Protein Structure Distribution in Sequence Space
Seanpit
> > On Jan 27, 12:38 pm, "Seanpit" <seanpitnos...@naturalselection.
> > Once the edge of this "magnetic field" is
> > reached, the minimum threshold is reached and further refinement
> > toward the maximum potential is no problem. It is the reaching of
> > this minimum threshold that is the problem. The island cluster of
> > potentially beneficial sequences represents the entire reach of the
> > potentially attractive "magnetic field". This entire reach is
> > completely isolated from all other island clusters and magnetic fields
> > at higher levels of functional complexity. The biosystem families you
> > speak of just are remotely clustered in one corner of sequence space
> > like you imagine. This notion of yours is way way off base.
>
> Evidence? I keep having to point out the obvious to you. The
> EVIDENCE (see the PNAS article and others that I have presented you)
> actually shows that the biologically useful proteins that *are*
> present in living organisms (and it doesn't matter whether they
> evolved or were created by the creation fairy) are NOT scattered
> throughout total structure space.
Even with regard to single protein systems, they are NOT clustered in
one tiny corner of sequence space. Look up even single protein maps
and you will see that they cover a wide range of sequence space. They
are not all clustered together like you imagine.
"Roughly speaking, however, distances are randomly distributed. This
means that, although only a small fraction of sequence space yields
uniquely folding sequences, sequence space is occupied nearly
uniformly. No "higher order" clustering (i.e., except the trivial case
of the homologous sequences) is visible.
Erich Bornberg-Bauer, "How Are Model Protein Structures Distributed in
Sequence Space?" Biophysical Journal, Volume 73, November 1997,
2393-2403
http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1181141&blobtype=pdf
So, you see, even at very low structural threshold levels, the
distribution of potentially beneficial structures is widespread and
fairly uniform. The clustering effects that are present at lower
levels rapidly decline at higher and higher threshold levels until the
high-level islands are very remotely separated in sequence space.
Sean Pitman
www.DetectingDesign.com
Perplexed in Peoria
"Seanpit" <seanpi...@naturalselection.0catch.com> wrote in message news:1170613322.7...@v45g2000cwv.googlegroups.com...
Thanks for the link, Sean. I haven't studied it carefully yet, but my
first impression is that they are not looking at (a sample of) real
biological proteins. Instead, they are looking at computer-generated
sets of hypothetical proteins which (based on their structural model)
ought to fold stably and reliably. But I need to read more carefully.
However, I was interested in your parenthetical comment in this:
No "higher order" clustering (i.e., except the trivial case
of the homologous sequences) is visible.
I have mostly responded to your postings as if they were merely a
critique of the evolutionary model rather than positive arguments for
some other model. But I am led to wonder how your favorite model
accounts for all that 'trivial' homology. Take, for example, the
20 or so aminoacyl-tRNA-synthases. Each shows considerable homology
across the entire tree of life (with the trees constructed from any
one of them being consistent with the others, except near the roots).
Furthermore, it seems that they are all homologous with each other -
suggesting that they arose from a common protein ancestor before the
organism-level LUCA. Why would that pattern arise in some other
model besides the evolutionary one?
Furthermore, there are partial homologies between these proteins and
many, many others - especially in the 'nucleotide fold' domain. That
certainly strikes me as a kind of 'clustering'. Do you hypothesize
that this 'nucleotide fold' motif is the only good way to solve the
problem of binding ATP? Isn't it more likely that it is the first
way of binding ATP to be discovered and that it was then copied into
other proteins that needed this fragment of function?
Ron O
>
> So, you see, even at very low structural threshold levels, the
> distribution of potentially beneficial structures is widespread and
> fairly uniform. The clustering effects that are present at lower
> levels rapidly decline at higher and higher threshold levels until the
> high-level islands are very remotely separated in sequence space.
>
>
> - Show quoted text -
My first reading of this paper doesn't seem to indicate any support
for your neutral gaps model being a problem. They are talking about
small peptides that can retain a basic structure with a large number
of "neutral substitutions, but they make no conclusions about the
activity of such structures. It is known from gene families that
basic structure can be retained while function is modified.
So how would studies like this do anything to change the fact that you
don't have a model that you can support in any fashion worth talking
about. What is your alternative explanation for the evolution of
proteins and what is your evidence for it. Recent genome studies
indicate that gene duplication is a lot more frequent than we had been
able to detect before. Gene duplication seems to be a mechanism that
would explain many protein families. Do you have a better
explanation? What is your evidence for your alternative? Claiming
that there is a problem when you don't even have a clue about a
possible viable alternative is pretty bogus don't you think?
Are you ever going to get around to presenting your alternative to
common descent and your evidence for your alternative that you claimed
to have that was better than the current scientific model? You
claimed to have such a model and evidence, so why putz around with
bogus neutral gaps if you have some killer evidence for your beliefs?
Let's see it.
Ron Okimoto
_Arthur
"Empirical fitness landscapes reveal accessible evolutionary paths"
by Frank J. Poelwijk, Daniel J. Kiviet, Daniel M. Weinreich and Sander
J. Tans ?
The paper seems to address your existential fears about hypothetical
barriers.
They studied a particular enzyme which is commonplace in bacteria, and
a "mutant" version, which is 100,000 times more efficient against
antibiotics like penicillin.
The new version of the protein/enzyme happens to be 5 mutations
distant from the canonical version.
Furthermore, the searchers have demonstrated that, in that case,
theres is a mutation pathway where ALL the intermediate forms
conferred increased anti-antibiotic functionality.
So, in that case, we have a smooth pathway to a NEW FUNCTIONALITY, a
100,000-fold improvement in antibiotic resistance.
While you're at it, do comment on the paper in the January issue of
Current Biology: "Continuous molecular evolution of protein-domain
structures by single amino acid changes. " Meier S, Jensen PR, David
CN, Chapman J, Holstein TW, Grzesiek S, Ozbek S. (2007)
Bobby Bryant
"_Arthur" <Art...@sympatico.ca> writes:
> D. Pitman, are you going to comment the new paper in Nature,
> "Empirical fitness landscapes reveal accessible evolutionary paths"
> by Frank J. Poelwijk, Daniel J. Kiviet, Daniel M. Weinreich and Sander
> J. Tans ?
>
> The paper seems to address your existential fears about hypothetical
> barriers.
s/fears/hopes/
--
Bobby Bryant
Reno, Nevada
Remove your hat to reply by e-mail.
Seanpit
> D.Pitman, are you going to comment the new paper in Nature,
> "Empirical fitness landscapes reveal accessible evolutionary paths"
> by Frank J. Poelwijk, Daniel J. Kiviet, Daniel M. Weinreich and Sander
> J. Tans ?
>
> The paper seems to address your existential fears about hypothetical
> barriers.
>
> They studied a particular enzyme which is commonplace in bacteria, and
> a "mutant" version, which is 100,000 times more efficient against
> antibiotics like penicillin.
The barriers I'm talking about are minimum structural threshold
barriers between what exists in a pool of options and the minimum
structural thresholds of novel potentially beneficial functions. Once
you have any type of function to at least some useful level of
functionality, further refinements, even to the point of 100,000 times
the prior efficiency, aren't a problem. The problem is getting the
particular function, like penicillinase, to even a minimum degree of
usefulness.
The penicillinase function, in particular, has never been shown to
evolve de novo - without this function already existing in the gene
pool to at least some degree of useful activity. This is interesting
partly because the penicillinase function does not have a very high
minimum structural threshold requirement (i.e., no more than 350 or so
specified residues at minimum).
> The new version of the protein/enzyme happens to be 5 mutations
> distant from the canonical version.
> Furthermore, the searchers have demonstrated that, in that case,
> theres is a mutation pathway where ALL the intermediate forms
> conferred increased anti-antibiotic functionality.
Yes, there are a large number of these single-step pathways that have
been identified for refinement of the same type of function where the
minimum threshold requirements have already been reached. The immune
system is another fine example of this sort of thing - of improvement
of the antibody binding function over time.
> So, in that case, we have a smooth pathway to a NEW FUNCTIONALITY, a
> 100,000-fold improvement in antibiotic resistance.
That's right - and there are many more examples of this sort of
refinement activity over time. It's a bit more difficult though when
you haven't reached the minimum threshold requirements for the
function in question at all. Gaining this threshold is the issue
here.
> While you're at it, do comment on the paper in the January issue of
> Current Biology: "Continuous molecular evolution of protein-domain
> structures by single amino acid changes. " Meier S, Jensen PR, David
> CN, Chapman J, Holstein TW, Grzesiek S, Ozbek S. (2007)
Tell me, does this paper talk about the observed evolution of even one
novel function that requires a minimum of more than 1000 specifically
arranged amino acid residues? If not, I'm not interested.
Sean Pitman
www.DetectingDesign.com
Seanpit
wrote:
> >http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1181141&blobtyp...
>
> > So, you see, even at very low structural threshold levels, the
> > distribution of potentially beneficial structures is widespread and
> > fairly uniform. The clustering effects that are present at lower
> > levels rapidly decline at higher and higher threshold levels until the
> > high-level islands are very remotely separated in sequence space.
>
> Thanks for the link,Sean. I haven't studied it carefully yet, but my
> first impression is that they are not looking at (a sample of) real
> biological proteins. Instead, they are looking at computer-generated
> sets of hypothetical proteins which (based on their structural model)
> ought to fold stably and reliably. But I need to read more carefully.
>
> However, I was interested in your parenthetical comment in this:
> No "higher order" clustering (i.e., except the trivial case
> of the homologous sequences) is visible.
> I have mostly responded to your postings as if they were merely a
> critique of the evolutionary model rather than positive arguments for
> some other model. But I am led to wonder how your favorite model
> accounts for all that 'trivial' homology. Take, for example, the
> 20 or so aminoacyl-tRNA-synthases. Each shows considerable homology
> across the entire tree of life (with the trees constructed from any
> one of them being consistent with the others, except near the roots).
> Furthermore, it seems that they are all homologous with each other -
> suggesting that they arose from a common protein ancestor before the
> organism-level LUCA. Why would that pattern arise in some other
> model besides the evolutionary one?
What about common design? - Why reinvent the wheel every time a wheel
would work just fine?
> Furthermore, there are partial homologies between these proteins and
> many, many others - especially in the 'nucleotide fold' domain. That
> certainly strikes me as a kind of 'clustering'.
I agree, but it isn't the same thing as the clustering of all types of
protein-based systems into one tiny corner of sequence space. This
limited clustering most certainly produces more closely spaced islands
of beneficial sequences. However, these islands do indeed drift
farther and farther apart as one moves up the ladder of minimum
structural threshold requirements.
> Do you hypothesize
> that this 'nucleotide fold' motif is the only good way to solve the
> problem of binding ATP? Isn't it more likely that it is the first
> way of binding ATP to be discovered and that it was then copied into
> other proteins that needed this fragment of function?
It most certainly isn't the only potentially viable way to achieve
this function. All functions have many possible structural solutions.
However, for ever one possibility that would work, there are trillions
upon trillions that won't work - and this ratio decreases,
exponentially, as one moves up the ladder of minimum structural
threshold requirements. This exponentially declining ratio rapidly
gives rise to the insurmountable non-beneficial gap problem and
evolutionary mechanisms simply stall out.
Sean Pitman
www.DetectingDesign.com
Seanpit
> >http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1181141&blobtyp...
>
> > So, you see, even at very low structural threshold levels, the
> > distribution of potentially beneficial structures is widespread and
> > fairly uniform. The clustering effects that are present at lower
> > levels rapidly decline at higher and higher threshold levels until the
> > high-level islands are very remotely separated in sequence space.
>
> >SeanPitmanwww.DetectingDesign.com-Hide quoted text -
>
> > - Show quoted text -
>
> My first reading of this paper doesn't seem to indicate any support
> for your neutral gaps model being a problem. They are talking about
> small peptides that can retain a basic structure with a large number
> of "neutral substitutions, but they make no conclusions about the
> activity of such structures. It is known from gene families that
> basic structure can be retained while function is modified.
The question here is one of the likely distribution of potentially
beneficial sequences within sequence space. Is this distribution
tightly clustered in one tiny corner of sequence space? Or, are these
potentially beneficial sequences distributed throughout sequence
space? The author's work and evaluation of existing protein-based
systems strongly support the latter view.
Certainly a structure can be modified with a corresponding
modification in the degree of function of a pre-established system.
However, the likelihood that a novel system of function can be found
in this manner is unlikely and becomes exponentially more and more
unlikely as one considers higher and higher minimum structural
threshold requirements.
> So how would studies like this do anything to change the fact that you
> don't have a model that you can support in any fashion worth talking
> about. What is your alternative explanation for the evolution of
> proteins and what is your evidence for it. Recent genome studies
> indicate that gene duplication is a lot more frequent than we had been
> able to detect before. Gene duplication seems to be a mechanism that
> would explain many protein families. Do you have a better
> explanation? What is your evidence for your alternative? Claiming
> that there is a problem when you don't even have a clue about a
> possible viable alternative is pretty bogus don't you think?
Are you actually trying to argue that a theory cannot be questioned
until one has some other way of explaining a particular phenomenon?
Really? That's a good one!
Beyond the fact that one doesn't have to have an answer before one can
raise questions about a proposed hypothesis or theory, there is indeed
a very good alternative to assuming evolutionary mechanisms did the
job in every case. Intelligent design is quite capable and should at
least be considered in such cases - just as would be proposed if
certain radiosignals were discovered by SETI scientists.
> Are you ever going to get around to presenting your alternative to
> common descent and your evidence for your alternative that you claimed
> to have that was better than the current scientific model? You
> claimed to have such a model and evidence, so why putz around with
> bogus neutral gaps if you have some killer evidence for your beliefs?
> Let's see it.
What do you think SETI scientists are looking for? They are in fact
looking for something that has such a large gap between it and what
non-deliberate processes are capable of achieving that some smart
alien intelligence is the most viable option. A clear demonstration
of non-beneficial gaps does the same thing for demonstrating that
evolutionary mechanisms are most unlikely to have crossed the gap
leaving intelligent deliberate processes as the most likely origin.
> Ron Okimoto
Sean Pitman
www.DetectingDesign.com
Perplexed in Peoria
"Seanpit" <seanpi...@naturalselection.0catch.com> wrote in message news:1170624588.1...@j27g2000cwj.googlegroups.com...
> On Feb 4, 11:06 am, "Perplexed in Peoria" <jimmene...@sbcglobal.net>
> wrote:
> > However, I was interested in your parenthetical comment in this:
> > No "higher order" clustering (i.e., except the trivial case
> > of the homologous sequences) is visible.
> > I have mostly responded to your postings as if they were merely a
> > critique of the evolutionary model rather than positive arguments for
> > some other model. But I am led to wonder how your favorite model
> > accounts for all that 'trivial' homology. Take, for example, the
> > 20 or so aminoacyl-tRNA-synthases. Each shows considerable homology
> > across the entire tree of life (with the trees constructed from any
> > one of them being consistent with the others, except near the roots).
> > Furthermore, it seems that they are all homologous with each other -
> > suggesting that they arose from a common protein ancestor before the
> > organism-level LUCA. Why would that pattern arise in some other
> > model besides the evolutionary one?
>
> What about common design? - Why reinvent the wheel every time a wheel
> would work just fine?
Well, common design explains the existence of homology. It doesn't
explain why when you construct twenty different phylogenetic trees
for the twenty different enzymes, those trees all agree with each other
on the shape of the crown groups.
Seanpit
wrote:
> "Seanpit" <seanpitnos...@naturalselection.0catch.com> wrote in messagenews:1170624588.1...@j27g2000cwj.googlegroups.com...
It does if the different groups have different by slightly different
functional needs for their slightly different systems and
environments. Nested patterns are often present within human-designed
systems.
Sean Pitman
www.DetectingDesign.com
_Arthur
0catch.com> wrote:
> > So, in that case, we have a smooth pathway to a NEW FUNCTIONALITY, a
> > 100,000-fold improvement in antibiotic resistance.
>
> That's right - and there are many more examples of this sort of
> refinement activity over time. It's a bit more difficult though when
> you haven't reached the minimum threshold requirements for the
> function in question at all. Gaining this threshold is the issue
> here.
>
You miss the point. The enzyme had another use, unrelated to
antibiotic resistance, and offered a negigible protection against
antibiotics.
If you are unwilling to call a 100,000-fold increase in activity A NEW
FUNCTIONALITY, then nothing at all will ever qualify as such, under
your unstated criteria.
> > While you're at it, do comment on the paper in the January issue of
> > Current Biology: "Continuous molecular evolution of protein-domain
> > structures by single amino acid changes. " Meier S, Jensen PR, David
> > CN, Chapman J, Holstein TW, Grzesiek S, Ozbek S. (2007)
>
> Tell me, does this paper talk about the observed evolution of even one
> novel function that requires a minimum of more than 1000 specifically
> arranged amino acid residues? If not, I'm not interested.
>
Yes, the paper makes no mention at all of any barrier linked to 1000,
or 666, or any other arbitray number of mutations. So, of course, you
wouldn't be interrested.
After all, there is no use for you to keep abreast of current
research, since the Pitman Law isn't based on biochemical research.
Biochemist Micheal Behe was so confident in his discovery of the
unevolvability of the immune system, that he didn't bother to follow
the research in the field. That level of confidence made a big
impression on the judge.
Seanpit
> On Feb 4, 4:23 pm, "Seanpit" <seanpitnos...@naturalselection.
>
> 0catch.com> wrote:
> > > So, in that case, we have a smooth pathway to a NEW FUNCTIONALITY, a
> > > 100,000-fold improvement in antibiotic resistance.
>
> > That's right - and there are many more examples of this sort of
> > refinement activity over time. It's a bit more difficult though when
> > you haven't reached the minimum threshold requirements for the
> > function in question at all. Gaining this threshold is the issue
> > here.
>
> You miss the point. The enzyme had another use, unrelated to
> antibiotic resistance, and offered a negigible protection against
> antibiotics.
> If you are unwilling to call a 100,000-fold increase in activity A NEW
> FUNCTIONALITY, then nothing at all will ever qualify as such, under
> your unstated criteria.
And you miss the point, if each single mutation is selectably
beneficial, as you claimed, then the antibiotic activity was not
negligible along the pathway but was selectable during each step in a
positive manner until the final 100,000-fold increase was realized.
Beyond this, even if the original starting point had no selectable
activity for the resulting function, the threshold level in this case
is only a few hundred specified residues - not even close to my
challenge of 1000 specified amino acid residues.
> > > While you're at it, do comment on the paper in the January issue of
> > > Current Biology: "Continuous molecular evolution of protein-domain
> > > structures by single amino acid changes. " Meier S, Jensen PR, David
> > > CN, Chapman J, Holstein TW, Grzesiek S, Ozbek S. (2007)
>
> > Tell me, does this paper talk about the observed evolution of even one
> > novel function that requires a minimum of more than 1000 specifically
> > arranged amino acid residues? If not, I'm not interested.
>
> Yes, the paper makes no mention at all of any barrier linked to 1000,
> or 666, or any other arbitray number of mutations. So, of course, you
> wouldn't be interrested.
What is the size of the evolved sequences? Hmmmm?
> After all, there is no use for you to keep abreast of current
> research, since the Pitman Law isn't based on biochemical research.
There are literally thousands of papers like this that all say pretty
much the same thing. As far as I am aware, not one of them actually
presents the observed evolution any system that requires a minimum
structural threshold of more than 1000 specified residues.
> Biochemist Micheal Behe was so confident in his discovery of the
> unevolvability of the immune system, that he didn't bother to follow
> the research in the field. That level of confidence made a big
> impression on the judge.
Please do present any research that shows any novel function evolving
that requires a minimum structural threshold of more than 1000
specified residues. I'd be most interested. I'm very interested in
following *relevant* research. Otherwise, I read plenty of articles
beyond those that are actually relevant to this discussion. I just
don't have time to read everything that everybody thinks I should
read. So, why not present something that's actually relevant for a
change? - along with a relevant quote for once?
Sean Pitman
www.DetectingDesign.com
Seanpit
protein systems within sequence space is presented in the following
link of the work of Jim Proctor and Andrew Torda (Hamburg University,
last update May, 2004):
http://www.zbh.uni-hamburg.de/wurst/protspace/ECCB_opt.huge.pdf
http://www.zbh.uni-hamburg.de/wurst/protspace/
Sean Pitman
www.DetectingDesign.com
Seanpit
_Arthur
0catch.com> wrote:
> Please do present any research that shows any novel function evolving
> that requires a minimum structural threshold of more than 1000
> specified residues.
You're the one with the bogus theory. Name me 3 known proteins that
you know for a fact that are 1000 amino-acids away than ANY possible
precursor known or unknown, with ANY possible biologically
And, while you were shifting goalposts, you aknowledged than it
doesn't seems to matter that an enzyme gains or lose a chemical
property by a factor of 100,000 in the process, it is still selectable
-- according to you.
For example, suppose a cell makes an enzyme that has an useful -- and
measurable -- capacity at digesting lactase. And that particular
enzyme has neglible efficiency at breaking down, say, crude oil.
Myself, I see no problem of envisionning a scenario where, after a
certain number of mutations (--does the number really matter? Why --
How ?) the mutated enzyme still presents a marginal lactase activity
but also a faint crude oil degrading functionality. And according to
your newly formulated criteria, the degree of functionality is
immateral, once aquired it can be selected for and improved a
thousandfold, nay, make that 100,000-fold.
Of course in their natural environment, most bacteria have no use for
a lactase-digesting enzyme, there are very few natural sources of
lactase. Or crude oil. Or penicilin.
So name me 3 known human or bacteria proteins that are surrounded by
an impassable moat of unfruited variants utterly devoid of ANY useful
chemical property, 1000 amino-acids deep.
Name me 3 first such proteins that come to your mind.
Robin Levett
Sean, before you throw out more references to papers that you can distort to
fit your requirements, isn't it about time you addressed the Choi and Kim
paper that Howard referred you to on 16 October last year? The one which
showed that proteins *in the real world* cluster into 4 families?
www.pnas.org/cgi/content/full/103/38/14056
Oh, and even a layman like me can see that you've got your interpretation of
the Bornberg-Bauer paper wrong. He specifically states that the HP protein
sequences he is examining are not uniformly distributed across sequence
space; see the last couple of paragraphs of the paper; and the RNA
sequences, that he says do "percolate through sequence space", do so in
such a way that "Within a number of mutations small compared to the length
of the sequence, the whole shape-space can be covered".
Even in the abstract he makes clear that "In analogy to protein families,
nets are dense and well-separated in sequence space".
--
Robin Levett
rle...@rlevett.ibmuklunix.net (unmunge by removing big blue - don't yahoo)
Ron O
0catch.com> wrote:
> On Feb 4, 11:28 am, "Ron O" <rokim...@cox.net> wrote:
>
>
>
>
>
> > >http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1181141&blobtyp...
>
> > > So, you see, even at very low structural threshold levels, the
> > > distribution of potentially beneficial structures is widespread and
> > > fairly uniform. The clustering effects that are present at lower
> > > levels rapidly decline at higher and higher threshold levels until the
> > > high-level islands are very remotely separated in sequence space.
>
>
> > > - Show quoted text -
>
> > My first reading of this paper doesn't seem to indicate any support
> > for your neutral gaps model being a problem. They are talking about
> > small peptides that can retain a basic structure with a large number
> > of "neutral substitutions, but they make no conclusions about the
> > activity of such structures. It is known from gene families that
> > basic structure can be retained while function is modified.
>
> The question here is one of the likely distribution of potentially
> beneficial sequences within sequence space. Is this distribution
> tightly clustered in one tiny corner of sequence space? Or, are these
> potentially beneficial sequences distributed throughout sequence
> space? The author's work and evaluation of existing protein-based
> systems strongly support the latter view.
No the real question is why you fool around with bogus junk like this,
that even you have to admit doesn't amount to squat in the face of all
the other data that we have, and don't bother to put up or shut up.
"Put up or shut up" is just an expression that you are probably well
aware of. It denotes frustration at the fact that you can obfuscate
the issue a dozen different ways, but you never come out and
demonstrate that you really have anything to discuss. If you aren't
willing to put forward the wonderful stuff that you claim to have
supporting your idea of what happened why do you spend so much time
shooting around the edges and never hitting the target? You make a
lot of noise, but that is all it is. What is your alternative, what
is the evidence for your alternative, and do a real critical analysis
of how it stacks up to the notion that you don't like. That is how an
honest person would approach the issue. They wouldn't keep lying
about what they have and pretending it is just too good to put
forward.
Getting back to this study, why would they have found anything any
different? The distributions donot tell you anything about how much
sequence space has to be searched to do a certain function. Sequence
space is so huge that even if you ran the simulation to check 10E12
sequences where would they all fall? There is also the fact that
their simulation also supports what we see in the molecular record.
Yockey came up with a shaky estimate that based on just what was known
about the various sequences when he made the estimate in the late
1970's that there were over 10E40 different cytochrome c sequences
that would function as cyt c just limiting the sequence to 104 amino
acid residues. These guys demonstrate that in their simulations over
half the amino acids residues can be replaced by mutation and the
internal structure isn't altered that much. They also admit that they
are only using hydrophobicity and we know that disulfide bonds are
very important, and that salt bridges (attraction between acidic and
basic amino acid R groups) are important. We can see that such sites
have changed in concert.
So where does this study leave you in terms of what you think is going
on? How could it possibly help the fact that your model is hopelessly
inadequate to explain the existing data. If you don't think that it
is, put it forward for evaluation. You can't deny that you were the
one that claimed that you had such a model and evidence, so why not
put it forward? Why jerk around with junk like this?
>
> Certainly a structure can be modified with a corresponding
> modification in the degree of function of a pre-established system.
> However, the likelihood that a novel system of function can be found
> in this manner is unlikely and becomes exponentially more and more
> unlikely as one considers higher and higher minimum structural
> threshold requirements.
Where do you get that from this paper? Any limited number of
sequences is going to have large gaps between them in sequence space.
What you need to know is how many of those sequences can provide the
functions that life needs. They do not appear to provide this answer
in the paper. Where is it?
>
> > So how would studies like this do anything to change the fact that you
> > don't have a model that you can support in any fashion worth talking
> > about. What is your alternative explanation for the evolution of
> > proteins and what is your evidence for it. Recent genome studies
> > indicate that gene duplication is a lot more frequent than we had been
> > able to detect before. Gene duplication seems to be a mechanism that
> > would explain many protein families. Do you have a better
> > explanation? What is your evidence for your alternative? Claiming
> > that there is a problem when you don't even have a clue about a
> > possible viable alternative is pretty bogus don't you think?
>
> Are you actually trying to argue that a theory cannot be questioned
> until one has some other way of explaining a particular phenomenon?
> Really? That's a good one!
No, we question our theories all the time, but nothing much changes
until a better explanation comes along that is more useful and
hopefully accurate than the one before. You can't just nit pick in
science. To actually do something you have to actually accomplish
something. No scientific theory is perfect, that is a fact and isn't
any news to anyone involved in science. Obfuscating the issue so that
you can continue to lie to yourself is not only counter productive,
but isn't worth jack in science or the real world except make your
self feel better somehow or to suck money out ot the rubes or make
them bend to your political whims because they really think that you
might have something. Do you still believe that you could do better
than the Ohio rubes and teach the real science of ID? It turned out
that you had been taken in by the IDiot lies and either were clueless
about how bogus ID science was or you were lying about how clueless
you were. Face the facts, you were either scammed by ID or you were
one of the scammers. Pick one and defend it.
>
> Beyond the fact that one doesn't have to have an answer before one can
> raise questions about a proposed hypothesis or theory, there is indeed
> a very good alternative to assuming evolutionary mechanisms did the
> job in every case. Intelligent design is quite capable and should at
> least be considered in such cases - just as would be proposed if
> certain radiosignals were discovered by SETI scientists.
Raise questions and then figure out how to do the research to solve
the problem. That is how science works. If we knew everything there
would be no science just technicians and librarians. You can't just
nay say because we all know (even you in your more lucid moments) that
your alternative is so much worse than the one that you don't like
that you don't even try to put it forward. Why not put it forward and
nit pick it? It would be much more fruitful and you can get definite
answers about what is wrong with it. That is the difference between
your nit picking and what happened to your notion. This sequence
space junk is at the limits of our understanding and we are far from
understanding it. Your model failed long ago based on well known and
accepted principles. A better alternative came along and it was
demonstrated to be better in so many ways that you don't stand a
chance. All you can do is obfuscate the issue and pretend that your
nit picking really matters, when if you did the same thing to your
alternative it would be no contest on which idea came up short.
>
> > Are you ever going to get around to presenting your alternative to
> > common descent and your evidence for your alternative that you claimed
> > to have that was better than the current scientific model? You
> > claimed to have such a model and evidence, so why putz around with
> > bogus neutral gaps if you have some killer evidence for your beliefs?
> > Let's see it.
>
> What do you think SETI scientists are looking for? They are in fact
> looking for something that has such a large gap between it and what
> non-deliberate processes are capable of achieving that some smart
> alien intelligence is the most viable option. A clear demonstration
> of non-beneficial gaps does the same thing for demonstrating that
> evolutionary mechanisms are most unlikely to have crossed the gap
> leaving intelligent deliberate processes as the most likely origin.
This is a stupid analogy because SETI is looking for a signal that
they can differentiate from a natural occurring signal. If all they
were looking for is something far away from what is known, three
pulsars in close proximity would be considered a SETI signal because
if it did occur only once in the Universe that would be as far away as
they could get. Get a clue. There are certain criteria that they
have to look for, and if and when they ever detect something the
debate will be one as to what that something is. If all they had was
looking at the different proteins and claiming that there was
intelligent signal there they would be doomed because we see those
protein sequences evolving even today.
Just demonstrate that your gaps exist, and then look at your
demonstration and compare it to what is wrong with your model and tell
us which one comes up short. Why keep obfuscating when you could nail
everyone with your model and evidence? Why can you see all that is
wrong with what you don't like, but you aren't willing to do the same
thing to your own model? Your methodology not only sounds bogus it is
bogus and you know it at some level, but insanity could be a defense.
You weren't too coherant when you were blathering about how you could
do better about teaching ID than the Ohio rubes, and I've pretty much
left your alone because of that mental break, but before you put up
your wonderful science of ID I'd like to see your alternative and the
evidence to back it up. Why claim that you have it if you aren't
willing to put it forward?
Your obfuscation tactics aren't just a little problem are they?
Obfuscation is all you have for the simple reason that you have
nothing else worth putting into the argument. If this isn't true, put
your junk forward and evaluate it for everyone. Someone that can talk
about problems in sequence space should be able to tell us why your
alternative comes up short compared to common descent, right?
Ron Okimoto
>
> > Ron Okimoto
>
> Sean Pitmanwww.DetectingDesign.com- Hide quoted text -
Seanpit
> On Feb 4, 5:19 pm, "Seanpit" <seanpitnos...@naturalselection.
>
> 0catch.com> wrote:
> > Please do present any research that shows any novel function evolving
> > that requires a minimum structural threshold of more than 1000
> > specified residues.
>
> You're the one with the bogus theory. Name me 3 known proteins that
> you know for a fact that are 1000 amino-acids away than ANY possible
You don't seem to understand the challenge. I'm not asking you to
present a case of a function evolving that was 1000aa away from any
possible precursor. I'm asking you to present a case of a function
evolve that requires of minimum of 1000 specifically arranged amino
acid residues to work - regardless of how far or close it may or may
not be from what came before.
Again, the gap distance is not the same thing as the minimum
structural threshold requirement. They are related, but they are not
the same. The likely gap distance is always much smaller than the
minimum threshold size.
> And, while you were shifting goalposts, you aknowledged than it
> doesn't seems to matter that an enzyme gains or lose a chemical
> property by a factor of 100,000 in the process, it is still selectable
> -- according to you.
That's what you claimed the author's of the paper your referenced said
- that each step along the pathway was functionally selectable. If
that is true, there is really no problem at all since there is no
functionally neutral gap. You started with an intact functional
system that already had, to a selectable degree, the function in
question - or isn't that really what the author's claimed?
> For example, suppose a cell makes an enzyme that has an useful -- and
> measurable -- capacity at digesting lactase. And that particular
> enzyme has neglible efficiency at breaking down, say, crude oil.
> Myself, I see no problem of envisionning a scenario where, after a
> certain number of mutations (--does the number really matter? Why --
> How ?) the mutated enzyme still presents a marginal lactase activity
> but also a faint crude oil degrading functionality. And according to
> your newly formulated criteria, the degree of functionality is
> immateral, once aquired it can be selected for and improved a
> thousandfold, nay, make that 100,000-fold.
That's right. Once the threshold requirements of the new function are
acquired to a selectable degree, further refinements aren't a problem.
> Of course in their natural environment, most bacteria have no use for
> a lactase-digesting enzyme, there are very few natural sources of
> lactase. Or crude oil. Or penicilin.
Right - -
> So name me 3 known human or bacteria proteins that are surrounded by
> an impassable moat of unfruited variants utterly devoid of ANY useful
> chemical property, 1000 amino-acids deep.
> Name me 3 first such proteins that come to your mind.
Again, that's not my claim for my 1000aa threshold (see above
explanation). There are many types of functions that require far more
than 1000 specifically arranged residues to work at all - even a
little bit. The flagellar motility system is a classic example,
requiring well over 10,000 specified residues. Ameboid motility,
exocitosis, pinocytosis, photosynthesis, eye-spot vision systems, etc.
all require thousands of specifically arranged amino acid residues
working together at the same time.
Sean Pitman
www.DetectingDesign.com
Seanpit
< snip >
> > What do you think SETI scientists are looking for? They are in fact
> > looking for something that has such a large gap between it and what
> > non-deliberate processes are capable of achieving that some smart
> > alien intelligence is the most viable option. A clear demonstration
> > of non-beneficial gaps does the same thing for demonstrating that
> > evolutionary mechanisms are most unlikely to have crossed the gap
> > leaving intelligent deliberate processes as the most likely origin.
>
> This is a stupid analogy because SETI is looking for a signal that
> they can differentiate from a natural occurring signal. If all they
> were looking for is something far away from what is known, three
> pulsars in close proximity would be considered a SETI signal because
> if it did occur only once in the Universe that would be as far away as
> they could get. Get a clue. There are certain criteria that they
> have to look for, and if and when they ever detect something the
> debate will be one as to what that something is. If all they had was
> looking at the different proteins and claiming that there was
> intelligent signal there they would be doomed because we see those
> protein sequences evolving even today.
Not true. We do not see protien sequences evolving even today at all
beyond very low levels of functional complexity - not a single example
goes beyond the 1000 specified amino acid residue structural threshold
requirement. Therefore, finding such a functional system significantly
beyond this threshold is most certainly the same thing as "a signal
that they [SETI] can differentiate from a natural occurring signal."
Why? Because it does not occur naturally at all and statistically it
cannot occur this side of a practical eternity of time.
< snip >
Sean Pitman
www.DetectingDesign.com
Seanpit
> Seanpit wrote:
> > An interesting 3D model for the distribution of existing small single-
> > protein systems within sequence space is presented in the following
> > link of the work of Jim Proctor and Andrew Torda (Hamburg University,
> > last update May, 2004):
>
> >http://www.zbh.uni-hamburg.de/wurst/protspace/ECCB_opt.huge.pdf
> >http://www.zbh.uni-hamburg.de/wurst/protspace/
>
> Sean, before you throw out more references to papers that you can distort to
> fit your requirements, isn't it about time you addressed the Choi and Kim
> paper that Howard referred you to on 16 October last year? The one which
> showed that proteins *in the real world* cluster into 4 families?
>
> www.pnas.org/cgi/content/full/103/38/14056
If you read the paper carefully, Choi and Kim do not say that proteins
form four families. Rather, they argue that protein folds can be
roughly categorized into four families. That's a big difference.
Also, consider the actual 3D model of their sequence space:
http://www.lbl.gov/Science-Articles/Archive/PBD-Universe-map-Kim.html
Notice in this model that even when it comes to very low-level protein
folding sequence space, the viable folds do not all overlap. Sure,
they are close together, but this is only to be expected at this very
low level of sequence space. It's kinda like the sequence space of 3-
letter words. They are all very closely clustered together like
this. However, this closeness of the potential steppingstones rapidly
expands as one moves up the ladder of minimum structural threshold
requirements.
> Oh, and even a layman like me can see that you've got your interpretation of
> the Bornberg-Bauer paper wrong. He specifically states that the HP protein
> sequences he is examining are not uniformly distributed across sequence
> space; see the last couple of paragraphs of the paper; and the RNA
> sequences, that he says do "percolate through sequence space", do so in
> such a way that "Within a number of mutations small compared to the length
> of the sequence, the whole shape-space can be covered".
That's right! The *whole* shape-space can be covered via relatively
small steps. This in fact means that the steppingstones here are
indeed distributed throughout sequence space. They are not clustered
together in one tiny corner. The fact that one can get across the
whole of sequence space without having to step very far from one to
the next steppingstone simply means that the ratio of steppingstones
vs. the non-viable "gap" options is rather high at this level of
minimum structural threshold requirements - as in the case of 3-letter
words. However, as you move up the ladder of threshold requirements,
this ratio drops off exponentially. As this happens, the
steppingstones drift apart rapidly. Pretty soon, it becomes very
difficult to take the same short steps and hit any steppingstone at
all.
> Even in the abstract he makes clear that "In analogy to protein families,
> nets are dense and well-separated in sequence space".
Exactly! And they cover the entire space! The nets are dense because
of the relatively high ratio that exists at such low levels of minimum
structural threshold requirements.
> Robin Levett
Sean Pitman
www.DetectingDesign.com
_Arthur
to count them ?
Also, the flagellar motility system is not a single protein, but an
assembly of approximatively 42 unique proteins.
Are you telling me that nothing prevents any single of those proteins
to be evolved individually by the cell, but that the whole *flagella*
is surrounded by some invisible "Pitman Gap" with the magic number
"1000aa" thrown in somewhere ?
I must know where you place your goalposts, you seem to be hiding them
begind a screen of fuzzy and ever-changing non-definitions and weasel-
concepts.
richardal...@googlemail.com
WHO specified the "1000 specified amino acid residue structural
threshold" and WHY is it relevant?
You have given no reason to think that it is anything other than an
arbitrary number you have pulled out of the air to falsify an
inaccurate model of evolution you have devised for no reason other
than to "falsify" it.
Novel functions can evolve without the need to cross your "1000
specified amino acid residue structural threshold".
There is no mechanism which prevents further evolution.
You may be able to fool the creationists with this sort of drivel, but
it is very clear that you can't fool anyone who knows anything about
the subject. Evidently your motive is to impress the creationists, not
to persuade the scientists, but as your whole argument is built on a
fabric of misrepresentation, distortion and outright falsehoods it is
deeply dishonest.
Evidently you are happy to use such dishonest methods to support your
case. You present your arguments here, and on your web sites knowing
perfectly well that they are bogus, based on unfounded assertion at
best and on outright falsehoods at worst, and would be utterly
demolished by any scientist with any knowledge of the subject were
they submitted to any form of academic review.
If you had a scrap of honesty you would submit your ideas to review.
I'm totally confident that you won't.
RF
Seanpit
> Remind me again what's a "specified residue", and how one is supposed
> to count them ?
All protein-based systems of function require a certain number of
specifically arranged amino acid residues. While flexibility of
arrangement can be tolerated, the degree of flexibility is often
fairly restricted. Several papers have been published about this sort
of thing to include papers by Sauer, Olsen, and Yockey. Estimates of
flexibility produce ratios for fairly specified 100aa systems of
around 1e-35 to 1e-65 or so.
> Also, the flagellar motility system is not a single protein, but an
> assembly of approximatively 42 unique proteins.
Actually, the number is a bit less than 42, but that's not the point.
The point is that all of the proteins (which are each made up of two
or three hundred fairly specified amino acid residues) in the
flagellar motility system have to be specifically arranged for the
overall system to work.
> Are you telling me that nothing prevents any single of those proteins
> to be evolved individually by the cell, but that the whole *flagella*
> is surrounded by some invisible "PitmanGap" with the magic number
> "1000aa" thrown in somewhere ?
The relatively small single proteins aren't a problem. What is a
problem is the assembly of many single proteins to produce a system
that requires a total of many thousands of amino acid residues to be
specifically arranged with each other at the same time. You just
can't add one protein together to gain the flagellar motility system
because of a lack of beneficial steppingstones that are actually that
close together.
The gaps between steppingstones at this level may not seem very big,
only a few dozen character changes in places along the pathway, but
these seemingly small gaps would require evolutionary mechanisms
trillions upon trillions of years to cross.
> I must know where you place your goalposts, you seem to be hiding them
> begind a screen of fuzzy and ever-changing non-definitions and weasel-
> concepts.
LOL - My goalposts have been just were they are now for many years.
My definitions have not changed. You just don't seem to understand
concepts that really are quite simple and intuitively obvious.
Sean Pitman
www.DetectingDesign.com
_Arthur
0catch.com> wrote:
> The relatively small single proteins aren't a problem. What is a
> problem is the assembly of many single proteins to produce a system
> that requires a total of many thousands of amino acid residues to be
> specifically arranged with each other at the same time. You just
> can't add one protein together to gain the flagellar motility system
> because of a lack of beneficial steppingstones that are actually that
> close together.
Why the blather about *protein* structures, why all along you really
meant the total combination of all the genes necessary for a multi-
protein structure ?
Ron O
Pathetic evasion. Sean what is good enough? Show us what is good
enough for you. Put up your alternative and the evidence for it so
that we can see just how much your bullpucky of only low level changes
in functional complexity really matters. If what we have is so bad,
what does that tell you about the pathetic junk that you have to
believe means anything? Really, show us what you think is good
enough.
Ron Okimoto
>
> < snip >
Seanpit
> > Not true. We do not see protein sequences evolving even today at all
> > beyond very low levels of functional complexity - not a single example
> > goes beyond the 1000 specified amino acid residue structural threshold
> > requirement.
>
> WHO specified the "1000 specified amino acid residue structural
> threshold" and WHY is it relevant?
If you look in scientific literature you will see something very
interesting. There are many examples of novel protein-based systems
evolving. However, all of these systems require significantly less
than 1000 specified amino acid residues. There isn't a single
example, in all of literature, of any real time evolution in action
that produces any novel function that requires at least 1000
specifically arranged residues working at the same time. Beyond this,
the number of examples drops off dramatically as one approaches this
1000aa mark.
If you don't understand why that is relevant, you must be deliberately
blind.
> You have given no reason to think that it is anything other than an
> arbitrary number you have pulled out of the air to falsify an
> inaccurate model of evolution you have devised for no reason other
> than to "falsify" it.
Show me just one example then of observed evolution in action beyond
this structural threshold.
> Novel functions can evolve without the need to cross your "1000
> specified amino acid residue structural threshold".
Novel functions that require at least 1000 specifically arranged
residues have never been observed to evolve. There are no real time
examples - period. Not one. Those functions that do evolve require
only a few hundred specified residues - like your cockroach milk
evolution example (only about 200 or so loosely specified residues
needed), which isn't even an observed example.
> There is no mechanism which prevents further evolution.
Then why doesn't evolution happen beyond the 1000aa threshold? What
makes evolution so common at levels below the 1000aa threshold, but
completely absent beyond this level?
> You may be able to fool the creationists with this sort of drivel, but
> it is very clear that you can't fool anyone who knows anything about
> the subject. Evidently your motive is to impress the creationists, not
> to persuade the scientists, but as your whole argument is built on a
> fabric of misrepresentation, distortion and outright falsehoods it is
> deeply dishonest.
You don't have the first clue what you are talking about here. You
don't understand your own proposed evolutionary mechanism and are
oblivious to the fact that this mechanism only works at levels well
below the 1000aa threshold.
> Evidently you are happy to use such dishonest methods to support your
> case. You present your arguments here, and on your web sites knowing
> perfectly well that they are bogus, based on unfounded assertion at
> best and on outright falsehoods at worst, and would be utterly
> demolished by any scientist with any knowledge of the subject were
> they submitted to any form of academic review.
Have at it then. Where are your devastating arguments? Hmmmm? Just
one example is all you need. Where is it?
> If you had a scrap of honesty you would submit your ideas to review.
What do you think I'm doing here? Don't you have a real argument of
your own?
> I'm totally confident that you won't.
LOL - whatever . . .
> RF
Sean Pitman
www.DetectingDesign.com
Seanpit
> > > This is a stupid analogy because SETI is looking for a signal that
> > > they can differentiate from a natural occurring signal. If all they
> > > were looking for is something far away from what is known, three
> > > pulsars in close proximity would be considered a SETI signal because
> > > if it did occur only once in the Universe that would be as far away as
> > > they could get. Get a clue. There are certain criteria that they
> > > have to look for, and if and when they ever detect something the
> > > debate will be one as to what that something is. If all they had was
> > > looking at the different proteins and claiming that there was
> > > intelligent signal there they would be doomed because we see those
> > > protein sequences evolving even today.
>
> > Not true. We do not see protein sequences evolving even today at all
> > beyond very low levels of functional complexity - not a single example
> > goes beyond the 1000 specified amino acid residue structural threshold
> > requirement. Therefore, finding such a functional system significantly
> > beyond this threshold is most certainly the same thing as "a signal
> > that they [SETI] can differentiate from a natural occurring signal."
> > Why? Because it does not occur naturally at all and statistically it
> > cannot occur this side of a practical eternity of time.
>
> Pathetic evasion. Sean, what is good enough? Show us what is good
> enough for you.
Do you have problems with reading comprehension Ron? I just pointed
out to you that no functional system that requires a minimum of more
than 1000 specified amino acid residues evolves. Why not go about
showing some examples beyond this threshold limitation? Why not
explain why there are no current examples of evolution in action
beyond this level? Why not explain why evolutionary mechanisms stall
out very rapidly as this threshold is approached?
> Put up your alternative and the evidence for it so
> that we can see just how much your bullpucky of only low level changes
> in functional complexity really matters. If what we have is so bad,
> what does that tell you about the pathetic junk that you have to
> believe means anything? Really, show us what you think is good
> enough.
Just one example would be fine Ron.
Seanpit
It really doesn't matter either way - a single or a multi-protein
structure would work just fine. What really matters is the total
number of specifically arranged amino acid residues that are
required. Those functions beyond the 1000aa level usually are made up
of independently coded proteins that are linked together in specific
arrangements with each other.
Sean Pitman
www.DetectingDesign.com
richardal...@googlemail.com
0catch.com> wrote:
> On Feb 5, 12:48 pm, richardalanforr...@googlemail.com wrote:
>
> > > Not true. We do not see protein sequences evolving even today at all
> > > beyond very low levels of functional complexity - not a single example
> > > goes beyond the 1000 specified amino acid residue structural threshold
> > > requirement.
>
> > WHO specified the "1000 specified amino acid residue structural
> > threshold" and WHY is it relevant?
>
> If you look in scientific literature you will see something very
> interesting. There are many examples of novel protein-based systems
> evolving. However, all of these systems require significantly less
> than 1000 specified amino acid residues. There isn't a single
> example, in all of literature, of any real time evolution in action
> that produces any novel function that requires at least 1000
> specifically arranged residues working at the same time. Beyond this,
> the number of examples drops off dramatically as one approaches this
> 1000aa mark.
So freaking what?
Evolution does not proceed by saltational leaps.
>
> If you don't understand why that is relevant, you must be deliberately
> blind.
>
> > You have given no reason to think that it is anything other than an
> > arbitrary number you have pulled out of the air to falsify an
> > inaccurate model of evolution you have devised for no reason other
> > than to "falsify" it.
>
> Show me just one example then of observed evolution in action beyond
> this structural threshold.
No, YOU need give a reason to think that it is anything other than an
arbitrary number you have pulled out of the air to falsify an
inaccurate model of evolution you have devised for no reason other
than to "falsify" it.
>
> > Novel functions can evolve without the need to cross your "1000
> > specified amino acid residue structural threshold".
>
> Novel functions that require at least 1000 specifically arranged
> residues have never been observed to evolve.
SO freaking what? Evolutionary theory does not require such
saltational leaps.
> There are no real time
> examples - period. Not one. Those functions that do evolve require
> only a few hundred specified residues - like your cockroach milk
> evolution example (only about 200 or so loosely specified residues
> needed), which isn't even an observed example.
What utter nonsense! If you have a better explanation for the evidence
presented by the authors of the paper, feel free to offer it. Their
conclusions are firmly based on that evidence.
>
> > There is no mechanism which prevents further evolution.
>
> Then why doesn't evolution happen beyond the 1000aa threshold? What
> makes evolution so common at levels below the 1000aa threshold, but
> completely absent beyond this level?
The fact that evolution does not proceed by saltational leaps.
The fact that your model is grossly and deliberately inacurate.
The fact that your models is not supported by a scrap of evidence.
The fact that your 1000aa threshold is completely arbitrary and not
founded on any evidence.
Your argument is no different from the facile creationist demand that
they will not "believe in" evolution unless they see a dog giving
birth to a cat. It is both ignorant and dishonest.
>
> > You may be able to fool the creationists with this sort of drivel, but
> > it is very clear that you can't fool anyone who knows anything about
> > the subject. Evidently your motive is to impress the creationists, not
> > to persuade the scientists, but as your whole argument is built on a
> > fabric of misrepresentation, distortion and outright falsehoods it is
> > deeply dishonest.
>
> You don't have the first clue what you are talking about here. You
> don't understand your own proposed evolutionary mechanism and are
> oblivious to the fact that this mechanism only works at levels well
> below the 1000aa threshold.
You have provided no evidence or argument whatsover to support your
assertion that it should. Your "1000aa threshold" is no more than an
arbitrary number you have pulled out of the air to falsify your own
personal model of evolution which you have devised for no reason other
than to falsify it.
>
> > Evidently you are happy to use such dishonest methods to support your
> > case. You present your arguments here, and on your web sites knowing
> > perfectly well that they are bogus, based on unfounded assertion at
> > best and on outright falsehoods at worst, and would be utterly
> > demolished by any scientist with any knowledge of the subject were
> > they submitted to any form of academic review.
>
> Have at it then. Where are your devastating arguments? Hmmmm? Just
> one example is all you need. Where is it?
>
No, what *YOU* need to do is to justify your assertion that such a
demand is reasonable based on evolutionary theory.
> > If you had a scrap of honesty you would submit your ideas to review.
>
> What do you think I'm doing here? Don't you have a real argument of
> your own?
>
What you are doing here is persisting in an utterly discredited
argunment which is based on nothing other than your unfounded
assertions and ignoring any evidence which demonstrates that it is
false. You mispresent and distort the words of the authors of the
papers you cite in support of your "theory", and ignore those parts of
the papers which don't suit you.
You are not submitting your ideas to review, something which I know
you won't because you are an intellectual coward who prefers to
pontificate on subjects about which you know very little to boost your
status in the creationist community rather than to learn about them
and make any genuine contribution to science.
> > I'm totally confident that you won't.
>
> LOL - whatever . . .
>
Which confirms that you are a moral and intellectual coward.
RF
> > RF
>
> Sean Pitmanwww.DetectingDesign.com
Ron O
You seem to have a comprehension problem. This whole schtick of yours
is just evasion. Where did you get the 1000 specified amino acids
junk? The average protein size is only 300 and you can't even explain
the evolutionary data of short proteins like cyt c that are only
around 100.
What is your alternative to common descent and the evidence for it?
We have reams of data using your "impossible" protein sequences that
tell us something that your model can't explain worth beans. If it
could you would have put it up years ago.
Lurkers should not be confused by Sean's evasion tactics. Any regular
knows what Sean has been up to for years. He made his common descent
claim a couple of years before Ohio hit the fan. He claimed that he
had an alternative model and evidence to back it up, what? Seven
years ago? He never backed up that claim. Right after the Ohio State
school board fiasco where the ID scam artists had to run the bait and
switch scam on the Ohio rubes in 2002 Sean claimed that he could do
better and that he had some real science to teach about ID, but he
never put it forward. The Ohio rubes were conned by the ID scam and
wanted to teach the science of ID, but all they got from the guys that
had perpetrated the ID scam was a replacement obfuscation scam that
didn't even mention that ID had ever existed. Sean claimed that there
was ID science to teach, but where is it? Why didn't it show up in
Dover when they needed it? Why hasn't Sean ever presented what he
claims exists?
Why dishonestly obfuscate about 1000 specified amino acids when you
know that you don't have jack as an alternative to the real science?
Sean has to explain the protein data that we have before he tries to
claim something about what we (and he) doesn't know. Sean knows for a
fact that he can't do what he claims or he wouldn't be waffling about
it for 7 years. We aren't talking about a few months or a couple of
years, but over half a decade of denial. It isn't that people are
being mean to Sean, it is that Sean is either incompetent or
dishonest. I've pretty much left him alone for several years because
I lean towards mental incompetence, but he seems to claim otherwise so
who is to argue?
>
> > Put up your alternative and the evidence for it so
> > that we can see just how much your bullpucky of only low level changes
> > in functional complexity really matters. If what we have is so bad,
> > what does that tell you about the pathetic junk that you have to
> > believe means anything? Really, show us what you think is good
> > enough.
>
> Just one example would be fine Ron.
Why the evasion Sean? After you make good on your common descent
claim may be we can get around to you demonstrating that your 1000
junk is biologically relevant. Of course the point would be moot
after you demonstrate that you are just a blowhard incompetent. I
didn't make your claim, you did that, so put up. How long will you be
in denial? 10 years? 20? More?
Why not be more honest and call your site creationistobfuscation101?
Ron Okimoto
>
> > Ron Okimoto
Vend
wrote:
> > Well, common design explains the existence of homology. It doesn't
> > explain why when you construct twenty different phylogenetic trees
> > for the twenty different enzymes, those trees all agree with each other
> > on the shape of the crown groups.
>
> It does if the different groups have different by slightly different
> functional needs for their slightly different systems and
> environments.
But why trees? and why the trees are consistent?
> Nested patterns are often present within human-designed
> systems.
You mean like a cd-player in a car?
Human designed object form generic graphs, not trees.
_Arthur
Seanpit
> > > Why the blather about *protein* structures, why all along you really
> > > meant the total combination of all the genes necessary for a multi-
> > > protein structure ?
>
> > It really doesn't matter either way - a single or a multi-protein
> > structure would work just fine. What really matters is the total
> > number of specifically arranged amino acid residues that are
> > required. Those functions beyond the 1000aa level usually are made up
> > of independently coded proteins that are linked together in specific
> > arrangements with each other.
>
> >SeanPitmanwww.DetectingDesign.com
>
> Blather.
You can lead a horse to water . . .
_Arthur
0catch.com> wrote:
>
> > > It really doesn't matter either way - a single or a multi-protein
> > > structure would work just fine. What really matters is the total
> > > number of specifically arranged amino acid residues that are
> > > required. Those functions beyond the 1000aa level usually are made up
> > > of independently coded proteins that are linked together in specific
> > > arrangements with each other.
>
>
> > Blather.
>
> You can lead a horse to water . . .
So the Pitman Gap you invented extends not around proteins, but rather
around biological structures, now ?
Seanpit
> > On Feb 6, 1:56 am, "Seanpit" <seanpitnos...@naturalselection.
> > > WHO specified the "1000 specified amino acid residue structural
> > > threshold" and WHY is it relevant?
>
> > If you look in scientific literature you will see something very
> > interesting. There are many examples of novel protein-based systems
> > evolving. However, all of these systems require significantly less
> > than 1000 specified amino acid residues. There isn't a single
> > example, in all of literature, of any real time evolution in action
> > that produces any novel function that requires at least 1000
> > specifically arranged residues working at the same time. Beyond this,
> > the number of examples drops off dramatically as one approaches this
> > 1000aa mark.
>
> So freaking what?
> Evolution does not proceed by saltational leaps.
You do understand, by now hopefully, that the 1000aa structural
threshold is not a measure of the step or "leap" size. It is a
measure of the minimum part requirement and degree of arrangement
needed to achieve a particular type of function regardless of how that
1000aa+ structure is produced. It is *possible* for such a functional
system to be just one point mutation away from something that already
exists within a population's gene pool. It is just that this
possibility is extremely *unlikely* at this level.
It is far far more likely that such a functional system would be
several dozen mutational steps away from anything that exists within a
population's gene pool - even if the population under consideration
consists of all living things on Earth (the likely distribution
follows a Poisson curve). Finding any novel beneficial function beyond
the 1000aa threshold, given the most likely minimum gap size, would
most certainly require a great many random mutation steps or "leaps";
exponentially more mutational steps and/or leaps than were needed
below this threshold. Of course, that means that exponentially more
time is required to achieve higher and higher minimum structural
threshold requirements - and that's a big big problem.
Small mutational steps simply do not add up to move a population up
the ladder of minimum structural threshold requirements. There just
aren't any examples of such evolution in action in all of literature -
not one. Your cockroach milk evolution example isn't even a real time
example and it doesn't cross a structural threshold of more than 200
or so loosely specified amino acid residues.
There are a great many such examples because the odds that such a
potentially beneficial function will be very close (within one or two
mutational steps) to what already exists within a gene pool are pretty
good, relatively speaking. However, the odds that this short distance
will also be a reality as one move up the ladder of minimum structural
threshold requirements drop exponentially.
> > If you don't understand why that is relevant, you must be deliberately
> > blind.
>
> > > You have given no reason to think that it is anything other than an
> > > arbitrary number you have pulled out of the air to falsify an
> > > inaccurate model of evolution you have devised for no reason other
> > > than to "falsify" it.
>
> > Show me just one example then of observed evolution in action beyond
> > this structural threshold.
>
> No, YOU need give a reason to think that it is anything other than an
> arbitrary number you have pulled out of the air to falsify an
> inaccurate model of evolution you have devised for no reason other
> than to "falsify" it.
I've already told you the reason. Don't tell me you still don't grasp
the significance of the fact that all examples of evolution "in
action" fall well below the 1000aa threshold. There is not a single
example beyond this level in all of literature. This threshold level
is not pulled out of thin air. It is presented in scientific
literature as the threshold that is never crossed. Please do explain
that - - if you can.
> > > Novel functions can evolve without the need to cross your "1000
> > > specified amino acid residue structural threshold".
>
> > Novel functions that require at least 1000 specifically arranged
> > residues have never been observed to evolve.
>
> SO freaking what? Evolutionary theory does not require such
> saltational leaps.
The 1000aa threshold has never been crossed by any series of
evolutionary steps, short or long, small or large. Small little steps
simply do not progress up the ladder of minimum structural threshold
requirements like you imagine. They only produce novel functions that
are below the 1000aa threshold. There is no progression up the ladder
- not one example.
> > There are no real time
> > examples - period. Not one. Those functions that do evolve require
> > only a few hundred specified residues - like your cockroach milk
> > evolution example (only about 200 or so loosely specified residues
> > needed), which isn't even an observed example.
>
> What utter nonsense! If you have a better explanation for the evidence
> presented by the authors of the paper, feel free to offer it. Their
> conclusions are firmly based on that evidence.
It doesn't matter Richard. Even if this example were actually
observed in real time, it is an example of crossing a threshold that
is far below the 1000aa threshold. The threshold crossed here is a
200aa threshold of loosely specified residues. That's not even
close! Even Barry Hall's lactase evolution example crosses a much
higher threshold of about 380aa that are much more specified.
There are much much better examples than your roach-milk example.
It's just that none of them come close to the 1000aa threshold.
< snip >
> RF
Sean Pitman
www.DetectingDesign.com
Seanpit
> So thePitmanGap you invented extends not around proteins, but rather
> around biological structures, now ?
Both. It is just that the gap is much smaller for smaller protein-
based functional structures (which usually include single proteins).
The larger the minimum structural size and specificity requirement the
larger the gap size. It's really very simple and downright intuitive.
Sean Pitman
www.DetectingDesign.com
Seanpit
> On 4 Feb, 23:02, "Seanpit" <seanpitnos...@naturalselection.0catch.com>
> wrote:
>
> > > Well, common design explains the existence of homology. It doesn't
> > > explain why when you construct twenty different phylogenetic trees
> > > for the twenty different enzymes, those trees all agree with each other
> > > on the shape of the crown groups.
>
> > It does if the different groups have different by slightly different
> > functional needs for their slightly different systems and
> > environments.
>
> But why trees? and why the trees are consistent?
Does an artists or designer of any kind have to have a reason that
appeals to you before you can detect design? This is the whole "No
intelligent designer would have done it that way" argument. Some
might say that about a Picasso painting if they were from an alien
planet. Yet, it is easy to detect a great deal of deliberate
intelligence behind a Picasso.
Beyond this, the nested hierarchy in nature makes a lot of creative
sense and is even beautifully elegant. The pattern is very similar to
patterns observed in highly technical human designs of integrated
systems - especially if a single designer or a small group of
designers were at work.
And, beyond this, the detection of design isn't about the detection of
a pattern that a mindless process is likely to produce. It is about
the detection of something that mindless processes are very unlikely
to produce. One cannot simply focus on one aspect of a phenomenon and
make a conclusive hypothesis about mindless or mindful origin. One
must consider all aspects of the phenomenon before a reliable
hypothesis can be established. While the nested pattern observed in
living things can indeed be explained by mindless evolutionary
processes, the functional aspects of living things, as they move
beyond very low levels of minimum structural threshold requirements,
are exponentially harder and harder to explain via mindless
evolutionary processes.
> > Nested patterns are often present within human-designed
> > systems.
>
> You mean like a cd-player in a car?
> Human designed object form generic graphs, not trees.
Not always . . . nested patterns can also be seen in human design.
Sean Pitman
www.DetectingDesign.com
richardal...@googlemail.com
0catch.com> wrote:
> > > > On Feb 5, 11:46 pm, richardalanforr...@googlemail.com wrote:
> > > On Feb 6, 1:56 am, "Seanpit" <seanpitnos...@naturalselection.
> > > > WHO specified the "1000 specified amino acid residue structural
> > > > threshold" and WHY is it relevant?
>
> > > If you look in scientific literature you will see something very
> > > interesting. There are many examples of novel protein-based systems
> > > evolving. However, all of these systems require significantly less
> > > than 1000 specified amino acid residues. There isn't a single
> > > example, in all of literature, of any real time evolution in action
> > > that produces any novel function that requires at least 1000
> > > specifically arranged residues working at the same time. Beyond this,
> > > the number of examples drops off dramatically as one approaches this
> > > 1000aa mark.
>
> > So freaking what?
> > Evolution does not proceed by saltational leaps.
>
> You do understand, by now hopefully, that the 1000aa structural
> threshold is not a measure of the step or "leap" size. It is a
> measure of the minimum part requirement and degree of arrangement
> needed to achieve a particular type of function regardless of how that
> 1000aa+ structure is produced. It is *possible* for such a functional
> system to be just one point mutation away from something that already
> exists within a population's gene pool. It is just that this
> possibility is extremely *unlikely* at this level.
>
So what?
> It is far far more likely that such a functional system would be
> several dozen mutational steps away from anything that exists within a
> population's gene pool - even if the population under consideration
> consists of all living things on Earth (the likely distribution
> follows a Poisson curve). Finding any novel beneficial function beyond
> the 1000aa threshold,
You have yet to explain why your "1000aa threshold" is of any
significance. Novel beneficial functions evolved with changes well
below this threshold.
What is so special about novel beneficial functions above this
arbitrary threshold?
> given the most likely minimum gap size, would
> most certainly require a great many random mutation steps or "leaps";
> exponentially more mutational steps and/or leaps than were needed
> below this threshold. Of course, that means that exponentially more
> time is required to achieve higher and higher minimum structural
> threshold requirements - and that's a big big problem.
Only in your model of evolution, which is formulated only so that you
can falsify it.
What mechanism prevents the accumulation of beneficial functions at
levels of change well below your arbitrary threshold?
>
> Small mutational steps simply do not add up to move a population up
> the ladder of minimum structural threshold requirements.
Why not?
> There just
> aren't any examples of such evolution in action in all of literature -
> not one.
There are very large numbers of papers which present of evidence for
evolution as a series of mutational steps in the literature.
Dismissing them as "not convincing", as is your habit, will not make
them go away.
> Your cockroach milk evolution example isn't even a real time
> example
So freaking what? Since when has observation in "real time" been a
requirement in science? You'll be insisting that I'm using the
"judicial method" next.
> and it doesn't cross a structural threshold of more than 200
> or so loosely specified amino acid residues.
>
Which demonstrates that novel functions can evolve at levels of change
well below your arbitrary threshold.
What mechanism prevents further changes to the genomenes of these
cockroaches?
> There are a great many such examples because the odds that such a
> potentially beneficial function will be very close (within one or two
> mutational steps) to what already exists within a gene pool are pretty
> good, relatively speaking. However, the odds that this short distance
> will also be a reality as one move up the ladder of minimum structural
> threshold requirements drop exponentially.
Once such a novel function has been acquired, what mechanism prevents
the acquisiting of another novel function? Or the loss of the acquired
function? This is, after all how evolutionary theory models the
evolution of more complex functions.
>
> > > If you don't understand why that is relevant, you must be deliberately
> > > blind.
>
> > > > You have given no reason to think that it is anything other than an
> > > > arbitrary number you have pulled out of the air to falsify an
> > > > inaccurate model of evolution you have devised for no reason other
> > > > than to "falsify" it.
>
> > > Show me just one example then of observed evolution in action beyond
> > > this structural threshold.
>
> > No, YOU need give a reason to think that it is anything other than an
> > arbitrary number you have pulled out of the air to falsify an
> > inaccurate model of evolution you have devised for no reason other
> > than to "falsify" it.
>
> I've already told you the reason.
No you haven't.
You have asserted over and over again that this is requirement, but
provided no evidence whatsoever to suggest that it has any meaning in
the real world.
> Don't tell me you still don't grasp
> the significance of the fact that all examples of evolution "in
> action" fall well below the 1000aa threshold.
The signifiance is that there is no requirement for changes above the
arbitrary threshold you have invented to evolution to carry on quite
happily.
> There is not a single
> example beyond this level in all of literature.
There are numerous example in the literature. The fact that you ignore
them, or pretend that they don't exist, or dismiss them without even
reading them as "unconvincing" is irrelevant. If you have a better
explanation for the evidence, or a better predictive model than
evolutionary theory, feel free to offer it.
> This threshold level
> is not pulled out of thin air. It is presented in scientific
> literature as the threshold that is never crossed.
Where?
> Please do explain
> that - - if you can.
>
The explanation is that you are persitently mispresenting the words of
a paper written over 30 years ago when our knowledge of the way in
which proteins function in genes was in its infancy.
> > > > Novel functions can evolve without the need to cross your "1000
> > > > specified amino acid residue structural threshold".
>
> > > Novel functions that require at least 1000 specifically arranged
> > > residues have never been observed to evolve.
>
> > SO freaking what? Evolutionary theory does not require such
> > saltational leaps.
>
> The 1000aa threshold has never been crossed by any series of
> evolutionary steps, short or long, small or large.
Why does it need to?
> Small little steps
> simply do not progress up the ladder of minimum structural threshold
> requirements like you imagine.
Why not?
Is there a mechanism which prevents the acquisition of further novel
functions once one has been acquired?
> They only produce novel functions that
> are below the 1000aa threshold. There is no progression up the ladder
> - not one example.
So what?
>
> > > There are no real time
> > > examples - period. Not one. Those functions that do evolve require
> > > only a few hundred specified residues - like your cockroach milk
> > > evolution example (only about 200 or so loosely specified residues
> > > needed), which isn't even an observed example.
>
> > What utter nonsense! If you have a better explanation for the evidence
> > presented by the authors of the paper, feel free to offer it. Their
> > conclusions are firmly based on that evidence.
>
> It doesn't matter Richard. Even if this example were actually
> observed in real time, it is an example of crossing a threshold that
> is far below the 1000aa threshold. The threshold crossed here is a
> 200aa threshold of loosely specified residues.
Quite so. It means that evolution can proceed perfectly well at levels
of change well below the arbitrary limit you have set.
What mechanism prevents the evolution of further novel functions?
> That's not even
> close! Even Barry Hall's lactase evolution example crosses a much
> higher threshold of about 380aa that are much more specified.
>
So what?
> There are much much better examples than your roach-milk example.
> It's just that none of them come close to the 1000aa threshold.
You have not explained why they need to.
Novel functions can evolve without any need to approach your arbitrary
threshold.
There is no mechanism to prevent further novel functions evolving.
>
> < snip >
Lets restore some of those snips, shall we?
> Then why doesn't evolution happen beyond the 1000aa threshold? What
> makes evolution so common at levels below the 1000aa threshold, but
> completely absent beyond this level?
The fact that evolution does not proceed by saltational leaps.
The fact that your model is grossly and deliberately inacurate.
The fact that your models is not supported by a scrap of evidence.
The fact that your 1000aa threshold is completely arbitrary and not
founded on any evidence.
Your argument is no different from the facile creationist demand that
they will not "believe in" evolution unless they see a dog giving
birth to a cat. It is both ignorant and dishonest.
> You don't have the first clue what you are talking about here. You
> don't understand your own proposed evolutionary mechanism and are
> oblivious to the fact that this mechanism only works at levels well
> below the 1000aa threshold.
You have provided no evidence or argument whatsover to support your
assertion that it should. Your "1000aa threshold" is no more than an
arbitrary number you have pulled out of the air to falsify your own
personal model of evolution which you have devised for no reason other
than to falsify it.
> Have at it then. Where are your devastating arguments? Hmmmm? Just
> one example is all you need. Where is it?
No, what *YOU* need to do is to justify your assertion that such a
demand is reasonable based on evolutionary theory.
> What do you think I'm doing here? Don't you have a real argument of
> your own?
What you are doing here is persisting in an utterly discredited
argunment which is based on nothing other than your unfounded
assertions and ignoring any evidence which demonstrates that it is
false. You mispresent and distort the words of the authors of the
papers you cite in support of your "theory", and ignore those parts of
the papers which don't suit you.
You are not submitting your ideas to review, something which I know
you won't because you are an intellectual coward who prefers to
pontificate on subjects about which you know very little to boost your
status in the creationist community rather than to learn about them
and make any genuine contribution to science.
> LOL - whatever . . .
richardal...@googlemail.com
....and not supported by a shred of evidence.
How do you explain that, Sean?
>
> Sean Pitmanwww.DetectingDesign.com
John Wilkins
I want to ask Sean a question. Do you think a 999aa change is possible?
--
John S. Wilkins, Postdoctoral Research Fellow, Biohumanities Project
University of Queensland - Blog: scienceblogs.com/evolvingthoughts
"He used... sarcasm. He knew all the tricks, dramatic irony, metaphor,
bathos, puns, parody, litotes and... satire. He was vicious."
_Arthur
Wat are the precise structural size and complete specificity
requirements of the bacterial flagellae ?
Seanpit
Greater than 10,000 fairly specified (1e-25 per 100aa) residues. If
you can come up with a threshold significantly less than this, I'd be
most interested.
Sean Pitman
www.DetectingDesign.com
Seanpit
> > > So freaking what?
> > > Evolution does not proceed by saltational leaps.
>
> > You do understand, by now hopefully, that the 1000aa structural
> > threshold is not a measure of the step or "leap" size. It is a
> > measure of the minimum part requirement and degree of arrangement
> > needed to achieve a particular type of function regardless of how that
> > 1000aa+ structure is produced. It is *possible* for such a functional
> > system to be just one point mutation away from something that already
> > exists within a population's gene pool. It is just that this
> > possibility is extremely *unlikely* at this level.
>
> So what?
Oh come on now! Think about it. If the odds that a short gap distance
actually exist decline exponentially with each increase in the minimum
structural threshold requirements, odds are that the actual minimum
gap distance will be greater. This means that the time it takes to
cross the gap is likely to be equivalently greater. Since the odds
change exponentially here, odds are that an exponentially greater
amount of time will be required to find a novel beneficial sequence at
a higher structural threshold level.
> > It is far far more likely that such a functional system would be
> > several dozen mutational steps away from anything that exists within a
> > population's gene pool - even if the population under consideration
> > consists of all living things on Earth (the likely distribution
> > follows a Poisson curve). Finding any novel beneficial function beyond
> > the 1000aa threshold,
>
> You have yet to explain why your "1000aa threshold" is of any
> significance. Novel beneficial functions evolved with changes well
> below this threshold.
How many times do I have to repeat myself? Novel beneficial functions
have evolved with the use of one or two or even three or four
mutational steps. However, and try and catch this point, the
resulting functional system did not require more than a few hundred
fairly specified residues in order to work to some selective
advantage.
It is because the resulting function was a low-level function that the
gaps size was so small. Odds are that no functional systems that have
higher minimum structural threshold requirements will be as close to
anything in any member of any population. These odds are
exponentially reduced with each step up the ladder. By the time the
1000aa level is considered, the odds that any gap will exist that is
only one or two mutations wide or even one or two dozen mutations wide
are extremely poor.
The odds follow a Poisson-type distribution. As one considers higher
and higher structural threshold requirements, the odds of a narrow gap
existing drop in such a way as to produce a Poisson distribution
pattern.
That is why the likely minimum gap distance is always much smaller
than the threshold level. However, a gap distance of just a few dozen
would require evolutionary mechanisms in a huge population of, say,
all living things on Earth, trillions upon trillions of years to
cross.
With each step up the ladder the ratio of potentially beneficial
steppingstone targets decreases exponentially. That's a fact. What
results is a widening of the gap between steppingstone targets as one
moves higher and higher up the ladder.
< snip rest - repetitive (both me and you) >
Sean Pitman
www.DetectingDesign.com
richardal...@googlemail.com
You don't.
You just have to provide an explanation for your assertion which is
supported by evidence.
Repeating the same assertion ad nauseam does not make it true.
> Novel beneficial functions
> have evolved with the use of one or two or even three or four
> mutational steps. However, and try and catch this point, the
> resulting functional system did not require more than a few hundred
> fairly specified residues in order to work to some selective
> advantage.
And the evidence you have to back this assertion is.......?
There is plenty of evidence both from studies of the genemones of
existing organisms and the fossil record that novel beneficial
functions *have* evolved involving a far greater number of
evolutionary steps that your arbitrary limit suggests.
Just to repeat a question I have asked many times and which you have
not answered:
What mechanism prevents the acquisition of more novel functions once
one has been acquired?
>
> It is because the resulting function was a low-level function that the
> gaps size was so small. Odds are that no functional systems that have
> higher minimum structural threshold requirements will be as close to
> anything in any member of any population. These odds are
> exponentially reduced with each step up the ladder. By the time the
> 1000aa level is considered, the odds that any gap will exist that is
> only one or two mutations wide or even one or two dozen mutations wide
> are extremely poor.
The evidence from the real world shows that this is not the case.
There is no evidence whatsoever to suggest that evolution stalls out
at any level.
So even though you deny the evidence from the real world, that
evidence shows that your model of evolution is wrong.
>
> The odds follow a Poisson-type distribution. As one considers higher
> and higher structural threshold requirements, the odds of a narrow gap
> existing drop in such a way as to produce a Poisson distribution
> pattern.
What mechanism prevents the acquisition of further novel functions
once one has been acquired?
Each time such novel function is acquired, we are back to square one.
Evolution, contrary to the model on which you insist, is not goal-
oriented.
>
> That is why the likely minimum gap distance is always much smaller
> than the threshold level. However, a gap distance of just a few dozen
> would require evolutionary mechanisms in a huge population of, say,
> all living things on Earth, trillions upon trillions of years to
> cross.
And how have you calculated "trillions upon trillions of years?
Surely this is not another number you have pulled out of the air?
>
> With each step up the ladder the ratio of potentially beneficial
> steppingstone targets decreases exponentially. That's a fact. What
> results is a widening of the gap between steppingstone targets as one
> moves higher and higher up the ladder.
"Higher and higher" eh?
This may come as news to you, but the idea of evolution as a great
chain of being was discredited about 200 years ago.
I suggest that you come to terms with the fact that you have
substantial gaps in your knowledge of evolutionary theory.
>
> < snip rest - repetitive (both me and you) >
Ah well.
I'll just put back all the questions you refuse to answer:
> Small mutational steps simply do not add up to move a population up
> the ladder of minimum structural threshold requirements.
Why not?
> There just
> aren't any examples of such evolution in action in all of literature -
> not one.
There are very large numbers of papers which present of evidence for
evolution as a series of mutational steps in the literature.
Dismissing them as "not convincing", as is your habit, will not make
them go away.
So where are the conclusions drawn by the authors of papers presenting
evidence for evolution as a series of mutational steps flawed?
You need to address the evidence, not simply ignore it.
> Your cockroach milk evolution example isn't even a real time
> example
Since when has observation in "real time" been a requirement in
science?
What mechanism prevents further changes to the genomenes of these
cockroaches?
Once such a novel function has been acquired, what mechanism prevents
the acquisiting of another novel function?
Or the loss of the acquired function?
This is, after all how evolutionary theory models the evolution of
more complex functions.
> > > If you don't understand why that is relevant, you must be deliberately
> > > blind.
> > > > You have given no reason to think that it is anything other than an
> > > > arbitrary number you have pulled out of the air to falsify an
> > > > inaccurate model of evolution you have devised for no reason other
> > > > than to "falsify" it.
> > > Show me just one example then of observed evolution in action beyond
> > > this structural threshold.
> > No, YOU need give a reason to think that it is anything other than an
> > arbitrary number you have pulled out of the air to falsify an
> > inaccurate model of evolution you have devised for no reason other
> > than to "falsify" it.
> I've already told you the reason.
No you haven't.
You have asserted over and over again that this is requirement, but
provided no evidence whatsoever to suggest that it has any meaning in
the real world.
So YOU need give a reason to think that it is anything other than an
arbitrary number you have pulled out of the air to falsify an
inaccurate model of evolution you have devised for no reason other
than to "falsify" it.
There are numerous example in the literature. The fact that you ignore
them, or pretend that they don't exist, or dismiss them without even
reading them as "unconvincing" is irrelevant. If you have a better
explanation for the evidence, or a better predictive model than
evolutionary theory, feel free to offer it.
> The 1000aa threshold has never been crossed by any series of
> evolutionary steps, short or long, small or large.
Why does it need to?
> Small little steps
> simply do not progress up the ladder of minimum structural threshold
> requirements like you imagine.
Why not?
Is there a mechanism which prevents the acquisition of further novel
functions once one has been acquired?
> They only produce novel functions that
> are below the 1000aa threshold. There is no progression up the ladder
> - not one example.
So what?
What mechanism prevents the evolution of further novel functions?
You have provided no evidence or argument whatsover to support your
RF
>
> Sean Pitmanwww.DetectingDesign.com
_Arthur
In other words, you have no clue how to measure the key value dictated
by your own quack theory that no one can make heads or tail of.
You cite the bacterial flagellae as a prime example of your theory,
but you miserably fail to measure is "fairly specified residues".
But we have your good word that it is certainly greater than 10,000
quatloos, from your own authority. By how much ? You cannot tell.
Any margin of error ? No margin necessary, because your whole concept
is an egregious error.
Vend
wrote:
> On Feb 6, 6:06 am, "Vend" <ven...@virgilio.it> wrote:
>
> > On 4 Feb, 23:02, "Seanpit" <seanpitnos...@naturalselection.0catch.com>
> > wrote:
>
> > > > Well, common design explains the existence of homology. It doesn't
> > > > explain why when you construct twenty different phylogenetic trees
> > > > for the twenty different enzymes, those trees all agree with each other
> > > > on the shape of the crown groups.
>
> > > It does if the different groups have different by slightly different
> > > functional needs for their slightly different systems and
> > > environments.
>
> > But why trees? and why the trees are consistent?
>
> Does an artists or designer of any kind have to have a reason that
> appeals to you before you can detect design? This is the whole "No
> intelligent designer would have done it that way" argument. Some
> might say that about a Picasso painting if they were from an alien
> planet. Yet, it is easy to detect a great deal of deliberate
> intelligence behind a Picasso.
Well, an unspecified designer could produce anything. That's why
asserting design without specifying anything about the designer is
unfalsifiable and therefore unscientific.
> Beyond this, the nested hierarchy in nature makes a lot of creative
> sense and is even beautifully elegant.
You mean like dolphins with non-functional elbow joints and without
gills?
> The pattern is very similar to
> patterns observed in highly technical human designs of integrated
> systems - especially if a single designer or a small group of
> designers were at work.
For instance?
> And, beyond this, the detection of design isn't about the detection of
> a pattern that a mindless process is likely to produce. It is about
> the detection of something that mindless processes are very unlikely
> to produce.
If I toss 1000 coins the specific sequence I obtain had an a priori
probability of 2^-1000: very unlikely. Do you detect that it wasn't
produced by a mindless process?
> One cannot simply focus on one aspect of a phenomenon and
> make a conclusive hypothesis about mindless or mindful origin. One
> must consider all aspects of the phenomenon before a reliable
> hypothesis can be established. While the nested pattern observed in
> living things can indeed be explained by mindless evolutionary
> processes, the functional aspects of living things, as they move
> beyond very low levels of minimum structural threshold requirements,
> are exponentially harder and harder to explain via mindless
> evolutionary processes.
You keep repeating this, but what is this exponential structural
threshold requirement and how do you know that it exists in biological
systems?
> > You mean like a cd-player in a car?
> > Human designed object form generic graphs, not trees.
>
> Not always . . . nested patterns can also be seen in human design.
Perhaps in some, but they are not the norm. Human designers constantly
mix technologies developed for unrelated applications.
This is what I would expect from an "intelligent" designer for any
reasonable meaning of the word "intelligent".
And we don't see this in biological systems.
Robin Levett
> On Feb 4, 8:19 pm, Robin Levett <rnlev...@yahoo.co.uk> wrote:
>> Seanpit wrote:
>> > An interesting 3D model for the distribution of existing small single-
>> > protein systems within sequence space is presented in the following
>> > link of the work of Jim Proctor and Andrew Torda (Hamburg University,
>> > last update May, 2004):
>>
>> >http://www.zbh.uni-hamburg.de/wurst/protspace/ECCB_opt.huge.pdf
>> >http://www.zbh.uni-hamburg.de/wurst/protspace/
>>
>> Sean, before you throw out more references to papers that you can distort
>> to fit your requirements, isn't it about time you addressed the Choi and
>> Kim
>> paper that Howard referred you to on 16 October last year? The one which
>> showed that proteins *in the real world* cluster into 4 families?
>>
>> www.pnas.org/cgi/content/full/103/38/14056
>
> If you read the paper carefully, Choi and Kim do not say that proteins
> form four families. Rather, they argue that protein folds can be
> roughly categorized into four families. That's a big difference.
I have read the paper carefully; you appear not to have done. Try this:
"Protein structures are more conserved than sequences in evolution, thus
most proteins in a given sequence family have similar or related molecular
structures."
Note, by the way, that Choi and Kim are dealing with real, not modelled,
proteins.
It is true that it is the protein structures that fall into 4 classes - but
it is also true that the many protein sequence families fall within those
same 4 classes.
> Also, consider the actual 3D model of their sequence space:
>
> http://www.lbl.gov/Science-Articles/Archive/PBD-Universe-map-Kim.html
>
> Notice in this model that even when it comes to very low-level protein
> folding sequence space, the viable folds do not all overlap. Sure,
> they are close together, but this is only to be expected at this very
> low level of sequence space. It's kinda like the sequence space of 3-
> letter words. They are all very closely clustered together like
> this. However, this closeness of the potential steppingstones rapidly
> expands as one moves up the ladder of minimum structural threshold
> requirements.
Interesting assertion. Any backup for it - it's not in the papers discussed
here.
>> Oh, and even a layman like me can see that you've got your interpretation
>> of
>> the Bornberg-Bauer paper wrong. He specifically states that the HP
>> protein sequences he is examining are not uniformly distributed across
>> sequence space; see the last couple of paragraphs of the paper; and the
>> RNA sequences, that he says do "percolate through sequence space", do so
>> in such a way that "Within a number of mutations small compared to the
>> length of the sequence, the whole shape-space can be covered".
>
> That's right! The *whole* shape-space can be covered via relatively
> small steps. This in fact means that the steppingstones here are
> indeed distributed throughout sequence space. They are not clustered
> together in one tiny corner. The fact that one can get across the
> whole of sequence space without having to step very far from one to
> the next steppingstone simply means that the ratio of steppingstones
> vs. the non-viable "gap" options is rather high at this level of
> minimum structural threshold requirements - as in the case of 3-letter
> words. However, as you move up the ladder of threshold requirements,
> this ratio drops off exponentially. As this happens, the
> steppingstones drift apart rapidly. Pretty soon, it becomes very
> difficult to take the same short steps and hit any steppingstone at
> all.
>
>> Even in the abstract he makes clear that "In analogy to protein families,
>> nets are dense and well-separated in sequence space".
>
> Exactly! And they cover the entire space! The nets are dense because
> of the relatively high ratio that exists at such low levels of minimum
> structural threshold requirements.
No they don't; neither Bornberg-Bauer nor Choi say this. Bornberg is
referring to RNA sequences as percolating through sequence space; the HP
protein sequences he is examining did *not* do so. "Dense and
well-separated in sequence space" does *not* mean "distributed throughout
sequence-space".
When you appreciate this you will realise that your comments above are
misconceived.
Choi, by the way, says this:
"The fact that most of proteins are structured and that the protein
structure space is very sparsely populated and restricted mostly to the
four elongated regions suggest that mutations in genes encoding proteins
have been constrained to those resulting in a structurally viable protein
occupying one of the four allowed regions of the protein structure space:
structural selection or ??designability?? (17, 18)."
which, if read "carefully", should tell you something.
--
Robin Levett
rle...@rlevett.ibmuklunix.net (unmunge by removing big blue - don't yahoo)
richardal...@googlemail.com
> <richardalanforr...@googlemail.com> wrote:
> > On Feb 6, 4:15 pm, "Seanpit" <seanpitnos...@naturalselection.
> > 0catch.com> wrote:
> > > On Feb 6, 7:58 am, "_Arthur" <Arth...@sympatico.ca> wrote:
>
> > > > So thePitmanGap you invented extends not around proteins, but rather
> > > > around biological structures, now ?
>
> > > Both. It is just that the gap is much smaller for smaller protein-
> > > based functional structures (which usually include single proteins).
> > > The larger the minimum structural size and specificity requirement the
> > > larger the gap size. It's really very simple and downright intuitive.
>
> > ....and not supported by a shred of evidence.
>
> > How do you explain that, Sean?
>
> I want to ask Sean a question.
No point. Sean doesn't answer questions. It's against his religion,
whatever that may be.
RF
John Wilkins
> On Feb 6, 6:41 pm, j.wilki...@uq.edu.au (John Wilkins) wrote:
> > <richardalanforr...@googlemail.com> wrote:
> > > On Feb 6, 4:15 pm, "Seanpit" <seanpitnos...@naturalselection.
> > > 0catch.com> wrote:
> > > > On Feb 6, 7:58 am, "_Arthur" <Arth...@sympatico.ca> wrote:
> >
> > > > > So thePitmanGap you invented extends not around proteins, but rather
> > > > > around biological structures, now ?
> >
> > > > Both. It is just that the gap is much smaller for smaller protein-
> > > > based functional structures (which usually include single proteins).
> > > > The larger the minimum structural size and specificity requirement the
> > > > larger the gap size. It's really very simple and downright intuitive.
> >
> > > ....and not supported by a shred of evidence.
> >
> > > How do you explain that, Sean?
> >
> > I want to ask Sean a question.
>
> No point. Sean doesn't answer questions. It's against his religion,
> whatever that may be.
>
> RF
>
> >Do you think a 999aa change is possible?
So I see. I wonder why he won't answer.
Seanpit
The calculation is based on the likely minimum number of specifically
arranged proteins needed to achieve flagellar motility. Each protein
part also has a likely minimum number of residues. Given this
information, the total likely minimum can be roughly estimated to at
least a useful degree.
If you think this estimate is significnatly off based, then by all
means, do present your own estimate of the likely minimum structural
requirements. I'd be most interested.
Sean Pitman
www.DetectingDesign.com
_Arthur
If your own metric has any significance, you should apply it yourself,
don't you think ?
"Each protein also has a likely minimum of residues" -- You mean you
haven't computed it ?? -- Can you ?????
Von R. Smith
Pulling numbers out of your ass isn't a "calculation". You keep
suggesting that you've done the math needed to arrive at this
estimate. You've taken math classes; you know what it means to "show
your work", and why it's at least as important as the answer itself.
So show us your work.
> If you think this estimate is significnatly off based, then by all
> means, do present your own estimate of the likely minimum structural
> requirements. I'd be most interested.
I'd be most interested in an answer to a question that I asked you a
few weeks ago that you never answered:
How many "fairly specified" residues are there in each of the proteins
in the 2,4-DNT cascade? And again, please show your work.
gregwrld
If Sean could back up his work with numbers he'd publish it - and you
just
know that ain'ta gonna happen.
Pigs don't fly - no matter how high you drop 'em!
gregwrld
_Arthur
> > > The calculation is based on the likely minimum number of specifically
> > > arranged proteins needed to achieve flagellar motility. Each protein
> > > part also has a likely minimum number of residues. Given this
> > > information, the total likely minimum can be roughly estimated to at
> > > least a useful degree.
>
See ? Professor Pitman almost seem to know how to calculate the Pitman
Coefficent of a dozen proteins !
Now, Sean, show me how it's done. Show me a table with how many Fairly
Specificated AAs each of the 42 or so proteins has, and how much is
the Pitman Fidge Factor you throw on top. And why.
Seanpit
> > > > The calculation is based on the likely minimum number of specifically
> > > > arranged proteins needed to achieve flagellar motility. Each protein
> > > > part also has a likely minimum number of residues. Given this
> > > > information, the total likely minimum can be roughly estimated to at
> > > > least a useful degree.
>
> Coefficent of a dozen proteins !
>
> Specificated AAs each of the 42 or so proteins has, and how much is
I have them listed on my website dealing with flagellar motility . . .
Ron O
0catch.com> wrote:
> On Feb 5, 5:15 pm, "Ron O" <rokim...@cox.net> wrote:
>
>
>
>
>
> > > > This is a stupid analogy because SETI is looking for a signal that
> > > > they can differentiate from a natural occurring signal. If all they
> > > > were looking for is something far away from what is known, three
> > > > pulsars in close proximity would be considered a SETI signal because
> > > > if it did occur only once in the Universe that would be as far away as
> > > > they could get. Get a clue. There are certain criteria that they
> > > > have to look for, and if and when they ever detect something the
> > > > debate will be one as to what that something is. If all they had was
> > > > looking at the different proteins and claiming that there was
> > > > intelligent signal there they would be doomed because we see those
> > > > protein sequences evolving even today.
>
> > > Not true. We do not see protein sequences evolving even today at all
> > > beyond very low levels of functional complexity - not a single example
> > > goes beyond the 1000 specified amino acid residue structural threshold
> > > requirement. Therefore, finding such a functional system significantly
> > > beyond this threshold is most certainly the same thing as "a signal
> > > that they [SETI] can differentiate from a natural occurring signal."
> > > Why? Because it does not occur naturally at all and statistically it
> > > cannot occur this side of a practical eternity of time.
>
> > Pathetic evasion. Sean, what is good enough? Show us what is good
> > enough for you.
>
> Do you have problems with reading comprehension Ron? I just pointed
> out to you that no functional system that requires a minimum of more
> than 1000 specified amino acid residues evolves. Why not go about
> showing some examples beyond this threshold limitation? Why not
> explain why there are no current examples of evolution in action
> beyond this level? Why not explain why evolutionary mechanisms stall
> out very rapidly as this threshold is approached?
>
> > Put up your alternative and the evidence for it so
> > that we can see just how much your bullpucky of only low level changes
> > in functional complexity really matters. If what we have is so bad,
> > what does that tell you about the pathetic junk that you have to
> > believe means anything? Really, show us what you think is good
> > enough.
>
> Just one example would be fine Ron.
>
> > Ron Okimoto
>
> Sean Pitmanwww.DetectingDesign.com- Hide quoted text -
>
> - Show quoted text -
So, how many more years of denial and evasion do you intend to wallow
through? Would an honest sane person keep up this kind of basket case
behavior? Remember you were the one to make the claims. The fact
that you won't make good on them says what about the viability of your
position?
Ron Okimoto
Seanpit
I did answer you many many times on this. Cascades are not the same
as systems of function where all the parts have to be in a specific
arrangement relative to each other at the same time. Cascades are
therefore much much less specified; no more functionally complex then
the most complex single part that does require all its residues to be
in specific orientation at the same time.
Sean
Seanpit
> > Novel beneficial functions
> > have evolved with the use of one or two or even three or four
> > mutational steps. However, and try and catch this point, the
> > resulting functional system did not require more than a few hundred
> > fairly specified residues in order to work to some selective
> > advantage.
>
> And the evidence you have to back this assertion is.......?
Do you have any counter examples? No? Then, that's the evidence?
> There is plenty of evidence both from studies of the genemones of
> existing organisms and the fossil record that novel beneficial
> functions *have* evolved involving a far greater number of
> evolutionary steps that your arbitrary limit suggests.
The fossil record is assumed to be evolutionary without any
understanding of how your proposed mechanism could have done the job.
The same is true of studies of sequence homologies. The assumption
that homologies must have arisen via the evolutionary mechanism is
just that, an assumption unsupported by any relevant statistical
analysis and completely devoid of any demonstration beyond extremely
low levels of functional complexity - i.e., evolution *only* produces
functional systems that have a minimum structural requirement that is
far less than 1000 specifically arranged amino acid residues.
> Just to repeat a question I have asked many times and which you have
> not answered:
> What mechanism prevents the acquisition of more novel functions once
> one has been acquired?
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.
The reason for this, yet again (to include the paragraph I wrote
before just below this one), is that there is a growing non-beneficial
gap that stalls out the existing evolutionary mechanism in an
exponential manner as one considers functional systems approaching the
1000aa structural threshold. Come on now. I'm sure you can remember
this for next time - - maybe . . .
> > It is because the resulting function was a low-level function that the
> > gaps size was so small. Odds are that no functional systems that have
> > higher minimum structural threshold requirements will be as close to
> > anything in any member of any population. These odds are
> > exponentially reduced with each step up the ladder. By the time the
> > 1000aa level is considered, the odds that any gap will exist that is
> > only one or two mutations wide or even one or two dozen mutations wide
> > are extremely poor.
>
> The evidence from the real world shows that this is not the case.
> There is no evidence whatsoever to suggest that evolution stalls out
> at any level.
Why then are all the examples of evolution in action well below the
1000aa threshold? Why doesn't evolution produce anything beyond this
threshold when it produces so much below it? You honestly don't see a
stalling out effect as the 1000aa is approached? Are you blind?
> So even though you deny the evidence from the real world, that
> evidence shows that your model of evolution is wrong.
Where is there any evidence at all dealing with explaining how the
actual mechanism does what it is otherwise merely assumed that it
does? All your "evidences" say nothing about how your proposed
mechanism works. They all, and I mean all, do nothing more than
assume the mechanism with a wave of the hand - not even an attempt to
evaluate the actual statistical likelihood of it really doing the job
for which it was invoked as an explanation.
Remember now, demonstrating the possibility is NOT the same thing as
demonstrating the likelihood.
> > The odds follow a Poisson-type distribution. As one considers higher
> > and higher structural threshold requirements, the odds of a narrow gap
> > existing drop in such a way as to produce a Poisson distribution
> > pattern.
>
> What mechanism prevents the acquisition of further novel functions
> once one has been acquired?
> Each time such novel function is acquired, we are back to square one.
> Evolution, contrary to the model on which you insist, is not goal-
> oriented.
You're wrong. Evolution is goal oriented in that if it didn't find
any other novel beneficial sequences in sequence space, evolution
wouldn't happen. Just because no specific potentially beneficial
sequence need be found doesn't mean that none need be found.
The problem is that higher-level potential beneficial targets become
more and more widely separated in the vast ocean of sequence space.
They are like steppingstones that start moving farther and farther
apart, in a linear manner, as one moves up the ladder of functional
complexity. That is way finding the higher and higher level targets
becomes exponentially harder and harder to do.
> > That is why the likely minimum gap distance is always much smaller
> > than the threshold level. However, a gap distance of just a few dozen
> > would require evolutionary mechanisms in a huge population of, say,
> > all living things on Earth, trillions upon trillions of years to
> > cross.
>
> And how have you calculated "trillions upon trillions of years?
> Surely this is not another number you have pulled out of the air?
I've listed the calculation on my website dealing with flagellar
evolution. If you disagree, I'd be most interested in your own
calculations of how much extra time it would take as one moves up the
ladder of minimum structural threshold requirements. Really, what
estimate would you give of the increased amount of time required to
reach the next higher rung of the ladder?
> > With each step up the ladder the ratio of potentially beneficial
> > steppingstone targets decreases exponentially. That's a fact. What
> > results is a widening of the gap between steppingstone targets as one
> > moves higher and higher up the ladder.
>
> "Higher and higher" eh?
> This may come as news to you, but the idea of evolution as a great
> chain of being was discredited about 200 years ago.
> I suggest that you come to terms with the fact that you have
> substantial gaps in your knowledge of evolutionary theory.
Different types of functional systems require different minimum
structural requirements. Some require more and some require less.
Those that require more are on "higher" rungs of the ladder of
functional complexity. That's a non-arguable fact.
> Ah well.
> I'll just put back all the questions you refuse to answer:
>
> > Small mutational steps simply do not add up to move a population up
> > the ladder of minimum structural threshold requirements.
>
> Why not?
I've already explained this? Why put back repeat questions that I've
answered a dozen times already? Bad memory? You don't seem to
remember or comprehend from one paragraph to the next within the same
post.
> > There just
> > aren't any examples of such evolution in action in all of literature -
> > not one.
>
> There are very large numbers of papers which present of evidence for
> evolution as a series of mutational steps in the literature.
> Dismissing them as "not convincing", as is your habit, will not make
> them go away.
As I've pointed out at least 50 times in this forum so far, not one of
these is an observed example of evolution in action. All observed
examples of evolution in action, and there are many of them, are well
below the 1000aa threshold.
> So where are the conclusions drawn by the authors of papers presenting
> evidence for evolution as a series of mutational steps flawed?
> You need to address the evidence, not simply ignore it.
The authors never go into any statistical analysis of the proposed
evolutionary mechanism. They all assume, without exception, that the
mechanism simply did the job. Many authors even use the word "assume"
when they employ the evolutionary mechanism. "We assume that gene
duplication combined with random mutations . . ." No actual
statistical evaluation of the odds of the mechanism actually working
according to the assumption is provided.
> > Your cockroach milk evolution example isn't even a real time
> > example
>
> Since when has observation in "real time" been a requirement in
> science?
I'm just saying that real time examples/testability are much more
reliable than assumptions. All real time examples of evolution in
action are well below the 1000aa threshold - to include this example
of yours which isn't even real time.
> What mechanism prevents further changes to the genomenes of these
> cockroaches?
Nothing prevents further evolutionary changes at low levels. However,
expanding non-beneficial gaps prevents further changes that produce
novel functions *above* the 1000aa threshold.
> Once such a novel function has been acquired, what mechanism prevents
> the acquisiting of another novel function?
Nothing if additional novel functions are also below the 1000aa
threshold.
> Or the loss of the acquired function?
Natural selection prevents the loss once the threshold structural
requirements of a novel beneficial function are actually realized.
> This is, after all how evolutionary theory models the evolution of
> more complex functions.
This model cannot work if the minimum structural threshold
requirements that are needed for more and more complex functions are
more and more separated from each other in sequence space.
Again, this is all repetitive stuff I've explained already - -
< snip rest >
Sean Pitman
www.DetectingDesign.com
Seanpit
> I want to askSeana question. Do you think a 999aa change is possible?
I did answer this question several days ago, but for some reason it
never showed up after I posted it. Go figure?
Anyway, of course a 999aa change is possible as is a 1000aa or
10,000aa change. Such changes happen all the time. It is just that
they never hit upon a novel type of functional system that has minimum
structural threshold requirements greater than 1000 specifically
arranged amino acid residues.
I've pointed this out many times in this forum already and even in
this thread, but perhaps you've missed it somehow? There's a big
difference between producing large changes and producing a novel
function that requires a large minimum structural threshold
requirement. The possibility of hitting such a high-level target
isn't the same thing as having good odds of hitting it.
> John S. Wilkins, Postdoctoral Research Fellow, Biohumanities Project
> University of Queensland - Blog: scienceblogs.com/evolvingthoughts
> "He used... sarcasm. He knew all the tricks, dramatic irony, metaphor,
> bathos, puns, parody, litotes and... satire. He was vicious."- Hide quoted text -
Sean Pitman
www.DetectingDesign.com
Seanpit
> <richardalanforr...@googlemail.com> wrote:
> > On Feb 6, 6:41 pm, j.wilki...@uq.edu.au (John Wilkins) wrote:
> > > <richardalanforr...@googlemail.com> wrote:
> > > > On Feb 6, 4:15 pm, "Seanpit" <seanpitnos...@naturalselection.
> > > > 0catch.com> wrote:
> > > > > On Feb 6, 7:58 am, "_Arthur" <Arth...@sympatico.ca> wrote:
>
> > > > > > So thePitmanGap you invented extends not around proteins, but rather
> > > > > > around biological structures, now ?
>
> > > > > Both. It is just that the gap is much smaller for smaller protein-
> > > > > based functional structures (which usually include single proteins).
> > > > > The larger the minimum structural size and specificity requirement the
> > > > > larger the gap size. It's really very simple and downright intuitive.
>
> > > > ....and not supported by a shred of evidence.
>
> > > > How do you explain that,Sean?
>
>
> > whatever that may be.
LOL - Oh please Richard! I dare say I've answered more questions of
yours than has any other creationist in this forum. I just don't have
the time to respond to everything. There are many many of you guys
and only one of me - - and I'm quite busy anyway with many other
things.
> > RF
>
> > >Do you think a 999aa change is possible?
>
> So I see. I wonder why he won't answer.
See seperate post in reply to this specific question:
> John S. Wilkins, Postdoctoral Research Fellow, Biohumanities Project
> University of Queensland - Blog: scienceblogs.com/evolvingthoughts
> "He used... sarcasm. He knew all the tricks, dramatic irony, metaphor,
> bathos, puns, parody, litotes and... satire. He was vicious."
Sean Pitman
www.DetectingDesign.com
Von R. Smith
No response?
>
> > > If you think this estimate is significnatly off based, then by all
> > > means, do present your own estimate of the likely minimum structural
> > > requirements. I'd be most interested.
>
> > I'd be most interested in an answer to a question that I asked you a
> > few weeks ago that you never answered:
> > How many "fairly specified" residues are there in each of the proteins
> > in the 2,4-DNT cascade? And again, please show your work.
>
> I did answer you many many times on this.
No, you didn't. An answer would consist of a number of residues for
each protein, along with an explanation of how you arrived at each
number. You have never provided this. If you have, please either
reproduce them or link me to a post where you provided them. Until
you do, my question remains unanswered.
> Cascades are not the same
> as systems of function where all the parts have to be in a specific
> arrangement relative to each other at the same time. Cascades are
> therefore much much less specified; no more functionally complex then
> the most complex single part that does require all its residues to be
> in specific orientation at the same time.
Right now, I am not asking you about the overall complexity of the
cascade; I am asking you about how many fairly specified residues
there are in each protein. Where are the numbers? Where is your work?
richardal...@googlemail.com
0catch.com> wrote:
> On Feb 6, 12:08 pm, richardalanforr...@googlemail.com wrote:
>
> > > Novel beneficial functions
> > > have evolved with the use of one or two or even three or four
> > > mutational steps. However, and try and catch this point, the
> > > resulting functional system did not require more than a few hundred
> > > fairly specified residues in order to work to some selective
> > > advantage.
>
> > And the evidence you have to back this assertion is.......?
>
> Do you have any counter examples? No? Then, that's the evidence?
So you have no evidence in other words.
If you propose a model, it's up to you to provide the evidence to
support it.
You have no evidence.
>
> > There is plenty of evidence both from studies of the genemones of
> > existing organisms and the fossil record that novel beneficial
> > functions *have* evolved involving a far greater number of
> > evolutionary steps that your arbitrary limit suggests.
>
> The fossil record is assumed to be evolutionary without any
> understanding of how your proposed mechanism could have done the job.
Are you serious?
I suggest that you educate yourself in evolutionary biology,
especially on the relationship between evolution and development. It's
called "evo-devo".
> The same is true of studies of sequence homologies. The assumption
> that homologies must have arisen via the evolutionary mechanism is
> just that, an assumption unsupported by any relevant statistical
> analysis and completely devoid of any demonstration beyond extremely
> low levels of functional complexity - i.e., evolution *only* produces
> functional systems that have a minimum structural requirement that is
> far less than 1000 specifically arranged amino acid residues.
I have no idea what you mean by this, and doubt that you do either.
We trace homologies by a number of different methods. We can identify
the genes whose expression causes limb buds to develope, and find the
same genes in a huge range of different animals doing the same job. We
know which genes intiate the division of the vertebral column into
different morphological zones, and find the same genes doing the same
job in zebrafish, chickens and mice. Because of that we assume that
such structures are homologous. We find the same basic pattern in the
layout of bones in the limbs of all tetrapods. All such limbs consist
of a single long bone, then a pair of long bones, and then a series of
bones of diminishing size organised usually as five digits. Even in
animals which do not have five digits when adult, we find that there
are five in embryos which are reabsorbed during ontogeny. Therefore is
is a reasonable assumption that the bones we indentify as humeri in
Tiktaalik, Cryptoclidus, Archaeopteryx, Homo and every other tetrapod
are homologues.
What's your explanation? Pure chance? And if it is "common
design" (which is not an explanation at all, but a post hoc
justifucation), how do you explain the fact that the tibia and fibula
of many ungulates develope as separate bones but fuse as the animal
matures to form a single structural element?
>
> > Just to repeat a question I have asked many times and which you have
> > not answered:
> > What mechanism prevents the acquisition of more novel functions once
> > one has been acquired?
>
> 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.
So what?
> They will all be at the same low level of minimum
> structural complexity or lower - not higher than the 1000aa threshold.
>
Why on earth do they need to be?
Evolution does not demand such saltational leaps.
Just because I can't jump 100 meters does not mean that I can't walk
across a football field.
> The reason for this, yet again (to include the paragraph I wrote
> before just below this one), is that there is a growing non-beneficial
> gap that stalls out the existing evolutionary mechanism in an
> exponential manner as one considers functional systems approaching the
> 1000aa structural threshold. Come on now. I'm sure you can remember
> this for next time - - maybe . . .
Once again you are making and unfounded assertion. You still have not
justified either the need for evolutionary processes to make the
saltational leap you insist is necessary, nor your "1000aa threshold"
as having any support from any evidence. Futhermore, you have
presented no evidence whatsoever that evolution "stalls out".
>
> > > It is because the resulting function was a low-level function that the
> > > gaps size was so small. Odds are that no functional systems that have
> > > higher minimum structural threshold requirements will be as close to
> > > anything in any member of any population. These odds are
> > > exponentially reduced with each step up the ladder. By the time the
> > > 1000aa level is considered, the odds that any gap will exist that is
> > > only one or two mutations wide or even one or two dozen mutations wide
> > > are extremely poor.
>
> > The evidence from the real world shows that this is not the case.
> > There is no evidence whatsoever to suggest that evolution stalls out
> > at any level.
>
> Why then are all the examples of evolution in action well below the
> 1000aa threshold?
Because there is no need whatsoever to invoke such saltational leaps
in evolutionary theory. Evolution can produce novel functions without
the need to break your "1000aa threshold".
> Why doesn't evolution produce anything beyond this
> threshold when it produces so much below it?
What explanation other than evolution do you have which explains the
gradation in forms we see in the fossil record representing the
modification of the jaw bones of reptiles into the ear bones of
mammals? Or the reduction of limb bones in fossil whales to form
flippers? Or the gradual modification of cursorial limb bones in
primitive sauropterygians into fully aquatic flippers in plesiosaurs?
The scientific explanation is that they evolved, and this theoretical
framework not only provides a sound explanation for these changes, but
makes predictions about the intermediate forms which we have not yet
found.
If your explanation is "common design", please provide a mechanism for
"common design" and make a prediction based on the limitations of that
mechanism about something we have not yet found in the fossil record.
> You honestly don't see a
> stalling out effect as the 1000aa is approached? Are you blind?
No I don't.
I see you waving your hands (metaphorically speaking), pulling numbers
out of the air, making unfounded assertion, not providing one scrap of
supporting evidence, and proposing a model of evolution which is not
supported by any scientific evidence which you have invented for no
reason other than to falsify it.
>
> > So even though you deny the evidence from the real world, that
> > evidence shows that your model of evolution is wrong.
>
> Where is there any evidence at all dealing with explaining how the
> actual mechanism does what it is otherwise merely assumed that it
> does? All your "evidences" say nothing about how your proposed
> mechanism works.
They most certainly do. The mechanisms of evolution impose very strict
constraints on what can and can't evolve. We know a lot about the
mechanisms of evoltion, and are learning more every week as research
progresses.
> They all, and I mean all, do nothing more than
> assume the mechanism with a wave of the hand -
This is utterly ridiculous. Do you seriously have no idea of the sheer
volume of research output in the field of "evo-devo"? That's all about
the mechanisms of evolution, and far from being assumed "with a wave
of the hand" is an vibrantly active area of research in which every
aspect of what we have learned about evolutionary mechanisms is
subjected to intense scrutiny at a fundamental level
> not even an attempt to
> evaluate the actual statistical likelihood of it really doing the job
> for which it was invoked as an explanation.
>
You have not made any serious proposal for a statistical method of
investigating anything, and your posts here show that your knowledge
of statistics is rather poor.
> Remember now, demonstrating the possibility is NOT the same thing as
> demonstrating the likelihood.
Which is completely irrelevant as you have not proposed any viable
model which can be subjected to statistical analysis.
>
> > > The odds follow a Poisson-type distribution. As one considers higher
> > > and higher structural threshold requirements, the odds of a narrow gap
> > > existing drop in such a way as to produce a Poisson distribution
> > > pattern.
>
> > What mechanism prevents the acquisition of further novel functions
> > once one has been acquired?
> > Each time such novel function is acquired, we are back to square one.
> > Evolution, contrary to the model on which you insist, is not goal-
> > oriented.
>
> You're wrong. Evolution is goal oriented in that if it didn't find
> any other novel beneficial sequences in sequence space, evolution
> wouldn't happen.
Quite so. But they do, and evolution carries on quite happily.
The point is that evolution is not moving towards a predetermined
target as you imply.
> Just because no specific potentially beneficial
> sequence need be found doesn't mean that none need be found.
And evolutionary mechanisms find these beneficial sequences.
>
> The problem is that higher-level potential beneficial targets become
> more and more widely separated in the vast ocean of sequence space.
No matter how many times you make this assertion, it will not become
true or represent any meaningful model of evolutionary theory.
> They are like steppingstones that start moving farther and farther
> apart, in a linear manner, as one moves up the ladder of functional
> complexity.
You have been presented with evidence that this is not the case, and
that protein sequences are not as specified as you insist, nor as
widely separated in sequence space as your "theory" demands. I suggest
that you address that evidence rather than misrepresenting the
conclusions of the authors of the papers are you have done.
> That is way finding the higher and higher level targets
> becomes exponentially harder and harder to do.
>
> > > That is why the likely minimum gap distance is always much smaller
> > > than the threshold level. However, a gap distance of just a few dozen
> > > would require evolutionary mechanisms in a huge population of, say,
> > > all living things on Earth, trillions upon trillions of years to
> > > cross.
>
> > And how have you calculated "trillions upon trillions of years?
> > Surely this is not another number you have pulled out of the air?
>
> I've listed the calculation on my website dealing with flagellar
> evolution.
You calculations are not based on the model for the evolution of the
bacterial flagellum which has been proposed by the biologist who have
worked on the material. Behe dismissed all this evidence without even
reading it as "unconvincing", so I guess you imagine that this is the
approach of a scientist to such material.
A word of advice: it isn't, and what's more it's deeply dishonest.
Your calculations are of no value, as they are based on a model of the
evolution of the flagellum which you have devised for no reason other
than to falsify it. I suggest that your approach is as honest as
Behe's.
> If you disagree, I'd be most interested in your own
> calculations of how much extra time it would take as one moves up the
> ladder of minimum structural threshold requirements. Really, what
> estimate would you give of the increased amount of time required to
> reach the next higher rung of the ladder?
Haven't a clue.
It's not my field, and in any case I don't place any value in
statistical calculations of such mechanisms. Science advances by
addressing what we don't know, and just because we cannot detail at
the smallest possible level the evolution of every system in every
living organism it does not mean that evolutionary theory is
falsified. So long as there are unknowns in our knowledge of the
mechanisms involved, no statistical calculation has any meaning. One
cannot attach a probability to an unknown mechanism.
>
> > > With each step up the ladder the ratio of potentially beneficial
> > > steppingstone targets decreases exponentially. That's a fact. What
> > > results is a widening of the gap between steppingstone targets as one
> > > moves higher and higher up the ladder.
>
> > "Higher and higher" eh?
> > This may come as news to you, but the idea of evolution as a great
> > chain of being was discredited about 200 years ago.
> > I suggest that you come to terms with the fact that you have
> > substantial gaps in your knowledge of evolutionary theory.
>
> Different types of functional systems require different minimum
> structural requirements. Some require more and some require less.
> Those that require more are on "higher" rungs of the ladder of
> functional complexity. That's a non-arguable fact.
And those "higher" levels can be reached in small incremental steps,
as the evidence from genetics and the fossil record demonstrates.
>
> > Ah well.
> > I'll just put back all the questions you refuse to answer:
>
> > > Small mutational steps simply do not add up to move a population up
> > > the ladder of minimum structural threshold requirements.
>
> > Why not?
>
> I've already explained this? Why put back repeat questions that I've
> answered a dozen times already? Bad memory? You don't seem to
> remember or comprehend from one paragraph to the next within the same
> post.
You have not explained this. You have merely repeated the assertion
that steps above a threshold level you have invented do not occur. You
have provided no evidence to support your assertions.
>
> > > There just
> > > aren't any examples of such evolution in action in all of literature -
> > > not one.
>
> > There are very large numbers of papers which present of evidence for
> > evolution as a series of mutational steps in the literature.
> > Dismissing them as "not convincing", as is your habit, will not make
> > them go away.
>
> As I've pointed out at least 50 times in this forum so far, not one of
> these is an observed example of evolution in action.
Why is there a need to observe evolution in action? Evolutionary
theory provides the best explanation for the evidence, and makes
predictions about unknown forms. There is no other theory in science
which provides any other explanation, nor makes any predictions.
> All observed
> examples of evolution in action, and there are many of them, are well
> below the 1000aa threshold.
So what?
This is evidence that evolution can produce novel functions without
the need to cross the arbitrary threshold you have invented.
>
> > So where are the conclusions drawn by the authors of papers presenting
> > evidence for evolution as a series of mutational steps flawed?
> > You need to address the evidence, not simply ignore it.
>
> The authors never go into any statistical analysis of the proposed
> evolutionary mechanism.
Why should they?
> They all assume, without exception, that the
> mechanism simply did the job. Many authors even use the word "assume"
> when they employ the evolutionary mechanism. "We assume that gene
> duplication combined with random mutations . . ." No actual
> statistical evaluation of the odds of the mechanism actually working
> according to the assumption is provided.
On what basis would you make a such a statistical evaluation?
The paper which details the evidence is there on the internet.
Come up with a proposal.
I should add that I have no idea how such a statistical evaluation
could be performed in any meaningful way.
>
> > > Your cockroach milk evolution example isn't even a real time
> > > example
>
> > Since when has observation in "real time" been a requirement in
> > science?
>
> I'm just saying that real time examples/testability are much more
> reliable than assumptions.
They are? It all depends on the nature of the evidence.
Nobody has observed the orbit of Pluto in "real time", but it's a
pretty good bet that it has been modelled acurately.
> All real time examples of evolution in
> action are well below the 1000aa threshold - to include this example
> of yours which isn't even real time.
>
Since when has observation in "real time" been a requirement for
science?
> > What mechanism prevents further changes to the genomenes of these
> > cockroaches?
>
> Nothing prevents further evolutionary changes at low levels. However,
> expanding non-beneficial gaps prevents further changes that produce
> novel functions *above* the 1000aa threshold.
You have provided no evidence whatsoever for "expanding non-beneficial
gaps". The molecular evidence cited by others on this thread suggests
that the "beneficial sequences" are closely clustered in phase space,
any not specific in the way you insist.
>
> > Once such a novel function has been acquired, what mechanism prevents
> > the acquisiting of another novel function?
>
> Nothing if additional novel functions are also below the 1000aa
> threshold.
So there is no mechanism which prevents the acquisition of "higher"
functions in a series of steps. This is, after all, the model of
evolution which is accepted by all working biologists.
Why do you insist on the need for saltational leaps?
>
> > Or the loss of the acquired function?
>
> Natural selection prevents the loss once the threshold structural
> requirements of a novel beneficial function are actually realized.
>
It does?
How?
We have many examples in biology of organisms which have lost acquired
functions or subverted them to other purposes. Are you suggesting that
this is impossible? If so, how do you explain the evidence?
> > This is, after all how evolutionary theory models the evolution of
> > more complex functions.
>
> This model cannot work if the minimum structural threshold
> requirements that are needed for more and more complex functions are
> more and more separated from each other in sequence space.
But they aren't, so your objection is not valid.
>
> Again, this is all repetitive stuff I've explained already - -
What you are doing here is persisting in an utterly discredited
argunment which is based on nothing other than your unfounded
assertions and ignoring any evidence which demonstrates that it is
false. You mispresent and distort the words of the authors of the
papers you cite in support of your "theory", and ignore those parts of
the papers which don't suit you.
You are not submitting your ideas to review, something which I know
you won't because you are an intellectual coward who prefers to
pontificate on subjects about which you know very little to boost your
status in the creationist community rather than to learn about them
and make any genuine contribution to science.
Which confirms that you are a moral and intellectual coward.
RF
>
> < snip rest >
>
> Sean Pitmanwww.DetectingDesign.com
John Wilkins
> On Feb 6, 10:41 am, j.wilki...@uq.edu.au (John Wilkins) wrote:
>
> > I want to askSeana question. Do you think a 999aa change is possible?
>
> I did answer this question several days ago, but for some reason it
> never showed up after I posted it. Go figure?
There's a functional gap involved.
>
> Anyway, of course a 999aa change is possible as is a 1000aa or
> 10,000aa change. Such changes happen all the time. It is just that
> they never hit upon a novel type of functional system that has minimum
> structural threshold requirements greater than 1000 specifically
> arranged amino acid residues.
>
> I've pointed this out many times in this forum already and even in
> this thread, but perhaps you've missed it somehow? There's a big
> difference between producing large changes and producing a novel
> function that requires a large minimum structural threshold
> requirement. The possibility of hitting such a high-level target
> isn't the same thing as having good odds of hitting it.
I don't get your point. If a 10aa mutation can hit a novel function,
then an 11aa muation can hit one. And so on, up to a 999aa mutation.
Hence, by mathematical induction, a 1000aa mutation can hit one. Yes,
the odds decrease inversely to the number of amino acid changes, but
that is very far from proving that there is a threshold at 1000aa.
So my question is really this: What makes it a threshold? As I
understand molecular genetics and protein biology, most mutations are
caused by point mutations, which are low in absolute change but high in
potential outcome, pr by duplications, which allow point mutations in
one of the paralogous pairs to, over time, accrue novel functions.
Nothing I know about this process suggests, nor have I read any science
that might suggest, that there is a limit to the amount of novelty that
can be formed this way. You are making, as I understand it from skimming
but not reading closely, a radical claim - there is a limit to the
amount of change, or the odds set up a threshold that limits change. But
I don't see this as necessary.
So, given that time and population size adds the odds up arithmetically,
the odds aainst reduce dramatically for any single novelty. Given also
that there are a *large* [in the mathematical sense] number of viable
novel functions that *might* work, it becomes effectively necessary that
large scale functional changes will occur. The onus, I suggest, is on
you to make the argument that there is a threshold.
Now you might do this in a number of ways. One might be to show
empirical evidence this occurs (and which would then call for
explanation given what we know, but you don't need to have an
explanation to show that it is a fact).
Another might be to show that it follows from our present knowledge of
the mathematical dynamics of molecular biology - that it is an
implication of stuff we *do* know, but which nobody before you or your
source has noticed before.
A third might be to show that there are novel facts in play - such as
contraints on protein conformations - that change the odds and the
argument from induction.
Have you done any of these things? In what I have read, I haven't seen
it, but I may have missed it. So far as I can tell, you merely assert
that functional novelty at 1000aa or above is not possible. And I say,
based on everything I have read about protein evolution, that it *is*.
Show me wrong. If you can, I will be the first to admit that I am. I
don't have the time to wade through large amounts of web-material on
your site. I find it too confusing. But if you have a simple page that
addresses this exact question clearly, post the link, and I'll copy the
relevant sections here and address them (one way or the other) point for
point. But if you can give a clear argument to this thread, I would
appreciate it.
--
Perplexed in Peoria
"John Wilkins" <j.wil...@uq.edu.au> wrote in message news:1htdi0i.1g1kpn9y3s8d0N%j.wil...@uq.edu.au...
That would truly be a cite for sorites.
John, I think that you are misinterpreting the nature of the 1000aa
'threshold'. It is not a physical, chemical, or biochemical threshold.
It is a threshold of incredulity. Sean is willing to believe, given
the age of the earth and the size of biological populations, that novel
functions can arise by chance. He is willing to concede that a novel
function requiring 500aa, say, might have arisen by chance, and since
evolved under NS to exquisite precision. He is even willing to concede
that since its origin, the proteins implementing this function have grown
in size by mutational accretion so that they are now 2000aa in length.
However, he is unwilling to believe that an evolving protein clade
could have originated by chance at a size greater than, say, 1000aa,
already implementing a selectable function, and evolving under NS
from there.
His choice of the number 1000 is fairly arbitrary. It is larger than
the limits of his credulity, but smaller than the size of novel
proteins which he assumes are required by evolutionary theory.
Sean, let me know if I have seriously distorted your thinking here.
richardal...@googlemail.com
0catch.com> wrote:
> On Feb 7, 3:51 am, j.wilki...@uq.edu.au (John Wilkins) wrote:
>
>
>
> > <richardalanforr...@googlemail.com> wrote:
> > > On Feb 6, 6:41 pm, j.wilki...@uq.edu.au (John Wilkins) wrote:
> > > > <richardalanforr...@googlemail.com> wrote:
> > > > > On Feb 6, 4:15 pm, "Seanpit" <seanpitnos...@naturalselection.
> > > > > 0catch.com> wrote:
> > > > > > On Feb 6, 7:58 am, "_Arthur" <Arth...@sympatico.ca> wrote:
>
> > > > > > > So thePitmanGap you invented extends not around proteins, but rather
> > > > > > > around biological structures, now ?
>
> > > > > > Both. It is just that the gap is much smaller for smaller protein-
> > > > > > based functional structures (which usually include single proteins).
> > > > > > The larger the minimum structural size and specificity requirement the
> > > > > > larger the gap size. It's really very simple and downright intuitive.
>
> > > > > ....and not supported by a shred of evidence.
>
> > > > > How do you explain that,Sean?
>
> > > > I want to askSeana question.
>
> > > No point.Seandoesn't answer questions. It's against his religion,
> > > whatever that may be.
>
> LOL - Oh please Richard! I dare say I've answered more questions of
> yours than has any other creationist in this forum. I just don't have
> the time to respond to everything. There are many many of you guys
> and only one of me - - and I'm quite busy anyway with many other
> things.
Making unfounded assertions is not answering questions, and no matter
how many times you repeat your unfounded assertions, they are still no
more than unfounded assertions.
You make assertions such as the one on your web site that rapid burial
is essential for exceptional preservation.
It isn't. There is an extensive literature on the subject of
taphonomy, and I have advised you of numerous papers, many of which
are available on-line, which show quite clearly and categorically that
your assertion is false.
It isn't, and your facile dismisal of this evidence on the grounds
that you are not convinced carries no weight whatsover. There is
little indication that you have read any of the material which shows
that you are wrong, and the fact that you have not changed your web
site demonstrates that you have no interest in supporting your
argument or learning about the subject. I can only surmise that you
maintain your web site only to give the impression of scholarship to
creationists who don't know any better.
It is evident from postings on this forum that you have managed to
fool some of them, though it is also evident that your supporters have
quite interpretations of the Biblical account than yours. Such
conflicts are apparently irrelevant to them. All that concerns them is
that someone using language which seems scientific supports some
aspect of their convictions.
The fact that you have coauthored an number of scientific papers
suggests that you understand the processes and nature of academic
publishing, and in particular the fact that no author can dismiss the
evidence offered against their conclusions on the grounds of argument
from incredulity. You have asserted that argument from incredulity has
a place in science. This statement is categorically false, and any
scientist arguing in any publication that they do no accept evidence
which contradicts their conclusions for no reason other than that they
are not convinced would be severely criticised by any competent
reviewer. If you are not convinced, you need to give the reasons *why*
you are not convinced and support your reasons with evidence.
Again, it may be that you think that you are making some sort of point
by the antics of evasion which you demonstrate on this forum, and
perhaps you can fool some creationists that you have some sort of
case. What is clear is that no scientist is taken in for a moment by
your pontification on subjects about which it quickly becomes clear
that your knowledge is severely limited. Perhaps this gives you some
sort of satisfaction, but if your ambition is to persuade any
scientist that your proposition has any merit whatsover, you need to
address the evidence.
RF
John Wilkins
> "John Wilkins" <j.wil...@uq.edu.au> wrote...
When you get to Plato's heaven, you are gonna pay for that.
>
> John, I think that you are misinterpreting the nature of the 1000aa
> 'threshold'. It is not a physical, chemical, or biochemical threshold.
> It is a threshold of incredulity. Sean is willing to believe, given
> the age of the earth and the size of biological populations, that novel
> functions can arise by chance. He is willing to concede that a novel
> function requiring 500aa, say, might have arisen by chance, and since
> evolved under NS to exquisite precision. He is even willing to concede
> that since its origin, the proteins implementing this function have grown
> in size by mutational accretion so that they are now 2000aa in length.
> However, he is unwilling to believe that an evolving protein clade
> could have originated by chance at a size greater than, say, 1000aa,
> already implementing a selectable function, and evolving under NS
> from there.
>
> His choice of the number 1000 is fairly arbitrary. It is larger than
> the limits of his credulity, but smaller than the size of novel
> proteins which he assumes are required by evolutionary theory.
>
> Sean, let me know if I have seriously distorted your thinking here.
That is also a good way to get Sean to clarify his claims. OK, Sean - is
this correct, and if so, why do you set the limit arbitrarily where you
do? Is it not arbitrary?
hersheyh
Isn't this number simply the total number of aa residues in some
specific bacterial flagella or some arbitrary large fraction thereof?
How do you calculate the number of "fairly specified" aa residues in
this *specific* case? How do you calculate the gap size from that
number of "fairly specified" aa residues? How do you deal with
mutations that produce chimeric proteins rather than point mutations?
How do you deal with proteins/protein structures in the eubacterial
flagella that have alternative useful *functions* that do not rely on
it being a part of a flagella? There are many *subfunctions* of parts
of different proteins in flagella; why do you focus entirely on a
single function of rotary motility? Given that one can, in principle
and also in practice, generate the *function* of rotary motility from
structures that have potential (and real) independent utilities in one
or a very few mutational step(s), why is the total number of aa
residues relevant to producing that *function*? Given that the
*function* of rotary motility can be generated by a similar linking of
pre-existing motor (but not the same one that eubacteria use) and whip-
containing pore (but not the same one that eubacteria use) in
archaebacteria and that there are even massive modifications of the
eubacterial flagella in different eubacteria (e.g. spirochaetes), why
do you think that the eubacterial flagella had to start from a random
useless sequence to produce the end result?
Curious minds want to know.
hersheyh
So, in mitochondria, the cascades that are represented by complexes
(proteins that adhere to one another and thereby increase the
efficiency of electron transfer within the complex) are evolutionarily
impossible because they adhere to one another whereas if they (less
efficiently) performed the same sequence as a cascade, they would be
"much much less specified"? How many mutational steps do you think
are necessary to cause proteins to adhere to one another to some
extent?
Seanpit
> Seanpit <seanpitnos...@naturalselection.0catch.com> wrote:
> > On Feb 6, 10:41 am, j.wilki...@uq.edu.au (John Wilkins) wrote:
>
> > > I want to askSeana question. Do you think a 999aa change is possible?
>
> > I did answer this question several days ago, but for some reason it
> > never showed up after I posted it. Go figure?
>
> There's a functional gap involved.
>
> > Anyway, of course a 999aa change is possible as is a 1000aa or
> > 10,000aa change. Such changes happen all the time. It is just that
> > they never hit upon a novel type of functional system that has minimum
> > structural threshold requirements greater than 1000 specifically
> > arranged amino acid residues.
>
> > I've pointed this out many times in this forum already and even in
> > this thread, but perhaps you've missed it somehow? There's a big
> > difference between producing large changes and producing a novel
> > function that requires a large minimum structural threshold
> > requirement. The possibility of hitting such a high-level target
> > isn't the same thing as having good odds of hitting it.
>
> I don't get your point. If a 10aa mutation can hit a novel function,
> then an 11aa muation can hit one.
Yes, but the odds of success for a given attempt are exponentially
less likely.
> And so on, up to a 999aa mutation.
> Hence, by mathematical induction, a 1000aa mutation can hit one.
That's true, but its about as likely as you winning the California
lottery 50 times in a row. Its possible, but very very unlikely at
this level this side of trillions upon trillions of years of time.
> Yes,
> the odds decrease inversely to the number of amino acid changes, but
> that is very far from proving that there is a threshold at 1000aa.
The odds decrease exponentially with the needed number of character
changes. The threshold is the point at which the mechanism clearly
looses ability to act in any sort of meaningful way. Statistically the
evolutionary mechanism just isn't believable any more as a creative
force beyond the 1000aa level; even for an extremely large population
of living things.
> So my question is really this: What makes it a threshold? As I
> understand molecular genetics and protein biology, most mutations are
> caused by point mutations, which are low in absolute change but high in
> potential outcome, pr by duplications, which allow point mutations in
> one of the paralogous pairs to, over time, accrue novel functions.
There are many types of mutations. Point mutations are only one type.
There are also duplication mutations and deletions and frame-shift
mutations ect. Without the help of natural selection, these mutations
are purely random. It is therefore natural selection that is suppose
to help evolution overcome the time problem that randomness creates.
However, natural selection is not in play until the novel beneficial
sequence is actually found via purely random searches of sequence
space. At higher levels of functional complexity, beyond the 1000aa
threshold, the gaps between potentially beneficial sequences are
enormous. The gaps are so enormous at this level that randomly
finding any beneficial sequence at this level requires an average time
of trillions upon trillions of years.
> Nothing I know about this process suggests, nor have I read any science
> that might suggest, that there is a limit to the amount of novelty that
> can be formed this way. You are making, as I understand it from skimming
> but not reading closely, a radical claim - there is a limit to the
> amount of change, or the odds set up a threshold that limits change. But
> I don't see this as necessary.
Then you don't understand the problem that exponentially increasing
time averages bring to the table.
> So, given that time and population size adds the odds up arithmetically,
> the odds aainst reduce dramatically for any single novelty.
That's true as long as you can increase the population's size
exponentially with each step of the structural threshold ladder. It
is just that population sizes have limits that are far too small to
cross the 1000aa threshold this side of a practical eternity of time.
> Given also
> that there are a *large* [in the mathematical sense] number of viable
> novel functions that *might* work, it becomes effectively necessary that
> large scale functional changes will occur. The onus, I suggest, is on
> you to make the argument that there is a threshold.
There are a large number of potentially beneficial functions within
high-level sequence space. However, there is a far far larger number
of non-beneficial sequences in high-level sequence space as well that
is exponentially greater than existed at lower levels. In other
words, it is the ratio of potentially beneficial vs. non-beneficial
that is important here - not so much the absolute number of
potentially beneficial sequences.
> Now you might do this in a number of ways. One might be to show
> empirical evidence this occurs (and which would then call for
> explanation given what we know, but you don't need to have an
> explanation to show that it is a fact).
>
> Another might be to show that it follows from our present knowledge of
> the mathematical dynamics of molecular biology - that it is an
> implication of stuff we *do* know, but which nobody before you or your
> source has noticed before.
>
> A third might be to show that there are novel facts in play - such as
> contraints on protein conformations - that change the odds and the
> argument from induction.
>
> Have you done any of these things? In what I have read, I haven't seen
> it, but I may have missed it. So far as I can tell, you merely assert
> that functional novelty at 1000aa or above is not possible. And I say,
> based on everything I have read about protein evolution, that it *is*.
I never said that crossing the 1000aa was impossible. I've said many
times that such a feat is possible. It is just extremely unlikely
this side of a practical eternity of time - like you winning the CA
Lottery 50 times in a row.
Tell me, why do you think all the examples of evolution "in action"
produce functions with far lower minimum structural threshold
requirements than 1000 specifically arranged amino acid residues?
What is your answer to this fact?
> Show me wrong. If you can, I will be the first to admit that I am. I
> don't have the time to wade through large amounts of web-material on
> your site. I find it too confusing. But if you have a simple page that
> addresses this exact question clearly, post the link, and I'll copy the
> relevant sections here and address them (one way or the other) point for
> point. But if you can give a clear argument to this thread, I would
> appreciate it.
I've done both.
> John S. Wilkins, Postdoctoral Research Fellow, Biohumanities Project
> University of Queensland - Blog: scienceblogs.com/evolvingthoughts
> "He used... sarcasm. He knew all the tricks, dramatic irony, metaphor,
> bathos, puns, parody, litotes and... satire. He was vicious."
Sean Pitman
www.DetectingDesign.com
hersheyh
0catch.com> wrote:
> > On Jan 29, 5:08 pm, "hersheyhv" <hersh...@indiana.edu> wrote:
> > > On Jan 27, 12:38 pm, "Seanpit" <seanpitnos...@naturalselection.
> > > Once the edge of this "magnetic field" is
> > > reached, the minimum threshold is reached and further refinement
> > > toward the maximum potential is no problem. It is the reaching of
> > > this minimum threshold that is the problem. The island cluster of
> > > potentially beneficial sequences represents the entire reach of the
> > > potentially attractive "magnetic field". This entire reach is
> > > completely isolated from all other island clusters and magnetic fields
> > > at higher levels of functional complexity. The biosystem families you
> > > speak of just are remotely clustered in one corner of sequence space
> > > like you imagine. This notion of yours is way way off base.
>
> > Evidence? I keep having to point out the obvious to you. The
> > EVIDENCE (see the PNAS article and others that I have presented you)
> > actually shows that the biologically useful proteins that *are*
> > present in living organisms (and it doesn't matter whether they
> > evolved or were created by the creation fairy) are NOT scattered
> > throughout total structure space.
>
> Even with regard to single protein systems, they are NOT clustered in
> one tiny corner of sequence space. Look up even single protein maps
> and you will see that they cover a wide range of sequence space. They
> are not all clustered together like you imagine.
>
> "Roughly speaking, however, distances are randomly distributed. This
> means that, although only a small fraction of sequence space yields
> uniquely folding sequences, sequence space is occupied nearly
> uniformly. No "higher order" clustering (i.e., except the trivial case
> of the homologous sequences) is visible.
>
> Erich Bornberg-Bauer, "How Are Model Protein Structures Distributed in
> Sequence Space?" Biophysical Journal, Volume 73, November 1997,
> 2393-2403
>
> http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1181141&blobtyp...
Poor Sean. He can't even see the difference between *structure space*
and *sequence space*. More of the same problem he has in
distinguishing between the words *functional complexity* and
*structure size*. The article he cites actually does little to
support his ideas. The authors, for example, state:
"It is certainly remarkable that for prototype sequence S , more than
half of all the residues may be mutated and up to four mutations at
the same time can be applied without altering the structure under the
condition that the sequence folds uniquely." p.2397
This, of course, is something I keep telling him. That overall
protein *structure* is only weakly correlated with *sequence* and that
*function* is usually an interaction of aspects of *structure* and
certain specific active aa sites within that structure. That is, the
number of *fully specified*aa residues, meaning aa's which must be
specific or identical in all proteins with a specific *function* is
generally a very small fraction of the total aa's in that protein.
Other aa residue sites can have various levels of deviation from
allowing one or two other aa's to allowing any, say, hydrophobic, to
allowing any aa but, say, proline. Sean continues to fail to state
what level of substitutability meets his criteria of that site being
"fairly specified".
It is not surprising to me that a mathematically specified type of
compact structure can be specified by different *sequences* widely
spaced in some hypothetical total *sequence* space. But that doesn't
mean that *real* proteins with such structures are widely scattered in
*structure* space; and the fact is that they are not so scattered.
Real proteins are clustered in *structure* space.
There are, as the authors also state (but Sean does not) certain
implicit assumptions in their theoretical model of proteins. First,
the ''structure' that they look for is the most stable and compact
ones rather than sequences that can flex and change shape. But
*functional* proteins (enzymes) typically are not so rigid and,
moreover, almost never can bind either substrate or product too
tightly. Indeed, it should optimally bind the chemical intermediate
between substrate and product best (but again not too tightly).
Such flexibility means that they can have secondary functionalities
and binding to other possible substrates that can be optimized.
Evolution works, after all, by *modification* of existing *functional*
structures rather than Sean's idea of inventing itself from some
random sequence of 1000 aas (or whatever) of no function whatsoever.
"Also, from an evolutionary point of view, it may well be important
for a biopolymer not to fold to a unique ground state (but to two or
more states with different functions) and not to lose flexibility of
adaptation by freezing in a "mutational trap." In a gedanken
experiment, one can easily imagine such sequences play a role in
bridging the gaps in sequence space between neutral sets. This might
be especially meaningful when only certain structural regions are
important for selection." p.2399
A second assumption that Sean makes, that the authors don't, is that
the proteins that actually exist in real organisms must somehow be a
random sampling of total structure or sequence space like their
hypothetical model of sequence space.
"A main result is that there are few frequent, and many rare
structures. This is consistent with considerations about the
limited number of natural protein folds (Chothia, 1992;
Orengo, 1994)" p. 2400.
Sean also implies that well-defined structures are rare, but the
authors know better:
"The small number of uniquely folding sequences is similar to the
fraction (1-5%) of stable, well defined structures that can be found
in samples of random sequences that were assembled from a ternary
hydrophobic-polar alphabet (QLR) (Davidson et al., 1995). In this and
from similar studies it was also concluded that a significant fraction
of
random sequences will fold uniquely and most probably to a frequent
structure. This is also very likely in this model, since frequent
structures are represented by neutral nets that span regions in
sequence space that are up to more than one-third of the diameter.
Real proteins preferably fold into a small number of "folds" (Chothia,
1992; Cordes et al., 1996; Orengo et al., 1994). These may correspond
to the frequent structures in this model. From there and from
considerations about the small fraction of sequence space that was
explored during evolution (Eigen, 1987), the assumption was drawn that
many structures were simply not found during evolution. This
corresponds to the obvious conclusions that rare structures are hard
to find in this model and have little capacity to adapt." p.2401
> So, you see, even at very low structural threshold levels, the
> distribution of potentially beneficial structures is widespread and
> fairly uniform. The clustering effects that are present at lower
> levels rapidly decline at higher and higher threshold levels until the
> high-level islands are very remotely separated in sequence space.
What I can see is Sean engaging in his strawman ideas and his bogus
use of numbers that represent total sequence size (or a large fraction
thereof) which only makes sense in a bogus strawman model of evolution
that implies that the total sequence size must be generated by a
random walk from a random sequence *maximally* distant from a
specified target. Sean has no way of calculating the number he does
need (the *minimum* number of mutational steps needed to produce a
'new' or modified or altered *function* from some existing functional
protein in an ancestral organism) from the large number he uses. He
typically refuses to even mention that his large numbers are
irrelevant.
>
> Sean Pitmanwww.DetectingDesign.co
Ron O
Can you really go 7 more years with your dishonest evasion? Do you
ever wonder why you have to evade the issues? Remember, you were the
one that made the claims, so why not either admit that you were wrong
or put up what you claim exists?
Ron Okimoto
John Wilkins
> On Feb 10, 9:06 pm, j.wilki...@uq.edu.au (John Wilkins) wrote:
> > Seanpit <seanpitnos...@naturalselection.0catch.com> wrote:
> > > On Feb 6, 10:41 am, j.wilki...@uq.edu.au (John Wilkins) wrote:
> >
> > > > I want to askSeana question. Do you think a 999aa change is possible?
> >
> > > I did answer this question several days ago, but for some reason it
> > > never showed up after I posted it. Go figure?
> >
> > There's a functional gap involved.
> >
> > > Anyway, of course a 999aa change is possible as is a 1000aa or
> > > 10,000aa change. Such changes happen all the time. It is just that
> > > they never hit upon a novel type of functional system that has minimum
> > > structural threshold requirements greater than 1000 specifically
> > > arranged amino acid residues.
> >
> > > I've pointed this out many times in this forum already and even in
> > > this thread, but perhaps you've missed it somehow? There's a big
> > > difference between producing large changes and producing a novel
> > > function that requires a large minimum structural threshold
> > > requirement. The possibility of hitting such a high-level target
> > > isn't the same thing as having good odds of hitting it.
> >
> > I don't get your point. If a 10aa mutation can hit a novel function,
> > then an 11aa muation can hit one.
>
> Yes, but the odds of success for a given attempt are exponentially
> less likely.
Have you done these calculations? I mean by this that you have computed
how many functional alternatives there are, and worked out how many
generations and individuals are need at realistic mutation rates to
figure out that the likelihood of getting *any* large functional novelty
is too low to be acceptable?
And have you included parallel processing, so to speak, of multiple
muations in a population (i.e., recombination of independently assorting
alleles due to sex)?
>
> > And so on, up to a 999aa mutation.
> > Hence, by mathematical induction, a 1000aa mutation can hit one.
>
> That's true, but its about as likely as you winning the California
> lottery 50 times in a row. Its possible, but very very unlikely at
> this level this side of trillions upon trillions of years of time.
Sure, but that is a serial one-hit process. Such processes are very
unique. Supose an appreciable fraction of California won, and when they
did, it increased their chances of winning again.
>
> > Yes,
> > the odds decrease inversely to the number of amino acid changes, but
> > that is very far from proving that there is a threshold at 1000aa.
>
> The odds decrease exponentially with the needed number of character
> changes. The threshold is the point at which the mechanism clearly
> looses ability to act in any sort of meaningful way. Statistically the
> evolutionary mechanism just isn't believable any more as a creative
> force beyond the 1000aa level; even for an extremely large population
> of living things.
So this is about what you find credible? I ask, because maths make some
unintuitive outcomes very likely indeed. So have you done the math?
Although I lack much mathematical knowledge, I'm sure there are those
here who would be more than willing to check your calculations and
assumptions. Please show the work. I am in no doubt I will find it
educational.
>
> > So my question is really this: What makes it a threshold? As I
> > understand molecular genetics and protein biology, most mutations are
> > caused by point mutations, which are low in absolute change but high in
> > potential outcome, pr by duplications, which allow point mutations in
> > one of the paralogous pairs to, over time, accrue novel functions.
>
> There are many types of mutations. Point mutations are only one type.
> There are also duplication mutations and deletions and frame-shift
> mutations ect. Without the help of natural selection, these mutations
> are purely random. It is therefore natural selection that is suppose
> to help evolution overcome the time problem that randomness creates.
I think you misunderstand the nature of "randomness" here. Evolutionary
randomness is merely a lack of direct correlation between the mutations
and the future usefulness they may have. But it doesn't follow that
cellular processes will reproduce any old changes - most such changes
will kill the cell (by which I mean if they are uncorrected by
correction by methylation pattern recognition). The issue is that
mutations that are at least viable can be sorted differentially, and
spread via sexual reproduction in a popualtion.
This makes natural selection in a sexual species an improbability
generator. There will be a viable outcome (or selection cannot apply)
that is unique (by definition) out of a possible field of large
combinations, that is more or less the fittest variant so far generated.
But this is no more unbelieveable than a Bridge hand.
> However, natural selection is not in play until the novel beneficial
> sequence is actually found via purely random searches of sequence
> space. At higher levels of functional complexity, beyond the 1000aa
> threshold, the gaps between potentially beneficial sequences are
> enormous. The gaps are so enormous at this level that randomly
> finding any beneficial sequence at this level requires an average time
> of trillions upon trillions of years.
Natural selection doesn't search the entirety of sequence space. It
searches only the adjacent sequences, within some small Hamming
distance. So it ramps up changes based on increasingly higher relative
fitnesses. This makes the times to fixation much smaller, and speeds up
the achievement time of larger aggregative changes piecemeal.
And you still haven't indicated why 1000aa is a threshold. Only that you
say it is.
>
> > Nothing I know about this process suggests, nor have I read any science
> > that might suggest, that there is a limit to the amount of novelty that
> > can be formed this way. You are making, as I understand it from skimming
> > but not reading closely, a radical claim - there is a limit to the
> > amount of change, or the odds set up a threshold that limits change. But
> > I don't see this as necessary.
>
> Then you don't understand the problem that exponentially increasing
> time averages bring to the table.
Explain them to me, like I was a 15 year old student.
>
> > So, given that time and population size adds the odds up arithmetically,
> > the odds aainst reduce dramatically for any single novelty.
>
> That's true as long as you can increase the population's size
> exponentially with each step of the structural threshold ladder. It
> is just that population sizes have limits that are far too small to
> cross the 1000aa threshold this side of a practical eternity of time.
Please show me how that works. I promise I will try to work through the
math, like I haven't since I was in school.
>
> > Given also
> > that there are a *large* [in the mathematical sense] number of viable
> > novel functions that *might* work, it becomes effectively necessary that
> > large scale functional changes will occur. The onus, I suggest, is on
> > you to make the argument that there is a threshold.
>
> There are a large number of potentially beneficial functions within
> high-level sequence space. However, there is a far far larger number
> of non-beneficial sequences in high-level sequence space as well that
> is exponentially greater than existed at lower levels. In other
> words, it is the ratio of potentially beneficial vs. non-beneficial
> that is important here - not so much the absolute number of
> potentially beneficial sequences.
That would only be relevant if you could show that functions are
randomly distributed through sequence space, and that they are sparsely
distributed, with nonfunctional regions in between. But that is to
presuppose an uncorrelated fitness landscape. I totally agree that in
such a landscape, selection would not work. But we do not have any
reason to think this is the case. Rather, we have biological reasons to
think that functional regions are more or less contiguous, and
mathematical reasons to think that in high dimensionality spaces, there
will be high fitness corridors (for the entire organism) that connect
nearly all regions of the space. So evolution can drive a population
between more distal regions stochastically to "find" a higher fitness
region. I suggest, given that you know more math than I d, that you go
read
Gavrilets, Sergey (2004), Fitness landscapes and the origin of species,
Monographs in population biology; v. 41. Princeton, N.J.; Oxford,
England: Princeton University Press.
The idea that there are nearly neutral pathways of high fitness between
regions was first proposed by Maynard Smith in 1970, for protein space,
and it has been extended a lot since.
>
> > Now you might do this in a number of ways. One might be to show
> > empirical evidence this occurs (and which would then call for
> > explanation given what we know, but you don't need to have an
> > explanation to show that it is a fact).
> >
> > Another might be to show that it follows from our present knowledge of
> > the mathematical dynamics of molecular biology - that it is an
> > implication of stuff we *do* know, but which nobody before you or your
> > source has noticed before.
> >
> > A third might be to show that there are novel facts in play - such as
> > contraints on protein conformations - that change the odds and the
> > argument from induction.
> >
> > Have you done any of these things? In what I have read, I haven't seen
> > it, but I may have missed it. So far as I can tell, you merely assert
> > that functional novelty at 1000aa or above is not possible. And I say,
> > based on everything I have read about protein evolution, that it *is*.
>
> I never said that crossing the 1000aa was impossible. I've said many
> times that such a feat is possible. It is just extremely unlikely
> this side of a practical eternity of time - like you winning the CA
> Lottery 50 times in a row.
>
> Tell me, why do you think all the examples of evolution "in action"
> produce functions with far lower minimum structural threshold
> requirements than 1000 specifically arranged amino acid residues?
> What is your answer to this fact?
Lack of resources to observe them. There are perhaps a few thousand
evolutionary biologists in the world, and while there are many more
molecular biologists, few of them are doing vertical studies of
population change over time. But I am unsure that you are correct. There
have been studies of much larger functional changes, mostly by
duplication of all or part of a genetic ORF.
>
> > Show me wrong. If you can, I will be the first to admit that I am. I
> > don't have the time to wade through large amounts of web-material on
> > your site. I find it too confusing. But if you have a simple page that
> > addresses this exact question clearly, post the link, and I'll copy the
> > relevant sections here and address them (one way or the other) point for
> > point. But if you can give a clear argument to this thread, I would
> > appreciate it.
>
> I've done both.
Unfortunately for me, not in this thread, where I can see it. Or if you
have, it has expired off my server.
--
Seanpit
> > > I don't get your point. If a 10aa mutation can hit a novel function,
> > > then an 11aa muation can hit one.
>
> > Yes, but the odds of success for a given attempt are exponentially
> > less likely.
>
> Have you done these calculations? I mean by this that you have computed
> how many functional alternatives there are, and worked out how many
> generations and individuals are need at realistic mutation rates to
> figure out that the likelihood of getting *any* large functional novelty
> is too low to be acceptable?
>
> And have you included parallel processing, so to speak, of multiple
> muations in a population (i.e., recombination of independently assorting
> alleles due to sex)?
Parallel processing doesn't increase the odds of success when it comes
to the average time needed for the first member of a population to
find a new beneficial target at a particular level of minimum
structural threshold requirements.
> > > And so on, up to a 999aa mutation.
> > > Hence, by mathematical induction, a 1000aa mutation can hit one.
>
> > That's true, but its about as likely as you winning the California
> > lottery 50 times in a row. Its possible, but very very unlikely at
> > this level this side of trillions upon trillions of years of time.
>
> Sure, but that is a serial one-hit process. Such processes are very
> unique. Supose an appreciable fraction of California won, and when they
> did, it increased their chances of winning again.
We are talking about a serial one-hit process here. The goal is for a
series of mutations of any kind to actually hit any potential
beneficial target in sequence space at a given level of structural
complexity. The very first time this happens for any *one* member of
a population, the game is over. And, finding one target at a given
level does not increase the odds of finding another novel beneficial
target for the population.
> > > Yes,
> > > the odds decrease inversely to the number of amino acid changes, but
> > > that is very far from proving that there is a threshold at 1000aa.
>
> > The odds decrease exponentially with the needed number of character
> > changes. The threshold is the point at which the mechanism clearly
> > looses ability to act in any sort of meaningful way. Statistically the
> > evolutionary mechanism just isn't believable any more as a creative
> > force beyond the 1000aa level; even for an extremely large population
> > of living things.
>
> So this is about what you find credible? I ask, because maths make some
> unintuitive outcomes very likely indeed. So have you done the math?
>
> Although I lack much mathematical knowledge, I'm sure there are those
> here who would be more than willing to check your calculations and
> assumptions. Please show the work. I am in no doubt I will find it
> educational.
The math is based on an exponential reduction in the ratio between
potentially beneficial and non-beneficial with each increase in the
minimum structural threshold requirement, which I discuss more below.
> > > So my question is really this: What makes it a threshold? As I
> > > understand molecular genetics and protein biology, most mutations are
> > > caused by point mutations, which are low in absolute change but high in
> > > potential outcome, pr by duplications, which allow point mutations in
> > > one of the paralogous pairs to, over time, accrue novel functions.
>
> > There are many types of mutations. Point mutations are only one type.
> > There are also duplication mutations and deletions and frame-shift
> > mutations ect. Without the help of natural selection, these mutations
> > are purely random. It is therefore natural selection that is suppose
> > to help evolution overcome the time problem that randomness creates.
>
> I think you misunderstand the nature of "randomness" here. Evolutionary
> randomness is merely a lack of direct correlation between the mutations
> and the future usefulness they may have. But it doesn't follow that
> cellular processes will reproduce any old changes - most such changes
> will kill the cell (by which I mean if they are uncorrected by
> correction by methylation pattern recognition). The issue is that
> mutations that are at least viable can be sorted differentially, and
> spread via sexual reproduction in a popualtion.
Neutral mutations cannot be stored preferentially over other types of
neutral mutations. Now, they can be stored preferentially over
detrimental mutations, but this doesn't help the odds of success when
it comes to finding functionally beneficial sequences at various
levels of minimum structural threshold requirements.
Neutral mutations are like a random walk through sequence space.
Detrimental mutations are like a random selection dart-throwing-type
step into sequence space. Both processes have essentially the same
odds of successfully finding a novel beneficial functional system.
> This makes natural selection in a sexual species an improbability
> generator. There will be a viable outcome (or selection cannot apply)
> that is unique (by definition) out of a possible field of large
> combinations, that is more or less the fittest variant so far generated.
> But this is no more unbelieveable than a Bridge hand.
Positive selection among a group of individuals relative to the parent
generation isn't about viability, it is about improved viability - an
increase in reproductive fitness over that attained by the parent
generation. If this improved reproductive fitness is not achieved,
there simply is no positive selection among the subsequent offspring
beyond that achieved by the parent generation.
> > However, natural selection is not in play until the novel beneficial
> > sequence is actually found via purely random searches of sequence
> > space. At higher levels of functional complexity, beyond the 1000aa
> > threshold, the gaps between potentially beneficial sequences are
> > enormous. The gaps are so enormous at this level that randomly
> > finding any beneficial sequence at this level requires an average time
> > of trillions upon trillions of years.
>
> Natural selection doesn't search the entirety of sequence space. It
> searches only the adjacent sequences, within some small Hamming
> distance. So it ramps up changes based on increasingly higher relative
> fitnesses. This makes the times to fixation much smaller, and speeds up
> the achievement time of larger aggregative changes piecemeal.
First off, natural selection isn't was does the searching. Random
mutations do that. Natural selection only selects after mutations
occur. Also, random mutations can indeed make either small or large
steps within sequence space. A multicharacter mutation can step
across the entire breadth of sequence space in a single bound.
The problem is that if there are no potential beneficial sequences
within a very short distance of any starting points in the existing
gene pool, a short-stepping random mutation isn't going to land on any
beneficial sequence so there will be no positive selection in any sort
of stepwise pathway made up of short little steps.
At higher levels of minimum structural threshold requirements, the
odds that a novel beneficial sequence will actually exist one or two
point mutations away drop off exponentially until you'd have a better
chance of winning the CA Lottery 50 times in a row in comparison.
> And you still haven't indicated why 1000aa is a threshold. Only that you
> say it is.
How many times do I have to point out to you that all examples of
evolution in action in literature never produce a novel system of
function that requires more than a few hundred specifically arranged
residues working together at the same time? Nothing even comes close
to the 1000aa level - not even when it comes to large populations with
very high mutation rates. If evolution stalls out in real time at
three to four hundred specified residues, and the stalling effect is
exponential in nature, the odds of anything reaching the 1000aa
quickly turn into trillions upon trillions of years.
The likely gap itself can also be estimated to a reasonable degree.
The minimum gap size grows linearly with each step up the ladder.
Not at higher levels of functional complexity beyond the 1000aa
threshold. There have been no papers or books dealing with this issue
of which I am aware. All of the papers and books out there only look
at very low levels of sequence space that are far less than the 1000aa
threshold. That is why there are interconnecting bridges or short
gaps between novel beneficial island clusters.
The problem is that as one moves up the ladder beyond these very low
structural threshold requirements sequence space expands so rapidly
via an exponential relative increase in non-beneficial sequences that
the increase in potentially beneficial sequences is hugely dwarfed.
The island clusters start to break apart. There just aren't enough
potentially beneficial sequences to stay connected. And, they
certainly do not all stay clustered in one tiny corner of sequence
space like many have suggested in this forum (Howard Hershey, John
Harshman, Richard Forrest, Ian Musgrave, Robin Goodfellow, etc). That
notion is demonstrably false by simply looking at current beneficial
high-level systems and noting that they are spread out all over
sequence space.
None of these have produced any novel function beyond the 1000aa
minimum structural threshold requirement. The fact that all examples
of evolution in action are well below this level is quite telling.
The very fact that low-level examples are so commonly observed even
with the limitations of the observers you mention here is very
interesting given the fact that no evolution is observed beyond the
level of a few hundred specified residues.
> > > Show me wrong. If you can, I will be the first to admit that I am. I
> > > don't have the time to wade through large amounts of web-material on
> > > your site. I find it too confusing. But if you have a simple page that
> > > addresses this exact question clearly, post the link, and I'll copy the
> > > relevant sections here and address them (one way or the other) point for
> > > point. But if you can give a clear argument to this thread, I would
> > > appreciate it.
>
> > I've done both.
>
> Unfortunately for me, not in this thread, where I can see it. Or if you
> have, it has expired off my server.
Go to my website and read the addendum to the Flagellar Evolution
essay.
> John S. Wilkins, Postdoctoral Research Fellow, Biohumanities Project
> University of Queensland - Blog: scienceblogs.com/evolvingthoughts
> "He used... sarcasm. He knew all the tricks, dramatic irony, metaphor,
> bathos, puns, parody, litotes and... satire. He was vicious."
Sean Pitman
www.DetectingDesign.com
Seanpit
> On Feb 10, 5:26 pm, "Seanpit" <seanpitnos...@naturalselection.
>
> 0catch.com> wrote:
> > On Feb 6, 12:08 pm, richardalanforr...@googlemail.com wrote:
>
> > > > Novel beneficial functions
> > > > have evolved with the use of one or two or even three or four
> > > > mutational steps. However, and try and catch this point, the
> > > > resulting functional system did not require more than a few hundred
> > > > fairly specified residues in order to work to some selective
> > > > advantage.
>
> > > And the evidence you have to back this assertion is.......?
>
>
> So you have no evidence in other words.
> If you propose a model, it's up to you to provide the evidence to
> support it.
> You have no evidence.
You don't understand how science works. A hypothesis stands as long
as no counter evidence comes along to falsify it. If you have no
evidence to counter my position, then my hypothesis stands and gains
more and more predictive value. No scientific hypothesis can ever be
positively proved this side of eternity. It can only be falsified.
It is much like my cow-jumping hypothesis. I hypothesize that no cow
will ever be able to jump over my house. I base this hypothesis upon
the limited set of cows that I have seen jump and by noting that no
cow that I have ever seen jump has ever come close to the jump needed
to clear my house. Now, all you have to do to falsify my cow jumping
hypothesis is show that my limited set of cows hasn't included a set
of cows that you know can indeed steadily improve their jumping
ability.
Do you know of such a set of cows of which I am unaware? If so,
please do present them by all means. Until you do, my hypothesis
gains predictive value.
I've made an observation that evolutionary mechanisms are able to
produce many novel systems of function that require just a few
specifically arranged amino acid residues. I've also noted that there
are far fewer examples when the minimum structural requirements move
up to one or two hundred. And, that there are just a handful of
examples when the threshold is at three or four hundred. I therefore
hypothesize that if the threshold is at 1000aa that the evolutionary
process (the cow) will not be able to jump over it (the house) in any
real time observation.
Beyond this, I can explain why such a stalling out effect occurs. It
is because of a linear expansion of non-beneficial gaps that surround
all potentially beneficial target sequences within sequence space at
higher and higher minimum structural threshold requirements. This
linear expansion in the non-beneficial gaps results in an exponential
expansion in the average number of random mutations that are needed to
cross the gap.
Its all very simple really - - unless you have some knowledge of some
other cows that can actually jump farther and farther than you have so
far presented.
> > > There is plenty of evidence both from studies of the genemones of
> > > existing organisms and the fossil record that novel beneficial
> > > functions *have* evolved involving a far greater number of
> > > evolutionary steps that your arbitrary limit suggests.
>
> > The fossil record is assumed to be evolutionary without any
> > understanding of how your proposed mechanism could have done the job.
>
> Are you serious?
> I suggest that you educate yourself in evolutionary biology,
> especially on the relationship between evolution and development. It's
> called "evo-devo".
Are you serous? Please, do present your evo-devo theory here and how
it explains cows that can jump higher and higher without any
exponential stalling effect . . .
> > The same is true of studies of sequence homologies. The assumption
> > that homologies must have arisen via the evolutionary mechanism is
> > just that, an assumption unsupported by any relevant statistical
> > analysis and completely devoid of any demonstration beyond extremely
> > low levels of functional complexity - i.e., evolution *only* produces
> > functional systems that have a minimum structural requirement that is
> > far less than 1000 specifically arranged amino acid residues.
>
> I have no idea what you mean by this, and doubt that you do either.
> We trace homologies by a number of different methods. We can identify
> the genes whose expression causes limb buds to develope, and find the
> same genes in a huge range of different animals doing the same job. We
> know which genes intiate the division of the vertebral column into
> different morphological zones, and find the same genes doing the same
> job in zebrafish, chickens and mice.
That's right . . .
> Because of that we assume that
> such structures are homologous.
They *are* homologous - - that part is not assumed. What is assumed
is that such homologous systems had a common evolutionary ancestor.
The problem with this assumption is that the homologous systems just
aren't homologous enough to overcome the non-beneficial gap problem or
the fact that this problem gets exponentially more and more serious
with each step up the minimum structural threshold requirement ladder.
> We find the same basic pattern in the
> layout of bones in the limbs of all tetrapods. All such limbs consist
> of a single long bone, then a pair of long bones, and then a series of
> bones of diminishing size organised usually as five digits. Even in
> animals which do not have five digits when adult, we find that there
> are five in embryos which are reabsorbed during ontogeny. Therefore is
> is a reasonable assumption that the bones we indentify as humeri in
> Tiktaalik, Cryptoclidus, Archaeopteryx, Homo and every other tetrapod
> are homologues.
That's right . . .
> What's your explanation? Pure chance? And if it is "common
> design" (which is not an explanation at all, but a post hoc
> justifucation), how do you explain the fact that the tibia and fibula
> of many ungulates develope as separate bones but fuse as the animal
> matures to form a single structural element?
Why is that a problem? You must argue at this point that no
intelligent designer would have done it that way. Problem is, that
isn't an argument from any understanding whatsoever as to how your
proposed mechanism could actually do the job. Your argument isn't
based on a scientific understanding of the process. It is only based
on your incredulity regarding the likelihood that any intelligent
being would have done it that way. You call that science?
At best, that is an extremely shaky assumption given the fact that the
designs that actually exist work very well. It also makes more and
more sense as we learn more and more about how these systems actually
integrate and function to perform the various tasks needed by various
types of living things. There are far less "vestigial" structures
today compared to just a few decades ago. The whole backward retina
argument that Dawkins made famous is now known to be completely
mistaken - i.e., it has many highly beneficial features given the
visual needs of those that have such a modification.
http://www.detectingdesign.com/humaneye.html
In short, the preservation of design makes a lot of sense and does not
in any way help to explain how your proposed mechanism could actually
do what you say it does. Talk about arguing from a lack of evidence.
You are devoted to your theory, not because you understand how the
mechanism behind your theory actually works, but because you cannot
comprehend how someone could have deliberately created what you see
before you? Really?
< snip >
Sean Pitman
www.DetectingDesign.com
Seanpit
> Seanpit wrote:
> > On Feb 4, 8:19 pm, Robin Levett <rnlev...@yahoo.co.uk> wrote:
> >> Seanpit wrote:
> >> > An interesting 3D model for the distribution of existing small single-
> >> > protein systems within sequence space is presented in the following
> >> > link of the work of Jim Proctor and Andrew Torda (Hamburg University,
> >> > last update May, 2004):
>
> >> >http://www.zbh.uni-hamburg.de/wurst/protspace/ECCB_opt.huge.pdf
> >> >http://www.zbh.uni-hamburg.de/wurst/protspace/
>
> >> Sean, before you throw out more references to papers that you can distort
> >> to fit your requirements, isn't it about time you addressed the Choi and
> >> Kim
> >> paper that Howard referred you to on 16 October last year? The one which
> >> showed that proteins *in the real world* cluster into 4 families?
>
> >>www.pnas.org/cgi/content/full/103/38/14056
>
> > If you read the paper carefully, Choi and Kim do not say that proteins
> > form four families. Rather, they argue that protein folds can be
> > roughly categorized into four families. That's a big difference.
>
> I have read the paper carefully; you appear not to have done. Try this:
>
> "Protein structures are more conserved than sequences in evolution, thus
> most proteins in a given sequence family have similar or related molecular
> structures."
Of course they do. However, structures or certain types of folds,
like amino acid residues, have to be in the proper order for the
function of the larger collective protein-based system to be
realized. While all protein-based systems share the same basic types
of fundamental structures, they do not share the same order with
regard to how these structures are arranged. Therein lies the
problem. How is the order achieved without the need to cross linearly
expanding non-beneficial gaps as one moves up the ladder of minimum
structural requirements?
> Note, by the way, that Choi and Kim are dealing with real, not modelled,
> proteins.
>
> It is true that it is the protein structures that fall into 4 classes - but
> it is also true that the many protein sequence families fall within those
> same 4 classes.
That just isn't true. The four classes mentioned here are dealing
with structural folds. When you are talking about large protein-based
systems make up of sequences of these folds, these systems do not fall
into four families at all. Why not? Because different protein systems
have different arrangements of the protein folds. These different
arrangements are scattered all over sequence space without clustering
in to four tightly knit family groups.
> > Also, consider the actual 3D model of their sequence space:
>
> >http://www.lbl.gov/Science-Articles/Archive/PBD-Universe-map-Kim.html
>
> > Notice in this model that even when it comes to very low-level protein
> > folding sequence space, the viable folds do not all overlap. Sure,
> > they are close together, but this is only to be expected at this very
> > low level of sequence space. It's kinda like the sequence space of 3-
> > letter words. They are all very closely clustered together like
> > this. However, this closeness of the potential steppingstones rapidly
> > expands as one moves up the ladder of minimum structural threshold
> > requirements.
>
> Interesting assertion. Any backup for it - it's not in the papers discussed
> here.
This hypothesis isn't discussed anywhere in literature. However, it
is intuitively obvious given certain facts. It is a fact that the
ratio of beneficial vs. non-beneficial sequences decreases
exponentially with each step up the minimum structural threshold
ladder. Now, unless all potentially beneficial targets somehow stay
clustered in one tiny corner of sequence space, this exponential
decline in ratio will, all by itself, create an uncrossable gap
problem very rapidly.
> >> Oh, and even a layman like me can see that you've got your interpretation
> >> of
> >> the Bornberg-Bauer paper wrong. He specifically states that the HP
> >> protein sequences he is examining are not uniformly distributed across
> >> sequence space; see the last couple of paragraphs of the paper; and the
> >> RNA sequences, that he says do "percolate through sequence space", do so
> >> in such a way that "Within a number of mutations small compared to the
> >> length of the sequence, the whole shape-space can be covered".
>
> > That's right! The *whole* shape-space can be covered via relatively
> > small steps. This in fact means that the steppingstones here are
> > indeed distributed throughout sequence space. They are not clustered
> > together in one tiny corner. The fact that one can get across the
> > whole of sequence space without having to step very far from one to
> > the next steppingstone simply means that the ratio of steppingstones
> > vs. the non-viable "gap" options is rather high at this level of
> > minimum structural threshold requirements - as in the case of 3-letter
> > words. However, as you move up the ladder of threshold requirements,
> > this ratio drops off exponentially. As this happens, the
> > steppingstones drift apart rapidly. Pretty soon, it becomes very
> > difficult to take the same short steps and hit any steppingstone at
> > all.
>
> >> Even in the abstract he makes clear that "In analogy to protein families,
> >> nets are dense and well-separated in sequence space".
>
> > Exactly! And they cover the entire space! The nets are dense because
> > of the relatively high ratio that exists at such low levels of minimum
> > structural threshold requirements.
>
> No they don't; neither Bornberg-Bauer nor Choi say this. Bornberg is
> referring to RNA sequences as percolating through sequence space; the HP
> protein sequences he is examining did *not* do so. "Dense and
> well-separated in sequence space" does *not* mean "distributed throughout
> sequence-space".
Look at the sequences yourself or even at the visual models. The
sequences are indeed distributed throughout sequence space. They
simply are not clustered together in one tiny corner like you imagine.
> When you appreciate this you will realise that your comments above are
> misconceived.
>
> Choi, by the way, says this:
>
> "The fact that most of proteins are structured and that the protein
> structure space is very sparsely populated and restricted mostly to the
> four elongated regions suggest that mutations in genes encoding proteins
> have been constrained to those resulting in a structurally viable protein
> occupying one of the four allowed regions of the protein structure space:
> structural selection or ??designability?? (17, 18)."
>
> which, if read "carefully", should tell you something.
If you look at the four "families" you can't help but notice that
these four families are fairly loosely defined and that they are not
clustered into four tiny round balls. Rather, they are quite spread
out with each approaching very different margins of sequence space.
One can get from one end of sequence space to the other by going down
different family arms of these viable protein folds.
This fairly loose distribution only gets worse as you move up the
ladder - exponentially worse.
> Robin Levett
Sean Pitman
www.DetectingDesign.com
_Arthur
0catch.com> wrote:
> How many times do I have to point out to you that all examples of
> evolution in action in literature never produce a novel system of
> function that requires more than a few hundred specifically arranged
> residues working together at the same time? Nothing even comes close
> to the 1000aa level
Professor Pitman, how many aa are involved in the bacterial flagella ?
Accurate count, please.
carlip...@physics.ucdavis.edu
> On Feb 10, 9:06 pm, j.wilki...@uq.edu.au (John Wilkins) wrote:
>> I don't get your point. If a 10aa mutation can hit a novel function,
>> then an 11aa muation can hit one.
> Yes, but the odds of success for a given attempt are exponentially
> less likely.
"Exponentially less likely" is a phrase I often hear from people who
don't know very much math. By itself, it doesn't mean anything --
depending on the "decay constant" in the exponent, an exponential
relation may be very different from a linear relation, or it may be
almost indistinguishable from a linear relation. (That is, if a<<1/N,
then e^{-aN} is very nearly equal to 1-aN.)
Is this just rhetoric, or are you claiming an actual calculation here?
If the latter, what is the value of the constant in the exponent? How,
exactly, did you determine (or measure) this value?
Steve Carlip
Von R. Smith
0catch.com> wrote:
> On Feb 10, 11:05 am, richardalanforr...@googlemail.com wrote:
>
>
>
>
>
> > On Feb 10, 5:26 pm, "Seanpit" <seanpitnos...@naturalselection.
>
> > 0catch.com> wrote:
> > > On Feb 6, 12:08 pm, richardalanforr...@googlemail.com wrote:
>
> > > > > Novel beneficial functions
> > > > > have evolved with the use of one or two or even three or four
> > > > > mutational steps. However, and try and catch this point, the
> > > > > resulting functional system did not require more than a few hundred
> > > > > fairly specified residues in order to work to some selective
> > > > > advantage.
>
> > > > And the evidence you have to back this assertion is.......?
>
> > > Do you have any counter examples? No? Then, that's the evidence.
>
> > So you have no evidence in other words.
> > If you propose a model, it's up to you to provide the evidence to
> > support it.
> > You have no evidence.
>
> You don't understand how science works. A hypothesis stands as long
> as no counter evidence comes along to falsify it. If you have no
> evidence to counter my position, then my hypothesis stands and gains
> more and more predictive value. No scientific hypothesis can ever be
> positively proved this side of eternity. It can only be falsified.
I have an hypothesis: Sean Pitman is full of shit and doesn't have a
clue about how science works. By your own standards, this hypothesis
stands until you falsify it. So go ahead, prove me wrong. Show that
there is any scientific case to back up your ideas that are as good as
the evidence you say isn't good enough for evolution.
richardal...@googlemail.com
0catch.com> wrote:
> On Feb 10, 11:05 am, richardalanforr...@googlemail.com wrote:
>
>
>
> > On Feb 10, 5:26 pm, "Seanpit" <seanpitnos...@naturalselection.
>
> > 0catch.com> wrote:
> > > On Feb 6, 12:08 pm, richardalanforr...@googlemail.com wrote:
>
> > > > > Novel beneficial functions
> > > > > have evolved with the use of one or two or even three or four
> > > > > mutational steps. However, and try and catch this point, the
> > > > > resulting functional system did not require more than a few hundred
> > > > > fairly specified residues in order to work to some selective
> > > > > advantage.
>
> > > > And the evidence you have to back this assertion is.......?
>
> > > Do you have any counter examples? No? Then, that's the evidence.
>
> > So you have no evidence in other words.
> > If you propose a model, it's up to you to provide the evidence to
> > support it.
> > You have no evidence.
>
> You don't understand how science works. A hypothesis stands as long
> as no counter evidence comes along to falsify it.
An hypothesis is formed by investigating the evidence and proposing a
model which can be tested with can explain that evidence. If you have
no evidence in the first place you cannot build an hypothesis.
I can assert that there is a small white teapot orbiting one of the
moons of Jupiter, but that does not form the basis of an hypothesis
unless I have some evidence for the existence of such a teapot.
> If you have no
> evidence to counter my position, then my hypothesis stands and gains
> more and more predictive value.
You need to start with evidence which is explained by your hypothesis,
and if there is an existing well-developed theory which has been
thoroughly tested over time you need to address all the evidence which
supports that theory and demonstrate that your hypothesis explains the
evidence better, and can make more acurate predictions.
> No scientific hypothesis can ever be
> positively proved this side of eternity. It can only be falsified.
Quite so. I suggest that you formulate an hypothesis which is not
based on unfounded assertions and can be tested against the evidence.
A flawed model of evolution devised for no reason other than to
falsify it is not an hypothesis in science.
>
> It is much like my cow-jumping hypothesis. I hypothesize that no cow
> will ever be able to jump over my house. I base this hypothesis upon
> the limited set of cows that I have seen jump and by noting that no
> cow that I have ever seen jump has ever come close to the jump needed
> to clear my house. Now, all you have to do to falsify my cow jumping
> hypothesis is show that my limited set of cows hasn't included a set
> of cows that you know can indeed steadily improve their jumping
> ability.
>
> Do you know of such a set of cows of which I am unaware? If so,
> please do present them by all means. Until you do, my hypothesis
> gains predictive value.
You have not presented any hypothesis with any predictive value.
>
> I've made an observation that evolutionary mechanisms are able to
> produce many novel systems of function that require just a few
> specifically arranged amino acid residues.
As has been pointed out to you by others, the degree to which such
amino acid residues need to be specifically arranged is far less than
your model demands.
> I've also noted that there
> are far fewer examples when the minimum structural requirements move
> up to one or two hundred.
Which poses not problem at all for evolutionary theory.
> And, that there are just a handful of
> examples when the threshold is at three or four hundred.
Again, so what?
> I therefore
> hypothesize that if the threshold is at 1000aa that the evolutionary
> process (the cow) will not be able to jump over it (the house) in any
> real time observation.
What you persistently ignore is the fact that evolutionary theory
proposes that evolution proceeds in small incremental steps, and that
there is no requirement in evolutionary theory for the saltational
leaps your flawed model demands. Novel functions are evolved at small
levels of change, and there is no mechanism with prevents further
changes happening.
>
> Beyond this, I can explain why such a stalling out effect occurs.
You cannot demonstrate that there is a stalling effect. Your "stalling
effect" is a prediction of your deliberately flawed model which you
cannot justify by reference to evidence.
> It
> is because of a linear expansion of non-beneficial gaps that surround
> all potentially beneficial target sequences within sequence space at
> higher and higher minimum structural threshold requirements. This
> linear expansion in the non-beneficial gaps results in an exponential
> expansion in the average number of random mutations that are needed to
> cross the gap.
Which is irrelevant as there is no requirement for such saltational
leaps in evolutionary theory as forumlated by the scientific
community.
>
> Its all very simple really - - unless you have some knowledge of some
> other cows that can actually jump farther and farther than you have so
> far presented.
You are in the position of arguing that because a cow cannot jump over
a house, a cow is incapable of walking around the house to get to the
other side.
>
> > > > There is plenty of evidence both from studies of the genemones of
> > > > existing organisms and the fossil record that novel beneficial
> > > > functions *have* evolved involving a far greater number of
> > > > evolutionary steps that your arbitrary limit suggests.
>
> > > The fossil record is assumed to be evolutionary without any
> > > understanding of how your proposed mechanism could have done the job.
>
> > Are you serious?
> > I suggest that you educate yourself in evolutionary biology,
> > especially on the relationship between evolution and development. It's
> > called "evo-devo".
>
> Are you serous? Please, do present your evo-devo theory here and how
> it explains cows that can jump higher and higher without any
> exponential stalling effect . . .
>
As I have pointed out, this is completely irrelevant analogy.
> > > The same is true of studies of sequence homologies. The assumption
> > > that homologies must have arisen via the evolutionary mechanism is
> > > just that, an assumption unsupported by any relevant statistical
> > > analysis and completely devoid of any demonstration beyond extremely
> > > low levels of functional complexity - i.e., evolution *only* produces
> > > functional systems that have a minimum structural requirement that is
> > > far less than 1000 specifically arranged amino acid residues.
>
> > I have no idea what you mean by this, and doubt that you do either.
> > We trace homologies by a number of different methods. We can identify
> > the genes whose expression causes limb buds to develope, and find the
> > same genes in a huge range of different animals doing the same job. We
> > know which genes intiate the division of the vertebral column into
> > different morphological zones, and find the same genes doing the same
> > job in zebrafish, chickens and mice.
>
> That's right . . .
>
> > Because of that we assume that
> > such structures are homologous.
>
> They *are* homologous - - that part is not assumed. What is assumed
> is that such homologous systems had a common evolutionary ancestor.
It's the best explanation we have, it makes predictions which can be
tested against the evidence, and it has not been falsified.
Do you have a better explanation?
> The problem with this assumption is that the homologous systems just
> aren't homologous enough
"Not homologous enough"? What the hell does that mean?
> to overcome the non-beneficial gap problem
You mean the "non-beneficial gap problem" which is a problem for your
deliberately flawed model of evolution?
There is no "non-beneficial gap problem" in evolutionary theory. It is
your invention, and is not supported by any evidence.
>or
> the fact that this problem gets exponentially more and more serious
> with each step up the minimum structural threshold requirement ladder.
The fact is that your model of evolution predicts the existence of
such gaps, yet you cannot identify any such gaps in the evidence. This
shows that you model is flawed, not that evolutionary theory is
flawed.
>
> > We find the same basic pattern in the
> > layout of bones in the limbs of all tetrapods. All such limbs consist
> > of a single long bone, then a pair of long bones, and then a series of
> > bones of diminishing size organised usually as five digits. Even in
> > animals which do not have five digits when adult, we find that there
> > are five in embryos which are reabsorbed during ontogeny. Therefore is
> > is a reasonable assumption that the bones we indentify as humeri in
> > Tiktaalik, Cryptoclidus, Archaeopteryx, Homo and every other tetrapod
> > are homologues.
>
> That's right . . .
>
> > What's your explanation? Pure chance? And if it is "common
> > design" (which is not an explanation at all, but a post hoc
> > justifucation), how do you explain the fact that the tibia and fibula
> > of many ungulates develope as separate bones but fuse as the animal
> > matures to form a single structural element?
>
> Why is that a problem? You must argue at this point that no
> intelligent designer would have done it that way.
No, you must present a testable hypothesis which could falsify your
assertion that an intelligent designer would have done it that way. To
do this, you need to propose an observation which could *NOT* be
explained in terms of an "intelligent designer".
> Problem is, that
> isn't an argument from any understanding whatsoever as to how your
> proposed mechanism could actually do the job.
What's wrong with the mechanisms which biolgists are researching?
Mutation, gene duplication, heterochrony, developmental constraints,
the actions of hox genes and other regulatory genes and so on? We seem
to be getting closer and closer to the answer all the time.
Why should be abandon all this in favour of your untestable assertion
that an "intelligent designer" did it?
> Your argument isn't
> based on a scientific understanding of the process.
I suggest that I have a pretty good understanding of the processes
involved, as I try to keep up-to-date with the literature on the
subject.
>It is only based
> on your incredulity regarding the likelihood that any intelligent
> being would have done it that way. You call that science?
My incredulity is based on the simple fact that you have offered
neither evidence nor a testable hypothesis as an alternative to the
scientific understanding of evolutionary mechanism.
>
> At best, that is an extremely shaky assumption given the fact that the
> designs that actually exist work very well.
So what? We have an excellent, extensively tested theory which
explains why they work very well.
> It also makes more and
> more sense as we learn more and more about how these systems actually
> integrate and function to perform the various tasks needed by various
> types of living things. There are far less "vestigial" structures
> today compared to just a few decades ago. The whole backward retina
> argument that Dawkins made famous is now known to be completely
> mistaken - i.e., it has many highly beneficial features given the
> visual needs of those that have such a modification.
So perhaps you can explain why all fish have the vertebrate retina,
whereas all cephalods, many of which occupy exactly the same
environment have more efficient eyes?
>
> http://www.detectingdesign.com/humaneye.html
>
A question which this link carefully avoids.
Oh, and by the way: you need to learn how to write decent HTML code.
> In short, the preservation of design makes a lot of sense
So how do you propose to test this hypothesis?
> and does not
> in any way help to explain how your proposed mechanism could actually
> do what you say it does. Talk about arguing from a lack of evidence.
So what evidence have you presented? All I have read is unfounded
assertion which are impossible to falsify.
Unless you can enlighten us all by proposing something which could
*NOT* be explained by you vague assertions about "common design",
"preservation of design", "intelligent designer" and so on?
> You are devoted to your theory, not because you understand how the
> mechanism behind your theory actually works, but because you cannot
> comprehend how someone could have deliberately created what you see
> before you? Really?
You have not proposed anything which can be supported by evidence or
tested in any way.
Could you give me a single reason why I should consider your
"explanation" as having any value whatsoever, especially as your main
argument is based on a model of evolution you have devised for no
reason other than to falsify it?
I consider this to be dishonest, by the way, just as I consider it to
be dishonest to refuse to even read the extensive evidence I have
cited which shows quite clearly and categorically that your statement
that rapid burial is required for excellent preservation is false.
Still, I'm not the one who is making myself look dishonest.
RF
>
> < snip >
>
> Sean Pitmanwww.DetectingDesign.com
Ron O
How many more years of denial, dishonest obfuscation, and evasion are
we going to get out of you, Sean?
You have to admit that it has been years, probably around 6 or 7
years, are you going to go for a full decade? Remember you made the
claims and never made good on them. Not only that, but you think that
just pretending that you never made them makes everything all right.
How bogus is that?
4 posts should make my point even to someone like you. You can go on,
but why?
Ron Okimoto
Von R. Smith
Heck, he can't even tell me how many specifically arranged residues
there are working together at the same time in each of the proteins in
the 2,4-DNT cascade. He doesn't even seem to have figured out why I'm
asking the question yet.
bro...@noguchi.mimcom.net
Actually, all Sean means by "exponentially less likely" is "I think
it's really, really unlikely, but I haven't got a clue about how to
model it", as you doubtless already know.
Seanpit
> > > > > And the evidence you have to back this assertion is.......?
>
> > > > Do you have any counter examples? No? Then, that's the evidence.
>
> > > So you have no evidence in other words.
> > > If you propose a model, it's up to you to provide the evidence to
> > > support it.
> > > You have no evidence.
>
> > You don't understand how science works. A hypothesis stands as long
> > as no counter evidence comes along to falsify it.
>
> An hypothesis is formed by investigating the evidence and proposing a
> model which can be tested with can explain that evidence. If you have
> no evidence in the first place you cannot build an hypothesis.
A hypothesis is built to explain an observation and make predictions
about the future. The observation in this case is simple: Lots of
functional systems evolve when they only require a few specifically
arranged residues in order to work to at least some degree of
usefulness. Fewer systems evolve when several hundred specified
residues are required and none evolve at all beyond this level.
There's not a single example of any novel function evolving by small
or large steps when that function requires a minimum of more than 1000
specifically arranged residues.
That's the observation. Evolution clearly has no difficulties
producing very small functional systems by seems to have a harder and
harder time producing larger and larger systems via small or large
steps. What hypothesis do you have to explain this obvious stalling
out effect? I say the answer is clearly the result of expanding non-
beneficial gaps between potentially beneficial sequences in sequence/
structure space.
> I can assert that there is a small white teapot orbiting one of the
> moons of Jupiter, but that does not form the basis of an hypothesis
> unless I have some evidence for the existence of such a teapot.
I have an actual observation that deserves explanation. There is in
fact a dramatic decline in evolution "in action" as one considers
greater and greater minimum structural threshold requirements of
protein-based systems. That's a fact clearly evident in scientific
literature. What explanation do you have? I've yet to see any
attempt at a reasonable hypothesis coming from your end.
< snip >
> > It is much like my cow-jumping hypothesis. I hypothesize that no cow
> > will ever be able to jump over my house. I base this hypothesis upon
> > the limited set of cows that I have seen jump and by noting that no
> > cow that I have ever seen jump has ever come close to the jump needed
> > to clear my house. Now, all you have to do to falsify my cow jumping
> > hypothesis is show that my limited set of cows hasn't included a set
> > of cows that you know can indeed steadily improve their jumping
> > ability.
>
> > Do you know of such a set of cows of which I am unaware? If so,
> > please do present them by all means. Until you do, my hypothesis
> > gains predictive value.
>
> You have not presented any hypothesis with any predictive value.
My hypothesis explains a clear observation with very high predictive
value that has yet to be challenged in any significant degree. The
evolutionary cows simply don't produce any novel systems of function
that are larger (in minimum structural requirements) than a few
hundred specifically arranged amino acid residues.
Now, don't come back with your "evolution doesn't work by saltational
steps" argument. Evolution has to take some sort of step, large or
small, to find potentially novel beneficial sequences out there in
sequence space. The problem is that neither small or large steps
actually find any novel beneficial sequences when the attached
function requires at minimum structural threshold of more than 1000
specifically arranged residues. In fact, it doesn't find anything
requiring more than a few hundred fairly specified residues.
> > I've made an observation that evolutionary mechanisms are able to
> > produce many novel systems of function that require just a few
> > specifically arranged amino acid residues.
>
> As has been pointed out to you by others, the degree to which such
> amino acid residues need to be specifically arranged is far less than
> your model demands.
What degree of specificity are you proposing? Those like Sauer,
Olsen, Yockey, Musgrave etc have demonstrated several types of
functional systems that have specificities greater than 1e-40 per
100aa. Even if you argue for a specificity of 1e-15 per 100aa
residues, your problems don't go away to any significant degree.
> > I've also noted that there
> > are far fewer examples when the
> > minimum structural requirements move
> > up to one or two hundred.
>
> Which poses not problem at all for evolutionary theory.
Oh really? How then do you explain this observation? What is it that
significantly reduces evolutionary potential at this level relative to
lower levels?
> > And, that there are just a handful of
> > examples when the threshold is at three or four hundred.
>
> Again, so what?
What's your explanation/hypothesis for this observation?
> > I therefore
> > hypothesize that if the threshold is at 1000aa that the evolutionary
> > process (the cow) will not be able to jump over it (the house) in any
> > real time observation.
>
> What you persistently ignore is the fact that evolutionary theory
> proposes that evolution proceeds in small incremental steps,
That's right! The problem is, evolution doesn't proceed by small or
large incremental steps at higher levels. It just doesn't happen at
the same rate that it happens at lower levels. It happens at a
markedly reduced rate that is many fold less than the rate it
progresses at lower levels.
I'm proposing that evolution cannot proceed up the ladder via small
incremental steps at the same rate because of the increasing non-
beneficial gap problem. The rate of evolution declines dramatically,
exponentially by greater than 10 fold per every additional 1aa
structural requirement (approaching 20 fold at higher and higher
levels).
> and that
> there is no requirement in evolutionary theory for the saltational
> leaps your flawed model demands.
I do not demand "saltational leaps" at all. I don't care how the
1000aa is crossed. It can be crossed by small little steps or large
leaps. Either way is fine with me. As long as a novel function is
produce that requires a minimum structural threshold of more than 1000
specifically arranged residues to work at all.
You do understand the difference now, hopefully, between a structural
threshold requirement and the size of a mutational step? They are not
the same thing as I've explained to you many times. The structural
requirements for a particular function are completely independent of
how that functional system is realized. It could be realized with a
single point mutation. It is just that if the functional system
requires a minimum of more than 1000 specifically arranged residues
the odds that it will exist within one point mutational step away from
anything that already exists within any genome are extremely remote.
> Novel functions are evolved at small
> levels of change, and there is no mechanism with prevents further
> changes happening.
Then why doesn't it actually happen at higher levels in real time at
the same rate that it happens at lower levels?
< snip >
> > Its all very simple really - - unless you have some knowledge of some
> > other cows that can actually jump farther and farther than you have so
> > far presented.
>
> You are in the position of arguing that because a cow cannot jump over
> a house, a cow is incapable of walking around the house to get to the
> other side.
Not true. I'm arguing that the cow cannot jump on top of the house.
There is no walking to the top of the house because there simply is no
pathway to the top of the house comprised of small steps which the cow
can actually climb at higher levels of functional complexity. And,
the trump card, no cows have ever been shown to end up on top of the
1000aa house in real time while many end up on houses that are smaller
than this. Explain that very real observation . . .
< snip >
> > They *are* homologous - - that part is not assumed. What is assumed
> > is that such homologous systems had a common evolutionary ancestor.
>
> It's the best explanation we have, it makes predictions which can be
> tested against the evidence, and it has not been falsified.
>
> Do you have a better explanation?
>
> > The problem with this assumption is that the homologous systems just
> > aren't homologous enough
>
> "Not homologous enough"? What the hell does that mean?
It means that the gaps between the homologies are too large to cross
via random mutation and function-based selection. Demonstrating
partial homology isn't enough to assume evolutionary ancestry. Why?
Because your proposed mechanism cannot cross a partial homology that
leaves a gap of more than a few dozen character differences this side
of a practical eternity of time (even if one considers a population
the size of all living things on Earth).
< snip >
> > Problem is, that
> > isn't an argument from any understanding whatsoever as to how your
> > proposed mechanism could actually do the job.
>
> What's wrong with the mechanisms which biolgists are researching?
> Mutation, gene duplication, heterochrony, developmental constraints,
> the actions of hox genes and other regulatory genes and so on? We seem
> to be getting closer and closer to the answer all the time.
Really? Where are there any examples of any of these types of
mutations producing any novel system of function with a minimum
structural threshold requirement of more than 1000 specifically
arranged residues? Where are there even any statistical analyses of
the potential of such evolutionary mechanisms beyond this level of
functional complexity?
> Why should be abandon all this in favour of your untestable assertion
> that an "intelligent designer" did it?
>
> > Your argument isn't
> > based on a scientific understanding of the process.
>
> I suggest that I have a pretty good understanding of the processes
> involved, as I try to keep up-to-date with the literature on the
> subject.
You've done nothing of the sort. You've just pointed out sequence and
structural similarities between high-level systems and then simply
asserted that evolutionary mechanisms clearly did the job. You've
presented no real time observation of evolution actually doing the job
nor have you presented any statistical analysis of the odds of
evolution actually doing the job at such levels. All you've done are
what all other scientists are doing - simply assuming that evolution
did the job. You've got nothing else here. How did evolution do the
job at such levels Forrest? What are the odds that your proposed
types of mutations are actually able to produce what you claim they
produced? Where are your calculations of the actual odds of success?
A simple assertion at this point just doesn't cut it.
> >It is only based
> > on your incredulity regarding the likelihood that any intelligent
> > being would have done it that way. You call that science?
>
> My incredulity is based on the simple fact that you have offered
> neither evidence nor a testable hypothesis as an alternative to the
> scientific understanding of evolutionary mechanism.
Yet you believe bald assertions that evolutionary mechanisms did the
job without any observational or statistical evidence beyond extremely
low levels of functional complexity?
> > At best, that is an extremely shaky assumption given the fact that the
> > designs that actually exist work very well.
>
> So what? We have an excellent, extensively tested theory which
> explains why they work very well.
Not beyond the 1000aa level you don't.
> > It also makes more and
> > more sense as we learn more and more about how these systems actually
> > integrate and function to perform the various tasks needed by various
> > types of living things. There are far less "vestigial" structures
> > today compared to just a few decades ago. The whole backward retina
> > argument that Dawkins made famous is now known to be completely
> > mistaken - i.e., it has many highly beneficial features given the
> > visual needs of those that have such a modification.
>
> So perhaps you can explain why all fish have the vertebrate retina,
> whereas all cephalods, many of which occupy exactly the same
> environment have more efficient eyes?
Cephalopods do not require high acuity vision nor do they have such
vision. High acuity vision requires much greater energy to maintain -
which is where the inverted retina design comes handily into play.
> >http://www.detectingdesign.com/humaneye.html
>
> A question which this link carefully avoids.
I actually discuss this question in fair detail if you actually care
to read the essay.
> Oh, and by the way: you need to learn how to write decent HTML code.
True . . .
< snip >
> RF
Sean Pitman
www.DetectingDesign.com
Seanpit
>
> > - Show quoted text -
>
> How many more years of denial, dishonest obfuscation, and evasion are
> we going to get out of you, Sean?
>
> You have to admit that it has been years, probably around 6 or 7
> years, are you going to go for a full decade? Remember you made the
> claims and never made good on them. Not only that, but you think that
> just pretending that you never made them makes everything all right.
> How bogus is that?
>
> 4 posts should make my point even to someone like you. You can go on,
> but why?
Ditto . . .
> Ron Okimoto
Sean Pitman
www.DetectingDesign.com
Seanpit
>
> > - Show quoted text -
>
> How many more years of denial, dishonest obfuscation, and evasion are
> we going to get out of you, Sean?
>
> You have to admit that it has been years, probably around 6 or 7
> years, are you going to go for a full decade? Remember you made the
> claims and never made good on them. Not only that, but you think that
> just pretending that you never made them makes everything all right.
> How bogus is that?
>
> 4 posts should make my point even to someone like you. You can go on,
> but why?
Ditto . . .
Do you actually have a real argument Ron? Is this the best you can
do? You don't have any substative response so you attempt a smoke
screen of lame personal insults?
Seanpit
> On Feb 15, 11:04 am, "_Arthur" <Arth...@sympatico.ca> wrote:
>
> > On Feb 15, 10:38 am, "Seanpit" <seanpitnos...@naturalselection.
>
> > 0catch.com> wrote:
> > > How many times do I have to point out to you that all examples of
> > > evolution in action in literature never produce a novel system of
> > > function that requires more than a few hundred specifically arranged
> > > residues working together at the same time? Nothing even comes close
> > > to the 1000aa level
>
> > Professor Pitman, how many aa are involved in the bacterial flagella ?
> > Accurate count, please.
I've already given you my estimate. Why do you want a repeat answer
the the very same question? What is your estimate?
> Heck, he can't even tell me how many specifically arranged residues
> there are working together at the same time in each of the proteins in
> the 2,4-DNT cascade. He doesn't even seem to have figured out why I'm
> asking the question yet.
I've already given you my answer to this question as well - many
times. What is your estimate for each individual protein?
Regardless, the point remains the same. This system is no more
complex, at least not to any significant degree, than its most complex
single protein part because the multiple parts are not required to be
specifically arranged with each other at the same time.
Sean Pitman
www.DetectingDesign.com
Seanpit
How many additional potentially beneficial structures do you think are
added with each additional 1aa structural requirement?
I propose that as one moves up the ladder of minimum structural
threshold requirements, 1aa at a time, the increase in potentially
beneficial sequences approaches a exponent of 1 while the increase in
non-beneficial sequences approaches an exponent of 20.
For example, the total number of meaningful sequences in the English
language system for 1-character sequences is about 3. This produces a
ratio of about 1 in 8 meaningful vs. non-meaningful sequences at this
level. The total number of meaningful 2-character sequences is about
96 or so (a 32 fold increase). The sequence space size for 2
character sequences is 26^2 = 676. This produces a ratio of
meaningful vs. non-meaningful of about 1 in 7. The total number of
meaningful 3-character sequences is about 972 (a 10 fold increase)
while the total sequence space size is 17,576 for a ratio of about 1
in 18. What about meaningful 7-character sequences? Counting
multiword phrases there are probably about 30,000 or so meaningful 7-
character sequences, which produces a ratio of less than 1 in
250,000.
Notice that the "exponential" increase in potentially meaningful
sequences is reduced with each level while the exponential increase in
non-meaningful sequences is increased toward and exponential of 26.
Adding the additional requirement that the sequence be not only
meaningful but beneficial as well only speeds up this process more
quickly so that the disparity between the increase in beneficial vs.
non-beneficial is accentuated more dramatically at lower levels.
The same basic pattern is present in all language/information systems,
to include genetics and protein-based functions.
How many 1aa systems are potentially beneficial from the perspective
of a given life form? 100% - right? The same is almost certainly
true of 2aa sequences. However, this pattern doesn't last long. The
increase in potentially beneficial sequences rapidly declines as one
moves up the ladder of specifically arranged residues 1aa at a time.
By the time the 100aa level is reached, the ratio of potentially
beneficial vs. non-beneficial is around 1e-40 to 1e-60 depending on
the degree of specificity one is considering (Sauer, Olsen, Yockey,
Musgrave, etc). This ratio continues to drop dramatically with
beneficial sequences being outpaced by non-beneficial sequences by
more than 10 fold given a specificity of 1e-40 per 100aa. As one
continues to move up the ladder the increase of non-beneficial
sequences outpaces the increase of potentially beneficial sequences
more and more, approaching a 20 fold differential (likely more than 20
fold given different potential 3D arrangements of the same sequence
residues).
At this point, the exponential declining ratio is clearly problematic
because it is such a severe decline. The only potentially valid
argument left is one of clustering of potentially beneficial sequences
within sequence space in such a way that evolution can progress
because these sequences are not evenly distributed throughout sequence
space. However, as long as there is at lease some distribution and
all the beneficial sequences are not simply clustered in one tiny
corner of sequence space, the degree of the exponential decline in the
ratio will rip apart the islands of beneficial sequences and make them
extremely isolated from each other very quickly at relatively low
levels of minimum structural threshold requirements.
> Steve Carlip
Sean Pitman
www.DetectingDesign.com
Ron O
>
> > > - Show quoted text -
>
> > How many more years of denial, dishonest obfuscation, and evasion are
> > we going to get out of you, Sean?
>
> > You have to admit that it has been years, probably around 6 or 7
> > years, are you going to go for a full decade? Remember you made the
> > claims and never made good on them. Not only that, but you think that
> > just pretending that you never made them makes everything all right.
> > How bogus is that?
>
> > 4 posts should make my point even to someone like you. You can go on,
> > but why?
>
> Ditto . . .
>
> Do you actually have a real argument Ron? Is this the best you can
> do? You don't have any substative response so you attempt a smoke
> screen of lame personal insults?
>
> > Ron Okimoto
>
>
> - Show quoted text -
Two posts of dishonest evasion.
Just give me one good reason why I should tell you how lame your
current argument is, when you have found out how lame all your others
were? How long have you been on your 1000 specified amino acid
schtick? What happened to your neutral gap schtick. Did you ever
find an example where a gap of 3 or 4 had to be crossed? Since the
answer is no, why do you think that expanding it to 1000 is going to
help you?
Face the facts, you can't even tell anyone if your 1000 specified
amino acid bull pucky is biologically relevant, and you've only been
on this current obfuscation scam for how long? A few months (I admit
that I don't really know because I don't read many of your posts)? I
am talking about your claim to actually have an argument that you
claim was just as good as the scientific argument. You were the one
to claim to have a model for your alternative to common descent and
the evidence to back it up around 7 years ago. 7 years of denial,
obfuscation and evasion. This isn't just a few weeks or months of
ignoring your latest scam, this is years of purposeful evasion on your
part. Just think if we were talking about Ray and his promised opus.
You've got him beat by years. How sad is that? Really, just step
back and imagine that we were talking about some other loser, what
would you think of that person?
You don't even deny the facts you just evade them, so you know that
you aren't on the up and up. You can't possibly call it honest, so
how do you justify it?
How sad is this last response? You are trying to claim that I am the
one that is evading the issues. Heck, I just ignore you most of the
time. What kind of loser would keep evading the issue by blaming
other people for their own lack of integrity and honesty?
Just think, all you would have had to do was think about the issues
for a few weeks and then come back and admit that you were wrong and
that you don't have anything worth putting forward at this time.
Instead we've had years of dishonest evasion and one obfuscation scam
after another, as if the scams replace the real issues. Face it, if
you had a real argument we would have seen it by now. You claim to
see all the holes in what you don't agree with, but why don't you
apply that intellect to your own junk and come to a reasonable
conclusion about it?
Ron Okimoto
Seanpit
> Two posts of dishonest evasion.
>
> Just give me one good reason why I should tell you how lame your
> current argument is, when you have found out how lame all your others
> were? How long have you been on your 1000 specified amino acid
> schtick? What happened to your neutral gap schtick. Did you ever
> find an example where a gap of 3 or 4 had to be crossed? Since the
> answer is no, why do you think that expanding it to 1000 is going to
> help you?
Can you show me any beneficial functional system that requires more
than 1000 specifically arranged amino acid residues that is within 3
or 4 residue changes of any other novel system of function? For
example, can you show me where the flagellar motility system is within
3 or 4 residue compared to any other novel system of function or even
one of its own independently functional subsystems?
Please do show some actual evidence Ron instead of this constant
blathering. It should be easy to do since you evidently claim that
such gaps do not exist. Where is your evidence supporting this
claim? Do you have just one example?
< snip >
Sean Pitman
www.DetectingDesign.com
Von R. Smith
0catch.com> wrote:
> On Feb 15, 8:29 pm, "Von R. Smith" <trakl...@gmail.com> wrote:
>
> > On Feb 15, 11:04 am, "_Arthur" <Arth...@sympatico.ca> wrote:
>
> > > On Feb 15, 10:38 am, "Seanpit" <seanpitnos...@naturalselection.
>
> > > 0catch.com> wrote:
> > > > How many times do I have to point out to you that all examples of
> > > > evolution in action in literature never produce a novel system of
> > > > function that requires more than a few hundred specifically arranged
> > > > residues working together at the same time? Nothing even comes close
> > > > to the 1000aa level
>
> > > Professor Pitman, how many aa are involved in the bacterial flagella ?
> > > Accurate count, please.
>
> I've already given you my estimate. Why do you want a repeat answer
> the the very same question? What is your estimate?
>
> > Heck, he can't even tell me how many specifically arranged residues
> > there are working together at the same time in each of the proteins in
> > the 2,4-DNT cascade. He doesn't even seem to have figured out why I'm
> > asking the question yet.
>
> I've already given you my answer to this question as well - many
> times.
Not unless "many" got redefined to mean "zero" while I wasn't
looking. But go ahead and prove my hypothesis wrong: either
reproduce the numbers you have given me "again and again" in this
thread once more, or link the post where you provided the numbers (and
explained how you got them). I'll make it simple: just give me the
estimate, and how you calculated it, for dntD.
> What is your estimate for each individual protein?
> Regardless, the point remains the same. This system is no more
> complex, at least not to any significant degree, than its most complex
> single protein part because the multiple parts are not required to be
> specifically arranged with each other at the same time.
Before I discuss this point any further, I want you state once more in
this thread, for the record, how you measure complexity. Give me a
metric. *One* metric that you will agree to apply consistently
throughout the discussion without trying to change the subject to
Bernoulli trials. Then, after we have nailed down the metric, we can
discuss the issue. Until then, I'm not going to waste my time with
your hand-wavings.
_Arthur
You gave me nothing. You're evading, again. And whaffling.
Seanpit
> > > Heck, he can't even tell me how many specifically arranged residues
> > > there are working together at the same time in each of the proteins in
> > > the 2,4-DNT cascade. He doesn't even seem to have figured out why I'm
> > > asking the question yet.
>
> > I've already given you my answer to this question as well - many
> > times.
>
> Not unless "many" got redefined to mean "zero" while I wasn't
> looking. But go ahead and prove my hypothesis wrong: either
> reproduce the numbers you have given me "again and again" in this
> thread once more, or link the post where you provided the numbers (and
> explained how you got them). I'll make it simple: just give me the
> estimate, and how you calculated it, for dntD.
There are many threads were I've discussed this topic with you at
great length. This is just one of them:
http://groups.google.com/group/talk.origins/msg/ba1934e940d34750?hl=en&
In this post you wrote the following:
_________
Math time:
The size of the sequence space for 1,888aa (the total length of the
four enzymes in question), is approximately 2e2456. If Sean's math
is
correct, and the proportion of functioning sequences is 2.5e-14 of
all
possible sequences, then there will be approximately 5e2442 possible
combinations of sequences that yield all four enzyme functions. If I
am correct, there will be about 2e2404 combinations that do so.
Let's
test this:
dntB is 548aa long. The size of the sequence space for 548aa is
approximately 1e713. If the proportion of sequences this length that
function as dntE is 1e-13, then there are about 1e700 possible
functioning sequences of this size.
dntAbAcAd is 745aa long, corresponding to a sequence space of size
2e969, with the total number of sequences this size performing the
enzyme's function being ~2e956.
dntD is 314aa long, corresponding to a sequence space of size 3e408,
corresponding to a total of 3e395 functioning sequences of that
length.
dngG is 281aa long. Sequence space size = approx 4e365; total number
of functioning sequences ~4e352.
By the Fundamental Principle of Counting (look it up if you don't
know
what that is, Sean) the total number of minimum-length permutations
yielding all four functions will be 1e700 * 2e953 * 3e395 * 4e352 ~
2e2404. (Gee, that number looks familiar!)
So, there are rougly 2e2404 possible functional permutations, out of
2e2456 possible sequences of that length. So the proportion of
possible sequences that work are -hey, look at that! about 1e-52!
Now, if I say that the order in which the four enzymes occur doesn't
matter, I can multiply the permutations by 4! to get about 5e2405
combinations. But your proportion of funcitoning sequences is still
about 1e-51.
OK, so my estimate was technically for permutations rather than
combinations. In the event, my math still beats up Sean's math.
So much for Sean's cascade rule for measuring specificity.
________
As I pointed out to you in that thread, the sequence space that holds
all four enzymes in this cascade is not the sequence space for 1,888aa
(~1e2456). Rather, the sequence space size that will hold all the
parts in this cascade at the same time is the space for the single
largest intact fully oriented piece in the cascade - none of which go
beyond the 1000 specifically arranged threshold requirement.
Of course, I've gone over this extensively with you before and for
some reason you just can't seem to figure it out (see following
example):
_________
> > Sean Pitman wrote:
> Von R. Smith wrote:
Sean Pitman wrote:
< snip >
> > For example, lets say that a system of function requires a minimum of 1
> > protein to work. This protein has to be at least 3aa in size and has
> > to be fully specified as far as the order of the resides within itself
> > in order to "work" at all. In other words, out of all the
> > possibilities in sequence space, only one 3aa sequence will be able to
> > do the job. What is the ratio of proteins with this particular
> > function in sequence space?
> >
> > The ratio is 1 in 8000 (20^3).
> >
> > Now, what if another system of function requires a minimum of two
> > proteins, each with the same size and specificity requirements as the
> > one above - just with two fully specified 3aa proteins instead of one?
> > What will the ratio be?
> >
> > The sequence space is still made up of 8000 potential 3aa proteins.
>
> No, the sequence space is 6.4e7 potential 6aa combinations. [for 3aa sequences ]
Not true. That would be the sequence space if each of the individual
residues were required to be oriented with each of the other residues
to make a single unified residue. The size of sequence space is not
increased by a system requiring independent proteins that do not have
interdependent orientation in order to achieve a given function.
This is your main confusion in understanding this problem. The
requirement for two 3aa sequences (each one fully specified) is not
the
same as the requirement for one fully specified 6aa sequence - not
even
close (explained yet again below).
> Specificity, as you yourself have defined it, is not a measurement of
> trials; it is measurement of degree of sequence conservation within a
> minimum sequence. In this example, we are proposing a system in which
> all six aa must occur in a particular order for the function to work.
Not true. What we have here is two 3aa sequences, each of which must
occur in a specific order within each 3aa, but not relative to the
other 3aa sequence. This is not the same as a specifically ordered
6aa
sequence. The ratios and odds of each are very different.
> Six "fully specified" amino acids for the function in question.
Two fully specified 3aa sequences or three fully specified 2aa
sequences or six fully specified 1aa sequences are not the same thing
as one fully specified 6aa sequence. They are all very different
things. You are trying to equate them, but they simply aren't the
same.
> The
> proportion of sequences that will work to those that will not is 1 in
> 6.4e7. If the two groups can be in either order, then the proportion
> doubles to 1 in 3.2e7.
Nope. You have the size of your sequence space wrong. The sequence
space size for two 3aa sequences is 20^3 or 8000 potential 3aa
sequences. Both of the fully specified 3aa sequences will be found
somewhere within this sequence space - 100%. This is not true of a
single fully specified 6aa sequence. It will not be found in 3aa
sequence space. It requires a 6aa sequence space to be found, which
ends up being a bit bigger at 6.4e7 in size.
> > Now, what happens to the ratio of this two-protein system requires that
> > the proteins not only be internally specified, but specifically
> > oriented relative to each other - no other orientation will do? What
> > happens to the overall specificity of the system? It shoots up
> > dramatically. What does this do to the ratio of what will work vs.
> > what will not work?
> > The ratio drops dramatically to 1 in 64,000,000 (20^6).
>
> Drops dramatically from what? I didn't see any estimate of the ratio
> of sequences that would work vs. ones that would not in your first
> example. Why not? Why switch metrics mid-argument?
The ratio of a fully specified 3aa sequence to sequence space is 1 in
8,000. The ratio of two fully specified 3aa sequences in sequence
space
is 2 in 8,000 or 1 in 4,000.
> If both pairs of 3aa sequences have one unique, fully-specified
> success, then the ratio that will work to those that will not work is
> the same in both cases: 1 in 6.4e7.
Not true. This is not how you solve the problem. You are equating two
3aa sequences with one 6aa sequence. You can't do this. They just
aren't the same thing. The odds of having both 3aa sequence, at the
same time, in a given genome, are much much higher than the odds of
having a single 6aa sequence - as described above.
< snip >
> > Not true. As explained above, the ratio of the sequences that can fill
> > the spot of at least one of the enzymes in the cascade is actually
> > higher than the ratio of a function that only requires the largest
> > enzyme (given the same degree of residue specificity).
>
> This is either a profound confusion on your part or a lame attempt at
> deflection. We are comparing the ratio of sequences that perform one
> particular step in the cascade to the ratio of sequences that perform
> *all* of them, not to the ratio of sequences that perform *any* of
> them.
Right - odds of having both 3aa sequences at the same time in a given
genome are much much greater than having a single 6aa sequence in a
given genome.
> > The number of
> > trials needed to find all of them is only the sum of the inverses of
> > each ratio.
>
> The number of trials is irrelevant. We are measuring total degree of
> sequence conservation (and hence proportions of sequences that will
> work to those that will not), not numbers of trials.
The number of trials is very relevant here because we are trying to
understand what it would take to get both 3aa sequences into a genome
in which they were not already present vs. one 6aa sequence. As it
turns out, it is much easier to get both 3aa sequences, at the same
time, than one 6aa sequence.
< snip repetitive confusion >
Sean Pitman
www.DetectingDesign.com
richardal...@googlemail.com
0catch.com> wrote:
> On Feb 15, 12:19 pm, richardalanforr...@googlemail.com wrote:
>
> > > > > > And the evidence you have to back this assertion is.......?
>
> > > > > Do you have any counter examples? No? Then, that's the evidence.
>
> > > > So you have no evidence in other words.
> > > > If you propose a model, it's up to you to provide the evidence to
> > > > support it.
> > > > You have no evidence.
>
> > > You don't understand how science works. A hypothesis stands as long
> > > as no counter evidence comes along to falsify it.
>
> > An hypothesis is formed by investigating the evidence and proposing a
> > model which can be tested with can explain that evidence. If you have
> > no evidence in the first place you cannot build an hypothesis.
>
> A hypothesis is built to explain an observation and make predictions
> about the future. The observation in this case is simple: Lots of
> functional systems evolve when they only require a few specifically
> arranged residues in order to work to at least some degree of
> usefulness. Fewer systems evolve when several hundred specified
> residues are required and none evolve at all beyond this level.
> There's not a single example of any novel function evolving by small
> or large steps when that function requires a minimum of more than 1000
> specifically arranged residues.
So what? That is not a requirement of evolutionary theory.
>
> That's the observation. Evolution clearly has no difficulties
> producing very small functional systems by seems to have a harder and
> harder time producing larger and larger systems via small or large
> steps. What hypothesis do you have to explain this obvious stalling
> out effect?
There is no "obvious stalling out effect".
You have presented a model of evolution which is different from any
proposed by any evolutionary scientist which predicts that such an
effect should exist, but not presented any evidence whatsoever that
such an effect exists.
This falsifies your model.
> I say the answer is clearly the result of expanding non-
> beneficial gaps between potentially beneficial sequences in sequence/
> structure space.
The answer is clearly that evolution can proceed quite happily with no
need whatsoever to take the saltational steps you demand.
>
> > I can assert that there is a small white teapot orbiting one of the
> > moons of Jupiter, but that does not form the basis of an hypothesis
> > unless I have some evidence for the existence of such a teapot.
>
> I have an actual observation that deserves explanation.
You have an assertion which does not require explanation, as it refers
to a phenomenon which does not exist and for which there is no
requirement in evolutionary theory.
> There is in
> fact a dramatic decline in evolution "in action" as one considers
> greater and greater minimum structural threshold requirements of
> protein-based systems.
Where is your evidence that such a "dramatic decline" exists? All the
evidence from the natural world suggests that there is no "dramatic
decline".
> That's a fact clearly evident in scientific
> literature.
No, it's an assertion you make based on a misinterpretation of a paper
which is over 20 years old. The scientific literature does not
describe any "dramatic decline" in evolutionary processes.
> What explanation do you have? I've yet to see any
> attempt at a reasonable hypothesis coming from your end.
>
What is wrong with the hypotheses which have been published in the
scientific literature over the past two centuries?
There has been extensive and rigorous testing of these hypotheses, and
they provide an excellent framework for understanding not just
evolution, but the whole sciences of biology and palaeontology.
Why should the fact that you present a flawed model of evolution which
you have devised only so that you can falsify it mean that I have to
produce any hypothesis at all? The only prediction made by you model,
that there should be discontiniuties in the nested hierarchy of all
living organisms is not supported by the evidence.
> < snip >
>
> > > It is much like my cow-jumping hypothesis. I hypothesize that no cow
> > > will ever be able to jump over my house. I base this hypothesis upon
> > > the limited set of cows that I have seen jump and by noting that no
> > > cow that I have ever seen jump has ever come close to the jump needed
> > > to clear my house. Now, all you have to do to falsify my cow jumping
> > > hypothesis is show that my limited set of cows hasn't included a set
> > > of cows that you know can indeed steadily improve their jumping
> > > ability.
>
> > > Do you know of such a set of cows of which I am unaware? If so,
> > > please do present them by all means. Until you do, my hypothesis
> > > gains predictive value.
>
> > You have not presented any hypothesis with any predictive value.
>
> My hypothesis explains a clear observation with very high predictive
> value that has yet to be challenged in any significant degree.
Your hypothesis is the model of evolution you have presented which
requires saltational leaps to gain "higher" functions.
You have not defined what you mean by "higher" functions, nor given
any way of judging if an acquired function is a "higher" function.
The only prediction your model appears to make is that functions
beyond an unspecified level of complexity cannot be acquired.
The evidence from the natural world suggests that such function can be
acquired, and that there is no need for the saltational leaps your
model demands.
This means that your model - which is the hypothesis you are
presenting - is falsified.
> The
> evolutionary cows simply don't produce any novel systems of function
> that are larger (in minimum structural requirements) than a few
> hundred specifically arranged amino acid residues.
There is no requirement whatsoever in evolutionary theory for such a
saltational leap.
There is no evidence that such saltational leaps are necessary.
>
> Now, don't come back with your "evolution doesn't work by saltational
> steps" argument. Evolution has to take some sort of step, large or
> small, to find potentially novel beneficial sequences out there in
> sequence space. The problem is that neither small or large steps
> actually find any novel beneficial sequences when the attached
> function requires at minimum structural threshold of more than 1000
> specifically arranged residues. In fact, it doesn't find anything
> requiring more than a few hundred fairly specified residues.
>
And the scientific literature tells us that there is no need to do
so. New functions can evolve without the need for the saltational
changes you demand.
This statement doesn't make much sense.
Are you telling us that it takes longer to evolve "higher" functions
than it does to evolve "lower" functions?
Frankly, so what?
>
> I'm proposing that evolution cannot proceed up the ladder via small
> incremental steps at the same rate because of the increasing non-
> beneficial gap problem.
And the evidence you have that there is such a "beneficial gap
problem" is what?
Your deliberately flawed model of evolution is not evidence.
> The rate of evolution declines dramatically,
> exponentially by greater than 10 fold per every additional 1aa
> structural requirement (approaching 20 fold at higher and higher
> levels).
And the evidence you have that there is such a dramatic decline" is
what?
Your deliberately flawed model of evolution is not evidence.
>
> > and that
> > there is no requirement in evolutionary theory for the saltational
> > leaps your flawed model demands.
>
> I do not demand "saltational leaps" at all. I don't care how the
> 1000aa is crossed. It can be crossed by small little steps or large
> leaps. Either way is fine with me. As long as a novel function is
> produce that requires a minimum structural threshold of more than 1000
> specifically arranged residues to work at all.
>
You ignore the evidence that such steps have been made.
> You do understand the difference now, hopefully, between a structural
> threshold requirement and the size of a mutational step? They are not
> the same thing as I've explained to you many times. The structural
> requirements for a particular function are completely independent of
> how that functional system is realized. It could be realized with a
> single point mutation. It is just that if the functional system
> requires a minimum of more than 1000 specifically arranged residues
> the odds that it will exist within one point mutational step away from
> anything that already exists within any genome are extremely remote.
So what evidence can you present which supports this assertion?
Your deliberately flawed model of evolution is not evidence.
>
> > Novel functions are evolved at small
> > levels of change, and there is no mechanism with prevents further
> > changes happening.
>
> Then why doesn't it actually happen at higher levels in real time at
> the same rate that it happens at lower levels?
Because such changes take more time, and are produced by the
accumulation of smaller changes.
>
> < snip >
>
> > > Its all very simple really - - unless you have some knowledge of some
> > > other cows that can actually jump farther and farther than you have so
> > > far presented.
>
> > You are in the position of arguing that because a cow cannot jump over
> > a house, a cow is incapable of walking around the house to get to the
> > other side.
>
> Not true. I'm arguing that the cow cannot jump on top of the house.
> There is no walking to the top of the house because there simply is no
> pathway to the top of the house comprised of small steps which the cow
> can actually climb at higher levels of functional complexity. And,
> the trump card, no cows have ever been shown to end up on top of the
> 1000aa house in real time while many end up on houses that are smaller
> than this. Explain that very real observation . . .
>
I have nothing to explain.
My analogy - that the cow can walk round the house - is a reasonable
description of the scientific explanation for the acquisition of
"higher" functions (a term for which you have provided no defintion or
means of measuring, by the way). Evolution does not proceed in
straight lines to a goal, which seems to be an underlying assumption
of your model.
> < snip >
>
> > > They *are* homologous - - that part is not assumed. What is assumed
> > > is that such homologous systems had a common evolutionary ancestor.
>
> > It's the best explanation we have, it makes predictions which can be
> > tested against the evidence, and it has not been falsified.
>
> > Do you have a better explanation?
>
> > > The problem with this assumption is that the homologous systems just
> > > aren't homologous enough
>
> > "Not homologous enough"? What the hell does that mean?
>
> It means that the gaps between the homologies are too large to cross
> via random mutation and function-based selection.
What the hell are "gaps between homologies"?
> Demonstrating
> partial homology isn't enough to assume evolutionary ancestry.
What the hell is "partial homology"?
> Why?
> Because your proposed mechanism cannot cross a partial homology that
> leaves a gap of more than a few dozen character differences this side
> of a practical eternity of time (even if one considers a population
> the size of all living things on Earth).
>
And the evidence you have to support this assertion is....?
Your deliberately flawed model of evolution is not evidence.
> < snip >
>
> > > Problem is, that
> > > isn't an argument from any understanding whatsoever as to how your
> > > proposed mechanism could actually do the job.
>
> > What's wrong with the mechanisms which biolgists are researching?
> > Mutation, gene duplication, heterochrony, developmental constraints,
> > the actions of hox genes and other regulatory genes and so on? We seem
> > to be getting closer and closer to the answer all the time.
>
> Really? Where are there any examples of any of these types of
> mutations producing any novel system of function with a minimum
> structural threshold requirement of more than 1000 specifically
> arranged residues?
How about the evolutionary series showing the way in which the bones
of the reptilain jaw became the bones of the mammalian ear for
starters?
> Where are there even any statistical analyses of
> the potential of such evolutionary mechanisms beyond this level of
> functional complexity?
I don't know.
Why don't you educate yourself in statistics, evolutionary theory,
genetics and so on and produce such an analysis.
>
> > Why should be abandon all this in favour of your untestable assertion
> > that an "intelligent designer" did it?
>
> > > Your argument isn't
> > > based on a scientific understanding of the process.
>
> > I suggest that I have a pretty good understanding of the processes
> > involved, as I try to keep up-to-date with the literature on the
> > subject.
>
> You've done nothing of the sort. You've just pointed out sequence and
> structural similarities between high-level systems and then simply
> asserted that evolutionary mechanisms clearly did the job. You've
> presented no real time observation of evolution actually doing the job
Since when has "real time observation" been a requirement for science?
> nor have you presented any statistical analysis of the odds of
> evolution actually doing the job at such levels.
Why on earth to I need to?
I have no idea how such a statistical analysis could be carried out,
as we are not dealing with processes to which is it possible to attach
meaningful measures of probability.
> All you've done are
> what all other scientists are doing - simply assuming that evolution
> did the job.
Do you have a better explanation?
> You've got nothing else here. How did evolution do the
> job at such levels Forrest?
By the processes of natural selection acting on variation in
populations of living organism. We may not know every detail of how
evolutionary processes did the job, but in the absence of any
alternative to the evolutionary model which can yield testable
predictions it seems a pretty good bet that we are thinking along the
right lines.
> What are the odds that your proposed
> types of mutations are actually able to produce what you claim they
> produced?
I don't know. I have no idea of how one can calculate the probability
of such events given the enormous number of unknown variables in the
process.
You don't know either, by the way: not only is your knowledge of
statistics demonstreated to be rather weak by reference to your
posting history, but you also lack knowledge of the processes by which
evolutionary theory models such events.
> Where are your calculations of the actual odds of success?
> A simple assertion at this point just doesn't cut it.
>
Bearing in mind that pretty well all you do is to make unfounded
assertions, this is somewhat ironic.
> > >It is only based
> > > on your incredulity regarding the likelihood that any intelligent
> > > being would have done it that way. You call that science?
>
> > My incredulity is based on the simple fact that you have offered
> > neither evidence nor a testable hypothesis as an alternative to the
> > scientific understanding of evolutionary mechanism.
>
> Yet you believe bald assertions that evolutionary mechanisms did the
> job without any observational or statistical evidence beyond extremely
> low levels of functional complexity?
I accept the model of evolution provided by evolutionary theory
because it is firmly based on the evidence, it produces testable
hypotheses and because it has not been falsified in spite of well over
a century of intense scrutiny. I know of no other theoretical
framework which makes any sense at all of the fossil record, the
diversity of living organisms, or the complex ways in which those
organisms interact.
It is a simple fact that you have offered neither evidence nor a
testable hypothesis as an alternative to the scientific understanding
of evolutionary mechanism.
So why should I change my acceptance of evolutionary theory?
>
> > > At best, that is an extremely shaky assumption given the fact that the
> > > designs that actually exist work very well.
>
> > So what? We have an excellent, extensively tested theory which
> > explains why they work very well.
>
> Not beyond the 1000aa level you don't.
>
You have no evidence to support this assertion.
> > > It also makes more and
> > > more sense as we learn more and more about how these systems actually
> > > integrate and function to perform the various tasks needed by various
> > > types of living things. There are far less "vestigial" structures
> > > today compared to just a few decades ago. The whole backward retina
> > > argument that Dawkins made famous is now known to be completely
> > > mistaken - i.e., it has many highly beneficial features given the
> > > visual needs of those that have such a modification.
>
> > So perhaps you can explain why all fish have the vertebrate retina,
> > whereas all cephalods, many of which occupy exactly the same
> > environment have more efficient eyes?
>
> Cephalopods do not require high acuity vision nor do they have such
> vision.
Bollocks. Learn some biology. Some cephalopods have better eyesight
that humans.
> High acuity vision requires much greater energy to maintain -
> which is where the inverted retina design comes handily into play.
>
> > >http://www.detectingdesign.com/humaneye.html
>
> > A question which this link carefully avoids.
>
> I actually discuss this question in fair detail if you actually care
> to read the essay.
>
> > Oh, and by the way: you need to learn how to write decent HTML code.
>
> True . . .
>
> < snip >
>
> > RF
>
> Sean Pitmanwww.DetectingDesign.com
A question which this link carefully avoids.
Oh, and by the way: you need to learn how to write decent HTML code.
> In short, the preservation of design makes a lot of sense
Seanpit
> On Feb 16, 1:57 am, carlip-nos...@physics.ucdavis.edu wrote:
>
>
>
>
>
> > Seanpit <seanpitnos...@naturalselection.0catch.com> wrote:
> > > On Feb 10, 9:06 pm, j.wilki...@uq.edu.au (John Wilkins) wrote:
>
> > [...]
>
> > >> I don't get your point. If a 10aa mutation can hit a novel function,
> > >> then an 11aa muation can hit one.
> > > Yes, but the odds of success for a given attempt are exponentially
> > > less likely.
>
> > "Exponentially less likely" is a phrase I often hear from people who
> > don't know very much math. By itself, it doesn't mean anything --
> > depending on the "decay constant" in the exponent, an exponential
> > relation may be very different from a linear relation, or it may be
> > almost indistinguishable from a linear relation. (That is, if a<<1/N,
> > then e^{-aN} is very nearly equal to 1-aN.)
>
> > Is this just rhetoric, or are you claiming an actual calculation here?
> > If the latter, what is the value of the constant in the exponent? How,
> > exactly, did you determine (or measure) this value?
>
> > Steve Carlip
>
> it's really, really unlikely, but I haven't got a clue about how to
> model it", as you doubtless already know.
With each additional fairly specified residue threshold requirement
beyond the 100aa level the additional non-beneficial sequences added
to the sequence space outpace the increase of beneficial sequences by
more than 10:1. This ratio only gets more and more unballanced as one
moves up the ladder - toward a ratio of 20:1 for every 1aa increase in
structural threshold requirements.
Therefore the odds that a novel beneficial functional structure will
continue to be within one or two character changes from anything that
exists within a population drop off quite dramatically as one moves up
the ladder beyond the 1000aa minimum threshold requirement.
Sean Pitman
www.DetectingDesign.com
hersheyh
0catch.com> wrote:
> On Feb 16, 3:59 am, "Ron O" <rokim...@cox.net> wrote:
>
> > Two posts of dishonest evasion.
>
> > Just give me one good reason why I should tell you how lame your
> > current argument is, when you have found out how lame all your others
> > were? How long have you been on your 1000 specified amino acid
> > schtick? What happened to your neutral gap schtick. Did you ever
> > find an example where a gap of 3 or 4 had to be crossed? Since the
> > answer is no, why do you think that expanding it to 1000 is going to
> > help you?
>
> Can you show me any beneficial functional system that requires more
> than 1000 specifically arranged amino acid residues that is within 3
> or 4 residue changes of any other novel system of function?
All of the new functions have been actually found to arise have arisen
from existing functional proteins by changes that are often 3-4
mutational steps (which is not the same as residue changes, but is
more accurate) or fewer from a previous protein(s).
But you merely *assert* that there actually exists "beneficial
functional systems that requires more than 1000 specifically arranged
amino acid residues". Nowhere have you presented a list of all the
"functional systems" that meet this requirement. Nowhere have clearly
specified how you determine the number of "fairly specified aa
residues" involved in "specific arrangement" for specific proteins.
All I have ever seen you present is some vague hints that there are
some 'systems' (and usually multiprotein systems) that somehow meet
your requirements. And then there suddenly is a vague hand-waving of
the number 1000 into existence and the false pretence that that number
refers to some sort of reality rather than representing a number you
pulled out of some dark nether region.
And you continually fail to acknowledge that the 1000 aa number is
irrelevant to the mechanism of evolution *unless* you can demonstrate
that the *real* number you need, the *minimum* (not average) gap size,
is strictly mathematically correlated with that large number.
Frankly, all you do is present a bogus large number (either total size
or some large fraction thereof) refering to hypothetical systems and
pretend that this number is relevant to something. It isn't.
> For
> example, can you show me where the flagellar motility system is within
> 3 or 4 residue compared to any other novel system of function or even
> one of its own independently functional subsystems?
Of course. I have already mentioned in the past that a novel form of
linkage between FliG and FliF to form a fusion protein and that this
new protein provides a novel linkage between a *pre-existing* system
that transports proteins along a whip-like channel to the outside (the
rotateable pore) and a motor subsystem that has the ability to convert
ATP into mechanical motion. Such systems exist in several different
forms in cells and have functions that do not include rotary
motility. Thus, this demonstrates how evolution actually works. The
total size of the end system doesn't matter. The number of mutational
steps required to reach the novel *function* from a state that lacked
that *function* is unrelated to the end size. But the same thing is
true for betagalactosidase activities. *Functional* levels of
betagalactosidase activity can either be produced by a single (or a
few) mutational steps in cells that have the ebg protein or it can be
much more difficult to generate in cells that lack that protein. That
is, the *mechanism* and number of mutational steps required is
dependent on the idiosyncratic presence or absence of a particular
possible precursor and is NOT a function of the size of the end
product.
Seanpit
> > > An hypothesis is formed by investigating the evidence and proposing a
> > > model which can be tested with can explain that evidence. If you have
> > > no evidence in the first place you cannot build an hypothesis.
>
> > A hypothesis is built to explain an observation and make predictions
> > about the future. The observation in this case is simple: Lots of
> > functional systems evolve when they only require a few specifically
> > arranged residues in order to work to at least some degree of
> > usefulness. Fewer systems evolve when several hundred specified
> > residues are required and none evolve at all beyond this level.
> > There's not a single example of any novel function evolving by small
> > or large steps when that function requires a minimum of more than 1000
> > specifically arranged residues.
>
> So what? That is not a requirement of evolutionary theory.
Many functional systems exist that require a minimum structural
threshold of many more than 1000 specified residues. Why does
evolution produce functional systems with lower-level requirements
quite easily in observable time but never produces any novel functions
beyond the 1000aa level in observable time?
This is simply a question as to why evolutionary mechanisms work so
well at low levels in a short period of time under laboratory
conditions, but not at all at higher levels beyond the 1000aa level?
What's your explanation?
> > That's the observation. Evolution clearly has no difficulties
> > producing very small functional systems by seems to have a harder and
> > harder time producing larger and larger systems via small or large
> > steps. What hypothesis do you have to explain this obvious stalling
> > out effect?
>
> There is no "obvious stalling out effect".
Oh please! Are you blind?! If evolution happens rapidly and very
commonly below structural thresholds of less than 20 or 30 residues,
less commonly at thresholds of 200-400 residues in the same period of
time, and not at all in this time period beyond the 1000aa threshold,
what does that tell you? How can you possibly argue, with any
seriousness, that is not an obvious stalling out effect?
> You have presented a model of evolution which is different from any
> proposed by any evolutionary scientist which predicts that such an
> effect should exist, but not presented any evidence whatsoever that
> such an effect exists.
I've not presented any other model of the evolutionary mechanism
besides the regular model that you evolutionists propose - random
mutation and natural selection. That's the proposed model I'm using.
It is just that this model shows a very clear stalling out effect as
you move up the ladder of minimum structural threshold requirements.
What is your explanation for this very clear phenomenon?
> This falsifies your model.
This is your model here. How does your model explain the stalling
effect that is in fact observed? My explanation is that non-
beneficial gaps are expanding. This model most certainly has not been
falsified in the least. A good way to falsify my hypothesis is to
actually present any evolutionary process in observable action
producing any novel function that requires a minimum of more than 1000
specifically arranged residues.
> > I say the answer is clearly the result of expanding non-
> > beneficial gaps between potentially beneficial sequences in sequence/
> > structure space.
>
> The answer is clearly that evolution can proceed quite happily with no
> need whatsoever to take the saltational steps you demand.
Where is your evidence for this? If evolution can proceed by small or
large steps up the ladder, why doesn't it happen with the same
commonality and at the same rapid rate that it happens at lower
levels?
> > > I can assert that there is a small white teapot orbiting one of the
> > > moons of Jupiter, but that does not form the basis of an hypothesis
> > > unless I have some evidence for the existence of such a teapot.
>
> > I have an actual observation that deserves explanation.
>
> You have an assertion which does not require explanation, as it refers
> to a phenomenon which does not exist and for which there is no
> requirement in evolutionary theory.
You're blind to the obvious man - I can show you many examples of
evolution in action. All of them produce novel functions that require
no more than a few hundred fairly specified residues. Not one of them
produces anything beyond the 1000aa threshold. That's a real
observation. There just isn't any way around it.
> > There is in
> > fact a dramatic decline in evolution "in action" as one considers
> > greater and greater minimum structural threshold requirements of
> > protein-based systems.
>
> Where is your evidence that such a "dramatic decline" exists? All the
> evidence from the natural world suggests that there is no "dramatic
> decline".
Not when it comes to observable evolution in action. All the evidence
of those cases were evolution has actually been demonstrated in real
time show a clear decline in evolutionary commonality and speed with
increasing structural threshold requirements.
< snip >
> > The
> > evolutionary cows simply don't produce any novel systems of function
> > that are larger (in minimum structural requirements) than a few
> > hundred specifically arranged amino acid residues.
>
> There is no requirement whatsoever in evolutionary theory for such a
> saltational leap.
> There is no evidence that such saltational leaps are necessary.
Again, I'm not asking for a leap here. The threshold requirement
isn't a measure of the step size or leap size. It is a measure of the
structural requirements of the resulting functional system. You can
produce this system by small or large steps. I'm not arguing that
large steps or "leaps" are required. How does evolution end up at
this higher level by any series of steps small or large?
> > Now, don't come back with your "evolution doesn't work by saltational
> > steps" argument. Evolution has to take some sort of step, large or
> > small, to find potentially novel beneficial sequences out there in
> > sequence space. The problem is that neither small or large steps
> > actually find any novel beneficial sequences when the attached
> > function requires at minimum structural threshold of more than 1000
> > specifically arranged residues. In fact, it doesn't find anything
> > requiring more than a few hundred fairly specified residues.
>
> And the scientific literature tells us that there is no need to do
> so. New functions can evolve without the need for the saltational
> changes you demand.
You must have a reading comprehension problem. Did you not understand
that I do not require any specific type of step, large or small,
saltational or otherwise. Evolution does require that a population
make some sort of series of steps in order for evolution to take
place. The question is, can any series of steps, small or large,
produce a novel system of function that requires a minimum structural
threshold requirement of more than 1000aa? Again, let me make this
clear to you, if possible (and I have my serious doubts if this is
actually possible), it doesn't matter what type of mutations you
choose. The odds of success are the same regardless.
> > > What you persistently ignore is the fact that evolutionary theory
> > > proposes that evolution proceeds in small incremental steps,
>
> > That's right! The problem is, evolution doesn't proceed by small or
> > large incremental steps at higher levels. It just doesn't happen at
> > the same rate that it happens at lower levels. It happens at a
> > markedly reduced rate that is many fold less than the rate it
> > progresses at lower levels.
>
> This statement doesn't make much sense.
> Are you telling us that it takes longer to evolve "higher" functions
> than it does to evolve "lower" functions?
YES!!!!!!
> Frankly, so what?
It doesn't just take a little bit longer to evolve higher-level
functions relative to lower-level functions. It takes exponentially
longer - approaching 20 times longer for every 1aa increase in the
minimum structural threshold requirement as one moves up the ladder
beyond the 1000aa threshold.
< snip >
> > The rate of evolution declines dramatically,
> > exponentially by greater than 10 fold per every additional 1aa
> > structural requirement (approaching 20 fold at higher and higher
> > levels).
>
> And the evidence you have that there is such a dramatic decline" is
> what?
The observation that the decline actually happens combined with the
obvious statistical decline in the ratio of beneficial vs. non-
beneficial with each step up the ladder.
> Your deliberately flawed model of evolution is not evidence.
The observation of a very real stalling out effect is very good
evidence - despite your deliberate blindness to the reality of this
observation.
> > > and that
> > > there is no requirement in evolutionary theory for the saltational
> > > leaps your flawed model demands.
>
> > I do not demand "saltational leaps" at all. I don't care how the
> > 1000aa is crossed. It can be crossed by small little steps or large
> > leaps. Either way is fine with me. As long as a novel function is
> > produce that requires a minimum structural threshold of more than 1000
> > specifically arranged residues to work at all.
>
> You ignore the evidence that such steps have been made.
Where have they ever been observed in real time? - as evolution "in
action? Why aren't they observed in real time while lower-level
examples are so commonly observed in real time? Your sequence data
homology comparisons have no explanatory power when it comes to
actually understanding the odds of your proposed mechanisms doing what
you merely assume they did.
> > You do understand the difference now, hopefully, between a structural
> > threshold requirement and the size of a mutational step? They are not
> > the same thing as I've explained to you many times. The structural
> > requirements for a particular function are completely independent of
> > how that functional system is realized. It could be realized with a
> > single point mutation. It is just that if the functional system
> > requires a minimum of more than 1000 specifically arranged residues
> > the odds that it will exist within one point mutational step away from
> > anything that already exists within any genome are extremely remote.
>
> So what evidence can you present which supports this assertion?
> Your deliberately flawed model of evolution is not evidence.
Again, the observation of evolution stalling out in its "real time"
potential is not a "model" and it is not flawed. It is very real.
> > > Novel functions are evolved at small
> > > levels of change, and there is no mechanism with prevents further
> > > changes happening.
>
> > Then why doesn't it actually happen at higher levels in real time at
> > the same rate that it happens at lower levels?
>
> Because such changes take more time, and are produced by the
> accumulation of smaller changes.
I'm not talking about the actual changes themselves. You'd think that
at least some populations would have accumulated the needed changes so
that the next step would produce a higher-level system in observable
time. Why doesn't this happen if these accumulations happen to
approach the threshold like you say?
> > > You are in the position of arguing that because a cow cannot jump over
> > > a house, a cow is incapable of walking around the house to get to the
> > > other side.
>
> > Not true. I'm arguing that the cow cannot jump on top of the house.
> > There is no walking to the top of the house because there simply is no
> > pathway to the top of the house comprised of small steps which the cow
> > can actually climb at higher levels of functional complexity. And,
> > the trump card, no cows have ever been shown to end up on top of the
> > 1000aa house in real time while many end up on houses that are smaller
> > than this. Explain that very real observation . . .
>
> I have nothing to explain.
> My analogy - that the cow can walk round the house - is a reasonable
> description of the scientific explanation for the acquisition of
> "higher" functions (a term for which you have provided no defintion or
> means of measuring, by the way). Evolution does not proceed in
> straight lines to a goal, which seems to be an underlying assumption
> of your model.
The cow cannot walk around the house unless there are closely spaced
steppingstones for the cow to step on each time. What happens if
these steppingstones become more and more widely spaced? What is the
cow going to walk on then?
The fact remains that the cow just doesn't end up on the other side of
the house in reality. No cows end up beyond the 1000aa threshold in
observable time. It just doesn't happen. That means that there are
no cows in any population that are even close to stepping across this
threshold. Because, if there were, they would be doing so, in
observable time, all the time. They aren't. There are no examples
that have ever been observed "in action". In other words, no one has
ever actually witnessed a cow crossing into 1000aa territory.
> > > "Not homologous enough"? What the hell does that mean?
>
> > It means that the gaps between the homologies are too large to cross
> > via random mutation and function-based selection.
>
> What the hell are "gaps between homologies"?
The gap is between sequences that are only partially homologous. The
functional differences between two sequences are the result of their
non-homologous parts. Therein lies the problem - the gap. How are
these non-homologous properties explained via your evolutionary
mechanisms? Remember each step in your explanation must offer some
sort of beneficial functional advantage over what came before.
> > Demonstrating
> > partial homology isn't enough to assume evolutionary ancestry.
>
> What the hell is "partial homology"?
Think about it. Even you can't be this dull witted.
> > > > Problem is, that
> > > > isn't an argument from any understanding whatsoever as to how your
> > > > proposed mechanism could actually do the job.
>
> > > What's wrong with the mechanisms which biolgists are researching?
> > > Mutation, gene duplication, heterochrony, developmental constraints,
> > > the actions of hox genes and other regulatory genes and so on? We seem
> > > to be getting closer and closer to the answer all the time.
>
> > Really? Where are there any examples of any of these types of
> > mutations producing any novel system of function with a minimum
> > structural threshold requirement of more than 1000 specifically
> > arranged residues?
>
> How about the evolutionary series showing the way in which the bones
> of the reptilain jaw became the bones of the mammalian ear for
> starters?
This is a series of morphologic variations assumed to be the result of
evolutionary processes. Again, the actual series of genetic mutations
has not been detailed nor evaluated in any sort of relevant
statistical manner as to the likelihood of random mutations and
natural selection actually being up to the job. You are left with
nothing more than your assumption that morphologic and genetic
similarities must always be the result of evolutionary change. That
assumption simply isn't supported beyond very low levels of functional
complexity.
> > Where are there even any statistical analyses of
> > the potential of such evolutionary mechanisms beyond this level of
> > functional complexity?
>
> I don't know.
> Why don't you educate yourself in statistics, evolutionary theory,
> genetics and so on and produce such an analysis.
Why don't you provide such an education? Where has anyone produced
any of this educational material at all?
> > > Why should be abandon all this in favour of your untestable assertion
> > > that an "intelligent designer" did it?
>
> > > > Your argument isn't
> > > > based on a scientific understanding of the process.
>
> > > I suggest that I have a pretty good understanding of the processes
> > > involved, as I try to keep up-to-date with the literature on the
> > > subject.
>
> > You've done nothing of the sort. You've just pointed out sequence and
> > structural similarities between high-level systems and then simply
> > asserted that evolutionary mechanisms clearly did the job. You've
> > presented no real time observation of evolution actually doing the job
>
> Since when has "real time observation" been a requirement for science?
Real time observation is very important in science, especially when it
actually happens at one level, but not at another. Beyond this, you
have no statistical analysis regarding your proposed mechanism doing
the job beyond very low levels either. You assumptions that it must
have happened that way just don't qualify as valid science.
> > nor have you presented any statistical analysis of the odds of
> > evolution actually doing the job at such levels.
>
> Why on earth to I need to?
> I have no idea how such a statistical analysis could be carried out,
> as we are not dealing with processes to which is it possible to attach
> meaningful measures of probability.
If you cannot evaluate your assumptions regarding the potential of
your proposed mechanism statistically, then it isn't science. Plain
and simple. Science is all about producing predictive value regarding
a proposed hypothesis. If your hypothesis is that a particular
mechanism can do the job, you have to produce some sort of odds
predicting how your mechanism will work in different situations - how
long it should take, etc. Otherwise, your mechanism is based on
nothing more solid than your bald statement that, "It just has to
work!"
> > All you've done are
> > what all other scientists are doing - simply assuming that evolution
> > did the job.
>
> Do you have a better explanation?
I do, but I don't need one before I can tell that your explanation is
based on nothing but hype and bald assertions.
> > You've got nothing else here. How did evolution do the
> > job at such levels Forrest?
>
> By the processes of natural selection acting on variation in
> populations of living organism. We may not know every detail of how
> evolutionary processes did the job, but in the absence of any
> alternative to the evolutionary model which can yield testable
> predictions it seems a pretty good bet that we are thinking along the
> right lines.
You don't know any statistical details about how random mutation and
natural selection did the job - none at all. This isn't a matter of
you kinda knowing how it happened. You don't have the first clue
beyond very low levels of functional complexity. Even when it comes
to low levels of functional complexity you really don't understand why
evolution works so well and so quickly. I do understand why. It is
because the non-beneficial gaps are so small at low levels. They can
be crossed by random mutations very rapidly. That's the most
reasonable answer - the one with the greatest predictive value.
> > What are the odds that your proposed
> > types of mutations are actually able to produce what you claim they
> > produced?
>
> I don't know. I have no idea of how one can calculate the probability
> of such events given the enormous number of unknown variables in the
> process.
> You don't know either, by the way: not only is your knowledge of
> statistics demonstreated to be rather weak by reference to your
> posting history, but you also lack knowledge of the processes by which
> evolutionary theory models such events.
I do know, by the way. At least I have a good basis for a rough
estimate. You, on the other hand, have absolutely no basis for making
any sort of estimate of evolutionary success or speed at any level.
< snip >
> > > > It also makes more and
> > > > more sense as we learn more and more about how these systems actually
> > > > integrate and function to perform the various tasks needed by various
> > > > types of living things. There are far less "vestigial" structures
> > > > today compared to just a few decades ago. The whole backward retina
> > > > argument that Dawkins made famous is now known to be completely
> > > > mistaken - i.e., it has many highly beneficial features given the
> > > > visual needs of those that have such a modification.
>
> > > So perhaps you can explain why all fish have the vertebrate retina,
> > > whereas all cephalods, many of which occupy exactly the same
> > > environment have more efficient eyes?
>
> > Cephalopods do not require high acuity vision nor do they have such
> > vision.
>
> Bollocks. Learn some biology. Some cephalopods have better eyesight
> that humans.
Ditto . . .
"The most advanced invertebrate eye is that of certain cephalopods.14
The major anatomical difference between the human eye and the advanced
cephalopod eye, such as the octopus, is the retina, which is not only
verted but also lacks a fovea centralis. As an underwater animal which
usually lives on the ocean bottom, the eye of the octopus is designed
to detect motion, not detail as is true of human eyes, and must
maximize its utilization of light since the ocean usually has little
or no light at its lower depths. Barnes notes:
The cephalopod eye undoubtedly forms an image, but the animal's visual
perception is certainly quite different from that of man, which is
greatly dependent upon interpretation by the brain. The cephalopod
optic connections appear to be especially adapted for analyzing
vertical and horizontal projections of objects in the visual field.
The visual system used by cephalopods is poorly understood partly
because understanding it is not a funding priority and partly because
it is so complex. Meglitsch notes: "The cephalopods have the most
highly developed nervous systems to be found in invertebrates, and
correspondingly complex behavior patterns."
In contrast to the claims of Dawkins et al., no evidence exists to
support the claim that even the most advanced verted eye is superior
to the inverted eye. As Ayoub asks:
[Would] "hundreds of thousands of vertebrate species-in a great
variety of terrestrial, marine and aerial environments-really see
better with a visual system used by a handful of exclusive marine
vertebrates? In the absence of any rigorous comparative evidence all
claims that the cephalopod retina is functionally superior to the
vertebrate retina remains entirely conjectural."
Judging by physiology, the verted cephalopod retina is clearly
inferior to the inverted retina. Wells notes:
Compared with the vertebrate retina, the retina of Octopus is very
simple. There are no equivalents of amacrine, bipolar or ganglion
cells in the cephalopod; peripheral processing of the visual input
must be much simpler.
The octopus eye also contains a complex nerve plexus posterior to the
receptors. Wells adds that the optic lobes must assume many of the
functions of the inverted retina in vertebrates so that the "apparent
relative simplicity of the cephalopod system is an illusion. It is a
matter of stacking; amacrines, bipolars and ganglion cells are all
there, but stuck onto the outer layer of the optic lobe rather than
onto the back of the retina."
Pechenik indicates that although cephalopods can perceive shape, light
intensity, and texture, they lack many of the advantages of an
inverted retina, such as the ability to perceive small details. The
visual system of the cephalopods is designed very differently than the
inverted eye in other ways to enable them to function in their dark,
water world. They can see only in black and white and have a narrow
range of vision compared to humans. Their photoreceptor cell
population is composed of only rods, and they contain a mere twenty
million retina receptor cells compared to 126 million in humans. The
rod's outer segments contain rhodopsin pigment that has a maximum
absorption in the blue-green part of the spectrum (475 nm), which is
the predominant color in their environment. Photons change the
rhodopsin to metarhodopsin and no further breakdown nor bleaching
occurs.
A second pigment in the octopus, retinochrome, has an absorption
maximum of 490 nm, which is more sensitive to dim light. It evidently
serves a supplementary role in the octopus vision system. Humans have
one rod type and three cone types. One cone type has a light frequency
of 430 nm (blue), another 530 nm (green), and the other 569 nm (red).
Further, in bright light the cephalopod's pupils become thin and slit-
shaped, and are held in a horizontal position by an organ called a
statocyst that uses gravity to determine the horizontal.25 Evidently
they scan a thin but wide area for information, indicating that their
visual world is considerably different from that of humans.
Grzimek notes that their visual process is "quite similar to that of
the batrachians, reptiles and insects. A 'photograph' of the recorded
image is not traced on the retina as in man; instead cephalopods
record and interpret as stimuli (pattern recognition ) only light and
color variations of a moving object." Importantly, the octopus "will
respond to certain motions as if they were prey, but will not react to
his normal food-objects when they are motionless." This observation of
the importance of motion in vision function is in harmony with the
observation that the octopus eye can be called "a compound eye with a
single lens" for the reason that the receptor cells are surrounded by
microvilli which form rhabdomeres. Each facet in a compound eye is
either on or off, and object movement produces a change in the on-and-
off pattern, similar to how a series of light bulbs produces the
illusion of movement by changing on-and-off patterns."
http://www.asa3.org/ASA/PSCF/2000/PSCF3-00Bergman.html
< snip rest >
> RF
Sean Pitman
www.DetectingDesign.com
Von R. Smith
0catch.com> wrote:
> On Feb 16, 5:30 am, "Von R. Smith" <trakl...@gmail.com> wrote:
>
> > > > Heck, he can't even tell me how many specifically arranged residues
> > > > there are working together at the same time in each of the proteins in
> > > > the 2,4-DNT cascade. He doesn't even seem to have figured out why I'm
> > > > asking the question yet.
>
> > > I've already given you my answer to this question as well - many
> > > times.
>
> > Not unless "many" got redefined to mean "zero" while I wasn't
> > looking. But go ahead and prove my hypothesis wrong: either
> > reproduce the numbers you have given me "again and again" in this
> > thread once more, or link the post where you provided the numbers (and
> > explained how you got them). I'll make it simple: just give me the
> > estimate, and how you calculated it, for dntD.
>
> There are many threads were I've discussed this topic with you at
> great length.
Yes, and in all that time you somehow forgot to answer the question:
How many specified residues are there in each protein of the 2,4-DNT
cascade?
You claim to have answered this question many times. An answer will
consist of a list of each protein, followed by the number of fairly-
specified residues there are in each one. Do you see such a list in
the text you quoted, or in the text of anything else you have
written? I don't.
<snip post in which Sean doesn't answer the question he claims to have
answered many many times>
Here, let me give you a fill-in-the-blank form.
1. There are ___________ fairly specified residues in dntAbAcAd, and
here is how I calculated that number:
2. There are ___________ fairly specified residues in dntB, and here
is how I calculated that number:
3. There are ___________ fairly specified residues in dntD, and here
is how I calculated that number:
4. There are ___________ fairly specified residues in dntE, and here
is how I calculated that number:
5. There are ___________ fairly specified residues in dntG, and here
is how I calculated that number:
Since, as you say, you have answered my question many many times, you
should have no problem filling in these blanks from one of your "many"
answers to my question. I am not interested in another avalanche of
unresponsive verbiage about 7-letter words or cows jumping over
houses. I want the numbers. We can argue about whether these numbers
"matter" to your 1000 residue challenge *after* you have demonstrated
that you can even estimate the number of fairly specified residues in
single proteins. If you can't or won't even do that, why should
anyone bother with you?
Seanpit
> On Feb 16, 10:49 am, "Seanpit" <seanpitnos...@naturalselection.
>
>
>
>
>
> 0catch.com> wrote:
> > On Feb 16, 5:30 am, "Von R. Smith" <trakl...@gmail.com> wrote:
>
> > > > > Heck, he can't even tell me how many specifically arranged residues
> > > > > there are working together at the same time in each of the proteins in
> > > > > the 2,4-DNT cascade. He doesn't even seem to have figured out why I'm
> > > > > asking the question yet.
>
> > > > I've already given you my answer to this question as well - many
> > > > times.
>
> > > Not unless "many" got redefined to mean "zero" while I wasn't
> > > looking. But go ahead and prove my hypothesis wrong: either
> > > reproduce the numbers you have given me "again and again" in this
> > > thread once more, or link the post where you provided the numbers (and
> > > explained how you got them). I'll make it simple: just give me the
> > > estimate, and how you calculated it, for dntD.
>
> > There are many threads were I've discussed this topic with you at
> > great length.
>
> Yes, and in all that time you somehow forgot to answer the question:
>
> How many specified residues are there in each protein of the 2,4-DNT
> cascade?
All require well less than 1000aa each at minimum. But, you already
know that. So, what's your point?
< snip >
Sean Pitman
www.DetectingDesign.com
Seanpit
> On Feb 16, 7:32 am, "Seanpit" <seanpitnos...@naturalselection.
>
> 0catch.com> wrote:
> > On Feb 16, 3:59 am, "Ron O" <rokim...@cox.net> wrote:
>
> > > Two posts of dishonest evasion.
>
> > > Just give me one good reason why I should tell you how lame your
> > > current argument is, when you have found out how lame all your others
> > > were? How long have you been on your 1000 specified amino acid
> > > schtick? What happened to your neutral gap schtick. Did you ever
> > > find an example where a gap of 3 or 4 had to be crossed? Since the
> > > answer is no, why do you think that expanding it to 1000 is going to
> > > help you?
>
> > Can you show me any beneficial functional system that requires more
> > than 1000 specifically arranged amino acid residues that is within 3
> > or 4 residue changes of any other novel system of function?
>
> All of the new functions have been actually found to arise have arisen
> from existing functional proteins by changes that are often 3-4
> mutational steps (which is not the same as residue changes, but is
> more accurate) or fewer from a previous protein(s).
Any specific examples? As I've noted extensively before, your FliG-
FliF example does not qualify because FliG is required for both
systems and there is no experimental setup where the independent
systems would link up with a simple fusion of FliG-FliF between
historically independently acting systems. The only example you have
of this situation actually occurring is in a system where flagellar
motility has already been pre-established.
< snip >
> Of course. I have already mentioned in the past that a novel form of
> linkage between FliG and FliF to form a fusion protein and that this
> new protein provides a novel linkage between a *pre-existing* system
> that transports proteins along a whip-like channel to the outside (the
> rotateable pore) and a motor subsystem that has the ability to convert
> ATP into mechanical motion. Such systems exist in several different
> forms in cells and have functions that do not include rotary
> motility. Thus, this demonstrates how evolution actually works.
Again, this example is only realized in systems that already have pre-
established flagellar motility. It is extremely unlikely that two
historically independently acting systems would be able to link up in
such a manner to produce flagellar motility which wasn't already there
historically. All you'd have to do to prove me wrong is produce such
a bacterium with both historically independently acting motor and
rotatable pore and see if they spontaneously link up via this sort of
covalent bonding you describe.
> The
> total size of the end system doesn't matter. The number of mutational
> steps required to reach the novel *function* from a state that lacked
> that *function* is unrelated to the end size.
Not true. There is a very strong relationship between the minimum
required size and specificity requirements for a functional system and
the likelihood that the needed subparts will be available in
sufficient order to self-assemble within just one or two mutational
steps of any kind.
> But the same thing is
> true for betagalactosidase activities. *Functional* levels of
> betagalactosidase activity can either be produced by a single (or a
> few) mutational steps in cells that have the ebg protein or it can be
> much more difficult to generate in cells that lack that protein. That
> is, the *mechanism* and number of mutational steps required is
> dependent on the idiosyncratic presence or absence of a particular
> possible precursor and is NOT a function of the size of the end
> product.
It is not was is possible, but what is probable. The odds that the
needed short distance will actually exist drop dramatically (10-20
fold) with each additional specified residue requirement. The fact
that only one starting point in the entire gene pool of a large
population was within such a short distance of any of a great many
potential lactase sequences/structures in sequence/structure space is
very telling given this relatively low level of functional/structural
complexity.
Sean Pitman
www.DetectingDesign.com
hersheyh
0catch.com> wrote:
> On Feb 16, 10:52 am, "Von R. Smith" <trakl...@gmail.com> wrote:
>
>
>
> > On Feb 16, 10:49 am, "Seanpit" <seanpitnos...@naturalselection.
>
> > 0catch.com> wrote:
> > > On Feb 16, 5:30 am, "Von R. Smith" <trakl...@gmail.com> wrote:
>
> > > > > > Heck, he can't even tell me how many specifically arranged residues
> > > > > > there are working together at the same time in each of the proteins in
> > > > > > the 2,4-DNT cascade. He doesn't even seem to have figured out why I'm
> > > > > > asking the question yet.
>
> > > > > I've already given you my answer to this question as well - many
> > > > > times.
>
> > > > Not unless "many" got redefined to mean "zero" while I wasn't
> > > > looking. But go ahead and prove my hypothesis wrong: either
> > > > reproduce the numbers you have given me "again and again" in this
> > > > thread once more, or link the post where you provided the numbers (and
> > > > explained how you got them). I'll make it simple: just give me the
> > > > estimate, and how you calculated it, for dntD.
>
> > > There are many threads were I've discussed this topic with you at
> > > great length.
>
> > Yes, and in all that time you somehow forgot to answer the question:
>
> > How many specified residues are there in each protein of the 2,4-DNT
> > cascade?
>
> All require well less than 1000aa each at minimum.
You mean that *each* protein in this cascade requires less than 1000
of whatever you mean by aa, don't you? Or do you mean the total in
all of the proteins of the cascade?
And that hand-waving smoke-and-mirrors number of 1000 is not the
answer that was asked for. He asked "How many specified residues are
there in each protein of the 2,4-DNT cascade? To answer that, you
have to come up with a specific number for each of the proteins (or
one for all of the proteins of the cascade). And you have to tell us
how you calculated that specific number.