On Dec 14, 11:37 am, Seanpit <seanpitnos...@naturalselection.
>>
>
>> > The likelihood
>> > that the actual gap size is as small as you need it to be (often
>> > suggested by you as being very close or equivalent to the minimum
>> > possible gap size), is based on the average gap size, which in turn is
>> > based on the ratio of targets to non-targets.
>>
>> Sean, the minimum possible gap size is NOT based on "average gap
>> size".
>
> That's completely irrelevant.
>
>> Neither is "minimum actual gap size".
>
> That's statistically mistaken. Minimum likely distances are indeed
> based on average distances. That is what the Poisson distribution is
> all about.
No, Sean, you are demonstrating your statistical ignorance again. The
Poisson distribution describes the probability of exactly k events occuring
within a fixed interval, given that the events occur at a known average rate
lambda = n/interval, and that the occurance of next event is independant of
distance from previous event. You have not demonstrated that you have met
the Poisson assumptions (especially event independance), and you have
incorrectly described what the Poisson distribution calculates.
Stuart
No it is not. It shows that to potentially go from Cytosome-C to some
other
functional protein, their at least 300 potential routes. We are
talking about a space
that has a large number of dimensions, which renders the below
statement silly.
The gap distance is the
> distance between the edge of one beneficial island cluster of
> sequences and the next closest edge of beneficial island sequences in
> sequence/structure space.
How do you know where that is and what it is? You have no clue.
>
> Do you see the distinction?
The distinction here is that observed sequence variability of CytoC is
measurable and suggests
a minimum of 100s of potential routes to new proteins, while your
concept of unbridegable
gaps between beneficial islands of functionality in a vast multi-
dimensional space is a figment
of your imagination.
- Because it is fundamentally important to
> understanding the problem of expanding gaps with increasing minimum
> threshold requirements.
What about genes and their respective coded for proteins that perform
different functions
in different species?
Take the PAX-6 homologs, in C-elegans it regulates the development of
the head. In humans it is
the master control gene for eye development.
One gene found in many beneficial islands of functionailty? Not only
does the sequence space have a large
number of dimensions; it is multiply connected in terms of
functionality as well.
Good luck analyzing that Sean.
Stuart
Ron O
0catch.com> wrote:
> On Dec 15, 8:05 am, Ron O <rokim...@cox.net> wrote:
>
> < snip pointless pejoratives >
You are so whacked that you probably don't even know what a pegorative
is. The facts are not pegoratives. Just because you have to snip and
run from your own claims, does not make them pegoratives. I'll put
them back so that anyone can see just what you think pegoratives are.
QUOTE SNIPPED material:
Let's see.... No admission that what I claim is all true. Just
claiming that the other guy has the problem and not Sean. Oh and
running away without addressing the issue. Gee, how predictable can
you get? How dishonest can you get? In the response to Lee above he
even lies about the rare moments. I would contend that Sean would
have to run through a whole lot of posts just to find some rare
instance where I didn't demonstrate that Sean was full of gas.
Sean do that, bring up the references, show that they are rare. You
should show that they are rare when I bothered to take you seriously.
That would be, what? More than 5 years ago? Just randomly take 50
of
my posts where I addressed the issues that you brought up and count
up
the times that I didn't set you on your can. You might find one such
post where you may have had some point, and probably not even that if
you only searched 50.
More than 5 years of you running a bogus obfuscation smoke screen,
when you know for a fact that you don't have jack to back it up.
END QUOTE:
More than 5 years of snipping and running. How dishonest and bogus
can you get?
>
> Finally - some actual arguments.
>
> > What does the actual data tell you about your bogus notions of protein
> > sequence space? Two species of bacteria with only 2000 proteins in
> > their genomes to mutate and they can evolve beta gal activity. How is
> > that possible if what you claim about sequence space is at all true?
>
> The odds are actually pretty good because the lactase function is at a
> pretty low level of minimum structural threshold requirements - i.e.,
> less than 400 fairly specified residues. The ratio of lactases vs.
> non-lactases at this level is actually pretty high. The same thing is
> true of other biosystems that are based on equivalently small single
> proteins. Such evolution actually happens fairly often at this
> level. But, it doesn't happen at all at higher levels - i.e., beyond
> the 1000aa threshold. That's what's most interesting about the gap
> problem. It is demonstrably exponential in nature.
Goal post shift to the mythical 1000aa threshold, that Sean has never
been able to verify exists. How low of a minimal threshold is Lactase
function? Just because you can't deny the data without looking more
like a clown than usual, how low is it?
You can't just make junk up and expect people to believe you,
especially since you are such a liar. You need confirmation. Where
is it? When have you or anyone ever established that this mythical
1000aa threshold exists? Put up or shut up. This bogus mytical
1000aa threshold argument must be getting lame even for you. Can you
go to someone like Behe and have him confirm this junk? No? Why
not? Pretending isn't demonstrating anything except your ability to
lie to yourself about this topic.
>
> > What is your alternative and the evidence to back it up? Doesn't
> > science have a verified means of getting what it needs for biological
> > evolution?
>
> Yes, it does. But, only at very low levels of minimum structural
> threshold requirements (i.e., well below the 1000aa threshold).
This again points out how lame your arguments are. Science has an
explanation. You can't deny it, you can only make up junk about some
mythical 1000aa threshold when you have to admit that you don't even
have anything as good as the low level explanation. You have jack.
You don't have an explanation for the 1000aa threshold crap either.
Put it forward if you claim to have one. Why should science have an
explanation for something that you can't even demonstrate exists in
nature?
>
> > What is your alternative? How does it match up with what
> > we can actually observe happening? How many species do you think Hall
> > tested and how related were they?
>
> Hall only tested one species - E. coli. But, the same thing is likely
> to happen in other species occasionally at this level of functional
> complexity.
Remember when you made your pegorative claims and tried to claim that
Hall didn't find any other species that could do the same trick as E.
coli? You ran away again, but not until I put the ref forward to
demonstrate why you had to run.
Here it is again.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=110764
Klebsiella is not E. coli.
>
> > Let's say that Hall tested 100
> > (unlikely). That would be just 200,000 protein sequences scored to
> > see if he could evolve beta gal activity and select for it. And it
> > worked, not just once, but at least twice.
>
> Actually, it only worked once. Hall did try to evolve Beta gal
> activity without the ebg sequence, but it didn't work. After about
> 40,000 generations of trying, Hall gave up and said that his double
> mutant colony had, "Limited evolutionary potential". This goes to
> show that even at the 400aa level evolution isn't always easy - even
> for a large population. The stalling out effect is starting to become
> clear at this level.
That was in E. coli. Read the Kleb paper. Remember what you ran from
last time? You've probably run so often that you can't keep track
anymore.
Hall never did the 40,000 generation experiment. What he did was a
series of single step selection experiments that may have amounted to
40,000 generations, but most likely did not. A generation before the
favorable mutation occurs is estimated to be 30-50 hours. This would
amount to 50,000 to 83,000 days, a minimum of 136 years of growing
bacteria. Did Hall ever run such an experiment? He might have run
136 experiments in parallel for a year, but that wouldn't be the same
would it? He probalby did even worse, and ran a bunch of experiments
for a couple of weeks. He would need to get a population to mutation
selection balance, and he never did, did he?
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=770439
Your own calculations indicated that once mutation selection balance
was reached in a population, jumping 2 or 3 mutational intervals was
not that rare. Hall's experiments never reached close to mutation
selection balance. He started with clonal populations at the same
start point every experiment. You know the difference, you prefer to
lie to yourself about it.
Remember it was your own calculations about the number of mutations in
a population at mutation selection balance that made you drop your 2
and 3 step gap for the 40 mutations gap, then there was this big leap
to the mythical 1000aa, when you never demonstrated that a gap of 3
had to be crossed. You even know why you can't demonstrate something
like that. It is because you need to know the starting protein
sequences, and you do not have that data. No one does.
>
> > What is the probability
> > that, that would happen if your bogus claims were correct about
> > protein sequence space and the number of viable sequences?
>
> Pretty good. Evolution happens quite often at this level actually.
> What you never seem to consider, however, is why evolution doesn't
> happen at higher levels?
The mythical higher levels that Sean can't even describe, let alone
have his own viable explanation for. If what science has is so bad,
what should that tell Sean about his alternative when he can't even
establish that it works at the lower levels?
>
> > You keep denying the antibody example, claiming that it isn't high
> > enough about something or other to satisfy you, but you have no
> > alternative do you? A maximum of 10E12 sequences are tested at any
> > time and the system works nearly all the time. Such a tiny fraction
> > of the sequence space has to be sampled to get funtional antibodies
> > that it makes your claims out to be a joke. You've known for years
> > that not only can they get antibody activity, but Abzymes demonstrate
> > that enzymatic function can evolve using the same system.
>
> Actually, the sequence space involved with antibody binding is quite
> small - only about 20^20 sequences. This sequence space can be
> exhaustively searched by a relatively small population of immune
> cells. Not a problem at this very low level.
And your evidence for this is...
Thought that you didn't have any. How did you come up with a number
so small? What about the Abzymes? Do you know how small a number of
amino acid residues that you are claiming account for the entire
immune response in the biosphere? It is only around 20 isn't it?
Even for you that number would have to be bogus.
>
> You see, all of your examples that you have ever presented are very
> low-level examples - every one. None of them comes remotely close to
> the 1000aa threshold where sequence space is the size of 20^1000.
> I've pointed this out to you many many times, but you act as if
> nothing was ever said. You don't even try to address this point, but
> act like it is completely irrelevant to the issue and go on presenting
> your low-level examples like they somehow explain away the problem.
They weren't such low level and irrelevant when you were on your 2 or
3 mutation gap kick, were they? What a joker. Where did you
establish this 1000aa threshold? When do you expect the Nobel prize?
Have you published, yet, or are you keeping it a secret? You can't
just make this junk up.
>
> > You know all this, but you keep blowing smoke. Not only that, but you
> > try to make it look like it is the other guys problem. That is just
> > sad.
>
> Just answer the question Ron. It isn't just smoke. It is a valid
> simple question. Why does evolution not produce any novel beneficial
> functional systems that require a minimum of more than 1000 fairly
> specified residues? Hmmmmm? Care to take a crack at answering that
> question?
Describe the 1000aa threshold so that someone can look for it and
determine that it is there. Why should I have to explain something
that doesn't even exist? What question am I supposed to answer? I
need to know what the threshold is before I can explain it. You have
never demonstrated that it even exists. How is anyone supposed to
explain the mythical 1000 aa threshold when only you know it is there,
but can't tell anyone else what it is? I'll answer "the question"
when you tell me how tall the invisible pink elephant is that is
standing next to you. Oh, geez, can't answer such a simple question,
you must be an idiot lamo.
>
> > Why not just put up or shut up? You don't deny that you made the
> > claims, so make good on them. It isn't my problem that you keep
> > running, it is your problem. You are doing the running and blowing
> > the smoke.
>
> This paragraph doesn't even make sense. I've presented some simple
> questions. Who is the one trying to avoid answering them? I've
> answered yours, why not at least try to answer mine? Instead, you
> continually present your usual low-level examples and an endless
> string of pejoratives? How is that helpful to me or anyone else who
> might also like to hear what you have to say regarding this question?
It would make sense if you hadn't snipped and run from what you can't
deal with for the past, geez, how long? Could it be 6 or 7 years for
the common descent claim? The ID stuff can't be more than 4 years,
but it is your problem.
What is your alternative to common descent and the evidence that you
claimed was just as good as what science had? What is the science of
ID that you would have taught to school kids when you were still
advocating the teach ID scam? Without the science, and no viable
alternative, who cares about the mythical 1000 aa threshold?
>
> > Ron Okimoto
>
> Sean Pitmanwww.DetectingDesign.com
DetectingDesign, what a bogus con job. All you are reduced to doing
is running the replacement obfuscation scam. Claiming links to the ID
scam when the other ID perps have a new scam that doesn't even mention
that ID ever existed makes you look like a moron.
Ron Okimoto
hersheyh
0catch.com> wrote:
> On Dec 14, 1:23 pm, hersheyh <hershe...@yahoo.com> wrote:
>
> > On Dec 14, 11:37 am, Seanpit <seanpitnos...@naturalselection.
>
> > 0catch.com> wrote:
> > > On Dec 13, 9:17 pm, hersheyh <hershe...@yahoo.com> wrote:
>
>
> > *****here is how Sean says he generates his numbers and what he says
> > they mean*****
> > "Well, first we have to calculate the likely gap size. Using an
> > average between the calculations of Yockey and Sauer, the ratio of
> > potential beneficial vs. non-beneficial for 100aa systems is about
> > 1e-40. This creates a ratio for a 1,000aa system of about
> > 1e-40^(1000/100) = 1e-400. So, the average gap size between
> > potentially beneficial sequences at this level would be about 308
> > residue differences - i.e., 20^308 = 1e400."
> > ******
>
> > The fact remains that you are *claiming* that the ratio
> > you ACTUALLY use to calculate "average gap size" represents "potential
> > beneficial vs non-beneficial" sequences
>
> I'm specifically talking about beneficial vs. non-beneficial at a
> given threshold level of minimum structural requirements - not just
> any and all levels.
Now. Look just above at what you wrote and tell me where, in the
description of the ratio you use in your further GIGO calculation of
"average gap size", there is even ANY mention of "threshold level of
minimum structural requirements"? I know that you always hand-wave
this vague concept into any discussion. But I sure don't see any
mention of it above where you are telling us how you calculate
"average gap size" at the 100aa level (not "average gap size" of those
proteins of 100 aa in size where I think the ratio of "sequences with
that specific function" to "total sequence space" is as small as
possible, extended by use of an equation which assumes that the
numerator does not change at all -- that only the denominator changes,
and taking the 20th root of the inverse of that ratio simply because
it appears to be related to random assembly of sequence space of part
of the original length and gives me a big number and calling that
number the "average gap size" without, of course, mentioning that this
is only the gap size of a protein with the appropriate "threshold
level of minimal structural requirements".
Can you please point out, in what you wrote, where you even *mention*
"threshold level of minimal structural requirements" much less
explained how that "level" is calculated?
What I see is you claiming that the ratio you gave is "potential
beneficial vs non-beneficial" sequences.
>
> > when, as you agree above, it
> > does not. Instead it is "a rough idea".
>
> I've always said it is a rough estimate.
Not in the appendix description. There you do NOT say that this
number is "a rough estimate". There you are saying that the ratio
that you cribbed from Yockey and Sauer *equals* or *is* the ratio of
"beneficial vs. non-beneficial" sequences. Without any
qualifications. Do you not see that this would be seen as disingenous
at best? I am not opposed to your correcting this "oversight" on your
part if you did not MEAN what you said, but just were engaged in
sloppy wording. I do object to your claiming that your description is
really good enough as is.
> We simply don't have enough
> information to be exact.
Then what you do is point that out in clear and coherent terms, not
simply pretend that the number you cribbed from Yockey and Sauer
equals the ratio of "beneficial vs. non-beneficial" sequences without
any of the qualifications you are now waving around to explain what
you really meant to say.
> This doesn't mean that it is impossible to
> have any idea at all as to the likely ratio that exists at a given
> threshold level.
It is, however, contemptible to state that the ratio for which there
are all these qualifications represents the ratio of "beneficial vs.
non-beneficial" sequences without adding all those qualifications.
Doing so implies a degree of accuracy you don't have. By not adding
the qualifiers you are waving around now, you are (intentionally or
not) implying there is no difference between the ratio of "beneficial
vs. non-beneficial" sequences and the ratio of "sequences which retain
all the functionality of cytochrome c or -- not 'and' -- similarly
highly conserved (higher level?) proteins vs. total sequence space".
In the latter description, for instance, you cannot claim that the
denominator represents "non-beneficial" sequences since we know that
the denominator includes many 'beneficial' sequences that are not
"cytochrome c" or -- not 'and' -- similar proteins.
I, again, would not be complaining so strongly if your description of
your calculation actually matched the math you are doing. It
doesn't. Period. Every thing you have said, every qualification you
have made tells us that your description doesn't match up with what
your math is claiming.
>
> I explain the reason why using such calculations does in fact give a
> pretty good idea as to the total number of beneficial targets that
> likely exist at a given threshold level.
And where, again, in your description [see below], is there even a
hint of "a given threshold level" much less a mathematical taking of
that concept into account? I am going by the description you actually
gave, not the one you might think you gave. If there is a discrepancy
between the two (and there obviously is), thank me and correct what
you actually gave so that it isn't misleading.
[snip]
>
> You just don't understand that these ratios are in fact roughly
> representative of the total at a given level.
> > > I never said that the CytoC or lambda repressor data represented all
> > > potentially beneficial sequences.
Sean, that is exactly what you said in the paragraph I quoted. You
said the ratio of Yockey and Sauer *is* *equal to* *the same as* the
ratio of "beneficial vs. non-beneficial" sequences at the 100aa
level. No qualification was presented. None. If you find it *in the
appendix where you calculate "average gap size", show me. If what you
*actually* said was not what you meant to say, then correct it. Don't
try to convince me that what you *actually* said really is what you
meant to say. Just tell me how you changed what you said to
accurately reflect what this ratio really means. Oh, I do hope it
tells us how to measure (quantitate) "level of functional complexity"
in a way that doesn't make that term simply a surrogate for "average
gap size" assuming that the sequence in question was randomly
assembled from scratch (or the mathematical equivalent). Besides,
single point mutations in even cytochrome c, would typically still
leave a protein that binds heme. Isn't binding heme a "function" that
has at least "potential benefit" in some context?
[snip]
>
> > > However, if you consider the specificity requirements
> > > for the average protein in a larger multiprotein system like a
> > > flagellar motility system, the ratio change involved isn't going to be
> > > remotely represented by a 2-fold extrapolation (a 10-fold
> > > extrapolation maybe).
>
> > How do you know that?
>
[snip]
If Sean corrects his ratio from being "beneficial vs. non-beneficial"
to being two proteins that *specifically* have the same "level of
structural complexity", then, and only then, does his particular
exponential equation make sense. But not for the reason he states.
Rather it is for a reason he doesn't mention, namely that his "average
gap size" is indistinguishable from any sensible "level of structural
complexity". IOW, Sean has gone from calling something "level of
functional/structural complexity or threshold of specificity" or
whatever to calling the same number "average gap size".
Let me show you how this works. Assume, for simplicity of argument,
that cytochrome c has 30.7 aa sites that are absolutely invariant and
69.7 aa sites that can be replaced by any aa. that would be a measure
of its level of functional complexity. This number was not
arbitrarily chosen. It was chosen because 20^30.7(the number of
sequences at this level of complexity that would have the 'function'
of cytochrome c)/20^100 (total number of sequences) = 10^-40. IOW,
this accurately describes number of sequences that function as
cytochrome c/total number of sequences. Those of you with long enough
memories might notice that 30.7 seems to register on some neurons.
There is a reason for that.
Now imagine a 1000 aa sequence (a 10-fold increase in total size) with
the same "level of sequence specificity (in this case, it would be 300
absolutely fixed sites and 700 sites where any aa would do). The
number of sequences that would have 'function' at this level of
complexity would be 20^700. Total sequence space would be 20^1000.
The ratio of 20^700/20^1000 = 10^-400. Just like Sean says. But then
how does Sean determine the "average gap size"? Ans: Why, by taking
the 20th root of 10^-400! And he is shocked! Shocked! that he comes
up with 307 aa as the "average gap size". Why he is shocked, I have
no idea because he *started out* with that assumption cleverly
disguised as "threshold level" or "level of complexity".
[snip]
hersheyh
Sorry. That should be the 20th root of 10^400 (the inverse of the
ratio). See, Sean. When I make a mistake, I don't have any problem
correcting it. Why do you?
hersheyh
0catch.com> wrote:
> On Dec 14, 1:23 pm, hersheyh <hershe...@yahoo.com> wrote:
>
> > On Dec 14, 11:37 am, Seanpit <seanpitnos...@naturalselection.
>
> > 0catch.com> wrote:
> > > On Dec 13, 9:17 pm, hersheyh <hershe...@yahoo.com> wrote:
>
>
> The presence or absence of a close sequence, like ebg, is indeed a
> function of the average gap distance. And, at this relatively low
> threshold level of about 400aa, this actual minimum gap distance of
> one is not that unlikely - statistically and in observed reality for a
> large population.
However, in another thread, Sean said that at a level of 300 aa, the
likely minimum gap distance was 4-5 dozen (it was one or two for a
sequence of 100aa). Sean asserted that it would be impossible, in
even a trillion years, to cross such a gap. Sean seems to think
numbers are completely fungible to his needs.
> However, the existence of such a small minimum
> approximating the smallest possible minimum is exponentially less
> likely at higher thresholds - both statistically and in observed
> reality (i.e., it has yet to be seen in reality beyond the 1000aa
> threshold).
Ah, yes. The imaginary 1000 aa threshold that quickly becomes the
1000 *minimum* threshold that quickly becomes something else. The end
justifies the numerology.
>
> < snip rest >
>
> Sean Pitmanwww.detectingDesign.com
Seanpit
> On Dec 15, 10:50 am, Seanpit <seanpitnos...@naturalselection.
>
> 0catch.com> wrote:
> > On Dec 15, 8:05 am, Ron O <rokim...@cox.net> wrote:
>
> > < snip pointless pejoratives >
>
> You are so whacked that you probably don't even know what a pegorative
> is. The facts are not pegoratives.
Personal attacks that have nothing to do with the questions presented
are needlessly pejorative and irrelevant.
< snip >
> > Finally - some actual arguments.
>
> > > What does the actual data tell you about your bogus notions of protein
> > > sequence space? Two species of bacteria with only 2000 proteins in
> > > their genomes to mutate and they can evolve beta gal activity. How is
> > > that possible if what you claim about sequence space is at all true?
>
> > The odds are actually pretty good because the lactase function is at a
> > pretty low level of minimum structural threshold requirements - i.e.,
> > less than 400 fairly specified residues. The ratio of lactases vs.
> > non-lactases at this level is actually pretty high. The same thing is
> > true of other biosystems that are based on equivalently small single
> > proteins. Such evolution actually happens fairly often at this
> > level. But, it doesn't happen at all at higher levels - i.e., beyond
> > the 1000aa threshold. That's what's most interesting about the gap
> > problem. It is demonstrably exponential in nature.
>
> Goal post shift to the mythical 1000aa threshold, that Sean has never
> been able to verify exists.
I think you are confusing the threshold limitation for the gap size.
The threshold size and the gap size are not the same thing. The
likely minimum gap distance is always smaller than the minimum
threshold limitation. But, what is interesting though about the
minimum gap distance is that it increases in a linear manner as the
minimum threshold limitations under consideration are increased.
So, for a threshold limitation of 1000 fairly specified residues, the
likely minimum gap distance would NOT be 1000 mutations wide - not
even close. Rather, the likely minimum gap distance would only be a
few dozen mutations wide at this level. However, this seemingly
small minimum gap distance would make evolution of a functional system
requiring a minimum of 1000aa very unlikely even over the course of
trillions of years of time - even for a bacterial colony the size of
all bacteria on Earth.
Now, let's look at a higher level system to see if higher-level
thresholds actually exist. Since you claim that higher level
thresholds do not exist, how many amino acids need to be coded for to
produce a flagellar motility system at minimum? (i.e. the threshold
size) Please, do give me your best estimate. As far as I can tell,
the answer is well over 10,000 fairly specified residue positions
coded for by an even greater number of codons of genetic real estate
(to include codes for non-structural proteins). A flagellar motility
system simply cannot be built with significantly fewer codons or
residues at all. If you think otherwise, please, do present your own
estimate.
> How low of a minimal threshold is Lactase
> function?
About 380aa.
> Just because you can't deny the data without looking more
> like a clown than usual, how low is it?
What data are you talking about here? What is your suggestion for the
minimum size requirement for the lactase function? Does it come
remotely close to the 1000aa threshold? No. Therefore, it is a
fairly low-level function. There are many examples of functional
systems that require only a few hundred fairly specified residues
evolving. There are no examples where the system requires over 1000
fairly specified residues - not one example of evolution beyond this
level in all of literature. And yes, many such systems do exist which
require many thousands of specified residue positions in every single
living thing. Here are just a few:
Flagellar motility, DNA transcription, RNA translation, vesicle
transport, ATP production, etc . . .
> You can't just make junk up and expect people to believe you,
> especially since you are such a liar. You need confirmation. Where
> is it? When have you or anyone ever established that this mythical
> 1000aa threshold exists?
After all the times I've presented this evidence I can't believe that
you would still be trying to suggest that no system exists which
requires a minimum of more than 1000aa to work. How can you suggest
such a thing and call yourself informed on this issue? If you don't
believe me, then by all means provide some sort of evidence showing
how a functioning flagellum or any other such system can be produced
with fewer than 1000 codons of genetic real estate . . .
> Put up or shut up. This bogus mytical
> 1000aa threshold argument must be getting lame even for you. Can you
> go to someone like Behe and have him confirm this junk? No? Why
> not? Pretending isn't demonstrating anything except your ability to
> lie to yourself about this topic.
I don't think you really understand the concept of minimum structural
threshold requirements after all this time.
> > > What is your alternative and the evidence to back it up? Doesn't
> > > science have a verified means of getting what it needs for biological
> > > evolution?
>
> > Yes, it does. But, only at very low levels of minimum structural
> > threshold requirements (i.e., well below the 1000aa threshold).
>
> This again points out how lame your arguments are. Science has an
> explanation. You can't deny it, you can only make up junk about some
> mythical 1000aa threshold when you have to admit that you don't even
> have anything as good as the low level explanation. You have jack.
> You don't have an explanation for the 1000aa threshold crap either.
> Put it forward if you claim to have one. Why should science have an
> explanation for something that you can't even demonstrate exists in
> nature?
Do you really not understand that all of your examples are of systems
that have very few minimum structural threshold requirements? They
just don't need very much to start working to at least some useful
level of activity - far fewer than 1000aa residues. How can you not
understand that concept? Simple functions like these are relatively
easy to evolve. More complex functions, on the other hand, are not
easy to evolve - - and in fact do not evolve. There is not a single
example of a more complex system actually evolving in all of
scientific literature. If you do know of such an example, beyond the
very simple systems you've already listed, then, by all means, present
this example.
You do understand that some types of functions are inherently more
complex than others - right? Would you say that flagellar motility
requires much more complexity than the single protein lactase
function? I sure hope you would agree to that.
> > > What is your alternative? How does it match up with what
> > > we can actually observe happening? How many species do you think Hall
> > > tested and how related were they?
>
> > Hall only tested one species - E. coli. But, the same thing is likely
> > to happen in other species occasionally at this level of functional
> > complexity.
>
> Remember when you made your pegorative claims and tried to claim that
> Hall didn't find any other species that could do the same trick as E.
> coli? You ran away again, but not until I put the ref forward to
> demonstrate why you had to run.
>
> Here it is again.
>
> http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubme...
>
> Klebsiella is not E. coli.
Interesting abstract. I was unaware of this particular experiment and
will have to obtain and read the full paper.
I do appreciate you bringing this paper to my attention, but I don't
see how it affects the main point at hand in the least. I mean, I
just noted for you that "the same thing is likely to happen in other
species occasionally at this level of functional complexity." Did you
miss that comment? After all, this level involves only a few hundred
fairly specified residues at most. This sort of thing is only to be
expected at such low levels - quite predictably in fact.
> > > Let's say that Hall tested 100
> > > (unlikely). That would be just 200,000 protein sequences scored to
> > > see if he could evolve beta gal activity and select for it. And it
> > > worked, not just once, but at least twice.
>
> > Actually, it only worked once. Hall did try to evolve Beta gal
> > activity without the ebg sequence, but it didn't work. After about
> > 40,000 generations of trying, Hall gave up and said that his double
> > mutant colony had, "Limited evolutionary potential". This goes to
> > show that even at the 400aa level evolution isn't always easy - even
> > for a large population. The stalling out effect is starting to become
> > clear at this level.
>
> That was in E. coli.
Right . . . and I'm sure the same thing would happen in other bacteria
as well. Delete the ebg equivalent in Klebsiella and the same
limitations would also be realized just as they were in E. coli - even
at this relatively low level.
> Read the Kleb paper. Remember what you ran from
> last time? You've probably run so often that you can't keep track
> anymore.
This sort of data though is always interesting to me and is always
relevant. Why not present more of this sort of argument instead of
your usual focus on personal attacks instead? This sort of
information is far more helpful and interesting to me and I'm sure to
others as well that your usual pointless personal attacks and
diatribe.
Beyond this, how does this paper help your position? All it is, at
the very most, is yet another example of low-level evolution - of a
novel system that requires far less than a minimum of 1000aa.
> Hall never did the 40,000 generation experiment. What he did was a
> series of single step selection experiments that may have amounted to
> 40,000 generations, but most likely did not. A generation before the
> favorable mutation occurs is estimated to be 30-50 hours. This would
> amount to 50,000 to 83,000 days, a minimum of 136 years of growing
> bacteria. Did Hall ever run such an experiment? He might have run
> 136 experiments in parallel for a year, but that wouldn't be the same
> would it? He probalby did even worse, and ran a bunch of experiments
> for a couple of weeks. He would need to get a population to mutation
> selection balance, and he never did, did he?
Under appropriate conditions, the generation of time of E. coli can be
as little as 20 minutes. In Hall's experiments, he significantly
increased the mutation rate and reduced the generation times.
In any case, this is really beside the point. The point is that Hall
studied enough generations to convince himself that his double mutant
E. coli did in fact have significantly "limited evolutionary
potential". That's the point. It is an interesting point because of
the relatively low level of complexity needed to achieve the lactase
function. It was somewhat surprising to Hall that evolutionary
potential would be so limited. This is a surprising conclusion
really. After all, all bacterial species can rapidly evolve
antibiotic resistance to just about any antibiotic that is presented
in sublethal levels. Why then should it be so difficult to evolve a
simple function like lactase in relative short order in just about any
lac negative bacterial colony as well? It is a very interesting
reason why evolution is so easy on the one hand, while being a lot
more difficult on the other, and then not at all at for functional
systems that require a bit more complexity.
> http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubme...
>
> Your own calculations indicated that once mutation selection balance
> was reached in a population, jumping 2 or 3 mutational intervals was
> not that rare.
That's right . . .
> Hall's experiments never reached close to mutation
> selection balance. He started with clonal populations at the same
> start point every experiment. You know the difference, you prefer to
> lie to yourself about it.
Hall's experiments didn't need to reach mutational balance (70,000
generations), because the gap size was only one mutation wide. A gap
of just one mutation is easy to cross for a large colony in a single
generation. And, this is exactly what happened.
> Remember it was your own calculations about the number of mutations in
> a population at mutation selection balance that made you drop your 2
> and 3 step gap for the 40 mutations gap, then there was this big leap
> to the mythical 1000aa, when you never demonstrated that a gap of 3
> had to be crossed.
The 1000aa threshold is not the gap size. I've had to explain this so
many times that I'm not quite sure why you haven't got this straight
yet. The 1000aa threshold represents those functional systems that
require this many amino acid parts in a fairly specific order to
work. The gap size is always, and I mean ALWAYS, smaller than the
minimum threshold limitation. The likely minimum gap distance at a
threshold level of 1000 fairly specified residues would probably only
be a few dozen residue changes wide - not 1000 by any means. It is
just that a gap of a few dozen residue changes would be uncrossable
this side of trillions of years of time - even for a colony the size
of all the bacteria on Earth.
> You even know why you can't demonstrate something
> like that. It is because you need to know the starting protein
> sequences, and you do not have that data. No one does.
We don't have to have the original protein data to have at least some
idea as to the likelihood that it would have been able to produce the
degree of functional complexity that we see in all living things. We
can get a very good idea based on the biosystems that do exist and the
limited evolutionary potential that we can see in play right now.
This information can be used to extrapolate to conditions that likely
existed in the past.
Also, without at least some idea as to the likely nature of past
conditions, your notions about the potential of the proposed
evolutionary mechanism of random mutation and function-based selection
are based on nothing more than wishful thinking - not evidence and
therefore not science.
> > > What is the probability
> > > that, that would happen if your bogus claims were correct about
> > > protein sequence space and the number of viable sequences?
>
> > Pretty good. Evolution happens quite often at this level actually.
> > What you never seem to consider, however, is why evolution doesn't
> > happen at higher levels?
>
> The mythical higher levels that Sean can't even describe, let alone
> have his own viable explanation for. If what science has is so bad,
> what should that tell Sean about his alternative when he can't even
> establish that it works at the lower levels?
This paragraph makes no sense to me. Evolution does work at low
levels of minimum structural threshold requirements. The lower the
level, the better it works - exponentially better. There is nothing
mysterious or mythical about the concept that some functions are more
complex than others in that they require more building blocks before
they can work. How on Earth is that such a mythical concept for you?
It should be downright obvious.
> > > You keep denying the antibody example, claiming that it isn't high
> > > enough about something or other to satisfy you, but you have no
> > > alternative do you? A maximum of 10E12 sequences are tested at any
> > > time and the system works nearly all the time. Such a tiny fraction
> > > of the sequence space has to be sampled to get funtional antibodies
> > > that it makes your claims out to be a joke. You've known for years
> > > that not only can they get antibody activity, but Abzymes demonstrate
> > > that enzymatic function can evolve using the same system.
>
> > Actually, the sequence space involved with antibody binding is quite
> > small - only about 20^20 sequences. This sequence space can be
> > exhaustively searched by a relatively small population of immune
> > cells. Not a problem at this very low level.
>
> And your evidence for this is...
As I've just explained to Howard, the typical length of an antigen
epitope is about 20 amino acid residues. So, the total number of
possible antigen epitopes is about 20^20 or
104,857,600,000,000,000,000,000,000 or ~100 trillion trillion. Since
there are trillions of different possible antigen epitopes, how does
one's immune system cope with such a variety of potential enemies?
Well, there are many immune cells produced by the body. In humans, in
particular, about 10^12 lymphocytes are present at any given time.
Not all the T-cells have different Y-shaped receptors, but many of
them do. Chances are that if enough non-self enemies get into the
body at least one of the immune cells will recognize the non-self
marker sequences or "antigens" located on this invader as "foreign" to
at least some useful degree. The odds that a single T-cell will
recognize a random epitope to at least some useful degree is about 1
in 10^12. So, does this mean it would take a trillion different T-
cells to cover all possible invaders? Well, no. The reason is
because an average cell or foreign invader "bug" has about 10^12
different epitopes. So, on average, a single T-cell will recognize at
least one of the potential antigen epitopes of a foreign invader.
http://www.detectingdesign.com/immunesystem.html
> Thought that you didn't have any.
Where did you get that idea?
> How did you come up with a number
> so small?
Because, antibody binding to antigens presented by antigen presenting
cells is only based on about 20 very loosely specified amino acid
residues.
> What about the Abzymes?
Abzymes require more than simple binding. Abzymes are antibodies
that, in addition to being able to bind, must also by able to
hydrolyze chemical bonds in a specific way to act as enzymes.
Enzymatic activity is far more complex than simple protein-binding
functions. It therefore has a much greater minimum size and
specificity requirement. For example, those abzymes that have
adequate levels of lactase activity equivalent to what might be useful
in a bacterium have minimum size requirements of several hundred
residues in a fair degree of specificity.
> Do you know how small a number of
> amino acid residues that you are claiming account for the entire
> immune response in the biosphere? It is only around 20 isn't it?
Yep - that's it.
> Even for you that number would have to be bogus.
It isn't bogus at all. It's a well-established fact. Look it up.
> > You see, all of your examples that you have ever presented are very
> > low-level examples - every one. None of them comes remotely close to
> > the 1000aa threshold where sequence space is the size of 20^1000.
> > I've pointed this out to you many many times, but you act as if
> > nothing was ever said. You don't even try to address this point, but
> > act like it is completely irrelevant to the issue and go on presenting
> > your low-level examples like they somehow explain away the problem.
>
> They weren't such low level and irrelevant when you were on your 2 or
> 3 mutation gap kick, were they? What a joker. Where did you
> establish this 1000aa threshold? When do you expect the Nobel prize?
> Have you published, yet, or are you keeping it a secret? You can't
> just make this junk up.
I've always said that Gaps of 2 or 3 mutations could be crossed in
relatively short order and I've always said that such small gap
distances become exponentially less and less likely with increasing
minimum structural threshold requirements. There's been no change in
this description of the problem at hand.
> > > You know all this, but you keep blowing smoke. Not only that, but you
> > > try to make it look like it is the other guys problem. That is just
> > > sad.
>
> > Just answer the question Ron. It isn't just smoke. It is a valid
> > simple question. Why does evolution not produce any novel beneficial
> > functional systems that require a minimum of more than 1000 fairly
> > specified residues? Hmmmmm? Care to take a crack at answering that
> > question?
>
> Describe the 1000aa threshold so that someone can look for it and
> determine that it is there. Why should I have to explain something
> that doesn't even exist? What question am I supposed to answer? I
> need to know what the threshold is before I can explain it. You have
> never demonstrated that it even exists. How is anyone supposed to
> explain the mythical 1000 aa threshold when only you know it is there,
> but can't tell anyone else what it is? I'll answer "the question"
> when you tell me how tall the invisible pink elephant is that is
> standing next to you. Oh, geez, can't answer such a simple question,
> you must be an idiot lamo.
What don't you understand about the concept of a minimum structural
threshold? It is a very simple concept. It is the minimum size and
specificity requirement of a system that is needed before it can work
to do a particular type of function. Some systems require a greater
minimum than do others. Many systems have a minimum that goes well
beyond the 1000aa threshold. Such systems never evolve. Only systems
with lesser threshold minimums have been shown to evolve - to include
all the examples you keep presenting.
How is that concept so difficult to understand?
> > > Why not just put up or shut up? You don't deny that you made the
> > > claims, so make good on them. It isn't my problem that you keep
> > > running, it is your problem. You are doing the running and blowing
> > > the smoke.
>
> > This paragraph doesn't even make sense. I've presented some simple
> > questions. Who is the one trying to avoid answering them? I've
> > answered yours, why not at least try to answer mine? Instead, you
> > continually present your usual low-level examples and an endless
> > string of pejoratives? How is that helpful to me or anyone else who
> > might also like to hear what you have to say regarding this question?
>
> It would make sense if you hadn't snipped and run from what you can't
> deal with for the past, geez, how long? Could it be 6 or 7 years for
> the common descent claim? The ID stuff can't be more than 4 years,
> but it is your problem.
>
> What is your alternative to common descent and the evidence that you
> claimed was just as good as what science had? What is the science of
> ID that you would have taught to school kids when you were still
> advocating the teach ID scam? Without the science, and no viable
> alternative, who cares about the mythical 1000 aa threshold?
If you'd at least try and answer the question as to why evolution
never produces anything more complex than systems requiring a minimum
of only a few hundred amino acid residues max, you'd start care about
this problem. It isn't easily dismissed for those who actually try to
solve it from the evolutionary perspective.
The alternative, of course, is ID. This is no scam if you can't
answer the question.
> DetectingDesign, what a bogus con job. All you are reduced to doing
> is running the replacement obfuscation scam. Claiming links to the ID
> scam when the other ID perps have a new scam that doesn't even mention
> that ID ever existed makes you look like a moron.
I present my own version of ID Theory on my website which, I must say,
is uniquely different from anything I've seen elsewhere. It really
doesn't matter to me what others are thinking or doing if it doesn't
make sense to me. I present ideas that do make sense to me on my
website. If that makes me look like a moron to you or anyone else -
so be it. I'm convinced by arguments that make sense to me; not who
agrees or doesn't agree with the arguments.
Seanpit
> On Dec 15, 12:07 pm, Seanpit <seanpitnos...@naturalselection.
>
> 0catch.com> wrote:
> > You equate a gap of 300 residue differences with specificity
> > flexibility. That is a fundamental error. The gap distance is the
> > distance between the edge of one beneficial island cluster of
> > sequences and the next closest edge of beneficial island sequences in
> > sequence/structure space.
> >SeanPitmanwww.DetectingDesign.com
>
> organism for 2 completely unrelated purposes, your 300aa PittMan Gap
> Theory would be falsified, would it not ?
>
> We would have a 0-gap, but each of the 2 functions would be the
> starting point of a new "cluster" of functional/useful proteins. The
> clusters would possibly diverge as measured in numbers of aa from the
> common single protein starting point. And at any time, one slightly
> different protein of either cluster could show an enzyme or binding
> property absent in the cluster, and branch off as a new cluster. We
> would now have 3 families of proteins, from a single "starting point".
>
> So, are you confident I cannot find a brain neurotransmitter protein
> with an analog used in the gut for digestion ? Or another
> neurotransmitter used as a polymer in spider silk ?
>
> Do you agree that the existence of any such protein would entirely
> destroy the Pittman Neuttral Gap theory ?
>
> I don't expect you to.
Exact or similar proteins are used all the time as parts of uniquely
different systems of function. That doesn't explain how one can get
from one particular starting point with one type of function to a
target with a uniquely different function. You see, to get the same
protein to be part of a uniquely different functional system, the
system itself much be different that the current system. This
requires a few changes. The minimum number of changes required to get
from one unique function to the other constitutes the gap distance.
This distance isn't "zero" as you suggest or the same system would
have both functions already without any changes needed at all. A
neurotransmitter requires a nervous system and a digestive enzyme
requires a GI system. Getting from one system to the other,
regardless of the fact that a number of similar proteins are used for
each system, is what creates the gap.
You see, you have to look at the function in question, not the single
protein that may be used as part of the system producing a given
function.
Sean Pitman
www.DetectingDesign.com
Seanpit
>
> > You equate a gap of 300 residue differences with specificity
> > flexibility. That is a fundamental error.
>
> No it is not. It shows that to potentially go from Cytosome-C to some
> other
> functional protein, their at least 300 potential routes. We are
> talking about a space
> that has a large number of dimensions, which renders the below
> statement silly.
CytoC is a fairly low-level function requiring a minimum of no more
than 100 fairly specified residues. The minimum likely gap distance
at this level is probably only a handful of residue changes (4 or 5) -
not even close to 300 changes which is well beyond the maximum of 100
in this case.
You don't seem to understand the concept of a gap distance.
> > The gap distance is the
> > distance between the edge of one beneficial island cluster of
> > sequences and the next closest edge of beneficial island sequences in
> > sequence/structure space.
>
> How do you know where that is and what it is? You have no clue.
There are some very good clues actually. Do a BLAST search to see
what the next closest system is to the one in question. The number of
differences between them is at least a good rough estimate of the
likely minimum gap distance.
> > Do you see the distinction?
>
> The distinction here is that observed sequence variability of CytoC is
> measurable and suggests
> a minimum of 100s of potential routes to new proteins, while your
> concept of unbridegable
> gaps between beneficial islands of functionality in a vast multi-
> dimensional space is a figment
> of your imagination.
Actually, the gap distance only concerns the distance of the most
direct route. For CytoC, closest distance to the next closest system
is far less than 100 residue changes.
Seanpit
> On Dec 15, 11:54 am, _Arthur <Arth...@sympatico.ca> wrote:
>
> > To chop down this saga to the bare outline,
> > some scientists, Yockey and Sauer, observed that the cytochrome
> > proteins of many species differed significantly (albeit with the same
> > basic structure), for the same overall functionality, and so their
> > genes differed.
>
> > sequence giving a biologically useful protein would be separated by
> > at least a 300 point mutations "gap" from *ANY* other protein of any
> > different function/usefulness.
>
> > Now the Pitt Man concedes that his 1000 number was a "rough estimate*,
> > which should make is 300 gap even rougher.
>
> > Of course, Pitts steadfastly refuses to correct his website, despite
> > the great many biological, mathematical, and logical absurdities
> > pointed to him, some of which he even very, very, very grudgingly half-
> > admitted, after years of handwaving, thread-pounding and
> > grandstanding.
>
> > Did I get any of it right ? Roughly ?
>
In agreeing with Arthur here, you show that you still don't grasp the
difference between sequence flexibility (i.e., the size of a target
island) and the distance between islands (i.e., the gap distance).
They aren't the same thing Howard. You, of all people, should know
this by now.
I can only assume that you support Arthur here because, and only
because, he is trying to oppose my position.
Sean Pitman
www.DetectingDesign.com
Seanpit
wrote:
>
> >> Sean, you are introducing a new variable here: "level of minimum
> >> structural threshold requirements".
>
> > This isn't a new variable. It has been the basis of my whole position
> > since the beginning. I don't know how many times I've used this very
> > same phrase for you directly in many many posts in the past? It has
> > to be over a 50 times. How can you not remember?
>
> Google is your friend. 4 hits on the phrase, all within the past week.
Yes, Google is your friend. Type in "minimum structural threshold
requirements" and the search will return 170 hits. And, if you type
that same search into Google Groups, you will get 475 hits, as of
today, going back over a year. Other variations on this phrase or
mention of essentially the same concept add even more hits.
In short, I'd hardly say this is a new concept since I've used this
very same phrase with Howard many many times.
Seanpit
wrote:
>
> >> Neither is "minimum actual gap size".
>
> > That's statistically mistaken. Minimum likely distances are indeed
> > based on average distances. That is what the Poisson distribution is
> > all about.
>
> No, Sean, you are demonstrating your statistical ignorance again. The
> Poisson distribution describes the probability of exactly k events occuring
> within a fixed interval,
That's right. How many targets are likely to be within a fixed
distance?
> given that the events occur at a known average rate
The average distance between targets is known.
> lambda = n/interval, and that the occurance of next event is independant of
> distance from previous event.
That's right . . .
> You have not demonstrated that you have met
> the Poisson assumptions (especially event independance), and you have
> incorrectly described what the Poisson distribution calculates.
The independence concept is only weakly relevant. The location of
targets in sequence space is not completely random. There is a loose
clustering effect. However, this effect is not significant enough to
affect the Poisson estimation to a significant degree.
The only way there would be a significant effect is if Howard notion
of all the potentially beneficial targets being clustered in one tiny
corner of sequence/structure space was in fact correct. The actual
distribution is far more random in appearance than Howard and others
in this forum seem to realize.
Sean Pitman
www.DetectingDesign.com
richardal...@googlemail.com
0catch.com> wrote:
> On Dec 15, 10:33 am, "R. Baldwin" <res0k...@nozirevBACKWARDS.net>
> wrote:
>
>
>
> > >> Sean, you are introducing a new variable here: "level of minimum
> > >> structural threshold requirements".
>
> > > This isn't a new variable. It has been the basis of my whole position
> > > since the beginning. I don't know how many times I've used this very
> > > same phrase for you directly in many many posts in the past? It has
> > > to be over a 50 times. How can you not remember?
>
> > Google is your friend. 4 hits on the phrase, all within the past week.
>
> Yes, Google is your friend. Type in "minimum structural threshold
> requirements" and the search will return 170 hits.
On the other hand, if you type in "level of minimum structural
threshold requirements" - i.e. you refer to it as a *variable*, you
get only a single hit, which, surprise, surprise, turn out to be the
reference you just made to it.
> And, if you type
> that same search into Google Groups, you will get 475 hits, as of
> today, going back over a year. Other variations on this phrase or
> mention of essentially the same concept add even more hits.
Here we go again: "Essentially the same" in Pitmanese means
"different" in English.
>
> In short, I'd hardly say this is a new concept since I've used this
> very same phrase with Howard many many times.
>
> http://www.google.com/search?hl=en&q=%22minimum+structural+threshold+...
>
> http://groups.google.com/groups?hl=en&q=%22minimum+structural+thresho...
No, the phrase you used was "minimum structural threshold
requirements".
By adding the words "level of " to that phrase, you are implying that
it is a variable which can be measured.
So how do we measure this variable?
Let's sit back and watch you evade again, shall we?
By the way, there's an outstanding question (well, many outstanding
questions, but let's try to get an answer for this one) you haven't
answered:
Who do you think has the intellectual capability to evaluate your
"theory"?
After all, it's clear that nobody on this forum thinks it's anything
more than a load of twaddle, so why waste your time and effort in
posting the same stuff over and over again?
Of course, my hypothesis is that you know that it's a load of twaddle,
and are posting here only because you think that it impresses the
creationists. Everything you have done so far verifies this
hypothesis.
RF
Ron O
0catch.com> wrote:
> On Dec 15, 1:40 pm, Ron O <rokim...@cox.net> wrote:
>
> > On Dec 15, 10:50 am, Seanpit <seanpitnos...@naturalselection.
>
> > 0catch.com> wrote:
> > > On Dec 15, 8:05 am, Ron O <rokim...@cox.net> wrote:
>
> > > < snip pointless pejoratives >
>
> > You are so whacked that you probably don't even know what a pegorative
> > is. The facts are not pegoratives.
>
> Personal attacks that have nothing to do with the questions presented
> are needlessly pejorative and irrelevant.
>
> < snip >
Still snipping and pretending. That isn't a pejorative that is a
fact. You can't run fast enough. Who do you think that you are
fooling? The problem is yours, you have to deal with it.
Can you even make yourself type out what you are running from?
Snipping it doesn't make it go away.
>
> > > Finally - some actual arguments.
>
> > > > What does the actual data tell you about your bogus notions of protein
> > > > sequence space? Two species of bacteria with only 2000 proteins in
> > > > their genomes to mutate and they can evolve beta gal activity. How is
> > > > that possible if what you claim about sequence space is at all true?
>
> > > The odds are actually pretty good because the lactase function is at a
> > > pretty low level of minimum structural threshold requirements - i.e.,
> > > less than 400 fairly specified residues. The ratio of lactases vs.
> > > non-lactases at this level is actually pretty high. The same thing is
> > > true of other biosystems that are based on equivalently small single
> > > proteins. Such evolution actually happens fairly often at this
> > > level. But, it doesn't happen at all at higher levels - i.e., beyond
> > > the 1000aa threshold. That's what's most interesting about the gap
> > > problem. It is demonstrably exponential in nature.
>
> > Goal post shift to the mythical 1000aa threshold, that Sean has never
> > been able to verify exists.
>
> I think you are confusing the threshold limitation for the gap size.
> The threshold size and the gap size are not the same thing. The
> likely minimum gap distance is always smaller than the minimum
> threshold limitation. But, what is interesting though about the
> minimum gap distance is that it increases in a linear manner as the
> minimum threshold limitations under consideration are increased.
This is stupid. You are going back to "it is a gap, but it isn't a
gap, it is only a gap when I want it to be a gap, and until I say
so." Just demonstrate that you have established the existence of this
mythical 1000aa threshold. You don't even know what it is.
What kind of threshold is it when the parts are independent and don't
have to evolve all together? It is just a bunch of small gaps that
you gave up on years ago.
>
> So, for a threshold limitation of 1000 fairly specified residues, the
> likely minimum gap distance would NOT be 1000 mutations wide - not
> even close. Rather, the likely minimum gap distance would only be a
> few dozen mutations wide at this level. However, this seemingly
> small minimum gap distance would make evolution of a functional system
> requiring a minimum of 1000aa very unlikely even over the course of
> trillions of years of time - even for a bacterial colony the size of
> all bacteria on Earth.
Define "fairly specified." You don't have to bother, I didn't think
that you could do it anyway it is just a rhetorical question. Sort of
like Behe and IC. What is the latest possible definition of IC
nowadays? The more parts something has the more IC it is? For Sean
it is the more gaps that aren't really gaps that you have that make
things "fairly, specified." We are back to gaps that aren't gaps, but
you know what the threshold is. What is the minimum gap distance for
a gap that isn't really a gap?
Do you ever read your junk? Do you just make this junk up as you go?
Do you ever look back on what you've already said about this gap
nonsense?
>
> Now, let's look at a higher level system to see if higher-level
> thresholds actually exist. Since you claim that higher level
> thresholds do not exist, how many amino acids need to be coded for to
> produce a flagellar motility system at minimum? (i.e. the threshold
> size) Please, do give me your best estimate. As far as I can tell,
> the answer is well over 10,000 fairly specified residue positions
> coded for by an even greater number of codons of genetic real estate
> (to include codes for non-structural proteins). A flagellar motility
> system simply cannot be built with significantly fewer codons or
> residues at all. If you think otherwise, please, do present your own
> estimate.
Why is this a higher level threshold? What is the threshold? Don't
you have to figure that out before you call it a higher level? I can
give you an estimate just as soon as you tell me how tall that
invisible pink elephant is that you have in your house. You know the
invisible one. It is probably right there standing beside you as you
read this.
Define "fairly specified." Sort of like describing that invisible
pink elephant. Did you know that it isn't really pink? Don't you
know what color it really is? What a loser. How do you expect anyone
to come up with an explanation for anything when you can't even
determine that it exists to explain?
All this bogus junk sounds sciency, but that is it. Demonstrate that
your 1000aa threshold exists. I'm still waiting. Did you know that
there are now two invisible pink elephants that aren't pink in your
house? These things sound stupid because they are stupid. Until you
can demonstrate that your 1000aa threshold is more than my assertion
about invisible pink elephants you have no argument.
>
> > How low of a minimal threshold is Lactase
> > function?
>
> About 380aa.
How bogus was that answer? Remember the last time you put it up? You
tell me what was wrong with that estimate. Just demonstrate that you
know what it is.
Does that mean that your threshold is just the number of amino acids
in the proteins involved? What are these gaps that aren't gaps
again? What do they have to do with the threshold?
Geez Louise, Lactase is a lower level threshold, but it is only a
third the size of your higher level threshold of 1000aa. What is that
definition of higher level thresholds again? If it is so easy to
evolve lactase function so as to make it insignificant to the
argument, what does that say about this 1000aa bogousity?
>
> > Just because you can't deny the data without looking more
> > like a clown than usual, how low is it?
>
> What data are you talking about here? What is your suggestion for the
> minimum size requirement for the lactase function? Does it come
> remotely close to the 1000aa threshold? No. Therefore, it is a
> fairly low-level function. There are many examples of functional
> systems that require only a few hundred fairly specified residues
> evolving. There are no examples where the system requires over 1000
> fairly specified residues - not one example of evolution beyond this
> level in all of literature. And yes, many such systems do exist which
> require many thousands of specified residue positions in every single
> living thing. Here are just a few:
What is the 1000 aa threshold?
What about the actual lactase data? What about the only data that you
have to work with? Where does it fit into this 1000 aa threshold?
You know why there are no examples, because you don't know of any.
You don't even know what a 1000aa threshold is, except to say that you
know it when you see it. Why should anyone believe you?
>
> Flagellar motility, DNA transcription, RNA translation, vesicle
> transport, ATP production, etc . . .
What is your alternative explanation? How long did it take for those
systems to evolve, and do you know the evolutionary path that you are
trying to claim could not have happened? If you claim to have this
knowledge spit it out. Are we going to go back to the gaps that
aren't really gaps, and arguments from ignorance?
Our best guess is that flagellar motility evolved a couple billion
years ago. There were life forms for around 2 billion years before
flagellum made their appearance. Map out how it could not have
happened. You are stuck with the same problem that all the other
IDiots have. To demonstrate your point you have to be able to claim
that all (ALL) possible evolutionary pathways have a probability so
low that it indicates that something else happened. Go for it. Isn't
it sad that you can't calculate the probability for even one
biologically relevant evolutionary path? The only calculation that
any IDiot has ever come up with is the biologically irrelevant
"tornado through a junkyard calculation." Demonstrate that you can do
what none of the other ID perps have been able to do.
>
> > You can't just make junk up and expect people to believe you,
> > especially since you are such a liar. You need confirmation. Where
> > is it? When have you or anyone ever established that this mythical
> > 1000aa threshold exists?
>
> After all the times I've presented this evidence I can't believe that
> you would still be trying to suggest that no system exists which
> requires a minimum of more than 1000aa to work. How can you suggest
> such a thing and call yourself informed on this issue? If you don't
> believe me, then by all means provide some sort of evidence showing
> how a functioning flagellum or any other such system can be produced
> with fewer than 1000 codons of genetic real estate . . .
We are back to codons, but they aren't really codons, because the
flagellum is made up of a lot of proteins, and just a few add up to
more than 1000 codons. So, you don't seem to know what your mythical
1000aa threshold is. Is it the number of codons, or the number of
gaps that aren't really gaps unless you want to claim that they are
gaps at some time, but that can change at any time?
There are now three invisible pink elephants that aren't pink in your
house. As soon as you can tell me how tall the mid sized one is, I'm
sure that I can come up with an explanation for your mythical 1000aa
threshold. That should happen about the time that pigs sprout wings
and fly, right?
>
> > Put up or shut up. This bogus mytical
> > 1000aa threshold argument must be getting lame even for you. Can you
> > go to someone like Behe and have him confirm this junk? No? Why
> > not? Pretending isn't demonstrating anything except your ability to
> > lie to yourself about this topic.
>
> I don't think you really understand the concept of minimum structural
> threshold requirements after all this time.
You apparently do not either. Is it codons? Are they the gaps that
aren't gaps? You know those gaps that do not have to be crossed all
at one time to break this threshold? Didn't you admit that? Sounds
like a pretty breakable threshold if you can inch up to it a little at
a time. I'd know if we could if you could tell us what it is.
>
> > > > What is your alternative and the evidence to back it up? Doesn't
> > > > science have a verified means of getting what it needs for biological
> > > > evolution?
>
> > > Yes, it does. But, only at very low levels of minimum structural
> > > threshold requirements (i.e., well below the 1000aa threshold).
>
> > This again points out how lame your arguments are. Science has an
> > explanation. You can't deny it, you can only make up junk about some
> > mythical 1000aa threshold when you have to admit that you don't even
> > have anything as good as the low level explanation. You have jack.
> > You don't have an explanation for the 1000aa threshold crap either.
> > Put it forward if you claim to have one. Why should science have an
> > explanation for something that you can't even demonstrate exists in
> > nature?
>
> Do you really not understand that all of your examples are of systems
> that have very few minimum structural threshold requirements? They
> just don't need very much to start working to at least some useful
> level of activity - far fewer than 1000aa residues. How can you not
> understand that concept? Simple functions like these are relatively
> easy to evolve. More complex functions, on the other hand, are not
> easy to evolve - - and in fact do not evolve. There is not a single
> example of a more complex system actually evolving in all of
> scientific literature. If you do know of such an example, beyond the
> very simple systems you've already listed, then, by all means, present
> this example.
I guy that claims that the age of the earth is wrong by 5 orders of
magnitude claiming that 380 and 1000 separate high and low levels of
whatever. Is there some disconnect here? The only difference between
high and low is that you can still lie about the high because we can't
explain it, because you can't tell us what it is. Evolution of the
low is low because we can observe it happening and you can't deny it
any longer. How bogus of a definition is that?
>
> You do understand that some types of functions are inherently more
> complex than others - right? Would you say that flagellar motility
> requires much more complexity than the single protein lactase
> function? I sure hope you would agree to that.
>
What is your definition of complexity? Flagellum obviously have more
moving parts, but they are still made of proteins. You don't have
computer operated widgets in there regulating the function. In fact
most of the flagellar proteins that have been studied are related to
other proteins in the bacteria that we know are doing something else.
We can't trace them all back to relatives because you know what 2
billion years of molecular evolution can do to protein sequences. So
it is different from the lactase evolution, how? By the number of
gaps that aren't really gaps unless you say so?
>
> > > > What is your alternative? How does it match up with what
> > > > we can actually observe happening? How many species do you think Hall
> > > > tested and how related were they?
>
> > > Hall only tested one species - E. coli. But, the same thing is likely
> > > to happen in other species occasionally at this level of functional
> > > complexity.
>
> > Remember when you made your pegorative claims and tried to claim that
> > Hall didn't find any other species that could do the same trick as E.
> > coli? You ran away again, but not until I put the ref forward to
> > demonstrate why you had to run.
>
> > Here it is again.
>
> >http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubme...
>
> > Klebsiella is not E. coli.
>
> Interesting abstract. I was unaware of this particular experiment and
> will have to obtain and read the full paper.
I'm sure that you saw it last time you ran. It is the same reference
that I put up the last time you made the same bogus claim. Isn't it
about time to run again?
>
> I do appreciate you bringing this paper to my attention, but I don't
> see how it affects the main point at hand in the least. I mean, I
> just noted for you that "the same thing is likely to happen in other
> species occasionally at this level of functional complexity." Did you
> miss that comment? After all, this level involves only a few hundred
> fairly specified residues at most. This sort of thing is only to be
> expected at such low levels - quite predictably in fact.
The reason for this is because you are dishonest and probably mentally
incompetent. Nothing, no amount of evidence, can change your mind,
even when you have to acknowledge its existence.
"Fairly specified" Must rank up there with "specified complexity,"
"irreducible complexity," "intelligent design," etc. How bogus did
all those turn out to be?
What was that intelligent design science that you would have taught to
school kids? What? No science? What are you arguing about?
What was that alternative to common descent that you had, and the
evidence to back it up? What? No alternative? Why are you arguing
about mythical thresholds if you don't have an alternative? Just
because it is the only pathetic thing that you can do doesn't mean
that you should be doing it.
It is only a personal attack to you because you know that you are
stupid to keep running and pretending. If you just started to be
straight, I wouldn't have to keep reminding you about what you are
lying about.
>
> Beyond this, how does this paper help your position? All it is, at
> the very most, is yet another example of low-level evolution - of a
> novel system that requires far less than a minimum of 1000aa.
>
It most definitely doesn't help yours. Remember when you were running
the Hall bull pucky for the first time? You were claiming that
crossing gaps of 3 were impossible. You hadn't come up with your
mythical 1000aa. The data showd that you were wrong, so at first you
jumped to 20 or 40 mutation gaps that were impossible, and it evolved
into this bogus claim of a whooping 1000aa.
At the very least it shows what a loser you are. Since you can't tell
us the difference between the two cases, and your own admissions seems
to be the difference between 380 and 1000. What are you arguing
about? All we have to do is divide up that 1000 into three parts and
you have no argument. So tell us what the 1000 is. You even admit
that you don't have to evolve all 1000 at a time. Even if the 1000
whatever exists, around 2 billion years of evolution took place before
flagellum evolved. We can still tell where a lot of the parts came
from.
In the face of that what do you have as an alternative?
>
> > Hall never did the 40,000 generation experiment. What he did was a
> > series of single step selection experiments that may have amounted
>
Snip what you can't deal with.
It is about time to run again.
Just remember to tell us the science of intelligent design that you
would have taught to school kids, and that alternative to common
descent that you claimed to have and the great evidence to back it up
that was just as good as the evidence science has for it's
alternative.
Sean, you are so lost that you are a guy that claims that being
reminded of what he claimed to be able to do, is a pegorative. Sure
it does make you out to be a loser, liar, and con artist, but heck,
whose fault is that? Who just keeps pretending and snipping and
running?
Ron Okimoto
R. Baldwin
> On Dec 15, 10:33 am, "R. Baldwin" <res0k...@nozirevBACKWARDS.net>
> wrote:
>>
>> >> Sean, you are introducing a new variable here: "level of minimum
>> >> structural threshold requirements".
>>
>> > This isn't a new variable. It has been the basis of my whole position
>> > since the beginning. I don't know how many times I've used this very
>> > same phrase for you directly in many many posts in the past? It has
>> > to be over a 50 times. How can you not remember?
>>
>> Google is your friend. 4 hits on the phrase, all within the past week.
>
> Yes, Google is your friend. Type in "minimum structural threshold
> requirements" and the search will return 170 hits. And, if you type
> that same search into Google Groups, you will get 475 hits, as of
> today, going back over a year. Other variations on this phrase or
> mention of essentially the same concept add even more hits.
>
> In short, I'd hardly say this is a new concept since I've used this
> very same phrase with Howard many many times.
>
You are such a dishonest man. Howard Hershey obviously put the entire phrase
"level of minimum structural threshold requirements"within quotes because it
appeared to be a new term that you hadn't defined yet.
Is your terminology squirmy on purpose? It sure appears to be.
R. Baldwin
> On Dec 15, 11:08 am, "R. Baldwin" <res0k...@nozirevBACKWARDS.net>
> wrote:
>>
>> >> Neither is "minimum actual gap size".
>>
>> > That's statistically mistaken. Minimum likely distances are indeed
>> > based on average distances. That is what the Poisson distribution is
>> > all about.
>>
>> No, Sean, you are demonstrating your statistical ignorance again. The
>> Poisson distribution describes the probability of exactly k events
>> occuring
>> within a fixed interval,
>
> That's right. How many targets are likely to be within a fixed
> distance?
No Sean, read for comprehension. It is the probability of finding an *exact
quantity* of events within the fixed interval. The probability mass function
is measured over the *quantity* variable. It is not "how many targets are
likely to be found within a fixed distance."
>
>> given that the events occur at a known average rate
>
> The average distance between targets is known.
>
>> lambda = n/interval, and that the occurance of next event is independant
>> of
>> distance from previous event.
>
> That's right . . .
Glad you agree, though above you clearly don't quite get it.
>
>> You have not demonstrated that you have met
>> the Poisson assumptions (especially event independance), and you have
>> incorrectly described what the Poisson distribution calculates.
>
> The independence concept is only weakly relevant. The location of
> targets in sequence space is not completely random. There is a loose
> clustering effect. However, this effect is not significant enough to
> affect the Poisson estimation to a significant degree.
Weaselly bull.
>
> The only way there would be a significant effect is if Howard notion
> of all the potentially beneficial targets being clustered in one tiny
> corner of sequence/structure space was in fact correct. The actual
> distribution is far more random in appearance than Howard and others
> in this forum seem to realize.
>
And you know this how? From some misinterpreted abstract of an article that
you didn't understand?
_Arthur
Oh, so the Pittman Gap is in "systems" of proteins, now ?
Now "systems" of proteins are surrounded by a functionless "neutral
gap" of 1000aa ??
You are not making any more sense that you were.
Ron O
Oops I thought that Sean had just snipped out the rest, but it was
Google that truncated the message.
So I'll continue.
> > Hall never did the 40,000 generation experiment. What he did was a
> > series of single step selection experiments that may have amounted to
> > 40,000 generations, but most likely did not. A generation before the
> > favorable mutation occurs is estimated to be 30-50 hours. This would
> > amount to 50,000 to 83,000 days, a minimum of 136 years of growing
> > bacteria. Did Hall ever run such an experiment? He might have run
> > 136 experiments in parallel for a year, but that wouldn't be the same
> > would it? He probalby did even worse, and ran a bunch of experiments
> > for a couple of weeks. He would need to get a population to mutation
> > selection balance, and he never did, did he?
>
> Under appropriate conditions, the generation of time of E. coli can be
> as little as 20 minutes. In Hall's experiments, he significantly
> increased the mutation rate and reduced the generation times.
Those were not the conditions of the experiment. Any bacteriologist
would know that E. coli can grow at a 20 minute doubling time, but
what were the selective conditions of the Hall experiment?
As far as I know the generation time only decreased once the favorable
mutation had occurred. For Hall to tell if some bacteria evolved
lactase function he would have to observe the faster growth rate under
selective conditions. The mutation rate did go up as later studies
showed because the bacteria under stress tend to make more mistakes
and sometimes SOS starts up. For the experiments where he removed EBG
and tried again, he would have been looking at the 30 to 50 hour
generation times unless you have some other assay that he could have
selected for. Hall knew that he wasn't getting the mutations that he
needed because nothing grew faster.
>
> In any case, this is really beside the point. The point is that Hall
> studied enough generations to convince himself that his double mutant
> E. coli did in fact have significantly "limited evolutionary
> potential". That's the point. It is an interesting point because of
> the relatively low level of complexity needed to achieve the lactase
> function. It was somewhat surprising to Hall that evolutionary
> potential would be so limited. This is a surprising conclusion
> really. After all, all bacterial species can rapidly evolve
> antibiotic resistance to just about any antibiotic that is presented
> in sublethal levels. Why then should it be so difficult to evolve a
> simple function like lactase in relative short order in just about any
> lac negative bacterial colony as well? It is a very interesting
> reason why evolution is so easy on the one hand, while being a lot
> more difficult on the other, and then not at all at for functional
> systems that require a bit more complexity.
No, you know for a fact that he didn't run the experiment that he
needed to run. When we went around this point before you had to admit
that if the population was allowed to reach mutation selection balance
that double and triple mutations would not be observed to be as rare
as Hall found. Hall started with clonal populations with nearly
identical genomes each time he started an experiment. He Would have
had to run the experiment in a chemostat until the population reached
mutation selection balance before it would be an actual test of
evolutionary capability. He never ran that experiment and you know
that he didn't or you would have put up the reference by now.
>
> >http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubme...
>
> > Your own calculations indicated that once mutation selection balance
> > was reached in a population, jumping 2 or 3 mutational intervals was
> > not that rare.
>
> That's right . . .
So what is your beef, and how does that impact your 1000aa threshold
that is composed of gaps that aren't really gaps, but they don't all
have to be crossed all at one time?
>
> > Hall's experiments never reached close to mutation
> > selection balance. He started with clonal populations at the same
> > start point every experiment. You know the difference, you prefer to
> > lie to yourself about it.
>
> Hall's experiments didn't need to reach mutational balance (70,000
> generations), because the gap size was only one mutation wide. A gap
> of just one mutation is easy to cross for a large colony in a single
> generation. And, this is exactly what happened.
His first experiements didn't have to. You made a stink about his
second set of experiments where he deleted EBG and claimed that it
meant that gaps of 2-3 could not be crossed. Don't you remember your
own arguments?
You were wrong. You admit it because you had to go from gaps of 2-3
to your 1000 aa bull pucky.
>
> > Remember it was your own calculations about the number of mutations in
> > a population at mutation selection balance that made you drop your 2
> > and 3 step gap for the 40 mutations gap, then there was this big leap
> > to the mythical 1000aa, when you never demonstrated that a gap of 3
> > had to be crossed.
>
> The 1000aa threshold is not the gap size. I've had to explain this so
> many times that I'm not quite sure why you haven't got this straight
> yet. The 1000aa threshold represents those functional systems that
> require this many amino acid parts in a fairly specific order to
> work. The gap size is always, and I mean ALWAYS, smaller than the
> minimum threshold limitation. The likely minimum gap distance at a
> threshold level of 1000 fairly specified residues would probably only
> be a few dozen residue changes wide - not 1000 by any means. It is
> just that a gap of a few dozen residue changes would be uncrossable
> this side of trillions of years of time - even for a colony the size
> of all the bacteria on Earth.
Here it is, the gaps that aren't gaps, but they are gaps when I want
them to be gaps.
Now we have "fairly specified order" of gap filling. What is that
definition of "fairly specified?"
Give us an example of a "gap size" that isn't really a gap that can't
be crossed in a trillion years. A specific example that anyone can
look up and verify exists would do your argument wonders.
>
> > You even know why you can't demonstrate something
> > like that. It is because you need to know the starting protein
> > sequences, and you do not have that data. No one does.
>
> We don't have to have the original protein data to have at least some
> idea as to the likelihood that it would have been able to produce the
> degree of functional complexity that we see in all living things. We
> can get a very good idea based on the biosystems that do exist and the
> limited evolutionary potential that we can see in play right now.
> This information can be used to extrapolate to conditions that likely
> existed in the past.
Demonstrate that you can support this claim. Just do it. Use your
flagellum example and tell us how large the gaps that aren't gaps had
to be if you don't know your starting point? Just verify that the
gaps were a dozen whatevers wide if you don't know what the sequence
was that you started with.
>
> Also, without at least some idea as to the likely nature of past
> conditions, your notions about the potential of the proposed
> evolutionary mechanism of random mutation and function-based selection
> are based on nothing more than wishful thinking - not evidence and
> therefore not science.
You are the guy that is claiming that you know these things. You are
the one that claims that you know that the flagellum was designed by
some intelligent designer. There is a lot about nature that we don't
know. You are the one claiming to have the answers. I just have to
stick with what we do know and since you have no viable alternative
you are screwed.
Where is your alternative to the evolutionary mechanism? Isn't it
strange that we can verify such mechanisms are working in nature, and
you don't have jack?
>
> > > > What is the probability
> > > > that, that would happen if your bogus claims were correct about
> > > > protein sequence space and the number of viable sequences?
>
> > > Pretty good. Evolution happens quite often at this level actually.
> > > What you never seem to consider, however, is why evolution doesn't
> > > happen at higher levels?
>
> > The mythical higher levels that Sean can't even describe, let alone
> > have his own viable explanation for. If what science has is so bad,
> > what should that tell Sean about his alternative when he can't even
> > establish that it works at the lower levels?
>
> This paragraph makes no sense to me. Evolution does work at low
> levels of minimum structural threshold requirements. The lower the
> level, the better it works - exponentially better. There is nothing
> mysterious or mythical about the concept that some functions are more
> complex than others in that they require more building blocks before
> they can work. How on Earth is that such a mythical concept for you?
> It should be downright obvious.
It makes no sense to you because you choose to remain ignorant. Your
alternative can't even be observed to work at the "lower" levels, so
what good is it? How does it compare against what we can establish is
working in nature?
Just define your mythical 1000aa threshold so that it can be
analyzed. Instead of rambling around pretending just do it. Your
problem is that if you ever do define it, all I have to do is break it
into three distinct parts and you are screwed because then it would
fall below your lower threshold of 380. You know that it is already
broken into two parts because we have the secretory part that is
obviously related to the working flagellum.
While you are at it you might want to tell everyone what your
alternative is so we know that you just aren't blowing smoke.
>
> > > > You keep denying the antibody example, claiming that it isn't high
> > > > enough about something or other to satisfy you, but you have no
> > > > alternative do you? A maximum of 10E12 sequences are tested at any
> > > > time and the system works nearly all the time. Such a tiny fraction
> > > > of the sequence space has to be sampled to get funtional antibodies
> > > > that it makes your claims out to be a joke. You've known for years
> > > > that not only can they get antibody activity, but Abzymes demonstrate
> > > > that enzymatic function can evolve using the same system.
>
> > > Actually, the sequence space involved with antibody binding is quite
> > > small - only about 20^20 sequences. This sequence space can be
> > > exhaustively searched by a relatively small population of immune
> > > cells. Not a problem at this very low level.
>
> > And your evidence for this is...
>
> As I've just explained to Howard, the typical length of an antigen
> epitope is about 20 amino acid residues. So, the total number of
> possible antigen epitopes is about 20^20 or
> 104,857,600,000,000,000,000,000,000 or ~100 trillion trillion.
This is the antigen, not the immunoglobin. This is just the average
antigen size. The antigen is the material that you inject into the
animal to induce the immune response.
Geez, I thought that you were talking about some minimal set of amino
acid residues that it would take to bind the antigen. It is more than
20, and that is the number that you need, not the number of residues
in the antigen.
Antigens do not have to be amino acids. Sugars bound to protein are
very effective antigens, and the way that they develop Abzymes is to
attach various other chemical constructs to create specific molecular
antigens.
>Since
> there are trillions of different possible antigen epitopes, how does
> one's immune system cope with such a variety of potential enemies?
> Well, there are many immune cells produced by the body. In humans, in
> particular, about 10^12 lymphocytes are present at any given time.
> Not all the T-cells have different Y-shaped receptors, but many of
> them do. Chances are that if enough non-self enemies get into the
> body at least one of the immune cells will recognize the non-self
> marker sequences or "antigens" located on this invader as "foreign" to
> at least some useful degree. The odds that a single T-cell will
> recognize a random epitope to at least some useful degree is about 1
> in 10^12. So, does this mean it would take a trillion different T-
> cells to cover all possible invaders? Well, no. The reason is
> because an average cell or foreign invader "bug" has about 10^12
> different epitopes. So, on average, a single T-cell will recognize at
> least one of the potential antigen epitopes of a foreign invader.
Well you have to start over and recalculate because the number of
antigens isn't important, and even if it was you have hugely
underestimated the number of them that there can be. You might as
well call them infinite because they are only limited to the chemical
constructs that we can make, and there are a lot of ways to put
together the existing elements. We can get binding of nucleotide
bases, unsaturated cyclic molecules with various chemical groups on
them. The list is limited by the imagination. The important fact is
that even with this tremendous number of antigens (we can make
synthetic antigens that have never been seen in nature) the antibodies
can respond and a useful one will evolve due to random mutation and
selection in only 10E12 events max. This is such a small fraction of
the protein sequence space available to the antibody that it is
essentially zero.
Proteins are just a lot more plastic that you can imagine. That is
only a problem for you.
>
> http://www.detectingdesign.com/immunesystem.html
Commercial advertizement showing that Sean was taken in by the
dishonest intelligent design scam, and doesn't have the brains to give
up on a scam when the other ID perps are running a new scam that
doesn't even mention that intelligent design ever existed.
>
> > Thought that you didn't have any.
>
> Where did you get that idea?
From your web site. Although I haven't been there for a while.
>
> > How did you come up with a number
> > so small?
>
> Because, antibody binding to antigens presented by antigen presenting
> cells is only based on about 20 very loosely specified amino acid
> residues.
Take it to the bank, you lost it with this argument, it doesn't even
make sense to talk about the antigen when it is the antibody that is
the important agent. Not only that but you have greatly
underestimated the number of possible antigens. You aren't just
dealing with twenty amino acids, there are probably hundreds of amino
acids found in nature that could work as antigens, not only that, but
sugars, nucleotide bases, and other chemical molecules can be attached
to amino acids and induce specific antibody binding.
>
> > What about the Abzymes?
>
> Abzymes require more than simple binding. Abzymes are antibodies
> that, in addition to being able to bind, must also by able to
> hydrolyze chemical bonds in a specific way to act as enzymes.
> Enzymatic activity is far more complex than simple protein-binding
> functions. It therefore has a much greater minimum size and
> specificity requirement. For example, those abzymes that have
> adequate levels of lactase activity equivalent to what might be useful
> in a bacterium have minimum size requirements of several hundred
> residues in a fair degree of specificity.
How do you know when the business end of the antibody is so much
larger than that?
Hey, and this evolution has to happen in less than 10E12 events. It
has to be lower level, right? So higher level is just three
antibodies strung together? They have evolved abzymes for more than
one step in an enzymatic path, but I don't recall if they did three,
it may have been just consecutive steps. If someone did develop an
abzyme biochemical pathway of 3 or more steps would that break your
1000 aa threshold? It would likely be over 1000 fairly specified
residues involved and you admit that not all 1000 have to happen at
one time.
>
> > Do you know how small a number of
> > amino acid residues that you are claiming account for the entire
> > immune response in the biosphere? It is only around 20 isn't it?
>
> Yep - that's it.
Well, I guess that you will just have to come up with another
argument, and take this stupid one off your web site.
>
> > Even for you that number would have to be bogus.
>
> It isn't bogus at all. It's a well-established fact. Look it up.
And, so what? It doesn't mean what you claim, just think about it for
a second and then hit the delete key at your web site. You wouldn't
want to be accused of misleading the ignorant rubes would you?
>
> > > You see, all of your examples that you have ever presented are very
> > > low-level examples - every one. None of them comes remotely close to
> > > the 1000aa threshold where sequence space is the size of 20^1000.
> > > I've pointed this out to you many many times, but you act as if
> > > nothing was ever said. You don't even try to address this point, but
> > > act like it is completely irrelevant to the issue and go on presenting
> > > your low-level examples like they somehow explain away the problem.
>
> > They weren't such low level and irrelevant when you were on your 2 or
> > 3 mutation gap kick, were they? What a joker. Where did you
> > establish this 1000aa threshold? When do you expect the Nobel prize?
> > Have you published, yet, or are you keeping it a secret? You can't
> > just make this junk up.
>
> I've always said that Gaps of 2 or 3 mutations could be crossed in
> relatively short order and I've always said that such small gap
> distances become exponentially less and less likely with increasing
> minimum structural threshold requirements. There's been no change in
> this description of the problem at hand.
This is a lie. Do I have to look up the ancient posts, or will you be
honest enough to at least admit that?
What did you use the Hall argument to support. It wasn't your 1000aa
threshold. You know that you were claiming that Hall could not jump a
gap of two or three when he removed the EBG gene. Why did gap
inflation start if this were true. Why the jump to 10 or 20 and the
rapid increase to 40, and now the 1000?
You can't even be honest with yourself, can you?
Just lay it out for everyone to see. Use a specific example and just
do it. Tell us what this mythical 1000aa threshold is.
>
> How is that concept so difficult to understand?
Do it. Just give us a specific example. You better make sure that I
can't divided it up into three parts or you will be screwed by your
own reasoning. Of course there is no more reason to believe that,
that reasoning is any sounder than the rest of your bull pucky.
You know there are now 4 invisible pink elephants that aren't pink in
your house. Now you can't pick out the mid sized one, so just
identify how tall the shortest one is. Gee, this is a wonderful way
to argue. Maybe I have a big future in the ID scam?
>
> > > > Why not just put up or shut up? You don't deny that you made the
> > > > claims, so make good on them. It isn't my problem that you keep
> > > > running, it is your problem. You are doing the running and blowing
> > > > the smoke.
>
> > > This paragraph doesn't even make sense. I've presented some simple
> > > questions. Who is the one trying to avoid answering them? I've
> > > answered yours, why not at least try to answer mine? Instead, you
> > > continually present your usual low-level examples and an endless
> > > string of pejoratives? How is that helpful to me or anyone else who
> > > might also like to hear what you have to say regarding this question?
>
> > It would make sense if you hadn't snipped and run from what you can't
> > deal with for the past, geez, how long? Could it be 6 or 7 years for
> > the common descent claim? The ID stuff can't be more than 4 years,
> > but it is your problem.
>
> > What is your alternative to common descent and the evidence that you
> > claimed was just as good as what science had? What is the science of
> > ID that you would have taught to school kids when you were still
> > advocating the teach ID scam? Without the science, and no viable
> > alternative, who cares about the mythical 1000 aa threshold?
>
> If you'd at least try and answer the question as to why evolution
> never produces anything more complex than systems requiring a minimum
> of only a few hundred amino acid residues max, you'd start care about
> this problem. It isn't easily dismissed for those who actually try to
> solve it from the evolutionary perspective.
Give a specific example and I'l go for it. Tell us what the 1000 aa
threshold is and maybe someone can explain it to you. You can't just
say flagellum and expect us to know what you are talking about, what
residues and why did you pick them?
>
> The alternative, of course, is ID. This is no scam if you can't
> answer the question.
What a joker. A dishonest political ploy is an explanation for
something that we can study in nature? So you admit that you do not
have a scientific alternative? So what is the beef?
Put up or shut up. Give something to explain. Define the 1000aa
threshold so that someone can look at it. I am interested in taking a
shot at it once you can describe what it is and demonstrate that it
exists. Really, all I have to do is divide and conquer, right. By
your own reasoning 380 is lower level. If you can describe the 1000
whatevers I can see if I can divide them up into small enough bites.
One of the invisible pink elephants that aren't pink that was in your
house, just decided to go on vacation, but you can still tell me how
tall the shortest one is, whenever you want to. Remember you have to
be able to verify your answer.
What if I just told you that my answer to your 1000aa bull pucky was
"four?" How would you contest that answer based on what the mythical
1000 aa threshold is? How would you know that it couldn't possibly be
four somethings?
>
> > DetectingDesign, what a bogus con job. All you are reduced to doing
> > is running the replacement obfuscation scam. Claiming links to the ID
> > scam when the other ID perps have a new scam that doesn't even mention
> > that ID ever existed makes you look like a moron.
>
> I present my own version of ID Theory on my website which, I must say,
> is uniquely different from anything I've seen elsewhere. It really
> doesn't matter to me what others are thinking or doing if it doesn't
> make sense to me. I present ideas that do make sense to me on my
> website. If that makes me look like a moron to you or anyone else -
> so be it. I'm convinced by arguments that make sense to me; not who
> agrees or doesn't agree with the arguments.
>
> > Ron Okimoto
>
> Sean Pitmanwww.DetectingDesign.com
Sean the con man, and proud of his work. Do you still lead off with
that dishonest emperor and no clothes routine? If biological
evolution has no clothes, what does that say about your alternative?
No lower level explanation, and no higher level explanation. No
explanation at all.
What was that science of intelligent design that you would have taught
to school kids? What is your alternative to common descent and the
evidence for it that is just as good as the evidence science has for
its alternative? You made those claims and all you can do is run and
pretend.
If you don't have the science, and you don't have an alternative, what
is your web site worth?
Ron Okimoto
Seanpit
< snip >
> > I think you are confusing the threshold limitation for the gap size.
> > The threshold size and the gap size are not the same thing. The
> > likely minimum gap distance is always smaller than the minimum
> > threshold limitation. But, what is interesting though about the
> > minimum gap distance is that it increases in a linear manner as the
> > minimum threshold limitations under consideration are increased.
>
> This is stupid. You are going back to "it is a gap, but it isn't a
> gap, it is only a gap when I want it to be a gap, and until I say
> so." Just demonstrate that you have established the existence of this
> mythical 1000aa threshold. You don't even know what it is.
>
> What kind of threshold is it when the parts are independent and don't
> have to evolve all together? It is just a bunch of small gaps that
> you gave up on years ago.
The threshold limitation is the minimum number of amino acid residues
or the minimum number of codons of DNA needed to code for a particular
type of biosystem function. The lactase function, for example,
requires a minimum of around 380aa in a fairly specific arrangement.
By "specific", I mean a flexibility of less than 1e100 or so per 100aa
(i.e., the size of the functional island).
This minimum structural threshold requirement is not the gap size at
all. The gap size is the measure of the distance between the edges of
the target islands. The gap size just so happens to increase, in a
linear manner, as one considers functional systems with greater and
greater minimum threshold requirements.
If you don't understand the difference between structural threshold
minimums and gaps between beneficial target sequences, you will not
understand anything further.
> > So, for a threshold limitation of 1000 fairly specified residues, the
> > likely minimum gap distance would NOT be 1000 mutations wide - not
> > even close. Rather, the likely minimum gap distance would only be a
> > few dozen mutations wide at this level. However, this seemingly
> > small minimum gap distance would make evolution of a functional system
> > requiring a minimum of 1000aa very unlikely even over the course of
> > trillions of years of time - even for a bacterial colony the size of
> > all bacteria on Earth.
>
> Define "fairly specified."
Function sequence flexibility of less than 1e30 per 100aa.
> You don't have to bother, I didn't think
> that you could do it anyway it is just a rhetorical question. Sort of
> like Behe and IC. What is the latest possible definition of IC
> nowadays? The more parts something has the more IC it is?
Not quite right. The more parts something has to have before it will
work to produce a particular function, the higher level of IC that
type of biosystem function has. That's my definition of IC. All
functional systems have certain amount of IC. It is just that some
systems have lower minimum structural requirements than do other
systems. They are therefore what I call "lower level systems".
> For Sean
> it is the more gaps that aren't really gaps that you have that make
> things "fairly, specified." We are back to gaps that aren't gaps, but
> you know what the threshold is. What is the minimum gap distance for
> a gap that isn't really a gap?
>
> Do you ever read your junk? Do you just make this junk up as you go?
> Do you ever look back on what you've already said about this gap
> nonsense?
You just don't understand that the minimum gap distance and structural
threshold minimums aren't the same thing. They are related to each
other, but they are by no means the same thing.
> > Now, let's look at a higher level system to see if higher-level
> > thresholds actually exist. Since you claim that higher level
> > thresholds do not exist, how many amino acids need to be coded for to
> > produce a flagellar motility system at minimum? (i.e. the threshold
> > size) Please, do give me your best estimate. As far as I can tell,
> > the answer is well over 10,000 fairly specified residue positions
> > coded for by an even greater number of codons of genetic real estate
> > (to include codes for non-structural proteins). A flagellar motility
> > system simply cannot be built with significantly fewer codons or
> > residues at all. If you think otherwise, please, do present your own
> > estimate.
>
> Why is this a higher level threshold? What is the threshold?
I just told you - greater than 10,000 fairly specified residues or
codons. That's the minimum number of parts that are required to
achieve the function of flagellar motility.
> Don't
> you have to figure that out before you call it a higher level? I can
> give you an estimate just as soon as you tell me how tall that
> invisible pink elephant is that you have in your house. You know the
> invisible one. It is probably right there standing beside you as you
> read this.
>
> Define "fairly specified." Sort of like describing that invisible
> pink elephant. Did you know that it isn't really pink? Don't you
> know what color it really is? What a loser. How do you expect anyone
> to come up with an explanation for anything when you can't even
> determine that it exists to explain?
>
> All this bogus junk sounds sciency, but that is it. Demonstrate that
> your 1000aa threshold exists. I'm still waiting. Did you know that
> there are now two invisible pink elephants that aren't pink in your
> house? These things sound stupid because they are stupid. Until you
> can demonstrate that your 1000aa threshold is more than my assertion
> about invisible pink elephants you have no argument.
Demonstrate that you can produce a system of flagellar motility with
significantly less than 10,000 amino acid residues or codons of
genetic real estate.
> > > How low of a minimal threshold is Lactase
> > > function?
>
> > About 380aa.
>
> How bogus was that answer? Remember the last time you put it up? You
> tell me what was wrong with that estimate. Just demonstrate that you
> know what it is.
>
> Does that mean that your threshold is just the number of amino acids
> in the proteins involved? What are these gaps that aren't gaps
> again? What do they have to do with the threshold?
Yes, the threshold is the minimum number of amino acid residues that
can produce a particular type of biosystem function - together with a
minimum degree of flexibility regarding sequence arrangement. Most
lactases use a fairly large number of residues - usually over 1000.
However, the minimum requirement for the lactase function seems to be
around 380aa. Getting a useful level of lactase activity with
significantly fewer proteins than this does not seem to be likely give
the available data.
> Geez Louise, Lactase is a lower level threshold, but it is only a
> third the size of your higher level threshold of 1000aa. What is that
> definition of higher level thresholds again?
Any system that requires a minimum of more than 1000 fairly specified
residues (as defined above) qualifies as a "higher-level" threshold.
> If it is so easy to
> evolve lactase function so as to make it insignificant to the
> argument, what does that say about this 1000aa bogousity?
You don't seem to understand the exponential nature of the problem.
What is reasonably easy at the 300 or 400 level is pretty much
impossible at the 1000aa level - because of the linear expansion of
the minimum gap distance between the available starting points and the
closest potential target. This linear expansion translates into an
exponential increase in the number of random walk steps/mutations
required to cross the gap.
That is why all of your examples of evolution in action are always low-
level examples. Not one of the examples that you have ever presented
requires a minimum of more than a few hundred fairly specified
residues to make the system in question work. In fact, there are no
examples at all beyond the 1000aa threshold in all of scientific
literature. Why do you think that might be?
> > > Just because you can't deny the data without looking more
> > > like a clown than usual, how low is it?
>
> > What data are you talking about here? What is your suggestion for the
> > minimum size requirement for the lactase function? Does it come
> > remotely close to the 1000aa threshold? No. Therefore, it is a
> > fairly low-level function. There are many examples of functional
> > systems that require only a few hundred fairly specified residues
> > evolving. There are no examples where the system requires over 1000
> > fairly specified residues - not one example of evolution beyond this
> > level in all of literature. And yes, many such systems do exist which
> > require many thousands of specified residue positions in every single
> > living thing. Here are just a few:
>
> What is the 1000 aa threshold?
How many times do I have to explain it? What do you not understand
about the statement that a functional biosystem requires a certain
minimum number of parts in a certain fairly specific arrangement
before it will work? How is that at all difficult to understand?
That IS the definition of the structural threshold minimum. A 1000aa
threshold minimum means that the system in question requires at least
1000 fairly specified residues. Simple. Shouldn't be that hard of a
concept to understand - should it?
> What about the actual lactase data? What about the only data that you
> have to work with? Where does it fit into this 1000 aa threshold?
The data on the lactase function clearly shows that its threshold
minimum is far less than 1000aa. The lactase minimum threshold is in
fact less than 380aa.
> You know why there are no examples, because you don't know of any.
And you don't either . . . Not beyond the 1000aa threshold.
> You don't even know what a 1000aa threshold is, except to say that you
> know it when you see it. Why should anyone believe you?
The 1000aa threshold is clearly defined. I really am finding it quite
difficult to understand your confusion when it comes to this seemingly
simple and straightforward definition.
> > > You can't just make junk up and expect people to believe you,
> > > especially since you are such a liar. You need confirmation. Where
> > > is it? When have you or anyone ever established that this mythical
> > > 1000aa threshold exists?
>
> > After all the times I've presented this evidence I can't believe that
> > you would still be trying to suggest that no system exists which
> > requires a minimum of more than 1000aa to work. How can you suggest
> > such a thing and call yourself informed on this issue? If you don't
> > believe me, then by all means provide some sort of evidence showing
> > how a functioning flagellum or any other such system can be produced
> > with fewer than 1000 codons of genetic real estate . . .
>
> We are back to codons, but they aren't really codons, because the
> flagellum is made up of a lot of proteins, and just a few add up to
> more than 1000 codons.
The flagellum is made up of a lot of proteins. It is the minimum
number of amino acid residues needed in all of the proteins, taken
together, that make up the minimum structural threshold for the
flagellar motility function. The minimum number of residues needed
for flagellar motility is not presented by the minimum number needed
for any one protein in the system. It is represented by the minimum
number needed to get flagellar motility. Multiprotein systems, like
the flagellum, cannot be produced with less than multiple proteins -
each of which has its own minimum structural requirements that produce
an overall minimum for the flagellar system.
Another way this minimum can be expressed is by the minimum amount of
genetic real estate that is needed to code for the flagellar system -
in codons. This minimum is also at least 10,000 codons.
< snip >
> > You do understand that some types of functions are inherently more
> > complex than others - right? Would you say that flagellar motility
> > requires much more complexity than the single protein lactase
> > function? I sure hope you would agree to that.
>
> What is your definition of complexity? Flagellum obviously have more
> moving parts, but they are still made of proteins.
Yes, a minimum of many proteins with many many more amino acid
building blocks total - as compared to a single protein system like
lactase. Lactase has a minimum need for less than 380aa while a
flagellum has a need for more than 10,000 specifically coded aa - at
minimum. See the difference in minimum requirements?
> You don't have
> computer operated widgets in there regulating the function. In fact
> most of the flagellar proteins that have been studied are related to
> other proteins in the bacteria that we know are doing something else.
Many of them do have a fair degree of sequence/structure homogeny.
That does not take away from the fact that the overall minimum
structural requirements for flagellar motility are greater than 10,000
fairly specified residues. It matters not how such a system evolved
or didn't evolve. The minimum threshold requirements stay the same.
Even if you showed 99.99999% homology to another pre-existing system,
this wouldn't change the fact that the minimum threshold requirements
are still the same. It might help you explain how this minimum was
realized by your evolutionary mechanism, by a reduction in the minimum
gap size, but it would not change the structure minimum requirements.
> We can't trace them all back to relatives because you know what 2
> billion years of molecular evolution can do to protein sequences. So
> it is different from the lactase evolution, how? By the number of
> gaps that aren't really gaps unless you say so?
It is just that the homologies that you think are so closely related
aren't nearly close enough for your mechanism to produce the needed
changes to get from one of your proposed homologous steppingstones to
the next. The needed mutational changes are far too many for your
mechanism of random mutation and function-based selection to actually
have done the job you say it did.
> > >http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubme...
>
> > > Klebsiella is not E. coli.
>
> > Interesting abstract. I was unaware of this particular experiment and
> > will have to obtain and read the full paper.
>
> I'm sure that you saw it last time you ran. It is the same reference
> that I put up the last time you made the same bogus claim. Isn't it
> about time to run again?
Not at all. I don't remember seeing this reference before. I don't
necessarily read all of your posts you know, since most of the time
you don't present any actual data or relevant references like this.
> > I do appreciate you bringing this paper to my attention, but I don't
> > see how it affects the main point at hand in the least. I mean, I
> > just noted for you that "the same thing is likely to happen in other
> > species occasionally at this level of functional complexity." Did you
> > miss that comment? After all, this level involves only a few hundred
> > fairly specified residues at most. This sort of thing is only to be
> > expected at such low levels - quite predictably in fact.
>
> The reason for this is because you are dishonest and probably mentally
> incompetent. Nothing, no amount of evidence, can change your mind,
> even when you have to acknowledge its existence.
Well, so far, all of your "evidences" consist of endless low-level
examples of evolution in action - examples that do not require more
than a few hundred fairly specified residues at minimum. How are such
examples suppose to explain anything beyond low-level evolution?
> "Fairly specified" Must rank up there with "specified complexity,"
> "irreducible complexity," "intelligent design," etc. How bogus did
> all those turn out to be?
None of these concepts are "bogus" at all - at least not as I define
these terms. ID, in particular, is used in mainstream science all the
time - to include forensic science, anthropology, and SETI.
> What was that intelligent design science that you would have taught to
> school kids? What? No science? What are you arguing about?
>
> What was that alternative to common descent that you had, and the
> evidence to back it up? What? No alternative? Why are you arguing
> about mythical thresholds if you don't have an alternative? Just
> because it is the only pathetic thing that you can do doesn't mean
> that you should be doing it.
There is a great deal of evidence. You just don't seem to recognize
it for what it is. One of the biggest reasons for this is that you
don't seem to understand the concept of minimum structural threshold
requirements.
> > > Read the Kleb paper. Remember what you ran from
> > > last time? You've probably run so often that you can't keep track
> > > anymore.
>
> > This sort of data though is always interesting to me and is always
> > relevant. Why not present more of this sort of argument instead of
> > your usual focus on personal attacks instead? This sort of
> > information is far more helpful and interesting to me and I'm sure to
> > others as well that your usual pointless personal attacks and
> > diatribe.
>
> It is only a personal attack to you because you know that you are
> stupid to keep running and pretending. If you just started to be
> straight, I wouldn't have to keep reminding you about what you are
> lying about.
Irrelevant personal attacks are those that attempt to attack the
opponents motives, or intelligence, or character. Those kinds of
attacks are simply not helpful. On the other hand, attacking the
argument at hand with relevant counterarguments is always helpful.
You see, you are going after the argument instead of the person.
Going after the person instead of the argument simply isn't helpful.
> > Beyond this, how does this paper help your position? All it is, at
> > the very most, is yet another example of low-level evolution - of a
> > novel system that requires far less than a minimum of 1000aa.
>
> It most definitely doesn't help yours.
How so? It is actually predicted by my model. There are in fact lots
of examples of evolution in action at this level in all kinds of
living things.
> Remember when you were running
> the Hall bull pucky for the first time? You were claiming that
> crossing gaps of 3 were impossible.
I've never claimed that crossing gaps of 3 were impossible. What I
said was that Hall thought that such gaps would be impossible to
cross. He therefore proposed some sort of magical non-Darwinian
guidance as perhaps being involved with the success of his early
experiments.
> You hadn't come up with your
> mythical 1000aa. The data showd that you were wrong, so at first you
> jumped to 20 or 40 mutation gaps that were impossible, and it evolved
> into this bogus claim of a whooping 1000aa.
Again, the 1000aa is the threshold limitation, NOT the minimum gap
size. Try to get this straight. The minimum gap size for the 1000aa
level is most likely a few dozen mutational changes. Do you see the
difference yet?
> At the very least it shows what a loser you are. Since you can't tell
> us the difference between the two cases, and your own admissions seems
> to be the difference between 380 and 1000. What are you arguing
> about? All we have to do is divide up that 1000 into three parts and
> you have no argument.
It would be nice for you if you could do that. But simply having
three different 333aa systems in the gene pool is not enough to
explain how a 1000aa system can be easily evolved. Not even close.
The fact that such a system has not been demonstrated to evolve in
real time should be a very good indication to you that your thinking
here might be just a little bit off.
> So tell us what the 1000 is. You even admit
> that you don't have to evolve all 1000 at a time. Even if the 1000
> whatever exists, around 2 billion years of evolution took place before
> flagellum evolved. We can still tell where a lot of the parts came
> from.
Two billion years is like a grain of sand in the universe compared to
the time needed to evolve a system with a 1000aa minimum threshold
requirement. Even trillions of years wouldn't be enough time. Yes,
it is true that the majority of the 1000aa needed to evolve a novel
system at this level is most likely already present in any given gene
pool. It is just that the few dozen changes needed to cross over from
what already exists to any novel functional system at this level are
more than enough to stall evolution completely out this side of a
practical eternity of time.
> In the face of that what do you have as an alternative?
The intelligent design-only hypothesis. No non-deliberate force of
nature comes remotely close to producing such higher-level systems.
Intelligent manipulation does. This is the same basis for SETI.
< snip >
hersheyh
0catch.com> wrote:
> On Dec 15, 10:33 am, "R. Baldwin" <res0k...@nozirevBACKWARDS.net>
> wrote:
>
>
>
> > >> Sean, you are introducing a new variable here: "level of minimum
> > >> structural threshold requirements".
>
> > > This isn't a new variable. It has been the basis of my whole position
> > > since the beginning. I don't know how many times I've used this very
> > > same phrase for you directly in many many posts in the past? It has
> > > to be over a 50 times. How can you not remember?
>
> > Google is your friend. 4 hits on the phrase, all within the past week.
>
> Yes, Google is your friend. Type in "minimum structural threshold
> requirements" and the search will return 170 hits. And, if you type
> that same search into Google Groups, you will get 475 hits, as of
> today, going back over a year. Other variations on this phrase or
> mention of essentially the same concept add even more hits.
>
> In short, I'd hardly say this is a new concept since I've used this
> very same phrase with Howard many many times.
Sean, I know full well that you have used the phrase many many times.
However, we were talking about your description of how *you* claimed
that *anyone* could use to calculate "average gap size". In that
description in your appendix there is no mention of "minimum
structural threshold requirements" as a variable in the "equation"
implied by your description. *If* you have now corrected that in your
appendix, fine. If not, you are still adding a hidden (new) variable
when you now claim that this aspect is important.
What is interesting is that you actually *can* calculate "minimum
structural threshold requirements" for the specified function (some
ability to act as an electron transport associated protein in a modern
system). *If* one accepts the Yockey calculation, he has calculated
the number of sequences that have the function of "cytochrome c
activity". Presumably you do accept that value. When you divide
that value by total sequence space for all proteins of that length
(100 aa), you claim that there is a ratio of roughly 10^-40.
Am I right so far?
Now, to me the phrase "minimum structural threshold requirements"
means "degree of sequence specificity" needed to have the specified
function. That is, the *idea* or *concept* behind the phrase "minimum
structural threshold requirements" is some measure of the extent to
which amino acids in a sequence length of 100 can be changed and still
retain the specified function. Because there is not just one sequence
that has cyt c activity, but many, "minimum structural threshold
requirements" is a measure of "sequence specificity for function".
Now we know that, in reality, different aa sites in cytochrome c are
partially variant to different extents, completely variant, or
completely invariant. But it would be nearly impossible to generate
an actual full description of "minimum structural threshold
requirements" or "degree of sequence specifity" from such real data,
and certainly not for mathematical amateurs like you and I. So you
use the phrase, but without clearly defining it or presenting it as a
quantitative description that can actually be calculated. It is just
a phrase representing the idea that some sequences have more stringent
sequence requirements than others.
Am I right so far?
Fortunately there *is* a way to calculate a good estimate of "degree
of sequence specificity" for cytochrome c. Namely, whatever the
degree of actual allowable variance in sequence, we do have a specific
number of sequences that must be produced: the number that, when
divided by total sequence space, gives us the ratio of 10^-40.
Because of that, we can choose any model of aa variation that can
generate that number. A simple model is one that assumes that there
are only two types of aa sites: those that are completely invariant
and those that are completely variant. Although the real sequences
would have aa sites that are partially variant, whatever the variance
really is, the same number of cyto c sequences must be produced. So
using the simple model that eliminates the difficulty of dealing with
aa sites that can vary somewhat will give us a result that is
mathematically equivalent to the many possible more complex
descriptions.
Are you following this?
In this simplified model, with only completely variant and invariant
aa's, the sequences that *have* cytochrome c function can only change
at the freely variant sites and that means that only these sites can
produce different functional cytochrome c's. The *invariant* sites
can never change, and thus do not produce *different* functional cyt c
sequences. We can estimate how many of the 100 aa's must be freely
variant (and thus have cytochrome c activity). The more aa's that are
invariant (and thus can have only one aa), the smaller the total
number of cytochrome c sequences and, consequently, the smaller the
ratio of the number of cytochrome c sequences to total sequence space
for proteins 100 aa long.
The 20th root of the number of cytochrome c sequences [estimated by
multiplying the rato of 10^-40 by total sequence space] would be an
estimate of the number of sites (in this model where we eliminate
sites that have partial variability) that are completely free to vary.
Am I right so far, Sean?
As the ratio of 10^-40 = 20^30.7/20^100, that would mean that the 20th
root of the numerator (the number of sequences in total sequence space
with cytochrome c function) is 30.7 or 31 aa's. The degree of
sequence *specificity* would be 100-31 = 69 aa's. That is, cytochrome
c, regardless of the actual specificity of its aa sites, is
mathematically equivalent to a protein in which 69% of its aa residues
are completely invariant and 31% are completely free to vary because
that is the ratio that would produce the number of functional (for cyt
c activity only, not for heme-binding or any other subset of the
protein's functions) sequences.
That would mean that any larger protein with the same degree of
"sequence specificity" or "minimum structural threshold" would also
have to have the mathematical equivalent of 69% of its aa residues
invariant with 31% completely free to vary. That is, if a protein
with the same "minimum structural threshold" or "functional level of
sequence specificity" as cyt c were 1000 aa long, the number of
completely variable aa's (under the assumption of only completely
variant and completely invariant, but producing the same number of
functional sequences) would be 307.
It is, of course, curious (but not, of course, if you actually do the
math) that 30.7 aa's is *also* what Sean calculates and claims
represents the "average gap size". That is 30.7 represents both the
number of aa sites in a 100 aa long protein with the "sequence
specificity" of cytochrome c that must (in a mathematical, not an
actual, sense) be completely free to vary *and* it also is the
"average gap size". And this relationship holds for longer proteins
that have what Sean considers the same degree of sequence specificity.
Both of these numbers vary linearly with increases in length (assuming
the same "minimum structural threshold" or "sequence specificity"
ratio).
Note on a couple of errors in previous posts. Unlike Sean, who
appears to have over-learned the lessons in medical school that
teaches physicians never to admit error to a patient and to bury their
mistakes and to assume that their status is like that in the comment
about why ministers and doctors make lousy pilots (One group thinks
they are near to God. The other thinks they are God.), I learned to
do science rather than practice the art of medicine. And Mother
Nature is an excellent humility-maker. I have no problem admitting
errors in my comments. Have done so in the past. Probably will in
the future. In fact, I do continue to *think* about what I say in
these threads after I say it and continue to try to poke holes in the
position that *I* [not the person I am commenting to] hold or think
about ways that what Sean (or any other poster) could be more right
than me. Fortunately, for my poor fragile ego, I do know a tad more
about biology than most creationist posters (and, alas for my ego, I
know that isn't saying much).
I do think I have a sense of when someone is posting bullshit GIGO and
waving their hands furiously. GIGO numerology is not always easy to
detect, and certainly can even fool *even* the person presenting it.
It can do so by a combination of wishful thinking, wanting
verification rather than testing for falsification, arrogance,
mathematical manipulations that don't do what one would like to think
they do, defining terms that are "fuzzy", not actually presenting
equations in which all the relevant terms are defined, and in which
the result is not described accurately and without bias, followed by
hand-waving that the numbers are "rough" or "crude" or are only meant
to show a "a pattern" -- even when they know them to be off by entire
orders of magnitude.:
Error #1:
The description of exponential growth this and recent posts is
different from my initial description, in which claimed that the
*number* of "beneficial" sequences did not change. I see now that I
made a math error. [You should try this sometime, Sean.] I was
wrong. The situation described is that both numerator and denominator
are increasing exponentially, but the numerator's starting number is
smaller. Thus, although *proportionally* there is no change with
increasing rate, at any given size point, the absolute numerical
difference between the numerator and denominator gets larger.
Think of it as compound interest, with time in the place of length.
If I start with 1000 dollars (the denominator) and the rate of
interest is 3%, my money will grow exponentially. And if you start
with 300 dollars (the numerator) and the rate of interest is also 3%,
that money will also grow exponentially. At any time point, the
person with the $300 starting point will have 30% as much money as the
person who started with $1000, but the absolute difference between
them will be larger than at any earlier time point.
Error # 2:
I believe I reversed the labels for what I call "completely free to
change" and "invariant" in an earlier post where I had not fully
thought through what the numbers would have meant. But, of course,
not thinking through what the numbers really mean is exactly the
problem that Sean has as well.
Neither error means that what Sean calls "average gap size" actually
is. I will leave it to Sean to explain why one will *always* get the
same number for "average gap size" and "number mathematically
equivalent to number of freely variant aa sites (if there were only
invariant and freely variant sites) for a specified protein function
for which we can estimate the number of different sequences that can
produce that specified function [but that specifically ignores
proteins that only have subfunctions of the specified function]."
>http://www.google.com/search?hl=en&q=%22minimum+structural+threshold+...
>
> http://groups.google.com/groups?hl=en&q=%22minimum+structural+thresho...
Seanpit
He would not need to run the experiment to mutation balance before a
gap of 2 or even 3 could be crossed in reasonable amount of time for a
population the size Hall was using. Do the math yourself and see.
> > >http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubme...
>
> > > Your own calculations indicated that once mutation selection balance
> > > was reached in a population, jumping 2 or 3 mutational intervals was
> > > not that rare.
>
> > That's right . . .
>
> So what is your beef, and how does that impact your 1000aa threshold
> that is composed of gaps that aren't really gaps, but they don't all
> have to be crossed all at one time?
The 1000aa threshold isn't the gap size. It is the minimum structural
requirements. The gap size for this level would be several dozen
mutational changes wide - which most certainly would need to be
crossed before a novel function at this level could be realized.
> > > Hall's experiments never reached close to mutation
> > > selection balance. He started with clonal populations at the same
> > > start point every experiment. You know the difference, you prefer to
> > > lie to yourself about it.
>
> > Hall's experiments didn't need to reach mutational balance (~70,000
> > generations), because the gap size was only one mutation wide. A gap
> > of just one mutation is easy to cross for a large colony in a single
> > generation. And, this is exactly what happened.
>
> His first experiements didn't have to. You made a stink about his
> second set of experiments where he deleted EBG and claimed that it
> meant that gaps of 2-3 could not be crossed. Don't you remember your
> own arguments?
The deletion of ebg in Hall's second set of experiments is very
interesting because after extended observation the lactase function
was not evolved. The observation was long enough that Hall got
frustrated and said that his ebg negative colony had, "limited
evolutionary potential."
Now, nowhere in this exchange did I say it was impossible to cross
gaps of just 2 or 3 character differences. I've said otherwise many
many times in fact.
> You were wrong. You admit it because you had to go from gaps of 2-3
> to your 1000 aa bull pucky.
You don't get it. The 1000aa is NOT the gap distance. I've always
said that small gaps, to include gaps of 2 or 3 or even over a dozen
mutational character changes could be crossed in evolutionary time
frames. But, the decline in evolvability is exponential in nature.
The only way to keep up is to increase the population size and/or
mutation rate. The problem here is that population sizes are limited
by limited environments and mutation rates are limited by their
lethality beyond a certain rate. So, at steady state population
sizes, evolutionary progress stalls out exponentially as the minimum
gap sizes increase - and they do in fact increase in a linear manner
as the structural threshold sizes increase.
< snip >
> > > > > You keep denying the antibody example, claiming that it isn't high
> > > > > enough about something or other to satisfy you, but you have no
> > > > > alternative do you? A maximum of 10E12 sequences are tested at any
> > > > > time and the system works nearly all the time. Such a tiny fraction
> > > > > of the sequence space has to be sampled to get funtional antibodies
> > > > > that it makes your claims out to be a joke. You've known for years
> > > > > that not only can they get antibody activity, but Abzymes demonstrate
> > > > > that enzymatic function can evolve using the same system.
>
> > > > Actually, the sequence space involved with antibody binding is quite
> > > > small - only about 20^20 sequences. This sequence space can be
> > > > exhaustively searched by a relatively small population of immune
> > > > cells. Not a problem at this very low level.
>
> > > And your evidence for this is...
>
> > As I've just explained to Howard, the typical length of an antigen
> > epitope is about 20 amino acid residues. So, the total number of
> > possible antigen epitopes is about 20^20 or
> > 104,857,600,000,000,000,000,000,000 or ~100 trillion trillion.
>
> This is the antigen, not the immunoglobin. This is just the average
> antigen size. The antigen is the material that you inject into the
> animal to induce the immune response.
Ever hear of an antigen epitope? It is the epitope that is important
here, not the total size of the antigen. The epitope is small. It is
obtained from processing by antigen presenting cells. This epitope is
what the binding site of the antibody binds to. The residues that
interact with the antigen epitope are also limited to about 20 or so
residues. So, the binding function of the immunoglobulin is indeed
based on just 20 or so residues. Other functions of the antibody are
what require the larger antibody size. The binding function however,
by itself, is quite simple.
< snip >
> >Since
> > there are trillions of different possible antigen epitopes, how does
> > one's immune system cope with such a variety of potential enemies?
> > Well, there are many immune cells produced by the body. In humans, in
> > particular, about 10^12 lymphocytes are present at any given time.
> > Not all the T-cells have different Y-shaped receptors, but many of
> > them do. Chances are that if enough non-self enemies get into the
> > body at least one of the immune cells will recognize the non-self
> > marker sequences or "antigens" located on this invader as "foreign" to
> > at least some useful degree. The odds that a single T-cell will
> > recognize a random epitope to at least some useful degree is about 1
> > in 10^12. So, does this mean it would take a trillion different T-
> > cells to cover all possible invaders? Well, no. The reason is
> > because an average cell or foreign invader "bug" has about 10^12
> > different epitopes. So, on average, a single T-cell will recognize at
> > least one of the potential antigen epitopes of a foreign invader.
>
> Well you have to start over and recalculate because the number of
> antigens isn't important, and even if it was you have hugely
> underestimated the number of them that there can be.
Not at all. Antibodies simply cannot specifically recognize antigen
epitopes that are larger than about 20aa or an equivalent number of
atoms - because that is the number of residue binding positions the
antibody has.
> You might as
> well call them infinite because they are only limited to the chemical
> constructs that we can make, and there are a lot of ways to put
> together the existing elements. We can get binding of nucleotide
> bases, unsaturated cyclic molecules with various chemical groups on
> them. The list is limited by the imagination. The important fact is
> that even with this tremendous number of antigens (we can make
> synthetic antigens that have never been seen in nature) the antibodies
> can respond and a useful one will evolve due to random mutation and
> selection in only 10E12 events max. This is such a small fraction of
> the protein sequence space available to the antibody that it is
> essentially zero.
You clearly don't understand the basis for how antibodies can actually
do their job. If antigen epitope sequence space were essentially
"infinite" as you claim, then a trillion or so antibodies could not do
their job effectively. It is because the antigen options are actually
quite limited that the immune system is able to work as effectively as
it does. After all, the odds of a randomly chosen antibody
recognizing or effectively binding to a particular antigen epitope are
about 1 in 10^12 (see reference). That would be impossible if your
notion of epitope space being "essentially infinite" were actually
true.
Jun Sun, David J. Earl, and Michael W. Deem, Glassy Dynamics in the
Adaptive Immune Response Prevents Autoimmune Disease, Physical Review
Letters, 95, 148104, September 30, 2005
http://www.mwdeem.rice.edu/djearl/autoimmune.pdf
> Proteins are just a lot more plastic that you can imagine. That is
> only a problem for you.
Proteins can be quite plastic indeed, but certainly not more than I
imagine.
> > > How did you come up with a number
> > > so small?
>
> > Because, antibody binding to antigens presented by antigen presenting
> > cells is only based on about 20 very loosely specified amino acid
> > residues.
>
> Take it to the bank, you lost it with this argument, it doesn't even
> make sense to talk about the antigen when it is the antibody that is
> the important agent.
Sure it does. The antibody cannot recognize more of an epitope than
will fit in its limited binding site.
> Not only that but you have greatly
> underestimated the number of possible antigens.
Not at all. Rather, you have greater overestimated the number of
effective antigen epitopes. Again, the odds of effective binding of Ab/
Ag are just 1 in a trillion. That's not very much of a sequence space
if you ask me.
> You aren't just
> dealing with twenty amino acids, there are probably hundreds of amino
> acids found in nature that could work as antigens, not only that, but
> sugars, nucleotide bases, and other chemical molecules can be attached
> to amino acids and induce specific antibody binding.
Again, effective antigen epitopes are indeed equivalent to no more
than about 20aa of sequence space. The immune system couldn't work if
you were correct. Look up the reference I gave you above.
> > > What about the Abzymes?
>
> > Abzymes require more than simple binding. Abzymes are antibodies
> > that, in addition to being able to bind, must also by able to
> > hydrolyze chemical bonds in a specific way to act as enzymes.
> > Enzymatic activity is far more complex than simple protein-binding
> > functions. It therefore has a much greater minimum size and
> > specificity requirement. For example, those abzymes that have
> > adequate levels of lactase activity equivalent to what might be useful
> > in a bacterium have minimum size requirements of several hundred
> > residues in a fair degree of specificity.
>
> How do you know when the business end of the antibody is so much
> larger than that?
The binding sites are what are important. The binding sites involve
only about 20aa.
> Hey, and this evolution has to happen in less than 10E12 events. It
> has to be lower level, right? So higher level is just three
> antibodies strung together?
You have this notion that it is an easy thing to just string existing
proteins together and end up with a higher level system. Sorry to
say, but that sort of simplistic thinking is simply wrong. The odds
of successfully stringing together existing proteins and ending up
with a higher level system are exponentially unlikely to hit upon any
novel beneficial system that has higher and higher minimum structural
requirements.
> They have evolved abzymes for more than
> one step in an enzymatic path, but I don't recall if they did three,
> it may have been just consecutive steps.
Enzymatic pathways are not more specified than each individual protein
in the pathway. Why? Because they do not require overall system
specificity as do systems like flagellar motility. The enzymes in
enzymatic pathways are part of a cascading system of function where
the individual protein parts do not need to be specifically arranged
relative to each other. This dramatically reduces the overall
complexity of the system.
> If someone did develop an
> abzyme biochemical pathway of 3 or more steps would that break your
> 1000 aa threshold?
No - because of a lack of the specificity requirement. Again,
cascading systems are no more structurally complex than their most
complex part that does require specific arrangement of its amino acid
building blocks relative to each other.
> It would likely be over 1000 fairly specified
> residues involved and you admit that not all 1000 have to happen at
> one time.
It might be over 1000 residues, but it would be specified. In other
words, all the amino acid parts would not be required to be in a
specific orientation relative to all the other amino acid building
blocks. Cascading systems are not like the flagellar system where all
of the parts must be specifically arranged relative to each other.
> > > Do you know how small a number of
> > > amino acid residues that you are claiming account for the entire
> > > immune response in the biosphere? It is only around 20 isn't it?
>
> > Yep - that's it.
>
> Well, I guess that you will just have to come up with another
> argument, and take this stupid one off your web site.
You need to read up a bit more on this topic.
> > > Even for you that number would have to be bogus.
>
> > It isn't bogus at all. It's a well-established fact. Look it up.
>
> And, so what? It doesn't mean what you claim, just think about it for
> a second and then hit the delete key at your web site. You wouldn't
> want to be accused of misleading the ignorant rubes would you?
Read up on the topic just a bit more.
> > I've always said that Gaps of 2 or 3 mutations could be crossed in
> > relatively short order and I've always said that such small gap
> > distances become exponentially less and less likely with increasing
> > minimum structural threshold requirements. There's been no change in
> > this description of the problem at hand.
>
> This is a lie. Do I have to look up the ancient posts, or will you be
> honest enough to at least admit that?
Sure - - please do look up where I said otherwise. It certainly
hasn't been in the last 5 years nor is such a statement anywhere on my
website.
> What did you use the Hall argument to support.
The start of the stalling out effect of evolutionary abilities even at
fairly low levels of functional complexity. While all bacterial
species would be able to quickly evolve a very low-level function like
antibiotic resistance to just about any antibiotic that was presented
in sublethal levels, it is not nearly that common for a bacterial
colony to be able to evolve even a simple single-protein enzyme.
> It wasn't your 1000aa threshold.
Yes, it was. For many years now I've had my 1000aa threshold out
there. I used Hall's experiments to show that on occasion simple
single protein functions may evolve up the a threshold of a few
hundred fairly specified residues - but not beyond the 1000aa
threshold. This challenge has been out there for many years.
> You know that you were claiming that Hall could not jump a
> gap of two or three when he removed the EBG gene.
The removal of ebg and the resulting lack of evolution in E. coli
proved that the gap involved was a bit bigger than one character
change - or even two or three. It basically proved that the *average*
gap distances for this level of complexity had in fact increased.
This increase in the average gap distance translates into a situation
where a minimum gap distance of one or two needed character changes is
exponentially less common than it was at lower levels.
> Why did gap
> inflation start if this were true. Why the jump to 10 or 20 and the
> rapid increase to 40, and now the 1000?
Again, the 1000aa threshold is not the gap distance. There has been
no increase in the challenge. The minimum gap distance that could not
be crossed in a reasonable amount of time has been and still is a few
dozen character changes wide. Your claim that the 1000aa number
represents what I call the "gap distance" is simply a strawman
mischaracterization of my true position.
> You can't even be honest with yourself, can you?
Why not stop building strawmen to misrepresent my position long enough
to see?
< snip >
Seanpit
wrote:
> "Seanpit" <seanpitnos...@naturalselection.0catch.com> wrote in message
Oh please! Don't tell me that you see a significant difference
between the phrase "minimum strcutral threshold requirements" and
"level of minimum structural threshold requirements"? Really? Come
on now! If you increase the minimum structural threshold
requirements, you have obviously move on to a higher level of those
requirements have you not?
Now, if that really wasn't obvious to you, I'm oh so sorry. But, I'm
not quite sure how you were confused by this or how I could have made
it any more clear.
Sean Pitman
www.DetectingDesign.com
hersheyh
0catch.com> wrote:
> On Dec 15, 10:44 am, hersheyh <hershe...@yahoo.com> wrote:
>
>
>
> > On Dec 15, 11:54 am, _Arthur <Arth...@sympatico.ca> wrote:
>
>
> In agreeing with Arthur here, you show that you still don't grasp the
> difference between sequence flexibility (i.e., the size of a target
> island) and the distance between islands (i.e., the gap distance).
> They aren't the same thing Howard. You, of all people, should know
> this by now.
Funny thing. I just posted a thread where I demonstrate (at least to
my current satisfaction) that sequence flexibility of cytochrome c,
specifically the number of aa sites that, mathematically, are freely
variable (in a mathematical model that assumes that there are only
"freely variable" and "invariant" aa sites -- which was done solely
because that simplifies the discussion) is exactly the same number you
call "average gap size".
> I can only assume that you support Arthur here because, and only
> because, he is trying to oppose my position.
I was making a joke. As indicated by the ;-)
>
> Sean Pitmanwww.DetectingDesign.com
Seanpit
>
> No, the phrase you used was "minimum structural threshold
> requirements".
> By adding the words "level of " to that phrase, you are implying that
> it is a variable which can be measured.
Minimum structural threshold requirements indicates a variable all by
itself. If the minimum is different for a different type of system,
this is a variation relative to a system where this minimum is
greater.
> So how do we measure this variable?
I've told you over and over and over again. The structural threshold
is a measure of the minimum number of residues, to include the degree
of specificity of arrangement, needed to produce a particular type of
functional system. I've also noted many many times that different
types of functional systems have different structural threshold
requirements.
< snip >
Sean Pitman
www.DetectingDesign.com
richardal...@googlemail.com
0catch.com> wrote:
> On Dec 16, 8:46 am, richardalanforr...@googlemail.com wrote:
>
>
>
> > No, the phrase you used was "minimum structural threshold
> > requirements".
> > By adding the words "level of " to that phrase, you are implying that
> > it is a variable which can be measured.
>
> Minimum structural threshold requirements indicates a variable all by
> itself.
No it doesn't. It implies a threshold level. That does not have to be
a variable. It could be fixed.
> If the minimum is different for a different type of system,
> this is a variation relative to a system where this minimum is
> greater.
>
> > So how do we measure this variable?
>
> I've told you over and over and over again.
No you haven't. You've asserted that it can be measured.
> The structural threshold
> is a measure of the minimum number of residues, to include the degree
> of specificity of arrangement, needed to produce a particular type of
> functional system.
So how does one measure it?
How can one attach a number to it?
You seem to operate in a weird parallel universe in which one can
carry out complex statistical analyses without using a dataset of
numbers, or measure a variable without applying any form of
measurement.
> I've also noted many many times that different
> types of functional systems have different structural threshold
> requirements.
No, you've asserted that they have. You have provided no methodology
whereby such a variable can be measured.
>
> < snip >
>
> Sean Pitmanwww.DetectingDesign.com
Oh, snipping th difficult question again, Sean?
Let's sit back and watch you evade again, shall we?
By the way, there's an outstanding question (well, many outstanding
questions, but let's try to get an answer for this one) you haven't
answered:
Who do you think has the intellectual capability to evaluate your
"theory"?
After all, it's clear that nobody on this forum thinks it's anything
more than a load of twaddle, so why waste your time and effort in
posting the same stuff over and over again?
Of course, my hypothesis is that you know that it's a load of twaddle,
and are posting here only because you think that it impresses the
creationists. Everything you have done so far verifies this
hypothesis.
Still verifying my hypothesis, Sean.
Keep it up!
Snip it again!
I'll post it again.
Each time you look even more evasive.
RF
richardal...@googlemail.com
I do.
Adding the words "level of" means that it is a variable which can be
measured.
> Really? Come
> on now! If you increase the minimum structural threshold
> requirements, you have obviously move on to a higher level of those
> requirements have you not?
>
> Now, if that really wasn't obvious to you, I'm oh so sorry. But, I'm
> not quite sure how you were confused by this or how I could have made
> it any more clear.
>
> Sean Pitmanwww.DetectingDesign.com
It's clear that you think that your critics on this forum are too
stupid and ignorant to understand your "theories".
It's clear that your critics think that you are dishonest,
mathematically incompetent and that you "theories" are a load of
unmitigated twaddle.
As it is evident that in your view you are casting the pearls of your
superior wisdom before swine, why do persist in doing so? After five
years of it you have made no converts, and none of your critics
harbours any lingering doubt that you are not dishonest and evasive.
So who do you think *is* capable of understanding your "theories", and
why do you not write them up and present them in a forum in which they
will be appreciated?
Of course, my hypothesis is that you know perfectly well that your
"theories" are a load of unmitigated bovine excrement, but so long as
you can gain the attention of the gullible and ignorant creationists
whose approval you evidently crave, you will carry on posting this
nonsense. It seems you have as much contempt for the critical
faculties of creationists as the scientists on this forum.
So far you have been very successful in verifying my hypothesis. I'd
say that it is close to being proved beyond reasonable doubt.
What do you think? After all, anyone reading your posts would think
that you must be the world's greatest authority on all things
scientific.
Why not give us the benefit of your immeasurable intellect and answer
the question?
RF
Seanpit
wrote:
>
> You are such a dishonest man. Howard Hershey obviously put the entire phrase
> "level of minimum structural threshold requirements"within quotes because it
> appeared to be a new term that you hadn't defined yet.
>
> Is your terminology squirmy on purpose? It sure appears to be.
Let me give you an example from way back in February of this year I
wrote:
"As I have explained to you many times before, more novel
functions can and do evolve once one has been acquired. It is just
that none of the new ones will have greater minimum structural
threshold requirements than the old ones. They will all be at the
same low level of minimum structural complexity or lower - not higher
than the 1000aa threshold."
http://groups.google.com/group/talk.origins/msg/617d1ff6acf21dc5
"So, you see, it is the type of function that has minimum
structural
threshold requirements. These different minimums are what I call
"levels of functional complexity" or "minimum structural threshold
requirements".
http://groups.google.com/group/talk.origins/msg/49ac8153dac91353
"By the time such a minimum gap distance is produced, the average
time required to evolve something new at such a level of minimum
structural threshold requirements has moved into trillions upon
trillions of years of average time."
"The greater the minimum structural threshold requirements of the
final product, the greater are the odds that more residue positions in
the subpart subsystems ... The evolutionary mechanism, when it works,
always works well shy of the 1000aa threshold level and drops off in
commonality and rate as the threshold ..."
"The E. coli in Hall's experiment were successful because the
functional system in question has a relatively low minimum structural
threshold requirement - not even close to the 1,000 level."
From July:
"What Ron and others like Howard Hershey don't seem to realize is
that
tiny gap distances that are only 1 or 2 or 3 mutational changes wide
are not always the most likely minimum gap distance at every level of
minimum structural threshold requirements."
http://groups.google.com/group/talk.origins/msg/0f26740218b32f9d
December of 2006:
"For low-level systems, this is a fine conclusion because it can
actually be demonstrated in real time and because it can be shown that
the gaps between old and new are quite small indeed. However, when it
comes to those systems that have greater minimum structural threshold
requirements, the case is not so clear."
October of 2006:
"And, this number of potentially non-beneficial options increases
exponentially when higher and higher levels of minimum structural
requirements are considered."
Need I go on? Who is being "dishonest" here?
Sean Pitman
www.DetectingDesign.com
Seanpit
wrote:
> "Seanpit" <seanpitnos...@naturalselection.0catch.com> wrote in message
>
> news:1a8d31d0-a7da-46cc...@d21g2000prf.googlegroups.com...
>
>
>
>
>
> > On Dec 15, 11:08 am, "R. Baldwin" <res0k...@nozirevBACKWARDS.net>
> > wrote:
>
> >> >> Neither is "minimum actual gap size".
>
> >> > That's statistically mistaken. Minimum likely distances are indeed
> >> > based on average distances. That is what the Poisson distribution is
> >> > all about.
>
> >> No, Sean, you are demonstrating your statistical ignorance again. The
> >> Poisson distribution describes the probability of exactly k events
> >> occuring
> >> within a fixed interval,
>
> > That's right. How many targets are likely to be within a fixed
> > distance?
>
> No Sean, read for comprehension. It is the probability of finding an *exact
> quantity* of events within the fixed interval. The probability mass function
> is measured over the *quantity* variable. It is not "how many targets are
> likely to be found within a fixed distance."
The fixed interval is the fixed distance of X character changes. The
"events" are the finding of target sequenes within this fixed
distance. How likely are targets to be found within a particular
distance is most certainly a product of the the ratio and distribution
of targets and it most certainly does closely follow a Poisson
distribution.
> >> given that the events occur at a known average rate
>
> > The average distance between targets is known.
>
> >> lambda = n/interval, and that the occurance of next event is independant
> >> of
> >> distance from previous event.
>
> > That's right . . .
>
> Glad you agree, though above you clearly don't quite get it.
>
>
>
> >> You have not demonstrated that you have met
> >> the Poisson assumptions (especially event independance), and you have
> >> incorrectly described what the Poisson distribution calculates.
>
> > The independence concept is only weakly relevant. The location of
> > targets in sequence space is not completely random. There is a loose
> > clustering effect. However, this effect is not significant enough to
> > affect the Poisson estimation to a significant degree.
>
> Weaselly bull.
You need to look at BLAST data a bit more carefully.
> > The only way there would be a significant effect is if Howard notion
> > of all the potentially beneficial targets being clustered in one tiny
> > corner of sequence/structure space was in fact correct. The actual
> > distribution is far more random in appearance than Howard and others
> > in this forum seem to realize.
>
> And you know this how? From some misinterpreted abstract of an article that
> you didn't understand?
If you understand it any better, please do explain your take on what
the data actually says - i.e., like the data from the paper written by
Choi and Kim for starters.
Sean Pitman
www.DetectingDesign.com
Seanpit
>
> > Minimum structural threshold requirements indicates a variable all by
> > itself.
>
> No it doesn't. It implies a threshold level. That does not have to be
> a variable. It could be fixed.
See:
http://groups.google.com/group/talk.origins/msg/0893dc44a735853b
Seanpit
>
> > > Is your terminology squirmy on purpose? It sure appears to be.
>
> > Oh please! Don't tell me that you see a significant difference
> > between the phrase "minimum strcutral threshold requirements" and
> > "level of minimum structural threshold requirements"?
>
> I do.
> Adding the words "level of" means
> that it is a variable which can be
> measured.
This is ridiculous weaseling . . .
See the following for my use of the word "level" together with the
phrase "minimum structural threshold requirements. I've used it in
discussions with you directly before - many times. You evidently have
very selective memory.
http://groups.google.com/group/talk.origins/msg/0893dc44a735853b
Sean Pitman
www.DetectingDesign.com
Seanpit
The gaps in question have always been between beneficially functional
protein systems.
> Now "systems" of proteins are surrounded by a functionless "neutral
> gap" of 1000aa ??
No. The 1000aa is NOT the gap size. I'm not sure how many times I
have to repeat myself here. The 1000aa is the minimum structural
threshold requirement that produces a gap size of a few dozen
character changes. In other words, the gap size is always much
smaller than the minimum structural threshold requirement.
> You are not making any more sense that you were.
That's because you still don't seem to understand the difference
between structural threshold sizes and gaps sizes. They aren't the
same thing.
Sean Pitman
www.DetectingDesign.com
Ron O
Second part:
>
> > You know why there are no examples, because you don't know of any.
>
> And you don't either . . . Not beyond the 1000aa threshold.
You are the guy that is claiming that they exist, shouldn't you have
an example? Engage brain and think before responding. Just a little
friendly advice.
>
> > You don't even know what a 1000aa threshold is, except to say that you
> > know it when you see it. Why should anyone believe you?
>
> The 1000aa threshold is clearly defined. I really am finding it quite
> difficult to understand your confusion when it comes to this seemingly
> simple and straightforward definition.
So, where is the example and the explanation for why you picked those
residues? Go for it. It is your argument, you demonstrate that it is
simple and straightforward. Just do it instead of making bogus
claims. How can anyone explain 1000 whatevers if you can't even tell
anyone what they are? Just go to your flagellar example pick them out
and show us what they are.
>
> > > > You can't just make junk up and expect people to believe you,
> > > > especially since you are such a liar. You need confirmation. Where
> > > > is it? When have you or anyone ever established that this mythical
> > > > 1000aa threshold exists?
>
> > > After all the times I've presented this evidence I can't believe that
> > > you would still be trying to suggest that no system exists which
> > > requires a minimum of more than 1000aa to work. How can you suggest
> > > such a thing and call yourself informed on this issue? If you don't
> > > believe me, then by all means provide some sort of evidence showing
> > > how a functioning flagellum or any other such system can be produced
> > > with fewer than 1000 codons of genetic real estate . . .
>
> > We are back to codons, but they aren't really codons, because the
> > flagellum is made up of a lot of proteins, and just a few add up to
> > more than 1000 codons.
>
> The flagellum is made up of a lot of proteins. It is the minimum
> number of amino acid residues needed in all of the proteins, taken
> together, that make up the minimum structural threshold for the
> flagellar motility function. The minimum number of residues needed
> for flagellar motility is not presented by the minimum number needed
> for any one protein in the system. It is represented by the minimum
> number needed to get flagellar motility. Multiprotein systems, like
> the flagellum, cannot be produced with less than multiple proteins -
> each of which has its own minimum structural requirements that produce
> an overall minimum for the flagellar system.
So where is the list and why did you pick them? How am I supposed to
explain how they could have evolved if you won't even tell me what I
am going to have to try to explain?
It sounds like the gaps that aren't gaps again. All the parts with
their own structural requirements. They don't all have to evolve at
the same time, but the whole 1000 matters for some reason even though
you can approach the threshold a little at a time.
>
> Another way this minimum can be expressed is by the minimum amount of
> genetic real estate that is needed to code for the flagellar system -
> in codons. This minimum is also at least 10,000 codons.
Gap inflation coming....
>
> < snip >
>
> > > You do understand that some types of functions are inherently more
> > > complex than others - right? Would you say that flagellar motility
> > > requires much more complexity than the single protein lactase
> > > function? I sure hope you would agree to that.
>
> > What is your definition of complexity? Flagellum obviously have more
> > moving parts, but they are still made of proteins.
>
> Yes, a minimum of many proteins with many many more amino acid
> building blocks total - as compared to a single protein system like
> lactase. Lactase has a minimum need for less than 380aa while a
> flagellum has a need for more than 10,000 specifically coded aa - at
> minimum. See the difference in minimum requirements?
Now Lactase is less than 380. So much for your minimum size. And the
flagellum is more than 10,000, but it used to have a threshold of
1000aa.
The average protein is 300 amino acid residues. Each would fall below
the 380 low level point, so what does the 10,000 have to do with it.
Lactase would be worth squat if you didn't have glycolytic pathway and
things like the Krebs cycle. There are probably more than 30 proteins
involved in making the flagellum, but how do they differ from lactase,
and why does it matter?
>
> > You don't have
> > computer operated widgets in there regulating the function. In fact
> > most of the flagellar proteins that have been studied are related to
> > other proteins in the bacteria that we know are doing something else.
>
> Many of them do have a fair degree of sequence/structure homogeny.
> That does not take away from the fact that the overall minimum
> structural requirements for flagellar motility are greater than 10,000
> fairly specified residues. It matters not how such a system evolved
> or didn't evolve. The minimum threshold requirements stay the same.
> Even if you showed 99.99999% homology to another pre-existing system,
> this wouldn't change the fact that the minimum threshold requirements
> are still the same. It might help you explain how this minimum was
> realized by your evolutionary mechanism, by a reduction in the minimum
> gap size, but it would not change the structure minimum requirements.
What a joker. The homology relationships between proteins supports
the scientific explanation. that the flagellum evolved. Your
designer could have designed the flagellum from scratch. Evolution
builds on what it already has. Similarity is evidence that the
flagellar proteins evolved from preexisting proteins. We can even
estimate how long ago the two proteins diverged.
If there was such a system with 99.999% similarity and joined to form
the flagellum we would likely have gotten into a time machine to see
the last pieces come together to form it around 2 billion years ago.
Any similar system today would be related, but not that closely. If
it were that closely related it would likely be derived from the
flagellum instead of being part of how it evolved. You are just
demonstrating what evolution would look like. We don't expect a whole
lot of change at any step. The previous structure would be nearly
identical to what came after. We only see differences between extant
flagellum because they evolved 2 billion years ago. A lot of parts
may be different and have evolved even if they were kept. We look at
all the flagellum and we can see that some parts have been lost, some
possibly gained and possibly lost and regained over time in the
various lineages. There is some core that seems to link the
eubacterial ones together, but the archea types and eukaryotic ones
look like they have a separate origin.
>
> > We can't trace them all back to relatives because you know what 2
> > billion years of molecular evolution can do to protein sequences. So
> > it is different from the lactase evolution, how? By the number of
> > gaps that aren't really gaps unless you say so?
>
> It is just that the homologies that you think are so closely related
> aren't nearly close enough for your mechanism to produce the needed
> changes to get from one of your proposed homologous steppingstones to
> the next. The needed mutational changes are far too many for your
> mechanism of random mutation and function-based selection to actually
> have done the job you say it did.
Another baseless assertion. Back it up if you can. Use real data to
do it.
>
> > > >http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubme...
>
> > > > Klebsiella is not E. coli.
>
> > > Interesting abstract. I was unaware of this particular experiment and
> > > will have to obtain and read the full paper.
>
> > I'm sure that you saw it last time you ran. It is the same reference
> > that I put up the last time you made the same bogus claim. Isn't it
> > about time to run again?
>
> Not at all. I don't remember seeing this reference before. I don't
> necessarily read all of your posts you know, since most of the time
> you don't present any actual data or relevant references like this.
That is probably because you snip and run all the time. I wouldn't
have the reference on my computer if it were not for you. I see that
you didn't deny that you made the same false claim before. Pretending
doesn't really work.
>
> > > I do appreciate you bringing this paper to my attention, but I don't
> > > see how it affects the main point at hand in the least. I mean, I
> > > just noted for you that "the same thing is likely to happen in other
> > > species occasionally at this level of functional complexity." Did you
> > > miss that comment? After all, this level involves only a few hundred
> > > fairly specified residues at most. This sort of thing is only to be
> > > expected at such low levels - quite predictably in fact.
>
> > The reason for this is because you are dishonest and probably mentally
> > incompetent. Nothing, no amount of evidence, can change your mind,
> > even when you have to acknowledge its existence.
>
> Well, so far, all of your "evidences" consist of endless low-level
> examples of evolution in action - examples that do not require more
> than a few hundred fairly specified residues at minimum. How are such
> examples suppose to explain anything beyond low-level evolution?
So, where are the low level evidences for your alternative? Don't
have any? Why would your alternative be better than the one with real
evidence?
>
> > "Fairly specified" Must rank up there with "specified complexity,"
> > "irreducible complexity," "intelligent design," etc. How bogus did
> > all those turn out to be?
>
> None of these concepts are "bogus" at all - at least not as I define
> these terms. ID, in particular, is used in mainstream science all the
> time - to include forensic science, anthropology, and SETI.
Forget SETI, just put up an example that we can look at and see if
your 1000 aa threshold means anything. Your rambling is bogus until
you can demonstrate that you actually have an argument.
>
> > What was that intelligent design science that you would have taught to
> > school kids? What? No science? What are you arguing about?
>
> > What was that alternative to common descent that you had, and the
> > evidence to back it up? What? No alternative? Why are you arguing
> > about mythical thresholds if you don't have an alternative? Just
> > because it is the only pathetic thing that you can do doesn't mean
> > that you should be doing it.
>
> There is a great deal of evidence. You just don't seem to recognize
> it for what it is. One of the biggest reasons for this is that you
> don't seem to understand the concept of minimum structural threshold
> requirements.
Put it up. Where is that evidence for your alternative to common
descent that you claimed to have that was just as good as what science
had? I'd like to see that first, but any evidence would be something
more than we've seen before.
>
> > > > Read the Kleb paper. Remember what you ran from
> > > > last time? You've probably run so often that you can't keep track
> > > > anymore.
>
> > > This sort of data though is always interesting to me and is always
> > > relevant. Why not present more of this sort of argument instead of
> > > your usual focus on personal attacks instead? This sort of
> > > information is far more helpful and interesting to me and I'm sure to
> > > others as well that your usual pointless personal attacks and
> > > diatribe.
>
> > It is only a personal attack to you because you know that you are
> > stupid to keep running and pretending. If you just started to be
> > straight, I wouldn't have to keep reminding you about what you are
> > lying about.
>
> Irrelevant personal attacks are those that attempt to attack the
> opponents motives, or intelligence, or character. Those kinds of
> attacks are simply not helpful. On the other hand, attacking the
> argument at hand with relevant counterarguments is always helpful.
> You see, you are going after the argument instead of the person.
> Going after the person instead of the argument simply isn't helpful.
So stop snipping and running. Stop lying about it and claiming
personal attacks when you know that if you weren't doing something
dishonest that there would be no reason for your claims of personal
attacks.
It doesn't do much good arguing about this junk with you for the
simple reason that you can't reason and act honestly.
Demonstrate that I'm wrong. Make good on your claims. Put up a real
example of your 1000aa threshold instead of just claiming that it
exists. Show us the residues and why you picked them.
>
> > > Beyond this, how does this paper help your position? All it is, at
> > > the very most, is yet another example of low-level evolution - of a
> > > novel system that requires far less than a minimum of 1000aa.
>
> > It most definitely doesn't help yours.
>
> How so? It is actually predicted by my model. There are in fact lots
> of examples of evolution in action at this level in all kinds of
> living things.
And you have squat for your alternative. It definitely doesn't help
yours, unless you think that evidence that molecular evolution happens
the way that we think helps you out.
>
> > Remember when you were running
> > the Hall bull pucky for the first time? You were claiming that
> > crossing gaps of 3 were impossible.
>
> I've never claimed that crossing gaps of 3 were impossible. What I
> said was that Hall thought that such gaps would be impossible to
> cross. He therefore proposed some sort of magical non-Darwinian
> guidance as perhaps being involved with the success of his early
> experiments.
What a liar. How many years ago was that? I'm going to have to go
back what? 5 or 6 years and try and pull out that crap. You aren't
worth it. You prove that I'm a liar, go back to the Hall junk around
2002 or 2001 and look up what you were claiming about when EBG was
removed, bring back the links so that we can all check out just what
you were claiming back then. Could it possibly be 2000? You should
know better than anyone else, and you'd also know what name that you
were posting under. I think that I may have been still on AOL and
Pokemoto and rokimoto at the U.
Until you do that, I will claim that you are a liar. I can't believe
that you don't remember your gap inflation.
>
> > You hadn't come up with your
> > mythical 1000aa. The data showd that you were wrong, so at first you
> > jumped to 20 or 40 mutation gaps that were impossible, and it evolved
> > into this bogus claim of a whooping 1000aa.
>
> Again, the 1000aa is the threshold limitation, NOT the minimum gap
> size. Try to get this straight. The minimum gap size for the 1000aa
> level is most likely a few dozen mutational changes. Do you see the
> difference yet?
So you do remember your gap inflation. You know that you are a liar.
Pretending is just what you do when you know that you don't have an
argument. No denial of the gap inflation, just junk about the
mythical 1000.
>
> > At the very least it shows what a loser you are. Since you can't tell
> > us the difference between the two cases, and your own admissions seems
> > to be the difference between 380 and 1000. What are you arguing
> > about? All we have to do is divide up that 1000 into three parts and
> > you have no argument.
>
> It would be nice for you if you could do that. But simply having
> three different 333aa systems in the gene pool is not enough to
> explain how a 1000aa system can be easily evolved. Not even close.
> The fact that such a system has not been demonstrated to evolve in
> real time should be a very good indication to you that your thinking
> here might be just a little bit off.
So you say, but we haven't seen them so we don't know do we? Nervous
about your 1000 aa threshold falling apart like your 3 gap? If you
provide an example we can start to evaluate the 1000aa threshold.
>
> > So tell us what the 1000 is. You even admit
> > that you don't have to evolve all 1000 at a time. Even if the 1000
> > whatever exists, around 2 billion years of evolution took place before
> > flagellum evolved. We can still tell where a lot of the parts came
> > from.
>
> Two billion years is like a grain of sand in the universe compared to
> the time needed to evolve a system with a 1000aa minimum threshold
> requirement. Even trillions of years wouldn't be enough time. Yes,
> it is true that the majority of the 1000aa needed to evolve a novel
> system at this level is most likely already present in any given gene
> pool. It is just that the few dozen changes needed to cross over from
> what already exists to any novel functional system at this level are
> more than enough to stall evolution completely out this side of a
> practical eternity of time.
But you have less than 10,000 years to do what you need done, so who
is worse off? If you are an old earther, what is your ID explanation
for why it took the designer a couple billion years to design the
flagellum? We have a pretty good idea why it could take that long to
evolve one because you have to get all the parts and evolve them from
other parts, but what is the design explanation?
What are these few dozen changes? I thought that we weren't talking
about those kinds of gaps. How do you know that a dozen had to be
crossed at any given time?
>
> > In the face of that what do you have as an alternative?
>
> The intelligent design-only hypothesis. No non-deliberate force of
> nature comes remotely close to producing such higher-level systems.
> Intelligent manipulation does. This is the same basis for SETI.
So, where is the science of ID that you would have taught to school
kids? No science, why take it seriously? No alternative, why run an
obfuscation scam?
SNIP and run. You are good at that.
Ron Okimoto
>
> < snip >
>
> > Ron Okimoto
>
> Sean Pitmanwww.DetectingDesign.com
Seanpit
>
> > > You know why there are no examples, because you don't know of any.
>
> > And you don't either . . . Not beyond the 1000aa threshold.
>
> You are the guy that is claiming that they exist, shouldn't you have
> an example? Engage brain and think before responding. Just a little
> friendly advice.
Systems with far greater minimum threshold requirements than 1000
fairly specified residues do exist. I've given you several examples -
to include the flagellum with its threshold of greater than 10,000
fairly specified residues.
What doesn't exist are any examples of random mutation and function-
based selection producing such a system. These evolutionary examples
are what don't exist. The high-level systems themselves most
certainly do exist.
How you can argue otherwise or act like you don't understand this
concept is truly a mystery.
> > > You don't even know what a 1000aa threshold is, except to say that you
> > > know it when you see it. Why should anyone believe you?
>
> > The 1000aa threshold is clearly defined. I really am finding it quite
> > difficult to understand your confusion when it comes to this seemingly
> > simple and straightforward definition.
>
> So, where is the example and the explanation for why you picked those
> residues?
How many times do I have to give you the examples before you
remember? Again one example is the flagellum which requires greater
than 10,000 specified residues at minimum. There are many other such
examples that go well beyond the 1000aa threshold minimum (which, as
already noted many times, is not the gap distance).
The reason why I draw the line at 1000aa is because the evolutionary
mechanism has never come remotely close producing any novel function
that require a minimum of 1000aa to work. The only examples of
evolution there are produce novel functions with minmum requirements
of only a few hundred fairly specified residues max.
> Go for it. It is your argument, you demonstrate that it is
> simple and straightforward. Just do it instead of making bogus
> claims. How can anyone explain 1000 whatevers if you can't even tell
> anyone what they are?
I've told you over and over again. The threshold limitation beyond
which I suggest evolution cannot go this side of trillions of years
involved finding novel functional systems that have a minimum
requirement of more than 1000 amino acid residues in a fairly
specific arrangement (i.e., less than 1e100 sequences per 100aa of
flexibility).
> Just go to your flagellar example pick them out
> and show us what they are.
The flagellum is an example of a system that has a threshold
requirement of at least 10,000 fairly specified residues. How can you
not understand that? What about the statement that it "takes at least
10,000 specifically arranged residues to build a flagellum" do you not
understand?
Until we can get past this point, there really is no point in
continuing with the rest. The rest of your questions will be answered
once you understand this first point.
< snip rest for now >
Sean Pitman
www.DetectingDesign.com
Seanpit
>
> > In agreeing with Arthur here, you show that you still don't grasp the
> > difference between sequence flexibility (i.e., the size of a target
> > island) and the distance between islands (i.e., the gap distance).
> > They aren't the same thing Howard. You, of all people, should know
> > this by now.
>
> Funny thing. I just posted a thread where I demonstrate (at least to
> my current satisfaction) that sequence flexibility of cytochrome c,
> specifically the number of aa sites that, mathematically, are freely
> variable (in a mathematical model that assumes that there are only
> "freely variable" and "invariant" aa sites -- which was done solely
> because that simplifies the discussion) is exactly the same number you
> call "average gap size".
According to Yockey anyway, the size of the CytoC island is 1e90
sequences. The ratio of CytoCs to non-CytoCs is therefore about 1 in
1e40 or 1e-40. Given a trillion potential beneficial functions with
these same minimum size and specificity requirements, the average gap
distance would be about 26 residue differences between islands and the
minimum likely gap distance would probably be around 4 or 5 for a
large population (along a Poisson distribution).
> > I can only assume that you support Arthur here because, and only
> > because, he is trying to oppose my position.
>
> I was making a joke. As indicated by the ;-)
Oh, so you do think Arthur is confused here? - just having a little
fun with Arthur? Is that it? ; )
Sean Pitman
www.DetectingDesign.com
_Arthur
So there are no gaps, and organisms can come up with new proteins and
new functions, by a succession of point mutations.
And now the Pittmann babbles about "protein systems" and "structural
threshold sizes".
What's the "structural reshold size" of an elephant's trunk ? Can you
compute it ?
Ron O
wrote. It wouldn't be snip and pretend again, would it?
And this is it?
>
> > > >http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubme...
>
> > > > Your own calculations indicated that once mutation selection balance
> > > > was reached in a population, jumping 2 or 3 mutational intervals was
> > > > not that rare.
>
> > > That's right . . .
>
> > So what is your beef, and how does that impact your 1000aa threshold
> > that is composed of gaps that aren't really gaps, but they don't all
> > have to be crossed all at one time?
>
> The 1000aa threshold isn't the gap size. It is the minimum structural
> requirements. The gap size for this level would be several dozen
> mutational changes wide - which most certainly would need to be
> crossed before a novel function at this level could be realized.
We are back to the gaps that aren't gaps. These not gaps are around
several mutational changes wide, but they aren't gaps, but they are
part of the 1000aa threshold. So can you put forward one of these
nongaps? One example?
>
> > > > Hall's experiments never reached close to mutation
> > > > selection balance. He started with clonal populations at the same
> > > > start point every experiment. You know the difference, you prefer to
> > > > lie to yourself about it.
>
> > > Hall's experiments didn't need to reach mutational balance (~70,000
> > > generations), because the gap size was only one mutation wide. A gap
> > > of just one mutation is easy to cross for a large colony in a single
> > > generation. And, this is exactly what happened.
>
> > His first experiements didn't have to. You made a stink about his
> > second set of experiments where he deleted EBG and claimed that it
> > meant that gaps of 2-3 could not be crossed. Don't you remember your
> > own arguments?
>
> The deletion of ebg in Hall's second set of experiments is very
> interesting because after extended observation the lactase function
> was not evolved. The observation was long enough that Hall got
> frustrated and said that his ebg negative colony had, "limited
> evolutionary potential."
Sure you made hay about it, but it didn't mean what you thought did
it? Gap inflation started once you realized that 3 wouldn't do.
>
> Now, nowhere in this exchange did I say it was impossible to cross
> gaps of just 2 or 3 character differences. I've said otherwise many
> many times in fact.
"Impossible" is probably the wiggle word here. Do you deny that you
made the claims about Hall demonstrating that gaps of two or three
were so unlikely as to be impossible to cross?
>
> > You were wrong. You admit it because you had to go from gaps of 2-3
> > to your 1000 aa bull pucky.
>
> You don't get it. The 1000aa is NOT the gap distance. I've always
> said that small gaps, to include gaps of 2 or 3 or even over a dozen
> mutational character changes could be crossed in evolutionary time
> frames. But, the decline in evolvability is exponential in nature.
> The only way to keep up is to increase the population size and/or
> mutation rate. The problem here is that population sizes are limited
> by limited environments and mutation rates are limited by their
> lethality beyond a certain rate. So, at steady state population
> sizes, evolutionary progress stalls out exponentially as the minimum
> gap sizes increase - and they do in fact increase in a linear manner
> as the structural threshold sizes increase.
Not a gap but made up of a bunch of gaps. So it isn't "impossible"
but it "stalls out."
>
> < snip >
>
This is quite a snip. It must be snip and pretend again.
Why not describe the 1000aa threshold so that it can be analyzed?
What about telling people your alternative so we know that you aren't
just blowing smoke?
I've already commented on this in another post. This is so loopy of
an argument that you should be embarassed for even thinking it up.
The functional antibody isn't just based on 20 residues. That may be
the usual epitope, but it isn't the only type of epitope and amino
acids don't zip up like DNA it takes a whole lot more amino acids to
form a pocket to specifically recognize those 20 residues. Not only
that but there have to be more amino acids that have to support the
binding site. They just don't hang in the air and their strucutral
backup has a lot to do with the shape of the binding site. Do you
deny that amino acids on opposite ends of the protein can influence
binding?
Concentrating on the size of the target was stupid even if it gave you
a number that you could live with to justify your continued ignorance
of the subject. It is the protein that does the binding that is the
most important. Just think for a second. You know that abzymes are
created during this process. You know that beta linkage catalysis can
be evolved and you claim that the minimum for this is 380. That is
far from 20 and lactose is only two sugar molecules instead of a
string of 20 amino acids. If it takes 380 amino acid residues to bind
and hydrolyze lactose, how many residues does it take to bind 20 amino
acids in such a way as to specifically recognize those 20 in that
order?
Take this argument off your page, it is bogus. Take it to the bank.
>
> < snip >
Snip what you can't counter. Snip and pretend. Sort of a long
established pattern.
>
>
> > >Since
> > > there are trillions of different possible antigen epitopes, how does
> > > one's immune system cope with such a variety of potential enemies?
> > > Well, there are many immune cells produced by the body. In humans, in
> > > particular, about 10^12 lymphocytes are present at any given time.
> > > Not all the T-cells have different Y-shaped receptors, but many of
> > > them do. Chances are that if enough non-self enemies get into the
> > > body at least one of the immune cells will recognize the non-self
> > > marker sequences or "antigens" located on this invader as "foreign" to
> > > at least some useful degree. The odds that a single T-cell will
> > > recognize a random epitope to at least some useful degree is about 1
> > > in 10^12. So, does this mean it would take a trillion different T-
> > > cells to cover all possible invaders? Well, no. The reason is
> > > because an average cell or foreign invader "bug" has about 10^12
> > > different epitopes. So, on average, a single T-cell will recognize at
> > > least one of the potential antigen epitopes of a foreign invader.
>
> > Well you have to start over and recalculate because the number of
> > antigens isn't important, and even if it was you have hugely
> > underestimated the number of them that there can be.
>
> Not at all. Antibodies simply cannot specifically recognize antigen
> epitopes that are larger than about 20aa or an equivalent number of
> atoms - because that is the number of residue binding positions the
> antibody has.
There are more than 20 amino acids found in nature that can act as
antigens. There are more R groups that we can put on. There are
sugar groups that can be part of this epitope. Just think for a
second, what does it mean when they claim that they can create
antibodies to antigens that have never been seen in nature. We can
put specific DNA sequences in as epitopes and have them specifically
recognized by antibodies. The number of possible epitopes is so much
larger than your calculations that it is a joke.
>
> > You might as
> > well call them infinite because they are only limited to the chemical
> > constructs that we can make, and there are a lot of ways to put
> > together the existing elements. We can get binding of nucleotide
> > bases, unsaturated cyclic molecules with various chemical groups on
> > them. The list is limited by the imagination. The important fact is
> > that even with this tremendous number of antigens (we can make
> > synthetic antigens that have never been seen in nature) the antibodies
> > can respond and a useful one will evolve due to random mutation and
> > selection in only 10E12 events max. This is such a small fraction of
> > the protein sequence space available to the antibody that it is
> > essentially zero.
>
> You clearly don't understand the basis for how antibodies can actually
> do their job. If antigen epitope sequence space were essentially
> "infinite" as you claim, then a trillion or so antibodies could not do
> their job effectively. It is because the antigen options are actually
> quite limited that the immune system is able to work as effectively as
> it does. After all, the odds of a randomly chosen antibody
> recognizing or effectively binding to a particular antigen epitope are
> about 1 in 10^12 (see reference). That would be impossible if your
> notion of epitope space being "essentially infinite" were actually
> true.
Figure it out for yourself. How do we produce antibodies that can
bind to specific DNA sequences if we can't use DNA as an antigen?
You keep repeating this 10^12 mantra, but you don't understand what it
is. In the mouse model where that number comes from, that is believed
to be the upper limit of the number of sequences that could have
possibly been tested during any given immune response. Out of that
number you get a successful antibody nearly every time. Anymore than
that and you have to claim that more cells than can be found in the
entire mouse body, and not just the immune cells would have had to
participate. These cells just don't die out rapidly and get replaced
either. It is true that you have to get tetnus boosters and things,
but it takes years to lose these cells. So you can't even rely on
exponential cell growth because you have to do something with all the
failures that are hanging around.
10E12 is the maximum number of protein sequence that could have
possibly been tested. This is all that could have possibly been
tested, not what the odds are for finding the correct antibody
sequence. It is more likely 10E10 or 10E11 for the actual number
tested.
If the odds of binding any epitope was 10E-12 as you contend the
immune response would likely fail more than half the time. It works
nearly all the time, so the odds of binding epitope must be a lot
greater than 10E-12.
The number of antigens is so much larger than you think that it is
mind boggling. There is no preset number that antibodies have to
identify. We haven't figured out the limit. The whole point is that
the immune system works nearly every time no matter what we have
thrown at it. How do you think that they evolve ATPase activity if
ATP or some analog can't be part of an epitope?
>
> Jun Sun, David J. Earl, and Michael W. Deem, Glassy Dynamics in the
> Adaptive Immune Response Prevents Autoimmune Disease, Physical Review
> Letters, 95, 148104, September 30, 2005
>
> http://www.mwdeem.rice.edu/djearl/autoimmune.pdf
>
> > Proteins are just a lot more plastic that you can imagine. That is
> > only a problem for you.
>
> Proteins can be quite plastic indeed, but certainly not more than I
> imagine.
More than you obviously know. Since you are wrong about the maximum
number of epitopes.
>
Google stop:
Ron Okimoto
hersheyh
0catch.com> wrote:
> On Dec 16, 1:53 pm, hersheyh <hershe...@yahoo.com> wrote:
>
>
>
> > > In agreeing with Arthur here, you show that you still don't grasp the
> > > difference between sequence flexibility (i.e., the size of a target
> > > island) and the distance between islands (i.e., the gap distance).
> > > They aren't the same thing Howard. You, of all people, should know
> > > this by now.
>
> > Funny thing. I just posted a thread where I demonstrate (at least to
> > my current satisfaction) that sequence flexibility of cytochrome c,
> > specifically the number of aa sites that, mathematically, are freely
> > variable (in a mathematical model that assumes that there are only
> > "freely variable" and "invariant" aa sites -- which was done solely
> > because that simplifies the discussion) is exactly the same number you
> > call "average gap size".
>
> According to Yockey anyway, the size of the CytoC island is 1e90
> sequences. The ratio of CytoCs to non-CytoCs is therefore about 1 in
> 1e40 or 1e-40.
That is the ratio I used.
> Given a trillion potential beneficial functions with
> these same minimum size and specificity requirements, the average gap
> distance would be about 26 residue differences between islands and the
> minimum likely gap distance would probably be around 4 or 5 for a
> large population (along a Poisson distribution).
Sean, in your appendix, the number for "average gap size" as *you*
calculated "average gap size" would not be 26 for cytochrome c. For
cytochrome c, it would have been 30.7, which is the 20th root of the
inverse of 10e-40. Do you just make up numbers whenever the urge to
make up a new number appears?
>[snip]
Ron O
>
> > > > How did you come up with a number
> > > > so small?
>
> > > Because, antibody binding to antigens presented by antigen presenting
> > > cells is only based on about 20 very loosely specified amino acid
> > > residues.
>
> > Take it to the bank, you lost it with this argument, it doesn't even
> > make sense to talk about the antigen when it is the antibody that is
> > the important agent.
>
> Sure it does. The antibody cannot recognize more of an epitope than
> will fit in its limited binding site.
And how much more than the binding site is needed for enzymatic
activity. Did you know that binding is just one aspect of enzymatic
activity. Did you know that amino acids don't just zip up like DNA
and that the binding pocket is a lot larger than 20 amino acids? Did
you consider the support structure needed to get that binding pocket
in that conformation? If lactase function requires 380, how could an
abzyme with the same activity require fewer? even though it is only
binding two sugar molecules instead of 20 amino acids? It isn't the
size of the epitope that matters. Get a clue.
>
> > Not only that but you have greatly
> > underestimated the number of possible antigens.
>
> Not at all. Rather, you have greater overestimated the number of
> effective antigen epitopes. Again, the odds of effective binding of Ab/
> Ag are just 1 in a trillion. That's not very much of a sequence space
> if you ask me.
What do you think that I've been saying. So few sequences have to be
tested to get binding that your 1000 aa threshold is a joke. It isn't
due to the small number of epitopes possible because there aren't just
20 amino acids that can form the epitope. All kinds of R groups can
be used, nucleotides and even specific DNA sequences, phenolics,
sugars, etc. All these possible epitopes and the immune system still
works nearly all the time. This means that every antibody sequence
tested (a maximum possible number of 10E12) has to be able to bind
multiple possible antigens because there are so many more antigens
that the number of antibody sequences that can possibly be tested. It
probably wouldn't work if there wasn't selection, preferential
amplification and selection again. Just like natural selection, in
fact, it is natural selection because you can't claim that the
designer is in there doing it, can you?
Just think what you are claiming if the odds were 1 in a trillion.
Why can I make a synthetic antigen that has never been seen in nature
and get an antibody to it? You only have a trillion chances, and yet
it works nearly every time. It works because you at first get weak
binding, and those cells are selected for amplification and more
mutations happen. These are selected and better binding gets
selected. This continues until you get an antibody that is able to do
the job effectively enough to stop the infection. It happens within a
maximum of 10E12 events. 10E12 is not the odds, it is the maximum
number of sequences that could have been tested. The odds have to be
less than this. It works just like natural selection because that is
what it is.
You've blown this one. You probably know it by what you have snipped.
>
> > You aren't just
> > dealing with twenty amino acids, there are probably hundreds of amino
> > acids found in nature that could work as antigens, not only that, but
> > sugars, nucleotide bases, and other chemical molecules can be attached
> > to amino acids and induce specific antibody binding.
>
> Again, effective antigen epitopes are indeed equivalent to no more
> than about 20aa of sequence space. The immune system couldn't work if
> you were correct. Look up the reference I gave you above.
You can repeat this as often as you like, but it just doesn't mean
what you claim. The epitope is not the antibody. It doesn't matter
what the antigen is, what matters is the protein sequence that binds
the antigen specifically. Specifically enough so that you can get
antibodies to specific DNA sequence.
>
> > > > What about the Abzymes?
>
> > > Abzymes require more than simple binding. Abzymes are antibodies
> > > that, in addition to being able to bind, must also by able to
> > > hydrolyze chemical bonds in a specific way to act as enzymes.
> > > Enzymatic activity is far more complex than simple protein-binding
> > > functions. It therefore has a much greater minimum size and
> > > specificity requirement. For example, those abzymes that have
> > > adequate levels of lactase activity equivalent to what might be useful
> > > in a bacterium have minimum size requirements of several hundred
> > > residues in a fair degree of specificity.
>
> > How do you know when the business end of the antibody is so much
> > larger than that?
>
> The binding sites are what are important. The binding sites involve
> only about 20aa.
That is the epitope size, not the size of the antibody pocket that
binds the epitope or even the support structure that is required to
create the pocket. Amino acids do not zip up like nucleotides. It
takes more than 20 to bind 20 specifically. Amino acids on the
opposite side of the protein from the binding site can affect the
structure of the binding site. Do you deny that? This argument of
yours is just full of baloney. Take it off your web site because you
know by now that it is bogus.
>
> > Hey, and this evolution has to happen in less than 10E12 events. It
> > has to be lower level, right? So higher level is just three
> > antibodies strung together?
>
> You have this notion that it is an easy thing to just string existing
> proteins together and end up with a higher level system. Sorry to
> say, but that sort of simplistic thinking is simply wrong. The odds
> of successfully stringing together existing proteins and ending up
> with a higher level system are exponentially unlikely to hit upon any
> novel beneficial system that has higher and higher minimum structural
> requirements.
So where is your example to demonstrate that this is wrong? Specific
proteins and residues would be nice. Where is it?
>
> > They have evolved abzymes for more than
> > one step in an enzymatic path, but I don't recall if they did three,
> > it may have been just consecutive steps.
>
> Enzymatic pathways are not more specified than each individual protein
> in the pathway. Why? Because they do not require overall system
> specificity as do systems like flagellar motility. The enzymes in
> enzymatic pathways are part of a cascading system of function where
> the individual protein parts do not need to be specifically arranged
> relative to each other. This dramatically reduces the overall
> complexity of the system.
So quantify it. Show us your example. Don't just claim that you know
what you are talking about, demonstrate it. You blew the antibody
example, why should anyone take your word on this?
>
> > If someone did develop an
> > abzyme biochemical pathway of 3 or more steps would that break your
> > 1000 aa threshold?
>
> No - because of a lack of the specificity requirement. Again,
> cascading systems are no more structurally complex than their most
> complex part that does require specific arrangement of its amino acid
> building blocks relative to each other.
You know it when you see it though, you just can't tell anyone else
what it is so that they can evaluate it.
>
> > It would likely be over 1000 fairly specified
> > residues involved and you admit that not all 1000 have to happen at
> > one time.
>
> It might be over 1000 residues, but it would be specified. In other
> words, all the amino acid parts would not be required to be in a
> specific orientation relative to all the other amino acid building
> blocks. Cascading systems are not like the flagellar system where all
> of the parts must be specifically arranged relative to each other.
Can you demonstrate that all the amino acid parts are required to be
in a specific orientation relative to all the other amino acid
building blocks in the flagellum? Thought not, because it isn't
true. You just have to look up how many different sequences make up
the various flagellum that are related by descent to know that a lot
of sequences can work, and they don't have to be in a specific order
relative to each other. So it can't be "all" it has to be a limited
number that is a subset of all, if that.
>
> > > > Do you know how small a number of
> > > > amino acid residues that you are claiming account for the entire
> > > > immune response in the biosphere? It is only around 20 isn't it?
>
> > > Yep - that's it.
>
> > Well, I guess that you will just have to come up with another
> > argument, and take this stupid one off your web site.
>
> You need to read up a bit more on this topic.
You have to remove it from your web site because you know it is bogus.
>
> > > > Even for you that number would have to be bogus.
>
> > > It isn't bogus at all. It's a well-established fact. Look it up.
>
> > And, so what? It doesn't mean what you claim, just think about it for
> > a second and then hit the delete key at your web site. You wouldn't
> > want to be accused of misleading the ignorant rubes would you?
>
> Read up on the topic just a bit more.
What a joker. You are the one that mistook the maximum number of
possible sequences tested for a probability, and messed up with the
epitope fiasco. Just face it even an epitope of 2 sugars (galactose
and glucose for lactose) would require more than 20 amino acids to
create the binding site on the antibody. The number of epitopes is
not just 20^20 because there are more than 20 different units that can
be part of that epitope. Sugars, nucleotides, just about any small
molecule that you can think of and not just the 20 amino acids coded
for.
>
> > > I've always said that Gaps of 2 or 3 mutations could be crossed in
> > > relatively short order and I've always said that such small gap
> > > distances become exponentially less and less likely with increasing
> > > minimum structural threshold requirements. There's been no change in
> > > this description of the problem at hand.
>
> > This is a lie. Do I have to look up the ancient posts, or will you be
> > honest enough to at least admit that?
>
> Sure - - please do look up where I said otherwise. It certainly
> hasn't been in the last 5 years nor is such a statement anywhere on my
> website.
This tells me that you know that you are lying. It was probably
before 2002 so it would be more than 5 years, and you would know this
better than anyone.
>
> > What did you use the Hall argument to support.
>
> The start of the stalling out effect of evolutionary abilities even at
> fairly low levels of functional complexity. While all bacterial
> species would be able to quickly evolve a very low-level function like
> antibiotic resistance to just about any antibiotic that was presented
> in sublethal levels, it is not nearly that common for a bacterial
> colony to be able to evolve even a simple single-protein enzyme.
It didn't work did it? It wasn't what you thought.
>
> > It wasn't your 1000aa threshold.
>
> Yes, it was. For many years now I've had my 1000aa threshold out
> there. I used Hall's experiments to show that on occasion simple
> single protein functions may evolve up the a threshold of a few
> hundred fairly specified residues - but not beyond the 1000aa
> threshold. This challenge has been out there for many years.
This is a lie. You only came up with this bogus mythical 1000aa after
the Hall junk.
Many years, but no denial that it wasn't always that way. How can you
do this kind of dishonest bogus junk?
>
> > You know that you were claiming that Hall could not jump a
> > gap of two or three when he removed the EBG gene.
>
> The removal of ebg and the resulting lack of evolution in E. coli
> proved that the gap involved was a bit bigger than one character
> change - or even two or three. It basically proved that the *average*
> gap distances for this level of complexity had in fact increased.
> This increase in the average gap distance translates into a situation
> where a minimum gap distance of one or two needed character changes is
> exponentially less common than it was at lower levels.
Sean, why do you even try? Does it make you feel better? Why not
just admit that you were wrong. Why kick around the issue and
obfuscate about it?
>
> > Why did gap
> > inflation start if this were true. Why the jump to 10 or 20 and the
> > rapid increase to 40, and now the 1000?
>
> Again, the 1000aa threshold is not the gap distance. There has been
> no increase in the challenge. The minimum gap distance that could not
> be crossed in a reasonable amount of time has been and still is a few
> dozen character changes wide. Your claim that the 1000aa number
> represents what I call the "gap distance" is simply a strawman
> mischaracterization of my true position.
It is only a gap when you want it to be gaps. It isn't a strawman
because that was your argument, and why gap inflation started. I see
that you don't deny the gap inflation. Does that make lying allright?
>
> > You can't even be honest with yourself, can you?
>
> Why not stop building strawmen to misrepresent my position long enough
> to see?
>
> < snip >
>
> > Ron Okimoto
>
> Sean Pitmanwww.DetectingDesign.com
Why not put up or shut up?
Where is that science of ID that you claimed that you could teach to
kids? Where is that alternative to common descent that you claimed to
have and the evidence for it that you claimed was just as good as the
evidence that science has. No science, no alternative, why run the
obfuscation scams?
snip and pretend.
Ron Okimoto
hersheyh
0catch.com> wrote:
> On Dec 16, 2:52 pm, Ron O <rokim...@cox.net> wrote:
>
>
>
> > > > You know why there are no examples, because you don't know of any.
>
> > > And you don't either . . . Not beyond the 1000aa threshold.
>
> > You are the guy that is claiming that they exist, shouldn't you have
> > an example? Engage brain and think before responding. Just a little
> > friendly advice.
>
> Systems with far greater minimum threshold requirements than 1000
> fairly specified residues do exist. I've given you several examples -
> to include the flagellum with its threshold of greater than 10,000
> fairly specified residues.
The archaean flagella is simpler than the eubacterial flagella. Many
of the proteins in the eubacterial flagella are not present in one or
another eubacteria. Since "minimum structural threshold" appears to
be, in practice, the smallest known protein/protein system that can
produce a specified function, which proteins are you adding together
to get this number? And why do you ignore the simpler archaean
flagella, which lacks many of the flagellin family of genes?
And your proposed mechanism does not even hint at any of the proposed
*real* evolutionary mechanisms, which all involve the presence of an
ancestral protein (or a duplicate) with a different function that gets
modified to produce a new, but related, function. There is no long
random search for any single protein, much less all of them all at
once.
> What doesn't exist are any examples of random mutation and function-
> based selection producing such a system. These evolutionary examples
> are what don't exist. The high-level systems themselves most
> certainly do exist.
>
> How you can argue otherwise or act like you don't understand this
> concept is truly a mystery.
>
> > > > You don't even know what a 1000aa threshold is, except to say that you
> > > > know it when you see it. Why should anyone believe you?
>
> > > The 1000aa threshold is clearly defined. I really am finding it quite
> > > difficult to understand your confusion when it comes to this seemingly
> > > simple and straightforward definition.
>
> > So, where is the example and the explanation for why you picked those
> > residues?
>
> How many times do I have to give you the examples before you
> remember? Again one example is the flagellum which requires greater
> than 10,000 specified residues at minimum. There are many other such
> examples that go well beyond the 1000aa threshold minimum (which, as
> already noted many times, is not the gap distance).
>
> The reason why I draw the line at 1000aa is because the evolutionary
> mechanism has never come remotely close producing any novel function
> that require a minimum of 1000aa to work.
What you mean is no evolutionary mechanism has done anything but
*modify* a previously existing system to produce a modified or 'novel'
function. When you are given examples of such modification, you find
some other reason to pretend that that is not what you want. Epitopes
are too simple a target. Whatever.
The only "example of evolution" you would accept is one that involves
crossing a large totally functionless gap. But we all agree that that
would not happen. But crossing large functionless gaps is *your*
model, not ours.
> The only examples of
> evolution there are produce novel functions with minmum requirements
> of only a few hundred fairly specified residues max.
>
> > Go for it. It is your argument, you demonstrate that it is
> > simple and straightforward. Just do it instead of making bogus
> > claims. How can anyone explain 1000 whatevers if you can't even tell
> > anyone what they are?
>
> I've told you over and over again. The threshold limitation beyond
> which I suggest evolution cannot go this side of trillions of years
> involved finding novel functional systems that have a minimum
> requirement of more than 1000 amino acid residues in a fairly
> specific arrangement (i.e., less than 1e100 sequences per 100aa of
> flexibility).
>
> > Just go to your flagellar example pick them out
> > and show us what they are.
>
> The flagellum is an example of a system that has a threshold
> requirement of at least 10,000 fairly specified residues. How can you
> not understand that?
Numbers you pull out of yer arse is not an answer.
Ron O
0catch.com> wrote:
> On Dec 16, 2:52 pm, Ron O <rokim...@cox.net> wrote:
>
>
>
> > > > You know why there are no examples, because you don't know of any.
>
> > > And you don't either . . . Not beyond the 1000aa threshold.
>
> > You are the guy that is claiming that they exist, shouldn't you have
> > an example? Engage brain and think before responding. Just a little
> > friendly advice.
>
> Systems with far greater minimum threshold requirements than 1000
> fairly specified residues do exist. I've given you several examples -
> to include the flagellum with its threshold of greater than 10,000
> fairly specified residues.
10,000 inflation raises its ugly head once Sean realized that his low
level specificity was only 380 compared to 1000.
Yes, so what evolutionary scenario are you claiming to have disproved
by not observing it happening?
There may have been 2 billion years of biological evolution before
there were flagellum. What do you expect to observe?
Remember the IDiot problem that they have admitted, that to make this
type of argument viable you have to discount every possible
biologically relevant evolutionary scenario. How many have you
discounted with your observations? None, right? We are talking
biologically relevant, and such experiments have never been done as
far as I know.
>
> What doesn't exist are any examples of random mutation and function-
> based selection producing such a system. These evolutionary examples
> are what don't exist. The high-level systems themselves most
> certainly do exist.
What scenario was tested? For the flagellum, what would you even
select for? How would you start the system evolving? We have clues,
it looks like you should get some ATPases to work for protein
transport, and build from there, so who did this experiment. If no
one has done it, that would be a good reason for not ever observing
it, along with the fact that it may have taken hundreds of millions of
years and various functional intermediates that didn't work for
motility to do it.
>
> How you can argue otherwise or act like you don't understand this
> concept is truly a mystery.
What concept? Your bogus mythical 1000aa threshold that you can't
even put up an example of? Just telling people to look at the
flagellum tells us squat. What is this threshold and what is it made
of. Use real proteins and show us.
>
> > > > You don't even know what a 1000aa threshold is, except to say that you
> > > > know it when you see it. Why should anyone believe you?
>
> > > The 1000aa threshold is clearly defined. I really am finding it quite
> > > difficult to understand your confusion when it comes to this seemingly
> > > simple and straightforward definition.
>
> > So, where is the example and the explanation for why you picked those
> > residues?
>
> How many times do I have to give you the examples before you
> remember? Again one example is the flagellum which requires greater
> than 10,000 specified residues at minimum. There are many other such
> examples that go well beyond the 1000aa threshold minimum (which, as
> already noted many times, is not the gap distance).
You can't just point to the flagellum and claim your job is done. You
are the one claiming some threshold, so you show us what it is. Use
the flagellum and use the proteins in it and show us that you know
what you are talking about.
>
> The reason why I draw the line at 1000aa is because the evolutionary
> mechanism has never come remotely close producing any novel function
> that require a minimum of 1000aa to work. The only examples of
> evolution there are produce novel functions with minmum requirements
> of only a few hundred fairly specified residues max.
The reason is that you pulled the number out of your butt and it
sounded good even if it stinks.
>
> > Go for it. It is your argument, you demonstrate that it is
> > simple and straightforward. Just do it instead of making bogus
> > claims. How can anyone explain 1000 whatevers if you can't even tell
> > anyone what they are?
>
> I've told you over and over again. The threshold limitation beyond
> which I suggest evolution cannot go this side of trillions of years
> involved finding novel functional systems that have a minimum
> requirement of more than 1000 amino acid residues in a fairly
> specific arrangement (i.e., less than 1e100 sequences per 100aa of
> flexibility).
Still no example, it doesn't look like you know what you are talking
about. Use the flagellum and show us what this threshold is. How can
we explain something if you can't tell us what it is?
>
> > Just go to your flagellar example pick them out
> > and show us what they are.
>
> The flagellum is an example of a system that has a threshold
> requirement of at least 10,000 fairly specified residues. How can you
> not understand that? What about the statement that it "takes at least
> 10,000 specifically arranged residues to build a flagellum" do you not
> understand?
Well what are a thousand of them or 100? This isn't an example, or
even a description that means anything. Take several of the proteins
and show us what is specified about them.
>
> Until we can get past this point, there really is no point in
> continuing with the rest. The rest of your questions will be answered
> once you understand this first point.
Once you can demonstrate that you have a point we can continue. This
is a farce. If you don't know what your threshold is just say that
and stop pretending.
If you know what it is, just take the flagellum and the proteins
involved and show us.
>
> < snip rest for now >
>
> Sean Pitmanwww.DetectingDesign.com
Snipping is what you are good at. It doesn't really solve your
problems, just thought that I'd tell you that.
When are you going to stop running and pretending? What good is this
1000aa threshold junk if you don't have the science to back up your
alternative and you don't even have a viable alternative? Why not put
up or shut up? You made the claims, you don't even deny making the
claims, you just pretend that you didn't and run.
Ron Okimoto
richardal...@googlemail.com
0catch.com> wrote:
> On Dec 16, 2:25 pm, richardalanforr...@googlemail.com wrote:
>
>
>
> > > > Is your terminology squirmy on purpose? It sure appears to be.
>
> > > Oh please! Don't tell me that you see a significant difference
> > > between the phrase "minimum strcutral threshold requirements" and
> > > "level of minimum structural threshold requirements"?
>
> > I do.
> > Adding the words "level of" means
> > that it is a variable which can be
> > measured.
>
> This is ridiculous weaseling . . .
>
> See the following for my use of the word "level" together with the
> phrase "minimum structural threshold requirements.
But not to give the meaning implied by the phrase.
> I've used it in
> discussions with you directly before - many times. You evidently have
> very selective memory.
>
> http://groups.google.com/group/talk.origins/msg/0893dc44a735853b
>
> Sean Pitmanwww.DetectingDesign.com
Oh, and talking about selective memories, you've been snipping the
difficult question again, Sean.
richardal...@googlemail.com
No Sean. That *doesn't'* support you.
R. Baldwin
"Seanpit" <seanpi...@naturalselection.0catch.com> wrote in message
news:c3a6584c-1892-48e4...@a35g2000prf.googlegroups.com...
I think you are, Sean. You are messy with terminology, and it appears to be
just to keep people from nailing you down. Even within this thread you used:
"level of minimum structural threshold requirements"
"low level of minimum structural complexity"
"levels of functional complexity" or "minimum structural threshold
requirements"
"greater minimum structural threshold requirements"
"higher and higher levels of minimum structural requirements"
These are all DIFFERENT! Yet when you are called on this lack of
consistency, you claim you are consistent. That is dishonest.
Now this may be a shock to you but "X", "level of X", and "levels of X" do
NOT MEAN THE SAME THING! If you only have one definition in mind, then use
ONE BLOODY PHRASE and quit changing it!
R. Baldwin
"level of X" implies a measure on X.
"levels of X", which you also use, implies that X follows a stairstep
function.
R. Baldwin
No, Sean, that does not make sense. You used the word "ratio" without
defining what ratio you are taking, and a distribution is not a number - it
is a probability mass function. You don't seem to be comprehending what a
Poisson probability mass function does. But, as usual, your vague language
makes it impossible to know what you really mean.
>
>> >> given that the events occur at a known average rate
>>
>> > The average distance between targets is known.
>>
>> >> lambda = n/interval, and that the occurance of next event is
>> >> independant
>> >> of
>> >> distance from previous event.
>>
>> > That's right . . .
>>
>> Glad you agree, though above you clearly don't quite get it.
>>
>>
>>
>> >> You have not demonstrated that you have met
>> >> the Poisson assumptions (especially event independance), and you have
>> >> incorrectly described what the Poisson distribution calculates.
>>
>> > The independence concept is only weakly relevant. The location of
>> > targets in sequence space is not completely random. There is a loose
>> > clustering effect. However, this effect is not significant enough to
>> > affect the Poisson estimation to a significant degree.
>>
>> Weaselly bull.
>
> You need to look at BLAST data a bit more carefully.
Why don't you provide YOUR methodology for analyzing BLAST data in a new
thread? That should be interesting.
>
>> > The only way there would be a significant effect is if Howard notion
>> > of all the potentially beneficial targets being clustered in one tiny
>> > corner of sequence/structure space was in fact correct. The actual
>> > distribution is far more random in appearance than Howard and others
>> > in this forum seem to realize.
>>
>> And you know this how? From some misinterpreted abstract of an article
>> that
>> you didn't understand?
>
> If you understand it any better, please do explain your take on what
> the data actually says - i.e., like the data from the paper written by
> Choi and Kim for starters.
>
The Choi and Kim paper did not say what you thought it did.
richardal...@googlemail.com
> On Dec 16, 8:33 pm, Seanpit <seanpitnos...@naturalselection.
>
> make up a new number appears?
>
> >[snip]
I presume that this is a rhetorical question....
RF
richardal...@googlemail.com
It's worth adding that the paper specifically states that it *can't*
show what he asserts that it shows.
RF
Ron O
I've abandoned him.
Sean:
If you look up the Hall EBG junk, just remember that the discussion
that we are talking about predates your 1000aa bullpucky. It may be
over 5 years in the past. It is before gap inflation and is one of
the reasons that you keep denying that you are talking about gaps. It
will be a good chance to look up 50 random posts of mine and seeing if
your assertion about them is bogus or not.;-)
What I'd like to see, but don't have much hope of seeing, is that you
make good on your past claims. They aren't just any claims, they cut
to the heart of what you think that you are doing. Without the
science, and without an alternative you have nothing to argue about.
All that you can do is blow smoke. You realize this. Pretending and
running is bogus to say the least, and the length of time that you
have been pretending and running makes it worse than that. How many
years has it been?
Ron Okimoto
Seanpit
> On Dec 16, 7:17 pm, Seanpit <seanpitnos...@naturalselection.
>
>
>
>
>
> 0catch.com> wrote:
> > On Dec 16, 2:52 pm, Ron O <rokim...@cox.net> wrote:
>
> > > > > You know why there are no examples, because you don't know of any.
>
> > > > And you don't either . . . Not beyond the 1000aa threshold.
>
> > > You are the guy that is claiming that they exist, shouldn't you have
> > > an example? Engage brain and think before responding. Just a little
> > > friendly advice.
>
> > Systems with far greater minimum threshold requirements than 1000
> > fairly specified residues do exist. I've given you several examples -
> > to include the flagellum with its threshold of greater than 10,000
> > fairly specified residues.
>
> 10,000 inflation raises its ugly head once Sean realized that his low
> level specificity was only 380 compared to 1000.
There is no inflation here Ron. The challenge is still at 1000aa
where it has been for many years. You asked for examples of systems
that required a minimum of more than 1000aa and I gave you several
examples. Why are you now trying to mischaracterize my position in
some other way?
> Yes, so what evolutionary scenario are you claiming to have disproved
> by not observing it happening?
I'm just showing a pattern. Evolution happens easily, commonly, and
quickly when minimum structural threshold requirements are few (i.e.,
less than 100 loosely specified residues - to include various forms of
antibiotic resistance, antibody specificity improvements, and the
like). When thresholds are more stringent, involving minimums of a
few hundred fairly specified residues (like lactase, nylonase, lambda
repressors, other single-protein enzymes and the like), evolution is
much less common. And, when minimum structural thresholds move beyond
the 1000aa level, evolution doesn't happen at all.
This phenomenon is a demonstrable fact. What is the reason for this
stalling out effect of the observed evolutionary mechanism in
action?
Well, statistically, evolution should be able to happen very quickly
if novel beneficial systems are only one or two character changes away
from something that already exists within the gene pool. The fact
that very low level functions evolve commonly and rapidly suggests
that all such functions are very close, not to just one, but to many
elements that exist within a large gene pool. That is why evolution is
so common and rapid at this very low level.
The reason why evolution is less common at thresholds requiring
minimums of a few hundred residues can be explained by potentially
beneficial targets being close to far fewer elements within a given
gene pool. Evolution might still be rapid since at this level since
all it takes is a target to be close to at least one element within
the gene pool. But, remove this one element, and evolution will not
happen nearly as rapidly. This feature was clearly demonstrated by
the experiments of Barry Hall in his work with E. coli.
So, what is the reason for the lack of evolution at thresholds that
seem to be only a little bit higher? - i.e., those systems requiring
at least 1000 fairly specified residues? Well, obviously, potential
targets at such levels are not "close" to anything within a given gene
pool. That's why evolution doesn't happen at all at such levels. And,
the odds of any higher-level target actually being close are so remote
as to make evolution beyond the 1000aa threshold statistically
impossible this side of trillions of years of time.
> There may have been 2 billion years of biological evolution before
> there were flagellum. What do you expect to observe?
Two billion years is remotely enough time to evolve any functional
system requiring the minimum structural requirements needed by the
flagellar motility system. Even a trillion years or a trillion
trillion years would be nearly enough time.
> Remember the IDiot problem that they have admitted, that to make this
> type of argument viable you have to discount every possible
> biologically relevant evolutionary scenario. How many have you
> discounted with your observations? None, right? We are talking
> biologically relevant, and such experiments have never been done as
> far as I know.
Yes, they have been done. The conclusion of intelligent design in
science, like anthropology, forensics, and SETI, is based on two
things. The first is that the phenomenon in question could be
manufactured by some process. The second is that no known non-
deliberate force of nature can do the job. Both of these features are
met in the flagellar motility system. Such a system could be
manufactured given a few more years of work with micro-engineering.
However, no known non-deliberate force of nature, not even random
mutation and function-based selection, come remotely close to this
level of functional complexity. This has been demonstrated by
millions of observations and experiments.
> > What doesn't exist are any examples of random mutation and function-
> > based selection producing such a system. These evolutionary examples
> > are what don't exist. The high-level systems themselves most
> > certainly do exist.
>
> What scenario was tested? For the flagellum, what would you even
> select for? How would you start the system evolving? We have clues,
> it looks like you should get some ATPases to work for protein
> transport, and build from there, so who did this experiment. If no
> one has done it, that would be a good reason for not ever observing
> it, along with the fact that it may have taken hundreds of millions of
> years and various functional intermediates that didn't work for
> motility to do it.
Lots of examples of evolution in action are available from nature for
which no specific experiment was set up - lots and lots. Antibiotic
resistance is a common example. The evolution of novel single-protein
enzymes and multi-protein enzymatic pathways is another. Yet, no
examples of higher-level systems have been observed to evolve in
nature or in any laboratory experiment where the resulting novel
system required a minimum of more than 1000 fairly specified residues
working together at the same time (like a flagellar motility system).
You argue that because no specific experiment has been done at this
level that it hasn't been tested and therefore it isn't a valid
scientific position. The same argument could be used to question the
scientific status of your position that the evolutionary mechanism of
random mutation and function-based selection actually did the job at
such high levels. That notion is also not tested much less
demonstrated beyond threshold of a few hundred fairly specified
residues. It doesn't even have a statistical basis. There are no
mathematical/statistical evaluations of the proposed evolutionary
mechanism at such levels published in literature - none whatsoever. It
is therefore not a scientific position by your own criteria. All it is
then is blind faith - nothing more.
> > How you can argue otherwise or act like you don't understand this
> > concept is truly a mystery.
>
> What concept? Your bogus mythical 1000aa threshold that you can't
> even put up an example of?
How can you say this when I just gave you an example of the flagellum
which requires a threshold of over 10,000aa?! Do you still not
understand the concept of a minimum structural threshold? These
thresholds DO exist. Every system has its own threshold minimums.
Some systems have greater minimums than others. And, many systems
have minimums that are in fact far greater than 1000aa.
> Just telling people to look at the
> flagellum tells us squat. What is this
> threshold and what is it made
> of. Use real proteins and show us.
The threshold for the flagellum is made up of real proteins and their
totals of amino acid residues. What is the minimum number of
flagellar parts that are needed before the system will work as a
flagellar motility system? What is the total number of amino acids
needed (all proteins combined)? Please do provide your own estimate.
I've already given you mine.
Sean Pitman
www.DetectingDesign.com
> > > > > You don't even know what a 1000aa threshold is, except to say that you
> > > > > know it when you see it. Why should anyone believe you?
>
> > > > The 1000aa threshold is clearly defined. I really am finding it quite
> > > > difficult to understand your confusion when it comes to this seemingly
> > > > simple and straightforward definition.
>
> > > So, where is the example and the explanation for why you picked those
> > > residues?
>
> > How many times do I have to give you the examples before you
> > remember? Again one example is the flagellum which requires greater
> > than 10,000 specified residues at minimum. There are many other such
> > examples that go well beyond the 1000aa threshold minimum (which, as
> > already noted many times, is not the gap distance).
>
> You can't just point to the flagellum and claim your job is done. You
> are the one claiming some threshold, so you show us what it is. Use
> the flagellum and use the proteins in it and show us that you know
> what you are talking about.
I already have. Take the minimum number of proteins in their most
trimmed down version needed to produce flagellar motility and count
the total number of amino acid residues. What number do you come up
with? Do your own estimate if you think mine is significantly off
base. I'd be most interested to see your own conclusion in this
regard. Do you think you could produce the same type of system with
the same functionality with less than 5,000 specifically coded residue
positions? - or 1000aa? If so, please do show me how . . .
< snip rest >
Sean Pitman
www.DetectingDesign.com
Seanpit
>
> > > So what is your beef, and how does that impact your 1000aa threshold
> > > that is composed of gaps that aren't really gaps, but they don't all
> > > have to be crossed all at one time?
>
> > The 1000aa threshold isn't the gap size. It is the minimum structural
> > requirements. The gap size for this level would be several dozen
> > mutational changes wide - which most certainly would need to be
> > crossed before a novel function at this level could be realized.
>
> We are back to the gaps that aren't gaps. These not gaps are around
> several mutational changes wide, but they aren't gaps, but they are
> part of the 1000aa threshold. So can you put forward one of these
> nongaps? One example?
This paragraph makes no sense. Non-gaps? What's that? It is the
minimum gap distance between something, anything, in a given gene pool
and the next closest potentially beneficial target that is important.
When the target in question requires a minimum of more than 1000
fairly specified residues, the likely minimum number of character
changes/mutations is going to be at least a few dozen. That's the
minimum gap size - a few dozen character changes.
Do you see the difference between threshold size and minimum gap size
now?
> > The deletion of ebg in Hall's second set of experiments is very
> > interesting because after extended observation the lactase function
> > was not evolved. The observation was long enough that Hall got
> > frustrated and said that his ebg negative colony had, "limited
> > evolutionary potential."
>
> Sure you made hay about it, but it didn't mean what you thought did
> it? Gap inflation started once you realized that 3 wouldn't do.
That's not true.
> > Now, nowhere in this exchange did I say it was impossible to cross
> > gaps of just 2 or 3 character differences. I've said otherwise many
> > many times in fact.
>
> "Impossible" is probably the wiggle word here. Do you deny that you
> made the claims about Hall demonstrating that gaps of two or three
> were so unlikely as to be impossible to cross?
Hall made this claim in his own paper. I specifically said that Hall's
assumptions here were mistaken many many times in this forum -
starting years ago when we first starting discussing this experiment
in this forum. Hall was mystified that his colony could cross a gap
of two mutations in a single generation. He was the only to claim
that this gap should have taken hundreds of thousands of years to
cross. I was the one to explain how such a gap could be crossed in
very short order given a colony of a few 100 billion individuals.
Your memory is faulty.
> > > You were wrong. You admit it because you had to go from gaps of 2-3
> > > to your 1000 aa bull pucky.
>
> > You don't get it. The 1000aa is NOT the gap distance. I've always
> > said that small gaps, to include gaps of 2 or 3 or even over a dozen
> > mutational character changes could be crossed in evolutionary time
> > frames. But, the decline in evolvability is exponential in nature.
> > The only way to keep up is to increase the population size and/or
> > mutation rate. The problem here is that population sizes are limited
> > by limited environments and mutation rates are limited by their
> > lethality beyond a certain rate. So, at steady state population
> > sizes, evolutionary progress stalls out exponentially as the minimum
> > gap sizes increase - and they do in fact increase in a linear manner
> > as the structural threshold sizes increase.
>
> Not a gap but made up of a bunch of gaps.
No - a single gap between what is and the next closest potentially
beneficial steppingstone.
> So it isn't "impossible"
> but it "stalls out."
It is never impossible - just very very unlikely this side of
trillions of years of time.
< snip >
> > Ever hear of an antigen epitope? It is the epitope that is important
> > here, not the total size of the antigen. The epitope is small. It is
> > obtained from processing by antigen presenting cells. This epitope is
> > what the binding site of the antibody binds to. The residues that
> > interact with the antigen epitope are also limited to about 20 or so
> > residues. So, the binding function of the immunoglobulin is indeed
> > based on just 20 or so residues. Other functions of the antibody are
> > what require the larger antibody size. The binding function however,
> > by itself, is quite simple.
>
> I've already commented on this in another post. This is so loopy of
> an argument that you should be embarassed for even thinking it up.
>
> The functional antibody isn't just based on 20 residues. That may be
> the usual epitope, but it isn't the only type of epitope and amino
> acids don't zip up like DNA it takes a whole lot more amino acids to
> form a pocket to specifically recognize those 20 residues.
You weren't talking about the whole function of the antibody - just
about the binding function of the antibody. The antibody has many more
functional elements to it than antibody binding. However, the binding
function alone is very simple. It only needs about 20aa to be
effective.
> Not only
> that but there have to be more
> amino acids that have to support the
> binding site.
The extra amino acids in this case are needed to provide structure for
the binding site so that conformational changes can be realized and
effectively used to signal the immune cell. These extra functional
features do indeed require extra amino acid residues. The binding
function alone, however, does not require these extra amino acids.
This particular functional aspect is very simple.
> They just don't hang in the air and their strucutral
> backup has a lot to do with the shape of the binding site. Do you
> deny that amino acids on opposite ends of the protein can influence
> binding?
>
> Concentrating on the size of the target was stupid even if it gave you
> a number that you could live with to justify your continued ignorance
> of the subject. It is the protein that does the binding that is the
> most important. Just think for a second. You know that abzymes are
> created during this process. You know that beta linkage catalysis can
> be evolved and you claim that the minimum for this is 380. That is
> far from 20 and lactose is only two sugar molecules instead of a
> string of 20 amino acids. If it takes 380 amino acid residues to bind
> and hydrolyze lactose, how many residues does it take to bind 20 amino
> acids in such a way as to specifically recognize those 20 in that
> order?
Binding is simple. Adding enzymatic activity or recognition of
binding on top of that is the addition of extra functionality that
does indeed increase the level of functional complexity. Abzymes with
lactase activity do in fact require over 380aa residues. That is
because enzymatic activity requires more than simple binding to
achieve effective hydrolysis of lactose.
This should be obvious to you. Come on now . . .
> > > Take it to the bank, you lost it with this argument, it doesn't even
> > > make sense to talk about the antigen when it is the antibody that is
> > > the important agent.
>
> > Sure it does. The antibody cannot recognize more of an epitope than
> > will fit in its limited binding site.
>
> And how much more than the binding site is needed for enzymatic
> activity.
Again, enzymatic activity is more complex than mere binding.
Effective enzymatic activity requires both specific binding and the
ability to hydrolyze specific bonds in the other molecule. That means
that the overall function is not as simple as the binding function
alone. The binding function, by itself, is very simple.
> Did you know that binding is just one aspect of enzymatic
> activity.
That's what makes enzymatic activity more complex than simple binding.
> Did you know that amino acids don't just zip up like DNA
> and that the binding pocket is a lot larger than 20 amino acids?
The reason why the binding pocket is larger than 20aa is because the
antibody, as an integral part of the immune system need to do a lot
more than just bind to the antigen epitope.
> Did
> you consider the support structure needed to get that binding pocket
> in that conformation? If lactase function requires 380, how could an
> abzyme with the same activity require fewer? even though it is only
> binding two sugar molecules instead of 20 amino acids? It isn't the
> size of the epitope that matters. Get a clue.
Get a clue? Who doesn't seem to understand the basic concept that
enzymatic activity and antibody activity is far more complex than
simple binding? - that the binding function, by itself, is very very
simple?
Seanpit
wrote:
>
> > October of 2006:
> > "And, this number of potentially non-beneficial options increases
> > exponentially when higher and higher levels of minimum structural
> > requirements are considered."
>
> > Need I go on? Who is being "dishonest" here?
>
> just to keep people from nailing you down. Even within this thread you used:
>
> "level of minimum structural threshold requirements"
> "low level of minimum structural complexity"
> "levels of functional complexity" or "minimum structural threshold
> requirements"
> "greater minimum structural threshold requirements"
> "higher and higher levels of minimum structural requirements"
>
> These are all DIFFERENT! Yet when you are called on this lack of
> consistency, you claim you are consistent. That is dishonest.
>
> Now this may be a shock to you but "X", "level of X", and "levels of X" do
> NOT MEAN THE SAME THING! If you only have one definition in mind, then use
> ONE BLOODY PHRASE and quit changing it!
You seem to have difficulty reading within context. I've made it very
clear over a very long time that I'm talking about different
functional systems having different minimum structural threshold
requirements. I've made it clear over a long time that I also refer
to these differences as "threshold minimums" or functional "levels".
I'm really at a loss, after all the time I've put into clarifying this
concept that anyone should be remotely confused.
Nothing is changing here. The concept is exactly the same as it has
been for years. It is very simple. Different systems have different
minimum structural requirements. They are therefore on what I call
different "levels" of minimum or irreducible complexity. If the part
requirement is reduce below this minimum threshold, the function in
question cannot be realized at all - not even a little bit.
There, is that really so hard to understand? Is that terminology
confusing for you still? If so, please do speak up and I'll try to
make it even more clear for you . . .
Sean Pitman
www.DetectingDesign.com
hersheyh
0catch.com> wrote:
> On Dec 15, 8:54 am, _Arthur <Arth...@sympatico.ca> wrote:
>
>
>
> > To chop down this saga to the bare outline,
> > some scientists, Yockey and Sauer, observed that the cytochrome
> > proteins of many species differed significantly (albeit with the same
> > basic structure), for the same overall functionality, and so their
> > genes differed.
>
> > Sean Pitt took that "1000 aa" divergence, and promulgated that *ANY*
> > sequence giving a biologically useful protein would be separated by
> > at least a 300 point mutations "gap" from *ANY* other protein of any
> > different function/usefulness.
>
> > Now the Pitt Man concedes that his 1000 number was a "rough estimate*,
> > which should make is 300 gap even rougher.
>
> > Of course, Pitts steadfastly refuses to correct his website, despite
> > the great many biological, mathematical, and logical absurdities
> > pointed to him, some of which he even very, very, very grudgingly half-
> > admitted, after years of handwaving, thread-pounding and
> > grandstanding.
>
> > Did I get any of it right ? Roughly ?
>
> Not even close. The differences in sequences that have a given
> function, like CytoC functionality, forms the degree of specificity
> that this function requires to work within a certain minimum size
> requirement. This specificity flexibility does not represent the gap
> distance. The gap distance is the distance between any sequence that
> can produce a beneficial function, like CytoC, and the next closest
> beneficial sequence that can produce a novel beneficial function that
> has the same or greater minimum structural threshold requirements.
>
> You equate a gap of 300 residue differences with specificity
> flexibility.
Actually, for a 1000 aa protein with the same level of sequence
specificity as cytochrome c, just like cytochrome c itself, the size
of "average gap size" and "specificity flexibility" (if that is
defined as the % of aa's that would be fully flexible, free to mutate
to any other aa and assuming that the aa's not free were completely
invariant) produce exactly the same number because, whatever the
actual nature of the "specificity flexibility, all such constructions
must produce the same number of different cyt c sequences. That means
that it is you, Sean, that equates the "average gap size" with
"specificity flexibility".
> That is a fundamental error. The gap distance is the
> distance between the edge of one beneficial island cluster of
> sequences and the next closest edge of beneficial island sequences in
> sequence/structure space.
That, however, is not the number you call "average gap distance". The
fundamental error is numerological GIGO on your part.
>
> Do you see the distinction? - Because it is fundamentally important to
> understanding the problem of expanding gaps with increasing minimum
> threshold requirements.
Sean, with each of your larger "minimum threshold requirements",
whether that be 1000 aa or 10,000 aa, it is perfectly clear that you
are *assuming* that there can be NO POSSIBLE functional intermediate.
That is assuming that all 1000 or 10,000 aa's in the end structure
arrived there by a mechanism of complete randomness with no
intermediate functional intermediate.
Somehow you think a mechanism of evolution involves the random
assembly of the *entire* structure all at once. AKA, the "747 in a
tornado" strawman version of evolution. Unless you can actually
demonstrate that there is no possible intermediates that have
*function* of some sort (not necessarily the *terminal* function you
ascribe as "the" teleologic function, which you seem to assume is the
only function that can possibly exist as an intermediate function),
you have no right to call the eubacterial flagella a system that meets
your requirement of having a "minimum threshold requirement" of 10,000
aa's and *assume* that it must form without a single functional
intermediate step.
>
> Sean Pitmanwww.DetectingDesign.com
Seanpit
wrote:
>
> > The fixed interval is the fixed distance of X character changes. The
> > "events" are the finding of target sequenes within this fixed
> > distance. How likely are targets to be found within a particular
> > of targets and it most certainly does closely follow a Poisson
> > distribution.
>
> No, Sean, that does not make sense. You used the word "ratio" without
> defining what ratio you are taking,
I've defined the ratio many times as the ratio of potential targets to
non-targets.
> and a distribution is not a number - it
> is a probability mass function.
That's right. The probability mass function of potential targets in
sequence space at higher and higher levels does in fact approximate a
fairly random distribution.
> You don't seem to be comprehending what a
> Poisson probability mass function does.
Yes, I do.
> But, as usual, your vague language
> makes it impossible to know what you really mean.
Not at all . . .
> >> > The independence concept is only weakly relevant. The location of
> >> > targets in sequence space is not completely random. There is a loose
> >> > clustering effect. However, this effect is not significant enough to
> >> > affect the Poisson estimation to a significant degree.
>
> >> Weaselly bull.
>
> > You need to look at BLAST data a bit more carefully.
>
> Why don't you provide YOUR methodology
> for analyzing BLAST data in a new
> thread? That should be interesting.
Why don't you present your evidence that the potential targets are
significantly clustered in one tiny corner of sequence space?
> >> > The only way there would be a significant effect is if Howard notion
> >> > of all the potentially beneficial targets being clustered in one tiny
> >> > corner of sequence/structure space was in fact correct. The actual
> >> > distribution is far more random in appearance than Howard and others
> >> > in this forum seem to realize.
>
> >> And you know this how? From some misinterpreted abstract of an article
> >> that you didn't understand?
>
> > If you understand it any better, please do explain your take on what
> > the data actually says - i.e., like the data from the paper written by
> > Choi and Kim for starters.
>
> The Choi and Kim paper did not say what you thought it did.
Oh yeah? The Choi and Kim paper clearly shows an increase in the
average distance between proteins in sequence/structure space with
increasing size requirements. It also shows that the loose clustering
of smaller protein systems becomes more and more loose at higher and
higher levels. And, this is still all dealing with very simple single-
protein systems. Just think what happens with multiprotein systems
like flagellar motility systems?! Your wishful thinking is just
that . . . Prove me wrong if you think otherwise. Prove that the
average gap distances do not increase with increasing minimum
structural requirements.
Sean Pitman
www.DetectingDesign.com
Seanpit
>
> > Given a trillion potential beneficial functions with
> > these same minimum size and specificity requirements, the average gap
> > distance would be about 26 residue differences between islands and the
> > minimum likely gap distance would probably be around 4 or 5 for a
> > large population (along a Poisson distribution).
>
> Sean, in your appendix, the number for "average gap size" as *you*
> calculated "average gap size" would not be 26 for cytochrome c. For
> cytochrome c, it would have been 30.7, which is the 20th root of the
> inverse of 10e-40. Do you just make up numbers whenever the urge to
> make up a new number appears?
You forget that the average gap size is affected by population size
and the number of potential targets. Depending upon your population
size and whatever number of potential targets you think most likely,
the average gap distance will change. In my example here, I didn't
use the same population size and I have you even more benefit of the
doubt regarding the number of potential targets.
Sean Pitman
www.DetectingDesign.com
Seanpit
> On Dec 16, 10:46 pm, Seanpit <seanpitnos...@naturalselection.
>
> 0catch.com> wrote:
> > On Dec 16, 2:15 pm, richardalanforr...@googlemail.com wrote:
>
> > > > Minimum structural threshold requirements indicates a variable all by
> > > > itself.
>
> > > No it doesn't. It implies a threshold level. That does not have to be
> > > a variable. It could be fixed.
Not in the context of the many times I've pointed out to you that
different functions having different minimums. I've also pointed to
you directly that I refer to these different minimum threshold
requirements that do in fact exist between different types of
functional systems as "levels". I've made this very clear to you
directly many times in the past. How you can then argue that I never
clarified this concept is beyond me.
> > See:
>
> >http://groups.google.com/group/talk.origins/msg/0893dc44a735853b
>
> No Sean. That *doesn't'* support you.
Yes, it does. It shows were I've explained this concept to you
directly before a number of times.
Seanpit
>
> > See the following for my use of the word "level" together with the
> > phrase "minimum structural threshold requirements.
>
> But not to give the meaning implied by the phrase.
You have extremely poor reading comprehension.This is what I wrote to
you directly back in February of this year:
"As I have explained to you many times before, more novel
functions can and do evolve once one has been acquired. It is just
that none of the new ones will have greater minimum structural
threshold requirements than the old ones. They will all be at the
same low level of minimum structural complexity or lower - not higher
than the 1000aa threshold."
http://groups.google.com/group/talk.origins/msg/617d1ff6acf21dc5
Tell me Richard, where is the basis for your confusion given this
context of what I've said to you directly many times before?
richardal...@googlemail.com
As others have pointed out, your terminology is so hopelessly confused
that it is hard to know what you have or haven't said. Mind you, your
habit of post hoc rationalisation when you make a mistake and
pretending that you meant something different from what you said
causes even more confusion.
Oh, and your STILL snipping the difficult questions, Sean.
How many times have you snipped this particular one? I think it's six
times so far.
mur...@tntech.edu
[...]
> You have extremely poor reading comprehension. [...[
Then please answer his question:
-----------
Who do you think has the intellectual capability to evaluate your
"theory"?
After all, it's clear that nobody on this forum thinks it's anything
more than a load of twaddle, so why waste your time and effort in
posting the same stuff over and over again?
----------------
>
> Tell me Richard, where is the basis for your confusion [...]
Then please answer his question:
-----------
Who do you think has the intellectual capability to evaluate your
"theory"?
After all, it's clear that nobody on this forum thinks it's anything
more than a load of twaddle, so why waste your time and effort in
posting the same stuff over and over again?
----------------
--DPM
>
> Sean Pitmanwww.DetectingDesign.com
hersheyh
Whoa. Just a moment here. Are you actually saying that you can
produce immunoglobins with *modification* of a few sites and transform
it from an immunoglobin that binds an entirely different site?
Wouldn't the "minimum structural threshold" be the *entire* length of
both the heavy and light chains? That is the "minimum structural
threshold" if you consistently apply your rule of "smallest known
protein that performs a function, which in this case is binding, for
the purpose of targeting for destruction, of epitope A. Now, it seems
that, in the case of immunoglobins, the "size" of the "minimum
structural threshold" is not the entire "system" (it is when you
discuss flagella and other examples), but a mere subset of sequences
within the proteins. So, Sean, how do you define "minimum structural
threshold"? Moreover, what we have here is a *change in function* of
*part* of a protein that completely changes its target. And
antibodies can, seemingly, be found to bind pretty much any possible
epitope, despite your claim that there are so many different epitopes
that it should take "trillions of years" to do so. And why aren't
there many, many, many, many completely functionless antibodies that
cannot bind to *any* epitope even if you say the "size" of the
sequence that is involved is 'only' 100 aa long? After all the ratio
of "potential beneficial vs. non-beneficial" is 10e-40 for sequences
100 aa long, right? Even if that is only a "rough" estimate, there
should be a lot of totally functionless antibodies (remember that
humans only have around 10^14 cells). After all, antibodies have to
bind reasonably tightly or they won't "function".
> When thresholds are more stringent, involving minimums of a
> few hundred fairly specified residues (like lactase, nylonase, lambda
> repressors, other single-protein enzymes and the like), evolution is
> much less common.
So you keep asserting. Yet it is quite clear that there is no
correlation between overall size and the number of mutational steps
required for lactase or nylonase. And I am quite sure that one could
arrange a series of selective steps involving small changes in target
sequence and selection for binding that target which would, at the end
of the co-evolutionary process, have resulted in a drastic change in
the sequence that the lambda repressor binds to. Each step in this co-
evolutionary process would have the same "function" as the original.
> And, when minimum structural thresholds move beyond
> the 1000aa level, evolution doesn't happen at all.
Aren't you assuming the entire process has to occur without any
possibility for a functional (but not necessarily the teleologic
function you assign) intermediate? Why would any evolutionary
theorist assume that? What they look for are proteins with similar
structure (sequence is sometimes a poorer stand-in) and related
function that can be *modified* to the new or modified function. Why
would they claim that this starting point must be so far away that it
is the same as assembling the entire new protein from scratch, like
assembling a 747 in a tornado?
>
> This phenomenon is a demonstrable fact.
Which phenomenon? We all agree that *if* the closest (not average)
functional sequence is a large number of completely functionless steps
away from a different or modified function, then the evolutionary
steps are unlikely to the extent that it won't always happen. But we,
but not you, point out that *when* evolution happens, it doesn't
happen that way. Do you understand the difference between your
theoretical "if" and the observed "when"?
> What is the reason for this
> stalling out effect of the observed evolutionary mechanism in
> action?
>
> Well, statistically, evolution should be able to happen very quickly
> if novel beneficial systems are only one or two character changes away
> from something that already exists within the gene pool.
And indeed that is *when* we see evolution.
> The fact
> that very low level functions evolve commonly and rapidly suggests
> that all such functions are very close, not to just one, but to many
> elements that exist within a large gene pool.
What is a "low level" function? Not a "minimum threshold" or any
other measure of total size. Total size does not define function.
Isn't that your claim wrt antibodies? Is a "high level" function a
function that has many subfunctions? How do you define "function"?
How do you define subfunction? Has a protein that has gained a
carboxy end form another protein that allows it to now interact with
two independent 'subsystems' based on this added subfunction gained a
"low level" function or a "high level" function?
> That is why evolution is
> so common and rapid at this very low level.
I don't see evolution as being more common and rapid among small
peptides. In fact, the rate of evolution of cytochrome c and histone
4B are among the slowest rates of evolution that we have observed.
OTOH, fibrinogen peptide has one of the fastest possible rates of
evolutionary change. Do you have any evidence to support your claim?
Or is it that, just like larger proteins, the ability to produce a new
or novel or modified *function* is dependent solely on the "actual
minimum gap size" available in actual organismal genomes. That is,
the evolution of an antibiotic resistant ribosome (a system of over
10,000 aa residues in size) can (and does) involve an "actual minimum
gap" of 1 aa change. The evolution of a 16 aa protein in an organism
that lacks any 16 aa protein sequence closer than 15 aa away from the
specified protein will not happen. The total size of the sequence and
whether that is a "minimum threshold level" is irrelevant. The
'level' of the end 'function' is irrelevant. Everything you say is
important is irrelevant. All that matters is the "actual minimum gap
size" for that particular process.
> The reason why evolution is less common at thresholds requiring
> minimums of a few hundred residues can be explained by potentially
> beneficial targets being close to far fewer elements within a given
> gene pool. Evolution might still be rapid since at this level since
> all it takes is a target to be close to at least one element within
> the gene pool. But, remove this one element, and evolution will not
> happen nearly as rapidly. This feature was clearly demonstrated by
> the experiments of Barry Hall in his work with E. coli.
Yes. What matters is the size of the "actual minimum gap". And that
number cannot be calculated from "average gap size" (nor even "likely
minimum gap size") even if your measurement of "average gap size"
really measured "average gap size".
> So, what is the reason for the lack of evolution at thresholds that
> seem to be only a little bit higher? - i.e., those systems requiring
> at least 1000 fairly specified residues?
It isn't the size of the product that is important. Unless you are
assuming that the way that evolutionary biologists say a 1000 aa
system is made is by completely random assembly from scratch with no
intermediate sequences of utility. They don't.
You mean by a mechanism that involves starting from some 1000 aa
system that is arbitrarily distant from the end product (your
calculation of "average gap size" does not do so). With no possible
pathway that involves functional intermediates.
Two. You need a subsytem that *functions* as a rotatable pore with
(probably) a whip. You need a subsystem that works as a "motor".
Both independently evolved rotary flagella are composed of subsystem
parts that performed these functions before the two subfunctions were
linked (by a short chain of mutational steps) to generate the function
of "motorized pore rotation".
> What is the total number of amino acids
> needed (all proteins combined)?
Irrelevant. All that matters is the length of the chain of mutations
that link the two previously existing *functional* subsystems (that
evolved for those functions) that produces the new *function* of motor-
generated rotation. I have presented a *model* system that shows that
some level of the end function could arise in as few as one mutational
step.
> Please do provide your own estimate.
> I've already given you mine.
>
> Sean Pitmanwww.DetectingDesign.com
>
>
>
> > > > > > You don't even know what a 1000aa threshold is, except to say that you
> > > > > > know it when you see it. Why should anyone believe you?
>
> > > > > The 1000aa threshold is clearly defined. I really am finding it quite
> > > > > difficult to understand your confusion when it comes to this seemingly
> > > > > simple and straightforward definition.
>
> > > > So, where is the example and the explanation for why you picked those
> > > > residues?
>
> > > How many times do I have to give you the examples before you
> > > remember? Again one example is the flagellum which requires greater
> > > than 10,000 specified residues at minimum. There are many other such
> > > examples that go well beyond the 1000aa threshold minimum (which, as
> > > already noted many times, is not the gap distance).
>
> > You can't just point to the flagellum and claim your job is done. You
> > are the one claiming some threshold, so you show us what it is. Use
> > the flagellum and use the proteins in it and show us that you know
> > what you are talking about.
>
> I already have. Take the minimum number of proteins in their most
> trimmed down version needed to produce flagellar motility and count
> the total number of amino acid residues. What number do you come up
> with?
And why do you think determining that number is relevant? What does
this number tell you if essentially all of the proteins are already
parts of functioning systems and only mutations needed to link
together these pre-existing systems is required to generate the
*function* of powered rotary motion? The only way that number would
have relevance is if the entire system could have no function
whatsoever unless it has the function of 'powered rotary motion'.
That is, if you could not start from pre-existing functional
subsystems, but had to build the *entire* system by random assembly
like a "747 in a tornado". Otherwise, such a calculation is worthless
GIGO.
> Do your own estimate if you think mine is significantly off
> base. I'd be most interested to see your own conclusion in this
> regard. Do you think you could produce the same type of system with
> the same functionality with less than 5,000 specifically coded residue
> positions? - or 1000aa? If so, please do show me how . . .
Why should I bother to produce a meaningless (wrt real evolution)
number?
>
> < snip rest >
>
> Sean Pitmanwww.DetectingDesign.com
Stuart
Its rather amusing, the parallels between this thread and the
expanding Earth thread.
The expanding earthers..
1. Pull numbers out of the thin air
2. Invent new terminology as they go along with vague definitons so
that you will never understand it.
3. Claim nobody familiar with established paradigms can understand it.
4. Point out the existing "assumptions" in the prevailing paradigm
while ignoring the ones they make.
psuedo-scientists of a feather flock together....
Stuart
John Stockwell
0catch.com> wrote:
> On Dec 11, 10:18 am, hersheyh <hershe...@yahoo.com> wrote:
>
> > Here is Sean's description of the calculation of "average gap
> > size"
>
> *****
>
> > "Well, first we have to calculate the likely gap size. Using an
> > average between the calculations of Yockey and Sauer, the ratio of
> > potential beneficial vs. non-beneficial for 100aa systems is about
> > 1e-40. This creates a ratio for a 1,000aa system of about
> > 1e-40^(1000/100) = 1e-400. So, the average gap size between
> > potentially beneficial sequences at this level would be about 308
> > residue differences - i.e., 20^308 = 1e400."
>
> *****
>
>
>
> > I have often accused Sean of numerology, or essentially of pulling
> > numbers out of his arse and claiming that they represent things that
> > they, in fact, do not represent. Take a look at the above calculation
> > which is the mathematical basis of just about all his sequence
> > arguments. You might think, unless you *actually* do some thinking,
> > that Sean is performing some hard-nosed mathematical analysis here
> > rather than merely manipulating numbers and assigning "scientific-
> > sounding" names to them. Thus, unless you actually look at what the
> > numbers mean, you might be fooled into thinking that Sean actually is
> > calculating "likely gap size" or "average gap size" by doing the above
> > mathematical manipulations of numbers, which are assumed to be based
> > on hard evidence, and that he is accurately telling us what the
> > numbers mean. Nothing could be further from the truth. In fact, I
> > think that the first person Sean 'fooled' by his mathematical
> > manipulations was Sean himself. He was fooled because he did not
> > actually think about what he was doing and let the fact that the
> > numbers he got seemed to "prove his point" cloud his thinking to the
> > point that he actually does think that the ratio he calculated was
> > "potential beneficial vs. non-beneficial", that there is his
> > exponential relationship between length and the above ratio, and that
> > he has calculated the "average gap size". Sean probably does think
> > that his numerology is a "mathematical proof" of the impossibility of
> > evolution.
>
> > Let me summarize the problems I see with the above calculation:
>
> > 1) The calculations of Yockey and Sauer do NOT give us the ratio of
> > "potential beneficial vs. non-benecial" sequences for 100aa systems.
> > They give us an estimate of the number of sequences that have
> > cytochrome c function and related sequence divided by the total number
> > of sequences at 100 aa level.
>
> Yockey's estimate is in fact dealing specifically with CytoC
> functionality. I've noted this several times on my website myself.
> Sauer and Olsen are dealing with lambda repressor functionality, not
> CytoC. What these and other similar estimates indicate is that a
> certain degree of required sequence specificity produces a certain
> ratio of sequences in sequence space that could produce some useful
> degree of functionality of the type in question.
>
> Obviously, this doesn't tell us how many potentially beneficial
> sequences of all kinds exist in 100aa sequence space. But, what it
> does do is illustrate a pattern of an exponentially declining ratio of
> beneficial vs. non-beneficial with increasing size and/or specificity
> requirements. In order to avoid this exponential increase, one would
> have to hypothesize that the number of different potentially
> beneficial sequences/structures increases at pretty much the same rate
> as the size of sequence/structure space increases with each increase
> in minimum structural threshold requirements. That notion simply
> isn't tenable to anyone who approaches this problem with a remotely
> candid mind. It isn't true in any language/information system that we
> know of and it isn't true for genetically based information systems
> either.
>
> That's the point. There is a clear pattern of exponentially
> increasing non-beneficial sequences relative to each increase in
> potentially beneficial sequences with each increase in minimum
> structural threshold requirements. This point should be so obvious as
> to be beyond argument.
>
>
>
> > Mathematically, if we call the
> > estimated number of sequences that have cytochrome c function C, and T
> > is the totality of sequence space for 100 aa long peptides, then the
> > equation that Sean is claiming represents as "potential beneficial vs.
> > non-beneficial" ratio is actually C/T. T can be mathematically
> > estimated as 20^le, where le is the length of the sequence, since
> > there are 20 possible amino acids at each position. Converting to
> > base 10, this would be 10^le^log20. Log 20 is about 1.3. So the
> > ratio, R(100), of what Sean calls "potential beneficial vs. non-
> > beneficial" sequences is really the equation:
>
> > R(le) = C/10^le^1.3 = 10^40 when le = 100.
>
> > Moreover, this relationship (the ratio of sequences with cytochrome c
> > function and sequence to all possible 100 aa long sequences) has ONLY
> > been determined (well, estimated) for the case where le = 100.
>
> That's because 100aa is fairly close to the minimum structural
> threshold requirement needed for CytoC. You can't produce a
> beneficial degree of CytoC functionality with just 50aa - no matter
> how they are arranged relative to each other.
>
> > 2) Problems with calling the numerator "potential beneficial
> > sequences". It should, in fact, be obvious to anyone that C, the
> > number of sequences that have cytochrome c-like function and sequence,
> > is NOT all possible "potential beneficial sequences". I think even
> > Sean sees that.
>
> Of course it's not. But, statistically, this point is pretty much
> irrelevant to the main issue. Again, given that one is looking for
> targets that require a minimum of at least 100aa with an equivalent
> degree of specificity as that required by CytoC functionality, the
> actual ratio of beneficial vs. non-beneficial is not going to be
> significantly different from the ratio of CytoC to non-CytoC in
> sequence/structure space.
>
> I've tried to explain this concept to you before, but I'll try again.
> Either you say that there is absolutely no way to get any idea at all
> as to the likely ratio of total targets to non-targets (which removes
> the scientific basis for your proposed mechanism by the way) or you
> try to use the available evidence to get as best as an idea as you
> can.
>
> One approach to determining the most likely number of potentially
> beneficial targets at a given threshold level is to consider how many
> total novel beneficial systems are in existence today in all living
> things at a given level. This number can be roughly known and it is
> not more than a trillion for the 100aa level. Even if it was 10
> trillion, it wouldn't make any significant difference. The reason for
> this is that 10 trillion uniquely different 100aa systems with the
> minimum degree of specificity of CytoC would take up no more than 1 in
> 1e27 sequences in sequence space. That is still a very tiny fraction
> of the available space of just over 1e130 sequences. The potential
> targets are still vastly outnumbered by non-beneficial sequences.
>
> This ratio only gets exponentially worse with increasing minimums.
> Keep the specificity requirement the same and raise the number of
> amino acid residues, the ratio drops exponentially. Keep the number
> of residues the same and raise the specificity, the ratio drops
> exponentially. That's the whole point.
>
> > But is it even *possible* to calculate the number of "potential
> > beneficial sequences"? The answer is 'sort of', but only in a squishy
> > soft way that allows one to say that "potential beneficial sequences"
> > are a heck of a lot more frequent than cytochrome c-like sequences.
>
> There might appear to be a "heck of a lot more" beneficial targets
> than CytoC targets - - at first approximation. But, when you compare
> this "heck of a lot" to the total size of sequence space, it is a tiny
> little spec of dust in the bottom of the bucket. It isn't remotely
> close, relative to the vast horde of non-beneficial sequences, to
> being a "heck of a lot".
>
> You have to starting thinking in relative terms here.
>
> > First we have the problem that "beneficial" is not an inherent feature
> > of a sequence, but a conditional one. Even the cytochrome c sequence
> > is not 'beneficial' in every situation or organism (think anaerobes).
> > And "potential" is important, since we cannot assume that a sequence
> > is useless until or unless we have a context to put it in.
>
> The context is any living thing in any particular environment. Take
> your pick. Whatever context you choose will have the same problem.
> The ratios are not going to be significantly different regardless of
> context. Bringing up the context is therefore irrelevant - a red
> herring.
>
> > But, if you understand how proteins actually work to produce
> > 'function' in organisms, we can think about this problem in a more
> > reasoned way than Sean has (i.e., by not assuming that the number of
> > cytochrome c-like sequences is a good stand-in for all "potential
> > beneficial sequences"). Proteins 'function' by providing surfaces
> > with affinity for biologically relevant structures or parts of
> > biologically relevant structures. Enzymes work because proteins bind
> > the substrates and products of the reaction less well than the
> > stressed intermediate. [Which is also why compounds related to
> > substrates or products but with equal or higher affinity for the
> > protein surface can be toxins or antibiotics.] Proteins also form
> > multimers and complex structures because of the affinity of small
> > patches of aa's on each protein for each other. Which biological
> > structure an amino acid sequence has affinity for determines its
> > 'function'. Moreover, because most biologically relevant structures
> > are small, the number of aa's involved in any particular binding
> > feature is also small. That is, the 'function' of proteins is a
> > consequence of the binding of epitopes by a small number of aa's.
> > That, of course, is the reason we can say, for example, that the
> > sequence of FliG involved in binding to
>
> ...
>
> read more >>
Sean,
Time and again, we have read your arguments about these
mysterious "gaps", what, for several years now? If you are so
competent and so certain, why don't you write
it up and publish the result in a reputable journal? Indeed, it would
go a long way to show us that you aren't merely the relgion drunk
fundy crank blowhard that we all think you are.
Indeed, while you are at it, if if is so easy to make these gaps, it
should be a snap to generate a bunch of them in fast replicating
species, such as bacteria.
Go ahead. Do some real science. Show us all up. Be a man. For
once.
-John
R. Baldwin
> On Dec 17, 12:34 am, "R. Baldwin" <res0k...@nozirevBACKWARDS.net>
> wrote:
>>
>> > The fixed interval is the fixed distance of X character changes. The
>> > "events" are the finding of target sequenes within this fixed
>> > distance. How likely are targets to be found within a particular
>> > distance is most certainly a product of the ratio and distribution
>> > of targets and it most certainly does closely follow a Poisson
>> > distribution.
>>
>> No, Sean, that does not make sense. You used the word "ratio" without
>> defining what ratio you are taking,
>
> I've defined the ratio many times as the ratio of potential targets to
> non-targets.
Wonderful. The last few posts, however, had to do with what a Poisson
Distribution *means*, so that is rather irrelavent, isn't it?
>
>> and a distribution is not a number - it
>> is a probability mass function.
>
> That's right. The probability mass function of potential targets in
> sequence space at higher and higher levels does in fact approximate a
> fairly random distribution.
>
>> You don't seem to be comprehending what a
>> Poisson probability mass function does.
>
> Yes, I do.
Your words indicate otherwise.
>
>> But, as usual, your vague language
>> makes it impossible to know what you really mean.
>
> Not at all . . .
I'm not the only one who finds so, Sean.
>
>> >> > The independence concept is only weakly relevant. The location of
>> >> > targets in sequence space is not completely random. There is a
>> >> > loose
>> >> > clustering effect. However, this effect is not significant enough
>> >> > to
>> >> > affect the Poisson estimation to a significant degree.
>>
>> >> Weaselly bull.
>>
>> > You need to look at BLAST data a bit more carefully.
>>
>> Why don't you provide YOUR methodology
>> for analyzing BLAST data in a new
>> thread? That should be interesting.
>
> Why don't you present your evidence that the potential targets are
> significantly clustered in one tiny corner of sequence space?
This is *your* theory, bub. It is *you* that needs to do the presenting. I
don't think you've got any evidence.
>
>> >> > The only way there would be a significant effect is if Howard notion
>> >> > of all the potentially beneficial targets being clustered in one
>> >> > tiny
>> >> > corner of sequence/structure space was in fact correct. The actual
>> >> > distribution is far more random in appearance than Howard and others
>> >> > in this forum seem to realize.
>>
>> >> And you know this how? From some misinterpreted abstract of an article
>> >> that you didn't understand?
>>
>> > If you understand it any better, please do explain your take on what
>> > the data actually says - i.e., like the data from the paper written by
>> > Choi and Kim for starters.
>>
>> The Choi and Kim paper did not say what you thought it did.
>
> Oh yeah? The Choi and Kim paper clearly shows an increase in the
> average distance between proteins in sequence/structure space with
> increasing size requirements. It also shows that the loose clustering
> of smaller protein systems becomes more and more loose at higher and
> higher levels. And, this is still all dealing with very simple single-
> protein systems. Just think what happens with multiprotein systems
> like flagellar motility systems?! Your wishful thinking is just
> that . . . Prove me wrong if you think otherwise. Prove that the
> average gap distances do not increase with increasing minimum
> structural requirements.
>
Why do you think Choi and Kim said their research showed the opposite of
what you did, Sean?
R. Baldwin
If there is one thing you have not been, it is clear.
>
> Nothing is changing here. The concept is exactly the same as it has
> been for years. It is very simple. Different systems have different
> minimum structural requirements. They are therefore on what I call
> different "levels" of minimum or irreducible complexity. If the part
> requirement is reduce below this minimum threshold, the function in
> question cannot be realized at all - not even a little bit.
>
> There, is that really so hard to understand? Is that terminology
> confusing for you still? If so, please do speak up and I'll try to
> make it even more clear for you . . .
>
Try this basic rule: one term, one definition. Don't change the terms, don't
change the definitions.
richardal...@googlemail.com
As has been pointed out, the way in which you use the phrase does not
necessarily imply the same meaning.
Scientists are very precise about how they use terms to avoid
ambiguity.
You should try learning some science, Sean.
Oh, and by the way, and talking about selective memories, you've been
hersheyh
Just a reminder of what Sean says is *the* way to calculate "average
gap size". We will now compare that with what he now claims he meant
to say. And follow up by showing a 'surprising' relationship.
***********
> "Well, first we have to calculate the likely gap size. Using an
> average between the calculations of Yockey and Sauer, the ratio of
> potential beneficial vs. non-beneficial for 100aa systems is about
> 1e-40. This creates a ratio for a 1,000aa system of about
> 1e-40^(1000/100) = 1e-400. So, the average gap size between
> potentially beneficial sequences at this level would be about 308
> residue differences - i.e., 20^308 = 1e400."
************
First, it was pointed out that the ratio he presents is NOT, in fact,
the ratio of "potential beneficial vs. non beneficial for 100aa
systems". Instead, it is an estimate of the number of sequences that
have cytochrome c or (not even "and") lamda repressor (both *specific*
100aa systems) functions divided by the number of all possible 100aa
sequences. Sean then said that the ratio was only meant to be "only a
rough estimate" or only meant to "show a pattern". I presume that
Sean has *already* corrected his wording to accurately describe what
this ratio *really* means. Whenever Sean tries to use the term
"average gap size" or "minimum likely gap size" or "ratio of
beneficial to no-beneficial", I will ask him how this value is
determined until he gets it right.
Sean also said he only meant to include to compare 100aa and 1000aa
systems that are at the same "specified threshold level" and that have
the same level of "functional complexity". Now, it is hard as hell to
get an operationally meaningful definition of these terms. But,
"specified threshold level" *seems* to mean that the protein (or part
of a protein/peptide or multiple proteins) presented is the smallest
known protein sequence(s) that has the *specified* function that Sean
is discussing.
I am willing to state that Sean does think that cytochrome c's roughly
100aa's represents its "threshold level" below which one cannot have
the "cytochrome c" function (even if a smaller portion of the protein
still binds to heme). Further, even though we now have cytochrome c's
"minimum threshold level" (namely 100aa's), there is still the fact
that cytochrome c's "functional complexity" has not be described.
But you will notice that not one of these qualifications of what Sean
is really measuring can be found in the above description of the ratio
he gives. Instead, Sean says the ratio is, that is "equals" or "the
same as" the ratio of "potential beneficial vs. non-beneficial for
100aa systems". Not 100aa systems with the "threshold level" and
"functional complexity" of cytochrome c. Yet he still gets the ratio
by dividing by total sequence space for *all* 100aa long sequences.
The best way to describe what Sean means by "functional complexity"
would be that it appears to represent the degree of "sequence
specificity" required to have a protein with the *specified*
function. Basically, many, actually most, of the aa sites in
cytochrome c (or pretty much any protein or protein system) are
"partially variant" and can change to some partial set of other aa's
without drastically affecting the specified *function*. A few sites
must have one and only one possible aa (is invariant) and other, again
typically a few, sites are "freely variable" and can be any aa.
So how to get a measure of "sequence specificity"? The answer is easy
once you know how many sequences exist that have the specified
function. In the case of cytochrome c/lambda repressor (or the
average protein composed of these two) which Sean obviously think do
meet the "minimum threshold level" of 100aa's, we, in fact, do know
the number of sequences that have those specified functions. It is
simply found by multiplying the ratio he gives us by total sequence
space for a 100aa long sequence. In the case of these two proteins,
the ratio 10^e-40 is actually 20^30.7/20^100. The base twenty is
used because that is the number of possible aa's at each site. That
means that the total number of functional cytochome c sequences is
20^30.7. That would be the total number of sequences regardless of
the distribution of aa sites among the three possibilities: partially
variable, freely variable, and invariant. Thus we can choose a simple
model among all possible models that are mathematically identical.
Namely, we can eliminate the category of partially variable, and ask
how many aa's in this 100 aa long sequence must (on average) be
effectively *invariant* and how many must (on average) be effectively
*freely variant* to produce the number of sequences that have
cytochrome c activity. This, of course, would also hold for any 100
aa protein that has the same level of "functional complexity" as
cytochrome c.
Since the invariant sites do not change, it is only the freely
variable sites that contribute to the larger number of sequences that
do have cytochrome c activity. The answer, then, obviously is 30.7
(the power to which 20 must be raised to generate the estimated number
of cytochrome c seqeunces) or 30.7% of the aa sites. This number is
the number of *freely variable* aa residues and is the estimate of
"sequence non-specificty". The number that represents "level of
functional complexity" or "level of sequence specificity" is 69.3 or
69.3% of the 100 aa's.
Now what Sean does is go through a series of calculations that appear
to be doing something, but really isn't doing anything. First, Sean
has already added the qualification that his putative 1000 aa sequence
is at the "minimum threshold". That is, no protein smaller than 1000
aa's can perform whatever function Sean thinks this protein performs.
He also demands that this sequence have the *same level* of
"functional complexity" or "sequence specificity" as cytochrome c.
Which means, of course, that he assumes that this protein also has,
using the argument above, 69.3% of its aa sites being effectively
invariant and 30.7% of its aa sites freely variant.
So how does he calculate the "average gap size", the putative number
of aa's that must change to go from the (nearest, average, maximally
distant) site to one that has the specified function? By taking the
20th root of the putative size of the number of sequences that have
that function (assuming both that 1000 is the 'minimum threshold'
*and* that this function has the same level of "sequence specificity"
as cytochrome c). That number, for a 1000 long protein, is, cue the
trumpets, 307. I.e., 30.7% of 1000. I.e. "the estimate of
effectively freely variant" aa sites in this 1000 long sequence with
the same "functional complexity" or "sequence specificity
requirements" as cytochrome c.
But without even going to the 1000 aa "minimum threshold level", it is
clear that the "average gap size" of cytochrome c is identical to the
"level of sequence non-specificity" when you have aa sequences that
both are at the same "minimum threshold level" and both have the same
level of "functional complexity" or "sequence specificity
requirements". For cytochrome c itself, the "average gap size" would
be 30.7.
Can Sean explain this interesting mathematical identity I have
'discovered' between "average gap size" and a measure of "level of
sequence non-specificity"? Why would "average gap size" increase as
the "level of sequence specificity/functional complexity" decreases,
which is what this identity implies? Why does Sean claim that
"average gap size" increases exponentially, when it is clear that the
increase is linear and basically a set % of total sequence "minimum
threshold size" for a given "level of sequence specificity"? Curious
minds want to know.
Ron O
0catch.com> wrote:
> On Dec 16, 8:18 pm, Ron O <rokim...@cox.net> wrote:
>
>
>
> > > > So what is your beef, and how does that impact your 1000aa threshold
> > > > that is composed of gaps that aren't really gaps, but they don't all
> > > > have to be crossed all at one time?
>
> > > The 1000aa threshold isn't the gap size. It is the minimum structural
> > > requirements. The gap size for this level would be several dozen
> > > mutational changes wide - which most certainly would need to be
> > > crossed before a novel function at this level could be realized.
>
> > We are back to the gaps that aren't gaps. These not gaps are around
> > several mutational changes wide, but they aren't gaps, but they are
> > part of the 1000aa threshold. So can you put forward one of these
> > nongaps? One example?
>
> This paragraph makes no sense. Non-gaps? What's that? It is the
> minimum gap distance between something, anything, in a given gene pool
> and the next closest potentially beneficial target that is important.
> When the target in question requires a minimum of more than 1000
> fairly specified residues, the likely minimum number of character
> changes/mutations is going to be at least a few dozen. That's the
> minimum gap size - a few dozen character changes.
No one claims that your arguments really make sense.
>
> Do you see the difference between threshold size and minimum gap size
> now?
A threshold made up of a lot of little gaps, but they aren't gaps,
because you know that if they are gaps your argument is bogus because
there is nothing prohibiting crossing the gaps. You can't even
establish that the gaps existed when the parts were coming together.
This seems to be winding down and Sean is preparing to run and pretend
again. He didn't even bother responding to most of the stuff.
Run and pretend.
What is your alternative to common descent and the evidence to back it
up that is just as good as what science has?
What is the science of intelligent design that you would have taught
to school kids?
Sean made these claims, but he has run from them for years. They
aren't just any claims, they are the heart of any argument that he
wants to make. If there is no science to the scam that he is running,
what is he arguing about? If he has no alternative, what could he
possibly accomplish by just obfuscating the issue and blow a lot of
smoke with no scientific content supporting his own claims?
Sean even knows he's lying. When confronted by his previous
obfuscation gap scam, his claim wasn't that he never ran such a scam,
but that, that scam hadn't been his argument for at least 5 years.
Heck, he's been running from his common descent alternative claim for
longer than that (could it be 6 or 7 years?).
I guess Sean can add this thread to the "rare" posts where I didn't
kick his butt when I addressed the issues. Just the junk he snips
should tell anyone, whose butt is getting kicked in this thread.
Sean admits to running this 1000aa threshold scam for years, and in
all that time he has never been able to demonstrate that it exists.
When asked for an example he claims a lot of bull-pucky about "fairly
specified" residues, but he never shows us what one looks like. He
only claims that they are there. He points to the flagellum, but that
is all. He knows that if he does point them out all they will be are
examples of his old gap argument. He knows that he can't even verify
that these gaps existed when the flagellum was evolving. He would
need a crystal ball that would tell him the protein sequences of the
progenitor proteins. We even know what proteins are related to most
of the ones that got incorporated into the flagellum, but related
isn't the same thing as knowing the sequence. We are dealing with 2
billion years of molecular evolution and Sean knows that all extant
flagellar proteins have very different sequences than they had then.
We know this, just by looking at other flagellum and observing how
much they have changed since the first one was evolved.
If Sean wants this argument to fly, he can provide an example that
anyone can evaluate. No one can just take his word that the threshold
exists, he has to demonstrate that it ever did.
Sean knows that he is sunk on this, but it is about the only ploy that
the creationists can still muster. It is just the old creationist
probability scam. It fails for the same reason that it has always
failed. Even the creationists can not calculate the probabilities.
Just get Sean to try. He can look up other efforts by his fellow scam
artists, and what would he come up with?
Sean just thinks that a 1000 whatevers is big enough to snow people in
the probability argument, but he even concedes that this threshold is
made up of a lot of smaller gaps (that he will claim are not gaps, but
then put a number on it like 12 or two dozen for the type of gap that
he is talking about), and that all the gaps do not have to come
together at one time. Yet, his argument depends on the 1000 meaning
something, but he can't demonstrate that it does. He can't even show
us one of the gaps that existed when he needs it to exist.
Sean there are now 5 invisible pink elephants that aren't pink
standing next to you. Tell me how tall the middle sized one is,
provide your evidence, and I am sure that I can answer your question
about the mythical 1000 aa threshold.
Sean, you need to demonstrate that the threshold exists. Take a
couple of the flagellar tail proteins and tell us what the gaps were
before they came together. Don't claim fairly specified, but provide
the residues and the reasons that you believe that the gaps existed.
This is where we get the "I am not talking about gaps" argument. So
what is the threshold? How can we argue about it if you can't tell us
what it is?
Recall my first response?
Are you going to run and pretend? If you can't make good on your
claims, what good is running a bogus obfuscation scam?
Take the epitope argument off you web page. It is bogus and you know
it by now. The size of the epitope does not have any bearing on how
many amino acids are required to bind it in the antibody protein.
Just the structural amino acids needed to get the binding site in the
right conformation is quite a number. Amino acids don't just float
around in solution and magically take the correct orientation. It
fooled you because it gave you a number that you could lie to yourself
about. There is no reason to lie to anyone else. Get it off your web
page.
Ron Okimoto
SNIP:
hersheyh
> On Dec 17, 11:35 am, Seanpit <seanpitnos...@naturalselection.
>
>
>
> 0catch.com> wrote:
> > On Dec 16, 8:18 pm, Ron O <rokim...@cox.net> wrote:
>
> > > > > So what is your beef, and how does that impact your 1000aa threshold
> > > > > that is composed of gaps that aren't really gaps, but they don't all
> > > > > have to be crossed all at one time?
>
> > > > The 1000aa threshold isn't the gap size. It is the minimum structural
> > > > requirements. The gap size for this level would be several dozen
> > > > mutational changes wide - which most certainly would need to be
> > > > crossed before a novel function at this level could be realized.
>
> > > We are back to the gaps that aren't gaps. These not gaps are around
> > > several mutational changes wide, but they aren't gaps, but they are
> > > part of the 1000aa threshold. So can you put forward one of these
> > > nongaps? One example?
>
> > This paragraph makes no sense. Non-gaps? What's that? It is the
> > minimum gap distance between something, anything, in a given gene pool
> > and the next closest potentially beneficial target that is important.
> > When the target in question requires a minimum of more than 1000
> > fairly specified residues, the likely minimum number of character
> > changes/mutations is going to be at least a few dozen. That's the
> > minimum gap size - a few dozen character changes.
>
> No one claims that your arguments really make sense.
Well, no one but Sean and people who know even less than he does.
The best I have gotten from Sean is that "minimum threshold size" is
the size of the smallest known sequence ("sequence" is either a
stretch of amino acids within a protein, e.g., immunoglobins, the
entire sequence of a protein, e.g., cytochrome c or lactase, or the
sum of the sequences of multiple proteins, e.g, the eubacterial
flagella) that performs a "specified function" (which means whatever
single function that Sean assigns). Except, of course, when it
doesn't mean that (the archaean flagella is smaller than the
eubacterial and many of the proteins of the eubacterial flagella are
dispensible in one or another eubacteria). Needless to say, Sean
applies whatever definition best suits his current needs.
But he is stuck with cytochrome c's "minimum threshold size" being 100
aa's because he uses the inverse of the ratio of sequences that have
cytochrome c function to total sequence space to calculate "average
gap size" for a protein with the "minimum threshold size" and
"sequence specificity/functional level" that has the "specified
function" of cytochrome c.
The "average gap size" is the number from which he hand-waves whatever
"likely minimum gap size" he wants or needs at the moment. And the
"average gap size" he calculates for cytochrome c is then simply
linearly increased with the size of other hypothetical proteins with
the often unstated (until pressed) assumptions of both a "minimum
threshold size" of, say, 1000aa and the same "functional level/
sequence specificity" as cytochrome c.
But Sean's claim that the 20th root of the number of 'non-cytochrome c
function' sequences per 'cytochrome c functional' sequence (this is
what the inverse of the ratio he uses means) really is "average gap
size" rather than merely the 20th root of an inverse ratio that tells
us how many "non-cytochrome c function" sequences there are per
"cytochrome c function" sequence has not been justified. Just because
he can come up with a smaller population and take the 20th root of it
doesn't mean that that number is "average gap size" in aa residues.
In any case, even *if* the 20th root of the population of sequences
that lack cyt c function per sequence that has cyt c funtion had
empirical meaning related to "gap size", this would only be the
"average gap size" for proteins that meet the assumptions of having a
"minimum threshold size" and "functional level of complexity/sequence
specificity" like that of cyt c. It would have no relationship to
"potential beneficial vs non-beneficial" sequences.
So, unless he can convince me otherwise, Sean has simply calculated an
arbitrary and irrelevant number that has no empirical meaning and
simply *named* that number "average gap size". That is GIGO
numerology. And, of course, every other term that depends on his
actually having a number that represents "average gap size".
[Note: in my last post, I made some math errors. If anyone other than
Sean is interested, I will be happy to post a correction. I wasn't
going to unless Sean actually is willing to defend his calculation of
"average gap size" as actually representing "average gap size",
because it is obvious to most readers that Sean engages in GIGO
numerology. It has not passed beneath my notice that the question of
what his "average gap size" really means is the one comment of my
initial challenge that he has not bothered to respond to.]
Seanpit
< snip >
> Why does Sean claim that
> "average gap size" increases exponentially, when it is clear that the
> increase is linear and basically a set % of total sequence "minimum
> threshold size" for a given "level of sequence specificity"? Curious
> minds want to know.
Come on Howard. Why build this strawman? You know it is a
misrepresentation because I've told you many many many many times that
both the average and minimum gap distances increase in a *linear*
manner with increasing minimum structural threshold requirements. Of
course the increase is linear! How many times have I pointed that out
to you directly?
Think about it for just a minute Howard. What happens to the average
number of random mutations needed to cross a minimum gap distance that
has just experiences a linear increase from what it was before? The
number of mutational steps increases exponentially. That's where the
exponential element comes into play. The gap distances increase
linearly while the random walk/selection distances increase
exponentially. Do you see the difference now?
Try not to forget this time.
Sean Pitman
www.DetectingDesign.com
hersheyh
[snip Sean's irrelevancies]
Sean, the number you call "average gap size" is nothing but 1) the
20th root of a population of sequences that is the population that one
gets when one divides the number of sequences in total sequence space
of a given size by the number of sequences that have a single
specified function that have that "minimum threshold size". That is,
if sequences that have the single specified function you named (e.g.,
cytochrome c) were not clustered in sequence space, but randomly
distributed, the population you calculated by inverting the Yockey
ratio would be the average number of sequences that lack the single
specified function per sequence that does. 2) Because the ratio of
Yockey is dependent upon the "sequence specificity" of the protein,
the number you call "average gap size" is also the number of
effectively completely invariant aa sites if you assumed that the
protein in question had only completely invariant aa sites and
completely free to vary sites (i.e., no sites in which only some aa
substitutions are allowed).
Neither description of the number you called "average gap size" has
anything to do with "average" or "gap size". In fact, the second
description is the largest possible gap size (the only possible
starting point for a "gap size" that is the effective (mathematical
equivalent of the) size of all the invariant sequences in a protein is
some sequence that doesn't have *any* of its effectively invariant
sites having the correct aa's (the sites that are effectively
completely free to vary are irrelevant to function). Putting back the
possibility of partially variant sites would not change that
conclusion. It would just make it harder to demonstrate.
The first description directly contradicts your idea of sequence space
arranged so that sequences that are similar in both sequence and,
especially, function are clustered.
IOW, your "average gap size" is nothing but bullshit GIGO numerology.
And that means that all your hand-waving numbers that follow,
especially "likely minimum gap size" is equally garbage.
Seanpit
> On Dec 21, 4:17 pm, Seanpit <seanpitnos...@naturalselection.
>
> 0catch.com> wrote:
> > On Dec 18, 7:51 am, hersheyh <hershe...@yahoo.com> wrote:
>
> [snipSean'sirrelevancies]
>
That's the minimum possible gap size Howard - not the average.
> the
> 20th root of a population of sequences that is the population that one
> gets when one divides the number of sequences in total sequence space
> of a given size by the number of sequences that have a single
> specified function that have that "minimum threshold size". That is,
> if sequences that have the single specified function you named (e.g.,
> cytochrome c) were not clustered in sequence space, but randomly
> distributed, the population you calculated by inverting the Yockey
> ratio would be the average number of sequences that lack the single
> specified function per sequence that does. 2) Because the ratio of
> Yockey is dependent upon the "sequence specificity" of the protein,
> the number you call "average gap size" is also the number of
> effectively completely invariant aa sites if you assumed that the
> protein in question had only completely invariant aa sites and
> completely free to vary sites (i.e., no sites in which only some aa
> substitutions are allowed).
The concept of the effective number of invariant residue positions is
helpful here. It sums up the total of partially variant sites.
Beyond this, the references to Yockey, Sauer, Olsen, etc., are only
meant to illustrate what specificity does to the ratio. It helps to
give a rough idea as to the likely total number of beneficial targets
in sequence space. Other papers, like Choi and Kim, help to give a
rough idea as to what happens to the distribution of targets with
increasing minimum structural threshold requirements - i.e., they do
not stay clustered together in one tiny corner of sequence space.
Rather, they spread out across the entire distance of sequence space -
from one side to the other. What clustering there is, becomes less
and less clustered. Both the average and minimum distances are in
fact increased, in a linear manner, with increasing structural
threshold requirements. That's a fact. You yourself recognize this
linear relationship (although you snipped it in this post), but don't
seem to grasp the exponential implications this linear relationship
has to random walk/selection as populations search within sequence
space.
> Neither description of the number you called "average gap size" has
> anything to do with "average" or "gap size".
Yes, it does. The average gap size is the average distance between a
given target and all other targets in sequence/structure space.
That's a simple concept and calculation as long as one has a fair idea
of how many targets exist within a given sequence/structure space.
> In fact, the second
> description is the largest possible gap size (the only possible
> starting point for a "gap size" that is the effective (mathematical
> equivalent of the) size of all the invariant sequences in a protein is
> some sequence that doesn't have *any* of its effectively invariant
> sites having the correct aa's (the sites that are effectively
> completely free to vary are irrelevant to function).
The largest possible gap size is the maximum size of the sequence
itself. The average gap size is smaller and the minimum likely gap
distance is smaller still. They are all different - kind of like how
the mean, median, and mode don't measure the same "averages".
> Putting back the
> possibility of partially variant sites would not change that
> conclusion. It would just make it harder to demonstrate.
The concept of partially variant sites has not been removed. It has
just been summarized in order to estimate the total number of targets
given a certain degree of partial variance of a certain number of
residue positions.
> The first description directly contradicts your idea of sequence space
> arranged so that sequences that are similar in both sequence and,
> especially, function are clustered.
This comment makes no sense. Sequences that are very similar in both
sequence and function are usually clustered pretty close together.
> IOW, your "average gap size" is nothing but bullshit GIGO numerology.
> And that means that all your hand-waving numbers that follow,
> especially "likely minimum gap size" is equally garbage.
This is nonsense. The average gap size is a simple mathematical
calculation. And, it does indeed play a role in identifying the most
likely minimum gap distance. At higher and higher minimum structural
threshold requirements, this likely minimum gap distance is NOT the
minimum possible gap distance like you suggest. That notion of yours
is especially inane. It could only be true if potential targets
remained just as clustered at higher levels as they were at lower
levels. All the evidence that we have strongly suggests that this
notion of yours just isn't true. Clustering demonstrably becomes less
and less clustered at higher and higher levels. That's a clear and
undeniable fact Howard. I'm not sure why you don't seem to be able to
accept that reality?
Sean Pitman
www.DetectingDesign.com
hersheyh
0catch.com> wrote:
> On Dec 21, 4:58 pm, hersheyh <hershe...@yahoo.com> wrote:
>
> > On Dec 21, 4:17 pm, Seanpit <seanpitnos...@naturalselection.
>
> > 0catch.com> wrote:
> > > On Dec 18, 7:51 am, hersheyh <hershe...@yahoo.com> wrote:
>
> > [snipSean'sirrelevancies]
>
> > Sean, the number you call "average gap size" is nothing but 1.
>
> That's the minimum possible gap size Howard - not the average.
If you were assembling a 100 aa protein from scratch, that would be
true. But you claim that is not what your mechanism proposes.
> > the
> > 20th root of a population of sequences that is the population that one
> > gets when one divides the number of sequences in total sequence space
> > of a given size by the number of sequences that have a single
> > specified function that have that "minimum threshold size". That is,
> > if sequences that have the single specified function you named (e.g.,
> > cytochrome c) were not clustered in sequence space, but randomly
> > distributed, the population you calculated by inverting the Yockey
> > ratio would be the average number of sequences that lack the single
> > specified function per sequence that does. 2) Because the ratio of
> > Yockey is dependent upon the "sequence specificity" of the protein,
> > the number you call "average gap size" is also the number of
> > effectively completely invariant aa sites if you assumed that the
> > protein in question had only completely invariant aa sites and
> > completely free to vary sites (i.e., no sites in which only some aa
> > substitutions are allowed).
>
> The concept of the effective number of invariant residue positions is
> helpful here. It sums up the total of partially variant sites.
It only simplifies the math and clarifies the thinking by taking one
'reality' among many that lead to the same number.
> Beyond this, the references to Yockey, Sauer, Olsen, etc., are only
> meant to illustrate what specificity does to the ratio.
That is NOT what your appendix says. Your appendix says, explicitly,
that you have calculated the "average gap size" and that the Yockey
ratio is the ratio of "potential beneficial vs. non-beneficial"
sequences. [Again, it IS the ratio of the number of sequences that
have a single *specified* function to total sequence space for all
sequences. You have NO idea at all about even the ratio of "known
beneficial to non-beneficial" sequences, much less "potential". And
the fact is that beneficial and non-beneficial are highly contingent
terms. Almost any protein sequence that can form a specific structure
*part* of the time probably can interact with some biological material
with the possibility of being "beneficial" under some circumstance.]
> It helps to
> give a rough idea as to the likely total number of beneficial targets
> in sequence space.
Not if you think that the number of invariant sites required for
cytochrome c function is both typical and that no other sequence but
those that have cytochrome c function can have any possible function
at all.
> Other papers, like Choi and Kim, help to give a
> rough idea as to what happens to the distribution of targets with
> increasing minimum structural threshold requirements - i.e., they do
> not stay clustered together in one tiny corner of sequence space.
> Rather, they spread out across the entire distance of sequence space -
> from one side to the other. What clustering there is, becomes less
> and less clustered.
Eye-balling a figure and imposing *your* and only *your*
interpretation on it when even the authors claim otherwise is called
bullshitting.
> Both the average and minimum distances are in
> fact increased, in a linear manner, with increasing structural
> threshold requirements.
Well duh. Your "average gap size" is nothing but a measure of
sequence specificity. It is, in fact, merely the % of a protein that
is "invariant" if only "invariant" and "freely variant" sites are
present. So if you increase "structural threshold requirements" [aka
sequence specificity] by 20 aa sites, the average gap size will also
increase by 20 aa sites. If you increase "structural threshold
requirements by 20%, the "average gap size will increase by 20%.
Identity works that way.]
> That's a fact. You yourself recognize this
> linear relationship (although you snipped it in this post), but don't
> seem to grasp the exponential implications this linear relationship
> has to random walk/selection as populations search within sequence
> space.
Evolution does not work by assembling sequences at random from scratch
or from some sequence that differs from the end sequence at each and
every invariant site. Models that propose this are GIGO "747 in a
tornado" models. But, as I keep saying, that is your model.
>
> > Neither description of the number you called "average gap size" has
> > anything to do with "average" or "gap size".
>
> Yes, it does. The average gap size is the average distance between a
> given target and all other targets in sequence/structure space.
A target *sequence* or a target *function* or a target *structure*? I
know that is what you *claim* is "average gap size". But the number
you calculate and call "average gap size" is the estimate of the
number of invariant sites in cytochrome c, which is a *specified*
function. Taken literally, your statement that "The average gap size
is the average distance between a given target and all other targets
in sequence/structure space." implies that the gap size is the empty
space between one sequence and another. It also implies that
sequences that have the cytochrome c are not "clustered" in sequence
space, but are randomly scattered around.
> That's a simple concept and calculation as long as one has a fair idea
> of how many targets exist within a given sequence/structure space.
Is that targets
> > In fact, the second
> > description is the largest possible gap size (the only possible
> > starting point for a "gap size" that is the effective (mathematical
> > equivalent of the) size of all the invariant sequences in a protein is
> > some sequence that doesn't have *any* of its effectively invariant
> > sites having the correct aa's (the sites that are effectively
> > completely free to vary are irrelevant to function).
>
> The largest possible gap size is the maximum size of the sequence
> itself.
Only for a sequence in which each and every aa site must be absolutely
invariant.
> The average gap size is smaller
Your *math* says that this number is *all* the effective number of
invariant sites in a protein with the *specified function*. For a
protein in which each site is invariant, the average gap size would be
the entire size of the protein. Your math does not say some vague
"smaller" number. It claims to have calculated *the* average gap
size. And the number calculated is *all* the effectively invariant
sites for sequences that have *the* *single* *specified* function.
The number of freely variable sites (be they 70%, 80%, or 99.99999% of
the length) don't change the "average gap size". Average gap size is
the same thing as sequence specificity.
> and the minimum likely gap
> distance is smaller still.
Minimum likely gap distance is a bull shit number that you wave
around. It is uncalculated.
> They are all different - kind of like how
> the mean, median, and mode don't measure the same "averages".
Is this supposed to make your non-calculation calculation of something
you fallaciously call "average gap size" somehow more real?
>
> > Putting back the
> > possibility of partially variant sites would not change that
> > conclusion. It would just make it harder to demonstrate.
>
> The concept of partially variant sites has not been removed. It has
> just been summarized in order to estimate the total number of targets
> given a certain degree of partial variance of a certain number of
> residue positions.
Is the above supposed to mean something? I introduced the idea of
removing partially variant size in order to give physical meaning to
the number you claim is "average gap size". Otherwise, the number
would not have any empirical reality and would be nothing but an
abstract number (the 20th root of an inverse ratio).
> > The first description directly contradicts your idea of sequence space
> > arranged so that sequences that are similar in both sequence and,
> > especially, function are clustered.
>
> This comment makes no sense. Sequences that are very similar in both
> sequence and function are usually clustered pretty close together.
Yes. And that means that sequences with structures similar to (and
convertable to) the ones that have the *specified function* reside
nearby. And many of these sequences will have potential beneficial
sequences that are subfunctions of the *specified function*. IOW,
even you are admitting that sequences that lack the *specified
function* (whatever other "potential beneficial functions" or
"potential beneficial subfunctionalities" they have) are NOT randomly
distributed in sequence space, but are *specifically* clustered
together.
This, of course, means that a model of evolution *like the
mathematical model you present* which involves complete randomness of
sequences has no empirical reality. It is pure GIGO math, even if you
could present an "average gap size".
>
> > IOW, your "average gap size" is nothing but bullshit GIGO numerology.
> > And that means that all your hand-waving numbers that follow,
> > especially "likely minimum gap size" is equally garbage.
>
> This is nonsense. The average gap size is a simple mathematical
> calculation.
One that does not produce anything close to something that could be
called "average gap size". What you claim is "average gap size" is
nothing but the total number of effectively invariant sites in a
*single* *specified* function. That number is not "average" and is
not "gap size" even in a completely randomized sequence space. Much
less in a sequence space where similar structures/sequences/
functionalities are clustered.
> And, it does indeed play a role in identifying the most
> likely minimum gap distance.
Not unless you can actually calculate "average gap size" rather than
merely bullshit your way to a number you claim is "average gap size".
Sean, the number you calculate, the 20th root of the inverse of the
ratio of sequences that have a *single* *specified* function to those
that lack that *single* *specific* function (*total sequence space for
a protein of that size being a fair substitute of the latter number),
if it has any real world meaning is as a measure of sequence
specificity (the effective number of invariant sites). That is NOT
"gap size" unless one ASSUMES that the starting sequence does not have
a match for any of the x invariant sites that the end sequence must
have. It certainly is not "average" anything.
> At higher and higher minimum structural
> threshold requirements, this likely minimum gap distance is NOT the
> minimum possible gap distance like you suggest. That notion of yours
> is especially inane. It could only be true if potential targets
> remained just as clustered at higher levels as they were at lower
> levels.
All that is required for the smaller numbers to be acheived is that
the "island" with the *single specified* function be surrounded by
similar sequences that have or could have had *potential*
functionality (although not the end specified function) in a non-
random way. Your argument claims that the sequences that do not have
the *specified* function must be randomly distributed in the "ocean"
of sequences. That is an explicit denial of the possibility of
sequences with subfunctions having any possible utility.
> All the evidence that we have strongly suggests that this
> notion of yours just isn't true. Clustering demonstrably becomes less
> and less clustered at higher and higher levels. That's a clear and
> undeniable fact Howard.
No. It is NOT an undeniable fact. It is bullshit. The sequences
that would surround an island at any "minimum threshold size" would
likely have very similar sequence and structure and would likely have
some if not most of the subfunctionality of the sequences that meet
the functional criteria you specified as "the" function. Such
sequences would likely have at least the potential of being functional
in their own right. Not every organism will have a protein in the
penumbra of the island. If not, then that island will not appear. If
so, then it can.
Again, proteins, at any level of "minimum threshold size" and
"sequence specificity", are NOT assembled randomly by chance alone.
They are *modified* from pre-existing sequences that have actual
functional utility but can be modified to different or modified
functionality.
hersheyh
Yes. I understand quite well that the numbers you calculate and claim
to *be* "average gap size" are NOT "average gap size", but only a hand-
waving approximation of something you derived from numbers available
to you that meet your real and only criteria: Being large enough to
seem to be "impossible" for evolution yet small enough so you don't
look completely foolish given actual examples of the evolution of new
'functions'.
These real examples, as would be predicted by the *real* theory of
evolution, arise by modification of pre-existing functional proteins
rather than by the strawman mechanism that starts a search (on
average) from some sequence that differs from the end *single
specified* function at each and every one of the aa's in the
'invariant' sites. [Aka, a modified "747 in a tornado" model of
evolution.]
Your pseudo-science quasi-math starts with a whole series of bogus
assumptions: 1) You assume that the number of 'potentially functional
sequences' in total sequence space for a protein of 100 aa in length
is identical to the number of sequences that have modern cytochrome c
function. You even admit that you are doing just this. [How you can
claim this assumption with a straight face, I don't know.] 2) You
assume that *all* the sequences that lack modern cytochrome c function
have no 'function' at all, actual or potential. [Again, how you can
claim that with a straight face, I don't know.] 3) You assume that
cytochrome c is a typical protein wrt its degree of "sequence
specificity". [We know this is not the case.] 4) You assume that
dividing total sequence space for a protein this size by sequences
that have the single specified function (cytochrome c) gives us a
number that has biological meaning wrt the *distribution* of sequences
in total sequence space. [The only model for which this would be the
case would be one in which cytochrome c sequences are randomly
distributed in total sequence space. Otherwise this ratio is only a
number that represents how many non-cytochrome c sequences there are
per cytochrome c sequence, but without any implications for the
distribution of these sequences in sequence space.] 5) You assume
that the 20th root of the above number represents "average gap size"
rather than an estimate of the degree "sequence specificity" by
estimating the 'effective number of invariant aa sites' in cytochrome
c. 6) You assume that larger proteins are merely cytochrome c writ
large.
In each of these assumptions, you have (inadvertantly or on purpose)
chosen the option that gives you the larger number.
Now, if all this were to be stated accurately rather than dishonestly
in Sean's web page, I would have no problem. But if Sean did that,
the flaws in his logic would be obvious to all but the dimmest of
readers. So, instead, Sean's web page claims that he has calculated
"average gap size" and he simply refers readers to counter-arguments
and claims that he is being "fair and balanced" by doing so.
Well, that is 'fair and balanced' only in the journalistic FOX-news
sense, not in the scientific sense. What Sean needs to do, is look
and see if he is accurately describing what his so-called calculation
of "average gap size" means. If he is not, and it is quite clear that
even he can see where it is not, he has to correct his description to
accurately describe what he is doing in these calculations, present
his equations, state his assumptions with clearly defined terms, etc.
If he finds that doing so means that he has to admit that he cannot
calculate "average gap size" with any sort of mathematical rigor, then
he has to say so and not pretend that he can calculate that number.
I will not hesitate to remind Sean of this each and every time he
returns here if I see that his web site is unchanged.
[snip]