exploring _all_ of sequence space -- done deal?
Kent Paul Dolan
I've forgotten who, but thanks, in any case.
Lo and behold, the document is _not_ behind a pay
wall!!
It is a very nice document, since the authors went
to the trouble completely to debunk what might be
called "Sean Pitman math", with the explicit
conclusion that the use of such math to "prove" the
need for divine intervention in creating the tree of
life is a bogus enterprise.
How much of protein sequence space
has been explored by life on Earth?
[...]
To further support this idea of a reduced alphabet
of amino acids, there are also very plausible
suggestions that the original amino acid repertoire
consisted of only four or five amino acids like
those found in the Miller--Urey experiments and the
Murchison meteorite (Miller et al. 1976), and that
the genetic code was initially limited to these few
amino acids that still predominate in proteins to
the current day (e.g. Trifonov 2000; Brooks et al.
2002; Ikehara 2002). Proteins with reduced amino
acid repertoires can fold and function successfully
(e.g. Cordes et al. 1996; Riddle et al. 1997; Plaxco
et al. 1998; Guo et al. 2004; Doi et al. 2005; López
de la Osa et al. 2007).
[...]
Finally, we conclude that the number 20^100 and
similar large numbers (e.g. Salisbury 1969; Maynard
Smith 1970; Mandecki 1998; Luisi 2003; Carrier 2004;
de Duve 2005) are simply ‘straw men’ advanced to
initiate discussion in the same spirit as the
‘Levinthal paradox’ of protein folding rates
(Levinthal 1969; Zwanzig et al. 1992). 20^100 is now
no more useful than the approximate 2×10^1834097
books present in Borges' (1999) fantastical ‘Library
of Babel’ and has no connection with the real world
of amino acids and proteins. Hence, we hope that our
calculation will also rule out any possible use of
this big numbers ‘game’ to provide justification for
postulating divine intervention (Bradley 2004;
Dembski 2004)
http://rsif.royalsocietypublishing.org/content/5/25/953.long
I can only add that after this analysis has been
cited into a discussion, any such attempt to use
"Sean Pitman math" to attempt "to provide
justification for postulating divine intervention"
is a dishonest enterprise, as well.
Life is, as usual when drop-kicking creationist
loons, good.
xanthian.
Seanpit
> Someone URLed this link a day or two ago,
> I've forgotten who, but thanks, in any case.
>
> Lo and behold, the document is _not_ behind a pay
> wall!!
>
> It is a very nice document, since the authors went
> to the trouble completely to debunk what might be
> justification for postulating divine intervention"
> is a dishonest enterprise, as well.
>
> Life is, as usual when drop-kicking creationist
> loons, good.
This paper is nonsense. The authors argue that because some types of
functional proteins are smaller than 100aa and because some types of
proteins have very low sequence specificity requirements that pretty
much all of sequence space could have been searched in just a few
billion years.
What these authors fail to realize is that not all protein-based
systems are created equal. Some systems do indeed require very few
amino acid building blocks and little sequence specificity. These, of
course, are on very low levels of functional complexity. Other
systems, however, require far more than the 100aa systems discussed by
the authors - at minimum. And, many of these systems require a
significant degree of specificity. These systems are on a much higher
level of functional complexity and therefore occupy much much larger
sequence spaces and also have exponentially lower ratios of
potentially beneficial vs. non-beneficial at these higher levels.
The authors of this paper do not even address the concept of different
levels of functional complexity. They only point out the obvious that
some types of functional systems are very very low level systems.
Well duh! What about those systems that are on much much higher
levels of minimum size and/or specificity requirements?
I can't believe such nonsense would actually convince anyone familiar
with the subject.
> xanthian.
Sean Pitman
www.DetectingDesign.com
Re: How much of protein sequence space has been explored by life on
Earth?
1. David T.F Dryden*,
2. Andrew R Thomson and
3. John H White
Kent Paul Dolan
> What these authors fail to realize is that not all
> protein-based systems are created equal.
They are what are usually called "experts".
You are what is usually called "a lunatic".
You being a non-entitiy, with no published peer
reviewed papers on this subject matter, they are not
responding to you.
They are arguing directly in response to the
dishonest sources of your fruitcake claims, Bradley
and Dembski.
They are fully conversant with those arguments.
Your pretense that there is something you know that
they have missed, is a thus a joke.
You argue as a well known cult-religion-motivated
invincibly ignorant biogenetics dunce.
They speak as recognized experts in their field.
You do not.
Your ill-motivated arguments, by naked ASSertion,
counter-factual and nature denying, do not a
competent rebuttal make.
They have provided fully documented arguments, with
54 complete citations to the relevant technical
literature.
You provide only bloviation.
They are competent in the subject matter whereof
they speak,
You are not.
You may continue your obvious dishonesty until the
sun burns down to a cinder.
No one will care a fig if you do, though many will
continue to enjoy yanking your chain, keeping you
in front of the spotlight as a figure of jest.
The experts have spoken.
You are now invincibly documented to be wrong in
every detail of your "Sean Pitman math".
You are now invincibly documented to be lying
through your teeth.
You are now demonstrated to have been doing so since
the inception of your dishonest arguments against
the theory of evolution, by now years past.
Strangely enough, even without this latest input,
most participants here have known that about you
for all those years, and told you so in blunt terms.
xanthian.
Steven L.
> Someone URLed this link a day or two ago,
> I've forgotten who, but thanks, in any case.
>
> Lo and behold, the document is _not_ behind a pay
> wall!!
>
> It is a very nice document, since the authors went
> to the trouble completely to debunk what might be
> called "Sean Pitman math", with the explicit
> conclusion that the use of such math to "prove" the
> need for divine intervention in creating the tree of
> life is a bogus enterprise.
I just read the paper.
Yes, it answers Pitman nicely.
But it also answers Gould and Sagan too--on a different subject:
"Protein sequence space is often viewed as a limitless desert of
maladjusted sequences with only a few oases of working sequences linked
by narrow pathways (Axe 2000, 2004). The navigation over this space by
natural selection is difficult and could take many different routes thus
resulting in organisms with largely different protein compositions. This
idea of contingency, if taken at the level of species, led Gould to
suggest that if one was to rerun the ‘tape of life’ then evolution would
take a totally different path and we, as a species, would only appear as
a highly improbable accident (Gould 1991; Luisi 2003; de Duve 2007a,b).
However, if there is any merit to our simple calculation then protein
sequence analysis provides no support for the idea of contingency at a
molecular level and it provides strong support for the ideas of
convergence (Conway Morris 2000, 2004; Dawkins 2005; Vermeij 2006; de
Duve 2007a,b). If one was to rerun the tape, then the protein
composition of organisms would be similar. "
That has implications for SETI too. We know that amino acids exist in
outer space. If "convergence" is true, then life forms elsewhere in the
Universe should be protein-based, and maybe even nucleic-acid-based.
Good paper!
--
Steven L.
Email: sdli...@earthlinkNOSPAM.net
Remove the NOSPAM before replying to me.
Steven L.
Sure. But that says that your argument becomes *less* applicable for
the early history of life on Earth, when the first microbes may have had
only a few different amino acids and low levels of functional
complexity; and your argument becomes *more* applicable for the later
history of life on Earth, when the full richness of sequence space of 20
amino acids emerged.
The first amino acid-based life forms on Earth didn't have high levels
of functional complexity. They were probably just barely good enough to
eke out a marginal living and reproduce. So the number of evolutionary
paths through sequence space was relatively small, back then.
I grant you that for larger, complex organisms with high levels of
functional complexity--the ones that evolved after the Cambrian
explosion--navigation through this richer sequence space became harder.
But some mechanisms were invented to speed up this process too, most
notably, SEX. Sex allows for a vast exploration of sequence space to
take place, as the male and female genes are reshuffled and recombined
through meiosis and zillions of sperm.
> The authors of this paper do not even address the concept of different
> levels of functional complexity. They only point out the obvious that
> some types of functional systems are very very low level systems.
> Well duh! What about those systems that are on much much higher
> levels of minimum size and/or specificity requirements?
>
> I can't believe such nonsense would actually convince anyone familiar
> with the subject.
May I forward your comments on to the author (except for the invective
about "nonsense")? Or would you like to do it yourself? His email
address is: david....@ed.ac.uk
Perhaps we can get a dialogue going between him and you. That would be
tremendously valuable to this NG.
wf3h
> What these authors fail to realize
sean is, at least, consistent.
SETI researchers are wrong because they don't agree with him
the mathematicians who developed the no free lunch theorem are wrong
because they don't agree with him
these guys are wrong....well...you get the picture.
sean's argument has devolved to the point where it's a parody of
itself. everyone is wrong if they disagree with sean. and his belief
in a 2000 year old failed idea?
why...it's the truth! we know that because he said it.
Perplexed in Peoria
> How much of protein sequence space
> has been explored by life on Earth?
>
> http://rsif.royalsocietypublishing.org/content/5/25/953.long
>
> I can only add that after this analysis has been
> cited into a discussion, any such attempt to use
> "Sean Pitman math" to attempt "to provide
> justification for postulating divine intervention"
> is a dishonest enterprise, as well.
It is a paper worth looking at. And the suggestion that the
'exploration of sequence space' might have taken place
back when the amino acid alphabet was smaller (and that
the alphabet and sequence space have since expanded)
is worth considering.
But I have to say that when they were computing their
upper bound on the number of sequences examined
(about 10^43) I thought that what they were doing *was*
Pitman math. Their 'lower bound' estimate of about
10^21 sequences strikes me as much more reasonable
as an extimate of how much of sequence space has been
explored.
So, I think that the answer to the title question has to be
"No, not a done deal. Not even close to all of sequence
space. But quite possibly enough of sequence space."
FLAME ON
I wish that every once in a while, I would get to read an abiogenesis
paper by someone working in a biology or biochemistry department,
rather than chemistry, physics, or computer science. Then, just maybe,
it might have some relevance to the process by which life originated
on this planet.
Furthermore, when the authors of a chemistry paper gratefully
acknowlege discussions with Simon Conway Morris, I'm afraid
it becomes impossible to take them very seriously.
FLAME OFF
Seanpit
Not remotely likely. The simplest living thing, even at a
theorectical limit, requires many systems that have minimum part
requirements of their own that go well beyond 100 fsaars - - even far
beyond 1000 fsaars.
> I grant you that for larger, complex organisms with high levels of
> functional complexity--the ones that evolved after the Cambrian
> explosion--navigation through this richer sequence space became harder.
> But some mechanisms were invented to speed up this process too, most
> notably, SEX. Sex allows for a vast exploration of sequence space to
> take place, as the male and female genes are reshuffled and recombined
> through meiosis and zillions of sperm.
Sex doesn't do squat when it comes to exploring sequence space
significantly faster. All sex does is allow for genetic recombination
of pre-established alleles. It doesn't help to find novel beneficial
alleles to any significant degree when these potentially beneficial
sequences become exponentially rarer and rarer with each step up the
ladder of functional complexity.
> > The authors of this paper do not even address the concept of different
> > levels of functional complexity. They only point out the obvious that
> > some types of functional systems are very very low level systems.
> > Well duh! What about those systems that are on much much higher
> > levels of minimum size and/or specificity requirements?
>
> > I can't believe such nonsense would actually convince anyone familiar
> > with the subject.
>
> May I forward your comments on to the author (except for the invective
> about "nonsense")? Or would you like to do it yourself? His email
> address is: david.dry...@ed.ac.uk
Please do. By all means. And do let me know what the author has to
say.
> Perhaps we can get a dialogue going between him and you. That would be
> tremendously valuable to this NG.
It would no doubt be interesting . . .
> Steven L.
> Email: sdlit...@earthlinkNOSPAM.net
> Remove the NOSPAM before replying to me.
Sean Pitman
www.DetectingDesign.com
Seanpit
> Kent Paul Dolan wrote:
> > Someone URLed this link a day or two ago,
> > I've forgotten who, but thanks, in any case.
>
> > Lo and behold, the document is _not_ behind a pay
> > wall!!
>
> > It is a very nice document, since the authors went
> > to the trouble completely to debunk what might be
> > conclusion that the use of such math to "prove" the
> > need for divine intervention in creating the tree of
> > life is a bogus enterprise.
>
> I just read the paper.
>
> Yes, it answers Pitman nicely.
How is that? It doesn't even address my argument of levels of
functional complexity and the exponential stalling out effect as
higher and higher levels are attempted by the mechanism of RM/NS.
This paper only deals with functional systems that are extremely low
level - much much lower level than even 100 fsaar systems. That's
complete nonsense when it comes to explaining the origin of truly
complex systems of function via RM/NS.
>
> But it also answers Gould and Sagan too--on a different subject:
>
> "Protein sequence space is often viewed as a limitless desert of
> maladjusted sequences with only a few oases of working sequences linked
> by narrow pathways (Axe 2000, 2004). The navigation over this space by
> natural selection is difficult and could take many different routes thus
> resulting in organisms with largely different protein compositions. This
> idea of contingency, if taken at the level of species, led Gould to
> suggest that if one was to rerun the ‘tape of life’ then evolution would
> take a totally different path and we, as a species, would only appear as
> a highly improbable accident (Gould 1991; Luisi 2003; de Duve 2007a,b).
> However, if there is any merit to our simple calculation then protein
> sequence analysis provides no support for the idea of contingency at a
> molecular level and it provides strong support for the ideas of
> convergence (Conway Morris 2000, 2004; Dawkins 2005; Vermeij 2006; de
> Duve 2007a,b). If one was to rerun the tape, then the protein
> composition of organisms would be similar. "
>
> That has implications for SETI too. We know that amino acids exist in
> outer space. If "convergence" is true, then life forms elsewhere in the
> Universe should be protein-based, and maybe even nucleic-acid-based.
>
> Good paper!
>
> --
> Steven L.
> Email: sdlit...@earthlinkNOSPAM.net
Seanpit
wrote:
> "Kent Paul Dolan" <xanth...@well.com> wrote in messagenews:gt2asc$c8p$1...@news.albasani.net...
>
> > How much of protein sequence space
> > has been explored by life on Earth?
>
> >http://rsif.royalsocietypublishing.org/content/5/25/953.long
>
> > I can only add that after this analysis has been
> > cited into a discussion, any such attempt to use
> > justification for postulating divine intervention"
> > is a dishonest enterprise, as well.
>
> It is a paper worth looking at. And the suggestion that the
> 'exploration of sequence space' might have taken place
> back when the amino acid alphabet was smaller (and that
> the alphabet and sequence space have since expanded)
> is worth considering.
A smaller alphabet doesn't really solve the problem. The minimum
structural threshold requirements for systems at different levels of
functional complexity remain essentially unchanged regardless of the
alphabet in use.
> But I have to say that when they were computing their
> upper bound on the number of sequences examined
> (about 10^43) I thought that what they were doing *was*Pitmanmath. Their 'lower bound' estimate of about
> 10^21 sequences strikes me as much more reasonable
> as an extimate of how much of sequence space has been
> explored.
There is a very big difference between the number of sequences
explored in a given span of time and the actual size of sequence space
that needs to be explored, on average, before any beneficial sequence
at a given level of functional complexity can expect to be realized.
The authors do not address this concept nor do they even seem to
comprehend the fact that every living thing, even the simplest living
thing, requires systems that have minimum structural threshold
requirements of their own that greatly surpass 100 fsaars.
> So, I think that the answer to the title question has to be
> "No, not a done deal. Not even close to all of sequence
> space. But quite possibly enough of sequence space."
Only enough of sequence space to find very very low level systems of
functional complexity. Certainly not remotely close to finding
anything beyond the 1000 fsaar level of functional complexity . . .
> FLAME ON
>
> I wish that every once in a while, I would get to read an abiogenesis
> paper by someone working in a biology or biochemistry department,
> rather than chemistry, physics, or computer science. Then, just maybe,
> it might have some relevance to the process by which life originated
> on this planet.
>
> Furthermore, when the authors of a chemistry paper gratefully
> acknowlege discussions with Simon Conway Morris, I'm afraid
> it becomes impossible to take them very seriously.
>
> FLAME OFF
Agreed.
Sean Pitman
www.DetectingDesign.com
Perplexed in Peoria
> On Apr 26, 4:13 pm, "Perplexed in Peoria" <jimmene...@sbcglobal.net>
> wrote:
> > 'exploration of sequence space' might have taken place
> > back when the amino acid alphabet was smaller (and that
> > the alphabet and sequence space have since expanded)
> > is worth considering.
>
> A smaller alphabet doesn't really solve the problem. The minimum
> structural threshold requirements for systems at different levels of
> functional complexity remain essentially unchanged regardless of the
> alphabet in use.
I'm not so sure of that. When I look at the question one way, my
intuition agrees with you. When I look at it a different way, my
intuition says that a smaller alphabet is a step in the right direction.
My conclusion is that my intuition cannot be trusted, and I need to
remain open minded.
Here is a thought experiment tending to show that smaller alphabets
help. Consider the problem of finding an RNA sequence which folds
into the famous 'cloverleaf' structure of tRNA. There are around
22 base pairs in the four stems. So with an alphabet of four bases
and a sequence size of 75, 31 bases are "don't care" and 22 of them
have to be complementary to the remaining 22.
That is, only one in 4^22 sequences will have the right cloverleaf
shape. Or, as I would prefer to put it, the specification of a
sequence satisfying that function takes 44 bits.
But now look at what is needed to achieve this function using an
alphabet of only two nucleic acid bases. Now, only one in 2^22
sequences satisfies the requirement. The specification needs only
22 bits.
Does this RNA sequence result transfer to protein sequences?
That is where my intuition is confused. But I do know that the
'function' of the amino acids at most sites in a typical protein
is to fit together nicely with some other amino acid elsewhere
in the same functional system.
'Rev Dr' Lenny Flank
> I can't believe such nonsense would actually convince anyone familiar
> with the subject.
But my dear Sean -- YOU have not convinced anyone familiar with the
subject.
In fact, everyone that you have shown your world-shattering sciencey
mathy stuff to, thinks it's horse shit.
Why is that, Sean?
Is it because the world's scientists are all engaged in an
international conspiracy against you?
Is it it because you really HAVE made the single most important
discovery of the 21st century, but are too stupid and incompetent to
explain it to anyone in such a manner that they can understand it and
grasp its genius?
Or is your mathy sciencey stuff really just full of shit, like
everyone thinks it is?
Which is it, Sean?
(snicker) (giggle) <------ yes, Sean, I am laughing at you
================================================
Lenny Flank
"There are no loose threads in the web of life"
Editor, Red and Black Publishers
http://www.RedandBlackPublishers.com
'Rev Dr' Lenny Flank
>
> How is that? It doesn't even address my argument
That's because your argument is just the same tired old "747 in a
tornado" bullshit that everyone laughed at 40 years ago.
Everyone but you seems to realize that evolution doesn't make things
all at once intact in one fell sdwoop by randomly assembling pieces.
Evolution works by modifying what is already there.
Which makes your entire "argument" . . . well . . . bullshit. (shrug)
R. Baldwin
news:453f9192-1ed9-487a...@q33g2000pra.googlegroups.com:
> On Apr 26, 3:00�pm, "Steven L." <sdlit...@earthlink.net> wrote:
>> Kent Paul Dolan wrote:
>> > Someone URLed this link a day or two ago,
>> > I've forgotten who, but thanks, in any case.
>>
>> > Lo and behold, the document is _not_ behind a pay
>> > wall!!
>>
>> > It is a very nice document, since the authors went
>> > to the trouble completely to debunk what might be
>> > called "SeanPitmanmath", with the explicit
>> > conclusion that the use of such math to "prove" the
>> > need for divine intervention in creating the tree of
>> > life is a bogus enterprise.
>>
>> I just read the paper.
>>
>> Yes, it answers Pitman nicely.
>
> How is that? It doesn't even address my argument of levels of
> functional complexity and the exponential stalling out effect as
> higher and higher levels are attempted by the mechanism of RM/NS.
> This paper only deals with functional systems that are extremely low
> level - much much lower level than even 100 fsaar systems. That's
> complete nonsense when it comes to explaining the origin of truly
> complex systems of function via RM/NS.
>
Sean is correct that the paper does not address his argument about
levels of functional complexity. The authors explicitly accept the
prevailing idea that protein evolution depends on simpler folds. This is
an idea that Sean simply ignores. The paper does not address the idea
that "levels of functional complexity" even exist, because they have
never been demonstrated to exist, and that concept is inconsistent with
a hierarchy based on families of protein sequences, protein structures,
and fold domains.
I doubt that any serious scientific article ever would address Sean's
"levels of functional complexity" because it has no basis in fact. There
is no reason to give it serious consideration.
As for the "exponential stalling out effect", for this to established,
not only would Sean would have to demonstrate why the prevailing
paradigm for protein evolution is erroneous, but that all conceivable
paradigms for protein evolution are erroneous. I doubt that he will even
attempt this, since he doesn't appear to understand the prevailing
paradigm at all.
Of course, if Sean believes I am not doing him justice, he could counter
my argument here, by completing the following:
"The prevailing paradigm for protein evolution is:"
unrestra...@hotmail.com
You haven't established that your 1000aa sequences have to be started
from scratch. This is, on the face of it, counter intuitive. It is
also refuted buy the evidence.
You haven't established that the sequences we do have which are that
long were the goal of evolution in any meaningful way.
You haven't established that *you have looked at all of the possible
useful mutations, and know the odds of them happening.
You haven't established that you know the evolutionary precursor to
any 1000aa genetic sequence.
Kermit
Kent Paul Dolan
> It doesn't even address my argument
Excuse me?
You are a *nobody*, no researcher is required to
address _your_ argument, it doesn't exist for
researchers because it is nowhere published in a
pertinent professional peer reviewed journal,
because even you know that it is garbage done for
your cult religion, not science.
> of levels of functional complexity and the
> exponential stalling out effect as higher and
> higher levels are attempted by the mechanism of
> RM/NS.
Well, first, because that argument is baseless word
salad.
The authors demonstrate convincingly that the
numbers you use to calculate your "trillions and
trillions of years..." are bogus numbers and that
the difficulty of the problem done with real numbers
does not rise at an exponential rate that causes
problems with exploring all of sequence space in the
time and with the number of living entities
available.
Second, because once _all_ of sequence space has
been explored, arguments based on any other factor
than exploring all of sequence space become
meaningless.
In particular, if sequence space has already all
been explored, it's long too late for your claims
that functional complexity makes that full
exploration impossible.
_All_ those "umbridgable" gaps have already been
bridged.
The article authors have given a cogent and
convincing argument that all of sequence space has
in all likelihood already been explored, and
certainly has had plenty of time and opportunity to
have been fully explored.
This leaves you like the little match girl, out in
the freezing cold of non-entityhood, looking in at
the warm flame of the light science casts on
reality, the gleaming reputations of real
contributors to science, and wishing you'd done some
real science instead of wasting your life dressed in
the rags of your dishonesty, trying to sell
worthless goods and arguing from a tested ground
truth base of squat for your never-clarified model
of adding functionality during speciation.
HTH
xanthian.
Kent Paul Dolan
> But I have to say that when they were computing
> their upper bound on the number of sequences
> examined (about 10^43) I thought that what they
> were doing *was* Pitman math.
Perhaps you misunderstood their intent.
They were trying to determine the maximum number of
sequences that could _possibly_ have been explored.
Of necessity, that requires them to use outrageously
optimistic assumptions, or they might miss that
maximum.
> Their 'lower bound' estimate of about 10^21
> sequences strikes me as much more reasonable as an
> extimate of how much of sequence space has been
> explored.
This, on the other hand, is the more important
bound, and is the bound someone with Pitman's cult
agenda would be challenging.
If it can be proved that this bound is wildly too
optimistic, then perhaps it is _not_ the case that
all of sequence space has already been explored.
That's why the authors used only extremely
pessimistic assumptions for how fast sequences were
being explored, in this case, to avoid
overestimating the smallest number of sequences that
would have been explored over evolutionary time.
HTH
xanthian.
Perplexed in Peoria
> Perplexed in Peoria wrote:
>
> > But I have to say that when they were computing
> > their upper bound on the number of sequences
> > examined (about 10^43) I thought that what they
> > were doing *was* Pitman math.
>
> Perhaps you misunderstood their intent.
>
> They were trying to determine the maximum number of
> sequences that could _possibly_ have been explored.
>
> Of necessity, that requires them to use outrageously
> optimistic assumptions, or they might miss that
> maximum.
>
> > Their 'lower bound' estimate of about 10^21
> > sequences strikes me as much more reasonable as an
> > extimate of how much of sequence space has been
> > explored.
>
> This, on the other hand, is the more important
> bound, and is the bound someone with Pitman's cult
> agenda would be challenging.
It is the bound anyone with an ounce of skepticism would
be challenging.
And as for "cult agendas", do you really think that the
"inevitable humans" agenda of Simon Conway Morris
which this paper promotes is any less religiously-based
and scientifically reprehensible than Pitman's agenda?
Don't you remember the brouhaha about Guillermo
Gonzalez and tenure? Gonzalez was selling essentially
the same snake oil that Conway Morris is.
> If it can be proved that this bound is wildly too
> optimistic, then perhaps it is _not_ the case that
> all of sequence space has already been explored.
Apparently you didn't 'do the math'. Their lower bound
didn't cover any but their lowest estimates for the total
size of sequence space.
> That's why the authors used only extremely
> pessimistic assumptions for how fast sequences were
> being explored, in this case, to avoid
> overestimating the smallest number of sequences that
> would have been explored over evolutionary time.
Except that their assumptions were not at all pessimistic.
They struck me as reasonable middle-balls.
Steven L.
First of all, the paper is not "promoting" Morris. The authors simply
claimed that their calculations are more supportive of a convergence
theory than they are of Gould's "freak accident" theory.
Gould and Pitman are actually on the same side when they claim that the
probability of a sentient technological species on Earth is very tiny.
It's just that Pitman believes it's so tiny as to be virtually impossible.
Secondly, while SETI proponents don't claim that humans are inevitable,
they do believe that sentient species capable of technological
civilizations are inevitable throughout the Universe, given sufficient
time. If they didn't believe that, they would have no reason to do
SETI--because it can't ever disprove that. And that's a convergence
theory too.
So the notion of convergence to at least intelligence and technology--to
a mind capable of comprehending the Universe--isn't "religiously based
and scientifically reprehensible." It's certainly speculative and
daring, but it has firm grounding in what we know from science.
If that meteorite hadn't wiped out the dinosaurs, would the descendants
of Troodon be worshiping God today? Would they have electricity,
airplanes, cell phones, etc.? That's convergence.
--
Steven L.
Email: sdli...@earthlinkNOSPAM.net
Seanpit
>
>
> You haven't established that your 1000aa sequences have to be started
> from scratch.
That's because they aren't started from scratch. They are never
maximally distant from a given genome.
> This is, on the face of it, counter intuitive. It is
> also refuted buy the evidence.
Exactly. The evidence shows that the distances between higher and
higher level beneficial sequences with novel functions increases in a
linear manner.
> You haven't established that the sequences we do have which are that
> long were the goal of evolution in any meaningful way.
The goal of the evolutionary mechanism of RM/NS is to find new
beneficial sequences. If it only finds neutral or detrimental
sequences, Darwinian-style evolution doesn't happen. While there is
no specific target to be sure, since the mechanism is mindless, there
are in fact targets upon which success or failure of the search
process is based.
> You haven't established that *you have looked at all of the possible
> useful mutations, and know the odds of them happening.
You don't have to look at all possible sequences in sequence space
before you can have a very good idea as to the ratio of beneficial vs.
non-beneficial. That's why it is a science. If you actually knew all
about all possible sequences, you wouldn't need science. Science is
about working with limited information. It isn't about producing
perfection.
> You haven't established that you know the evolutionary precursor to
> any 1000aa genetic sequence.
That's because an evolutionary precursor is statistically unlikely to
have ever existed. If you think otherwise, were is your statistical
analysis that shows that such a precursor is actually likely to have
existed and that your proposed mechanism is remotely likely to have
done the job this side of trillions of years of time? All I see from
your end are fairytale just-so stories and bravado - no real science
or statistical analysis of any kind.
> Kermit
Sean Pitman
www.DetectingDesign.com
Seanpit
> On Apr 26, 7:24 pm, Seanpit <sean...@gmail.com> wrote:
>
>
>
> > How is that? It doesn't even address my argument
>
> That's because your argument is just the same tired old "747 in a
> tornado" bullshit that everyone laughed at 40 years ago.
>
> Everyone but you seems to realize that evolution doesn't make things
> all at once intact in one fell sdwoop by randomly assembling pieces.
> Evolution works by modifying what is already there.
That's right. Evolution does work by modifying what is already
there. The problem here is that if the gaps between what is already
there and the next closest beneficial sequence are too large, a
successful modification will not happen this side of trillions of
years of time - on average. That's the entire problem with your
proposed mechanism of RM/NS beyond extremely low levels of functional
complexity. The gaps between what is already there and higher level
functional systems are simply too large for your mechanism to work in
what anyone would call a reasonable amount of time.
If you think otherwise, you should be able to produce some odds
analysis to support your theory. But, you can't. All you have are
fairytale just-so stories about how it is possible without any
consideration of the likelihoods of your stories. That's not
science. That's just your active imagination at work.
> Which makes your entire "argument" . . . well . . . bullshit. (shrug)
Prove it. Produce some statistical analysis that proves me wrong. It
should be easy if you guys actually have some real scientific backing
like you claim you have.
> ================================================
> Lenny Flank
> "There are no loose threads in the web of life"
>
> Editor, Red and Black Publishershttp://www.RedandBlackPublishers.com
Sean Pitman
www.DetectingDesign.com
Seanpit
wrote:
>
> Sean is correct that the paper does not address his argument about
> levels of functional complexity. The authors explicitly accept the
> prevailing idea that protein evolution depends on simpler folds. This is
> an idea that Sean simply ignores. The paper does not address the idea
> that "levels of functional complexity" even exist, because they have
> never been demonstrated to exist, and that concept is inconsistent with
> a hierarchy based on families of protein sequences, protein structures,
> and fold domains.
You're mistaken. Sure proteins are based on relatively simple folds.
I do in fact address this idea very clearly in my essay on the
flagellar motility system. The problem is that higher level systems
require many of these simple folds at minimum - many many more
compared to the simple systems discussed in your paper here. In fact,
the minimum structural threshold for a system like the flagellar
motility system requires over 10,000 fairly specified amino acid
residues working together at the same time. The number of unique
folds is relatively few, but that is irrelevant to the problem of
levels of functional complexity.
> I doubt that any serious scientific article ever would address Sean's
> "levels of functional complexity" because it has no basis in fact. There
> is no reason to give it serious consideration.
Oh come on. It is obvious that some systems are far more complex and
have a far greater minimum structural requirement than do other
systems. Don't tell me that you cannot tell which systems are more or
less functionally complex. That's just nonsense.
> As for the "exponential stalling out effect", for this to established,
> not only would Sean would have to demonstrate why the prevailing
> paradigm for protein evolution is erroneous, but that all conceivable
> paradigms for protein evolution are erroneous. I doubt that he will even
> attempt this, since he doesn't appear to understand the prevailing
> paradigm at all.
It is easy to show that the prevailing paradigm for protein evolution
is erroneous beyond very very low levels of functional complexity.
First off, it just doesn't happen beyond levels that require more than
a few hundred fairly specified residues at minimum. There isn't one
example of evolution in action in all of literature beyond the 1000aa
level - not one. And, statistically, it is very unlikely to ever be
realized this side of trillions of years of time.
If you think otherwise, by all means, produce some real statistical
analysis, some real science, to prove me wrong. So far, the very best
you guys have come up with are these endless examples of low level
evolution and your fairytale stories about how higher level evolution
could have happened without any consideration of the likelihood of
your stories. Without at least some statistical analysis, they have no
predictive value and therefore simply are not "science". They are
just-so stories. That's it.
> Of course, if Sean believes I am not doing him justice, he could counter
> my argument here, by completing the following:
>
> "The prevailing paradigm for protein evolution is:"
Evolution works on what came before. That is the prevailing paradigm
for protein evolution. The problem is that the gaps between what came
before or what already exists in a given genome and the next
potentially beneficial sequence in sequence space (with a novel
function) grows linearly with each increase in the functional
complexity of the systems in question. That is why evolutionary
progress is so limited to very very low levels of functional
complexity and why it has never ever been observed beyond the 1000
fsaar level.
Sean Pitman
www.DetectingDesign.com
wf3h
>
> Prove it. Produce some statistical analysis that proves me wrong. It
> should be easy if you guys actually have some real scientific backing
> like you claim you have.
>
scientific backing? did sean really request this?
a guy who:
-has never provided a mechanism for his own ideas
-uses a failed analogy rather than a mechanism as 'proof' of his
argument
-arbitrarily excludes natural processes based solely on his religious
beliefs
-arbitrarily asserts every scientist who disagrees with him is wrong
-uses the most commonly used WRONG idea in history (creationism) yet
asserts it's right
has complained about someone else's view of science?
Seanpit
wrote:
You're thinking about this wrong. The question is, what is the
minimum specificity requirement needed to produce the system in
question. In this case, even given our characters in the alphabet,
the minimum specificity needed is in fact 1 in 2^22.
You see, the alphabet doesn't really matter. It is the minimum
requirements of the system that matter. You assume that the system
would have to use all the letters of the alphabet. That is an
incorrect assumption. The system in question, at minimum, may not
need to use all the letters of the alphabet. It is therefore the
system that dictates the level of complexity, not the alphabet.
> Does this RNA sequence result transfer to protein sequences?
> That is where my intuition is confused. But I do know that the
> 'function' of the amino acids at most sites in a typical protein
> is to fit together nicely with some other amino acid elsewhere
> in the same functional system.
Again, the size of the alphabet that can be worked with is irrelevant
to the problem. Levels of functional complexity are not defined by the
alphabet, but by the minimum structural threshold requirement of the
system in question - a minimum requirement that is not bound to use
all the characters that are available.
Sean Pitman
www.DetectingDesign.com
TomS
<fba9446e-6e7c-4ca2...@k19g2000prh.googlegroups.com>, Seanpit
stated..."
>
>On Apr 26, 7:37=A0pm, "'Rev Dr' Lenny Flank" <lfl...@yahoo.com> wrote:
>> On Apr 26, 7:24=A0pm, Seanpit <sean...@gmail.com> wrote:
>>
>>
>>
>> > How is that? =A0It doesn't even address my argument
>>
>> That's because your argument is just the same tired old "747 in a
>> tornado" bullshit that everyone laughed at 40 years ago.
>>
>> Everyone but you seems to realize that evolution doesn't make things
>> all at once intact in one fell sdwoop by randomly assembling pieces.
>> Evolution works by modifying what is already there.
>
>That's right. Evolution does work by modifying what is already
>there. The problem here is that if the gaps between what is already
>there and the next closest beneficial sequence are too large, a
>successful modification will not happen this side of trillions of
>years of time - on average. That's the entire problem with your
>proposed mechanism of RM/NS beyond extremely low levels of functional
>complexity. The gaps between what is already there and higher level
>functional systems are simply too large for your mechanism to work in
>what anyone would call a reasonable amount of time.
>
>If you think otherwise, you should be able to produce some odds
>analysis to support your theory. But, you can't. All you have are
>fairytale just-so stories about how it is possible without any
>consideration of the likelihoods of your stories. That's not
>science. That's just your active imagination at work.
The odds analysis is easy.
The alternatives are natural causes and more-than-natural causes.
The number of possible states resulting from more-than-natural
causes is larger than the number of possible states resulting
from natural causes. (More-than-natural causes can do more than
natural causes.)
Therefore, the probability that a given state will result from
more-than-natural causes is less than the probability that given
state will result from natural causes.
N(more-than-natural) > N(natural)
Therefore
P(more-than-natural) = N(chosen states)/N(more-than-natural)
<
N(chosen states)/N(natural) = P(natural)
--
---Tom S.
"As scarce as truth is, the supply has always been in excess of the demand."
attributed to Josh Billings
richardal...@googlemail.com
> On Apr 26, 7:37 pm, "'Rev Dr' Lenny Flank" <lfl...@yahoo.com> wrote:
>
> > On Apr 26, 7:24 pm, Seanpit <sean...@gmail.com> wrote:
>
> > > How is that? It doesn't even address my argument
>
> > That's because your argument is just the same tired old "747 in a
> > tornado" bullshit that everyone laughed at 40 years ago.
>
> > Everyone but you seems to realize that evolution doesn't make things
> > all at once intact in one fell sdwoop by randomly assembling pieces.
> > Evolution works by modifying what is already there.
>
> That's right. Evolution does work by modifying what is already
> there. The problem here is that if the gaps between what is already
> there and the next closest beneficial sequence are too large, a
> successful modification will not happen this side of trillions of
> years of time - on average.
So, Sean.
Identify *ANY* protein used in *ANY* biological system which is
isolated from its nearest neighbours in the sequence space of proteins
by a gap too large to be crossed other than by a large number of
intermediate steps which would take "trillions of years".
If you can't, it demonstrates that your whole argument is utterly
bogus.
Of course, we know that you can't, you know that you can't, and that
the only reason why you continue to promote your silly "theory" is
that you want to impress the creationists who you can count on for
uncritical acceptance of anything couched in scientific-sounding
language which appears to support their cause.
You won't write it up as an academic paper and submit it for
publication because you know perfectly well that no editor of any
academic journal would treat it as anything other than a joke. Your
excuse that *NO* editor of *ANY* academic journal has a "candid mind"
and *ALL* are brainwashed by the evolutionist elite is so
transparently facile - not to say dishonest - that only a creationist
could accept it. You know that you have nothing of any scientific
value to offer, which is why you just post the same old nonsense over
and over again in forums such as this rather than demonstrating the
strength of your convictions by actually *trying* to get it published.
RF
wf3h
> On Apr 26, 8:40 pm, "R. Baldwin" <res0k...@nozirevBACKWARDS.net>
> wrote:
>
>
>
> > Sean is correct that the paper does not address his argument about
> > levels of functional complexity. The authors explicitly accept the
> > prevailing idea that protein evolution depends on simpler folds. This is
> > an idea that Sean simply ignores. The paper does not address the idea
> > that "levels of functional complexity" even exist, because they have
> > never been demonstrated to exist, and that concept is inconsistent with
> > a hierarchy based on families of protein sequences, protein structures,
> > and fold domains.
>
> You're mistaken. Sure proteins are based on relatively simple folds.
> I do in fact address this idea very clearly in my essay on the
> flagellar motility system. The problem is that higher level systems
> require many of these simple folds at minimum - many many more
> compared to the simple systems discussed in your paper here. In fact,
> the minimum structural threshold for a system like the flagellar
> motility system requires over 10,000 fairly specified amino acid
> residues working together at the same time. The number of unique
> folds is relatively few, but that is irrelevant to the problem of
> levels of functional complexity.
what constitutes 'working together at the same time'?
the average number of amino acids in any specific protein fold is a
few hundred at best. most aa's in a protein don't do much. so if your
argument is that 10,000 aa's have to evolve all at once, this is
simply wrong.
and how does 'design' handle this? the fact is, it doesn't. it doesn't
at all. it's completely unable to specify ANY method which can
confront a problem you yourself have generated.
> > As for the "exponential stalling out effect", for this to established,
> > not only would Sean would have to demonstrate why the prevailing
> > paradigm for protein evolution is erroneous, but that all conceivable
> > paradigms for protein evolution are erroneous. I doubt that he will even
> > attempt this, since he doesn't appear to understand the prevailing
> > paradigm at all.
>
> It is easy to show that the prevailing paradigm for protein evolution
> is erroneous beyond very very low levels of functional complexity.
> First off, it just doesn't happen beyond levels that require more than
> a few hundred fairly specified residues at minimum. There isn't one
> example of evolution in action in all of literature beyond the 1000aa
> level - not one. And, statistically, it is very unlikely to ever be
> realized this side of trillions of years of time.
this makes no sense at all. first, we know that most protein
folds...the active areas of proteins...are a few hundred amino acid
units in length, NOT thousands.
and, without a mechanism of knowing how amino acid chains
develop....apart from evolution...we simply do not know WHAT causes
them to change. it's an unknown. so to say that the change is
statistically impossible is nonsense. the mechanism may be very simple
indeed. we just haven't found it.
THEN to reject the LOGICAL assumption...an unknown process...in favor
of one that has FAILED....creationism...is mind blowing. this type of
reasoning stopped science dead in its tracks for the last 2000 years.
>
> If you think otherwise, by all means, produce some real statistical
> analysis, some real science, to prove me wrong. So far, the very best
> you guys have come up with are these endless examples of low level
> evolution and your fairytale stories about how higher level evolution
> could have happened without any consideration of the likelihood of
> your stories. Without at least some statistical analysis, they have no
> predictive value and therefore simply are not "science". They are
> just-so stories. That's it.
and your argument? the creationist one?
care to cite a SINGLE example of a success in THAT area?
oh. you can't. after using this argument for TWO MILLENIA....you still
can't point to a single success.
>
> > Of course, if Sean believes I am not doing him justice, he could counter
> > my argument here, by completing the following:
>
> > "The prevailing paradigm for protein evolution is:"
>
> Evolution works on what came before. That is the prevailing paradigm
> for protein evolution. The problem is that the gaps between what came
> before or what already exists in a given genome and the next
> potentially beneficial sequence in sequence space (with a novel
> function) grows linearly with each increase in the functional
> complexity of the systems in question. That is why evolutionary
> progress is so limited to very very low levels of functional
> complexity and why it has never ever been observed beyond the 1000
> fsaar level.
>
and as you admit, creationism has never been observed anywhere at any
time under any circumstances.
yet you think it's right. IOW evidence be damned, your church has the
answer.
thanks, sean. after seeing your 2000 year history of failure, i think
i'll take my business elsewhere.
pol...@msx.dept-med.pitt.edu
> On Apr 26, 10:20 pm, unrestrained_h...@hotmail.com wrote:
>
>
>
> > You haven't established that your 1000aa sequences have to be started
> > from scratch.
>
> That's because they aren't started from scratch. They are never
> maximally distant from a given genome.
>
> > This is, on the face of it, counter intuitive. It is
> > also refuted buy the evidence.
>
> Exactly. The evidence shows that the distances between higher and
> higher level beneficial sequences with novel functions increases in a
> linear manner.
Golly ! All these years BEFORE, you were bellowing it was an
EXPONENTIAL increase !
Now you stepped it down to merely linear. Why ? Reality slapping you
so hard it generated a tiny crack in your belief shield, and a small
glimmer of light got in ?
> > You haven't established that the sequences we do have which are that
> > long were the goal of evolution in any meaningful way.
>
> The goal of the evolutionary mechanism of RM/NS is to find new
> beneficial sequences. If it only finds neutral or detrimental
> sequences, Darwinian-style evolution doesn't happen. While there is
> no specific target to be sure, since the mechanism is mindless, there
> are in fact targets upon which success or failure of the search
> process is based.
Good thing that neutral and beneficial sequences can be found by
'Darwinian-style' evolution.
In REALITY, success is defined NOT as 'how closely does this sequence
conform to one of Lord Pitman's delusional, teleological endpoints',
but rather 'does this sequence grant an advantage over OTHER existing
sequences in this environ ?'
> > You haven't established that *you have looked at all of the possible
> > useful mutations, and know the odds of them happening.
>
> You don't have to look at all possible sequences in sequence space
> before you can have a very good idea as to the ratio of beneficial vs.
> non-beneficial.
Too bad your silly 'ratio' ignores the effects of selection, and
retains ALL sequences (beneficial AND deleterious) each generation -
only by retaining all sequences does your silly ratio bloating happen.
Since you desperately NEED the ratio to bloat (so you have an excuse
to invoke the unknowable whim of an unknown external intelligence that
somehow did something sometime in the past), you ignore selection at
every step.
> That's why it is a science. If you actually knew all
> about all possible sequences, you wouldn't need science. Science is
> about working with limited information. It isn't about producing
> perfection.
>
> > You haven't established that you know the evolutionary precursor to
> > any 1000aa genetic sequence.
>
> That's because an evolutionary precursor is statistically unlikely to
> have ever existed.
By your 'model', the 'odds' of a 100 amino acid sequence having a
useful fold is about :
20^ln(100)/20^100, or about 1 in 10^174.
REAL WORLD experiments show the odds of a 100 amino acid sequence
having a selectable function is :
1 in 10^9 to 1in 10^15.
Given that your 'model' is off by over 100 orders of magnitude for
even the SMALLEST protein, why, EXACTLY, should anyone take your
claims about anything seriously ?
In your 'model', chimeric genes should not exist, since you
'determined' the 'odds' of one existing are too small.
Examination of REALITY reveals that several chimeric genes exist.
Given that reality conflicts with your 'model', will you claim that
REALITY is at fault, and it is 'obvious' than an unknown intelligence
somehow did something to generate chimeric genes for some reason ?
> If you think otherwise, were is your statistical
> analysis that shows that such a precursor is actually likely to have
> existed and that your proposed mechanism is remotely likely to have
> done the job this side of trillions of years of time? All I see from
> your end are fairytale just-so stories and bravado - no real science
> or statistical analysis of any kind.
>
> Sean Pitmanwww.DetectingDesign.com
Where is your statistical analysis that shows the odds an external
intelligence that could create DNA sequences existed billions of years
ago ? Your willful incredulity is evidence of nothing except the fact
you are willfully incredulous.
Your 'odds' are based on the silly idea that there is ONE (and ONLY
ONE) viable target for evolution to find, and that it MUST stagger
through all of neutral sequence space before finding it.
But what you 'calculated' are NOT the odds the flagellum would form -
what you 'calculated' was the odds that amino acids would fall
together all at once PURELY BY CHANCE to form the observed flagellum.
Calculating the odds of an event happening AFTER it happened is silly
- it makes even the most mundane events look nigh impossible.
Example : take a deck of cards and shuffle them. Deal them out, and
note the order of the cards.
The odds that the cards would be dealt out in that particular order is
1/52!, or 1/8.069 x 10^67.
Given the 'odds' of that sequence showing up, would you 'conclude' an
external intelligence DIDIT ?
Those odds would only be impressive if you called the order BEFORE the
cards were dealt; looking at them afterwards then declaring the
results 'too improbable' is just plain silly. Yet that is essentially
what you're doing with your flagellum 'calculations'.
Seanpit
> On Apr 27, 11:14 am, Seanpit <sean...@gmail.com> wrote:
>
>
>
>
>
> > On Apr 26, 10:20 pm, unrestrained_h...@hotmail.com wrote:
>
> > > You haven't established that your 1000aa sequences have to be started
> > > from scratch.
>
> > That's because they aren't started from scratch. They are never
> > maximally distant from a given genome.
>
> > > This is, on the face of it, counter intuitive. It is
> > > also refuted buy the evidence.
>
> > Exactly. The evidence shows that the distances between higher and
> > higher level beneficial sequences with novel functions increases in a
> > linear manner.
>
> Golly ! All these years BEFORE, you were bellowing it was an
> EXPONENTIAL increase !
>
> Now you stepped it down to merely linear. Why ? Reality slapping you
> so hard it generated a tiny crack in your belief shield, and a small
> glimmer of light got in ?
Why not actually go back and try to read what I've written for years
in this forum for comprehension? The increase in gap distance is
linear. The increase in the average time needed to cross the gap is
exponential. Therefore, the average time to success increases
exponentially as the gap distance increases linearly.
> > > You haven't established that the sequences we do have which are that
> > > long were the goal of evolution in any meaningful way.
>
> > The goal of the evolutionary mechanism of RM/NS is to find new
> > beneficial sequences. If it only finds neutral or detrimental
> > sequences, Darwinian-style evolution doesn't happen. While there is
> > no specific target to be sure, since the mechanism is mindless, there
> > are in fact targets upon which success or failure of the search
> > process is based.
>
> Good thing that neutral and beneficial sequences can be found by
> 'Darwinian-style' evolution.
>
> In REALITY, success is defined NOT as 'how closely does this sequence
> conform to one of LordPitman'sdelusional, teleological endpoints',
That's the number of viable folds - not the number of beneficial
sequences. You haven't yet grasped the difference between folds and
sequences nor have you grasped the concept of minimum specificity
requirements.
> REAL WORLD experiments show the odds of a 100 amino acid sequence
> having a selectable function is :
>
> 1 in 10^9 to 1in 10^15.
>
> Given that your 'model' is off by over 100 orders of magnitude for
> even the SMALLEST protein, why, EXACTLY, should anyone take your
> claims about anything seriously ?
This published number deals with all systems smaller than 100aa
regardless of type or minimum sequence specificity requirements. It
does not deal with systems that require at least 100aa that are
"fairly specified" as I've defined this term. For example, some of
the functional systems used in this calculation are only proteins that
simply bind to other proteins or sequences. Simple binding to at
least some useful level isn't a very complex function and doesn't
require very much sequence specificity.
My calculations, on the other hand, are right in line with published
estimates of those like Yockey, Sauer, Max, and Olsen which do deal
more with higher levels of sequence specificity and minimum size
requirements.
> In your 'model', chimeric genes should not exist, since you
> 'determined' the 'odds' of one existing are too small.
>
> Examination of REALITY reveals that several chimeric genes exist.
Of course they exist. They just don't produce novel beneficial
functional systems beyond 1000 fsaars. There's not a single example
of the production of any chimeric gene or protein that crosses this
threshold level.
Rather, it is like someone always drawing a Royal Flush - 100 times in
a row. Would you believe that just happened without intelligent
input? Come on now. Start thinking for yourself for a change . . .
Sean Pitman
www.DetectingDesign.com
Seanpit
<richardalanforr...@googlemail.com> wrote:
> On Apr 27, 4:19 pm, Seanpit <sean...@gmail.com> wrote:
>
>
>
>
>
> > On Apr 26, 7:37 pm, "'Rev Dr' Lenny Flank" <lfl...@yahoo.com> wrote:
>
> > > On Apr 26, 7:24 pm, Seanpit <sean...@gmail.com> wrote:
>
> > > > How is that? It doesn't even address my argument
>
> > > That's because your argument is just the same tired old "747 in a
> > > tornado" bullshit that everyone laughed at 40 years ago.
>
> > > Everyone but you seems to realize that evolution doesn't make things
> > > all at once intact in one fell sdwoop by randomly assembling pieces.
> > > Evolution works by modifying what is already there.
>
> > That's right. Evolution does work by modifying what is already
> > there. The problem here is that if the gaps between what is already
> > there and the next closest beneficial sequence are too large, a
> > successful modification will not happen this side of trillions of
> > years of time - on average.
>
> So,Sean.
> Identify *ANY* protein used in *ANY* biological system which is
> isolated from its nearest neighbours in the sequence space of proteins
> by a gap too large to be crossed other than by a large number of
> intermediate steps which would take "trillions of years".
>
> If you can't, it demonstrates that your whole argument is utterly
> bogus.
Yep, that would be true if in fact there were no examples of higher
level systems that are in fact remotely isolated. But, alas, there
are many such systems. The flagellar motility system is a classic
example. It requires a minimum of around 10,000 fairly specified
amino acid residues (fsaars). And, it is remotely isolated from the
next closest beneficial system at the same level or lower levels of
functional complexity by gaps that are far too large to cross this
side of many trillions of years of time.
> Of course, we know that you can't, you know that you can't, and that
> the only reason why you continue to promote your silly "theory" is
> that you want to impress the creationists who you can count on for
> uncritical acceptance of anything couched in scientific-sounding
> language which appears to support their cause.
Think again. The evidence is overwhelmingly on my side of this
issue. You're the one, on the other hand, who has absolutely no
statistical basis to believe that the mechanism of RM/NS can do much
of anything beyond levels of complexity that are far lower than the
1000 fsaar level.
> You won't write it up as an academic paper and submit it for
> publication because you know perfectly well that no editor of any
> academic journal would treat it as anything other than a joke. Your
> excuse that *NO* editor of *ANY* academic journal has a "candid mind"
> and *ALL* are brainwashed by the evolutionist elite is so
> transparently facile - not to say dishonest - that only a creationist
> could accept it. You know that you have nothing of any scientific
> value to offer, which is why you just post the same old nonsense over
> and over again in forums such as this rather than demonstrating the
> strength of your convictions by actually *trying* to get it published.
Try to counter it yourself, using something other than fairytale just-
so stories and bravado, for a change . . .
> RF
Sean Pitman
www.DetectingDesign.com
Seanpit
> "On Mon, 27 Apr 2009 08:19:37 -0700 (PDT), in article
Congratulations, you just falsified the very basis of SETI.
Remember, everything is natural here. It is just that some natural
mechanisms are driven by natural intelligence and some are driven by
mindless processes.
> ---Tom S.
> "As scarce as truth is, the supply has always been in excess of the demand."
> attributed to Josh Billings
Sean Pitman
www.DetectingDesign.com
wf3h
and natural intelligences are driven by mindless processes as well.
TomS
<640b8aa2-87e6-4ff2...@v23g2000pro.googlegroups.com>, Seanpit
stated..."
>
>On Apr 27, 8:47=A0am, TomS <TomS_mem...@newsguy.com> wrote:
>> "On Mon, 27 Apr 2009 08:19:37 -0700 (PDT), in article
>pit
>> stated..."
>>
>>
>>
>>
>>
>> >On Apr 26, 7:37=3DA0pm, "'Rev Dr' Lenny Flank" <lfl...@yahoo.com> wrote:
>> >> On Apr 26, 7:24=3DA0pm, Seanpit <sean...@gmail.com> wrote:
>>
>> >> > How is that? =3DA0It doesn't even address my argument
>>
>> >> That's because your argument is just the same tired old "747 in a
>> >> tornado" bullshit that everyone laughed at 40 years ago.
>>
>> >> Everyone but you seems to realize that evolution doesn't make things
>> >> all at once intact in one fell sdwoop by randomly assembling pieces.
>> >> Evolution works by modifying what is already there.
>>
>> >there. =A0The problem here is that if the gaps between what is already
>> >there and the next closest beneficial sequence are too large, a
>> >successful modification will not happen this side of trillions of
>> >proposed mechanism of RM/NS beyond extremely low levels of functional
>> >functional systems are simply too large for your mechanism to work in
>> >what anyone would call a reasonable amount of time.
>>
>> >If you think otherwise, you should be able to produce some odds
>> >fairytale just-so stories about how it is possible without any
>> >science. =A0That's just your active imagination at work.
>>
>> [...snip...]
>>
>> The odds analysis is easy.
>>
>> The alternatives are natural causes and more-than-natural causes.
>>
>> The number of possible states resulting from more-than-natural
>> causes is larger than the number of possible states resulting
>> from natural causes. (More-than-natural causes can do more than
>> natural causes.)
>>
>> Therefore, the probability that a given state will result from
>> more-than-natural causes is less than the probability that given
>> state will result from natural causes.
>>
>> N(more-than-natural) > N(natural)
>>
>> Therefore
>>
>> <
>> N(chosen states)/N(natural) =3D P(natural)
>
>Congratulations, you just falsified the very basis of SETI.
>
>Remember, everything is natural here. It is just that some natural
>mechanisms are driven by natural intelligence and some are driven by
>mindless processes.
Let's see if I understand you correctly.
You are saying that the extra-terrestrial intelligences that SETI
is looking for are more-than-natural.
You are saying that the "Intelligent Designer(s)" of ID are natural.
You are saying that your "intelligent designers" are either
unconcerned with, or incapable of, driving some events.
You have no "odds analysis" to support your "theory". You have a
half-analysis, at best, claiming a small probability for whatever
you don't like, but never contemplating a comparison.
(By the way, I would have hoped that you would have been clever
enough to realize that "odds analysis" is just as sound if one
replaces "more-than-natural"/"natural" with "driven by natural
intelligence"/"driven by mindless processes".)
--
Steven L.
Which is what, exactly?
As Ken Miller and others have pointed out, the type III secretory system
of some bacteria is homologous to the basal body of the bacterial
flagellum. A subset of the proteins in the basal body of the flagellum
make up this other structure in some bacteria.
Do you know of some other beneficial system that is closer in sequence
space to the bacterial flagellum than the type III secretory system?
> Think again. The evidence is overwhelmingly on my side of this
> issue. You're the one, on the other hand, who has absolutely no
> statistical basis to believe that the mechanism of RM/NS can do much
> of anything beyond levels of complexity that are far lower than the
> 1000 fsaar level.
Here's the problem: I know of biological systems that are extremely
complex; so do you. But to prove that such a system is truly remotely
isolated in sequence space, one would have to survey *all other
biological systems* to prove that none is sufficiently close in
sequence space. And given how many species (and their peculiar protein
sequences) are now extinct, that's a job you can never finish.
When Behe began harping on bacterial flagella, evidently he was unaware
of the type III secretory system and its homologies. As Ken Miller and
others have pointed out, this system is clearly close to the flagellum's
basal body "motor" in sequence space, because a subset of the type III
secretory system's proteins also occur in the basal body "motor" of the
flagellum. So either one evolved from the other, or they must share a
common ancestor.
It would be easy for Behe to overlook this, because a microbe uses this
secretory system as a way to inject its toxins into victim cells,
something which at first glance hsa nothing to do with the way flagella
propel other microbes. You wouldn't think to look for this near the
sequence subspace of flagella. But "inject" is an active behavior, that
requires a cellular motor. So this motor could get readily adapted to
do other active behaviors--like whipping cellular flagella. And so
Behe, and you, are wrong. Cellular motors of quite different functions
from quite different species are close to each other in sequence space.
You would have the same problem with cellular respiration. It sure
looks complex, as if it's isolated in some corner of sequence space far
from simpler biological systems:
http://upload.wikimedia.org/wikipedia/commons/7/74/CellRespiration.svg
But the enzymes which compose the Krebs cycle didn't just pop into
existence by the chemical finagling of some Grand Designer. No, they
have their own evolutionary history too. They evolved from the
essentially similar proteins in the ancient bacteria that eventually got
incorporated into eukaryotes as mitochondria:
Sequence space isn't laid out as random biological systems as "islands"
in sequence space with few relationships to their neighbors. The
relationships are there. These examples show how a comprehensive survey
of sequence space would show it to be densely interconnected, not
isolated points as you're claiming.
--
Steven L.
Email: sdli...@earthlinkNOSPAM.net
Seanpit
> On Apr 27, 11:29 am, Seanpit <sean...@gmail.com> wrote:
>
>
>
>
>
> > On Apr 26, 8:40 pm, "R. Baldwin" <res0k...@nozirevBACKWARDS.net>
> > wrote:
>
> > > levels of functional complexity. The authors explicitly accept the
> > > prevailing idea that protein evolution depends on simpler folds. This is
> > > that "levels of functional complexity" even exist, because they have
> > > never been demonstrated to exist, and that concept is inconsistent with
> > > a hierarchy based on families of protein sequences, protein structures,
> > > and fold domains.
>
> > You're mistaken. Sure proteins are based on relatively simple folds.
> > I do in fact address this idea very clearly in my essay on the
> > flagellar motility system. The problem is that higher level systems
> > require many of these simple folds at minimum - many many more
> > compared to the simple systems discussed in your paper here. In fact,
> > the minimum structural threshold for a system like the flagellar
> > motility system requires over 10,000 fairly specified amino acid
> > residues working together at the same time. The number of unique
> > folds is relatively few, but that is irrelevant to the problem of
> > levels of functional complexity.
>
> what constitutes 'working together at the same time'?
An enzymatic cascading system is made of separately acting proteins
that work in sequential order - not at the same time like in a
flagellar motility system where all work together at the same time in
a specific unified order.
> the average number of amino acids in any specific protein fold is a
> few hundred at best.
Correct. But many systems required many different "folds" working
together in a very specific arrangement.
> most aa's in a protein don't do much. so if your
> argument is that 10,000 aa's have to evolve all at once, this is
> simply wrong.
No one said that they had to all evolve at once. That's not true at
all. Evolution is based on changes to pre-established systems that
came before. Larger systems are not produced from scratch . . .
> and how does 'design' handle this? the fact is, it doesn't. it doesn't
> at all. it's completely unable to specify ANY method which can
> confront a problem you yourself have generated.
Not true. Human-level technology can produce such sequences and is
even getting very close to producing novel information at this level
beyond simply copying it from what already exists on the nano-scale.
> > > As for the "exponential stalling out effect", for this to established,
> > > not only wouldSeanwould have to demonstrate why the prevailing
> > > paradigm for protein evolution is erroneous, but that all conceivable
> > > paradigms for protein evolution are erroneous. I doubt that he will even
> > > attempt this, since he doesn't appear to understand the prevailing
> > > paradigm at all.
>
> > It is easy to show that the prevailing paradigm for protein evolution
> > is erroneous beyond very very low levels of functional complexity.
> > First off, it just doesn't happen beyond levels that require more than
> > a few hundred fairly specified residues at minimum. There isn't one
> > example of evolution in action in all of literature beyond the 1000aa
> > level - not one. And, statistically, it is very unlikely to ever be
> > realized this side of trillions of years of time.
>
> this makes no sense at all. first, we know that most protein
> folds...the active areas of proteins...are a few hundred amino acid
> units in length, NOT thousands.
You forget about multiprotein systems - like the flagellar motility
system.
> and, without a mechanism of knowing how amino acid chains
> develop....apart from evolution...we simply do not know WHAT causes
> them to change. it's an unknown. so to say that the change is
> statistically impossible is nonsense. the mechanism may be very simple
> indeed. we just haven't found it.
Science is based on what is currently known - not on what might become
known in the future. And, based on what is currently known, right
now, it is in fact statistically impossible for the mechanism of RM/NS
to do what you guys claim it did.
> THEN to reject the LOGICAL assumption...an unknown process...in favor
> of one that has FAILED....creationism...is mind blowing. this type of
> reasoning stopped science dead in its tracks for the last 2000 years.
Human-level intelligence has not failed.
> > If you think otherwise, by all means, produce some real statistical
> > analysis, some real science, to prove me wrong. So far, the very best
> > you guys have come up with are these endless examples of low level
> > evolution and your fairytale stories about how higher level evolution
> > could have happened without any consideration of the likelihood of
> > your stories. Without at least some statistical analysis, they have no
> > predictive value and therefore simply are not "science". They are
> > just-so stories. That's it.
>
> and your argument? the creationist one?
>
> care to cite a SINGLE example of a success in THAT area?
Human-level intelligence and technology? - lots of examples.
>
> oh. you can't. after using this argument for TWO MILLENIA....you still
> can't point to a single success.
You're confusing an attempt to prove God with an attempt to
demonstrate at least human-level intelligence and creativity - big
difference.
> > > Of course, ifSeanbelieves I am not doing him justice, he could counter
> > > my argument here, by completing the following:
>
> > > "The prevailing paradigm for protein evolution is:"
>
> > Evolution works on what came before. That is the prevailing paradigm
> > for protein evolution. The problem is that the gaps between what came
> > before or what already exists in a given genome and the next
> > potentially beneficial sequence in sequence space (with a novel
> > function) grows linearly with each increase in the functional
> > complexity of the systems in question. That is why evolutionary
> > progress is so limited to very very low levels of functional
> > complexity and why it has never ever been observed beyond the 1000
> > fsaar level.
>
> and as you admit, creationism has never been observed anywhere at any
> time under any circumstances.
>
> yet you think it's right. IOW evidence be damned, your church has the
> answer.
>
> thanks,sean. after seeing your 2000 year history of failure, i think
> i'll take my business elsewhere.
You are again confusing beliefs in God with beliefs in that at least
human-level intelligence is required to explain certain phenomena.
They aren't the same argument Bob - not at all.
Sean Pitman
www.DetectingDesign.com
Seanpit
Not without a very very high level of informational complexity which
entails a very complex and specified physical arrangement of parts.
It is the informational complexity of a system that is in question
here. This informational complexity must be pre-established on a very
high level before it can produce true "artifacts" that are clearly
identifiable as true artifacts.
Sean Pitman
www.DetectingDesign.com
Seanpit
> "On Mon, 27 Apr 2009 09:34:20 -0700 (PDT), in article
Where did I say that? Didn't I just say that everything is natural
here? There is nothing about the theory I'm presenting that invokes
anything that is "more-than-natural".
> You are saying that the "Intelligent Designer(s)" of ID are natural.
Yes. The argument is that at least human-level intelligence was
required. There is no argument for the need for anything other than
very natural levels of intelligence here.
> You are saying that your "intelligent designers" are either
> unconcerned with, or incapable of, driving some events.
I don't understand this question? Of course the intelligent designers
are capable of "driving some events". That is how they can be
detected as intelligent by what they produce.
> You have no "odds analysis" to support your "theory". You have a
> half-analysis, at best, claiming a small probability for whatever
> you don't like, but never contemplating a comparison.
Have you actually read my odds analysis? I do indeed comtemplate the
alternate model of RM/NS. It doesn't come remotely close to doing the
job. What other alternate model did you have in mind? And, where is
your statistical support for this model?
> (By the way, I would have hoped that you would have been clever
> enough to realize that "odds analysis" is just as sound if one
> replaces "more-than-natural"/"natural" with "driven by natural
> intelligence"/"driven by mindless processes".)
Not at all. Science can detect natural levels of intelligence.
Science cannot detect the need for "more-than-natural" levels of
intelligence. Big big difference.
> ---Tom S.
> "As scarce as truth is, the supply has always been in excess of the demand."
> attributed to Josh Billings
Sean Pitman
www.DetectingDesign.com
Kent Paul Dolan
> The goal of the evolutionary mechanism of RM/NS is
> to find new beneficial sequences.
What part of "evolution is not teleological" do you
remain too pig ignorant to accept?
xanthian.
Oh, right: without "evolution being teleological",
your arguments are even more meaningless, since
"bridging large gaps" is no necessity for evolving,
and so then you cannot debunk evolution by positing
large gaps it _must_ bridge to operate.
Kent Paul Dolan
> Prove it. Produce some statistical analysis that
> proves me wrong. It should be easy if you guys
> actually have some real scientific backing like
> you claim you have.
You have been given this information many times, and
each time you have ignored or rejected it. Here it
is again.
Creatures in nature are observed by scientists to
evolve, entirely unassisted by intelligent design
input, in ways not at all mysterious, and that
evolution is observed to include large new
functionality improvements, like bacteria becoming
able to use vitamin C as a source of nourishment.
That, probablistically, shows a 100% certainty that
your argument is constructed entirely of cowpats.
There, your long demanded probabilistic argument has
been provided to you, yet again. Now, you respond
with the long demanded mathematical and biological
model under which your teleological version of
evolution is supposed to be operating.
xanthian.
Seanpit
> Seanpit wrote:
>
> > The goal of the evolutionary mechanism of RM/NS is
> > to find new beneficial sequences.
>
> What part of "evolution is not teleological" do you
> remain too pig ignorant to accept?
What part of evolution doesn't happen unless novel beneficial
sequences are found don't you understand? Evolution doesn't have to
happen - that's for sure. But, for evolution to actually be realized,
novel beneficial sequences must be found.
>
> xanthian.
>
> Oh, right: without "evolution being teleological",
> your arguments are even more meaningless, since
> "bridging large gaps" is no necessity for evolving,
> and so then you cannot debunk evolution by positing
> large gaps it _must_ bridge to operate.
Sean Pitman
www.DetectingDesign.com
Seanpit
None of these "improvements" or examples of evolution in action
produce anything beyond the 1000 fairly specified amino acid
threshold. These low-level examples are the very same as those
presented by the authors of the paper you've just listed here in this
thread. The fact remains that the mechanism of RM/NS can only explain
these low-level examples and no further. It cannot explain higher
levels of functional complexity. That's where the rub comes in.
That's where the evolutionary mechanism stalls out.
> xanthian.
Sean Pitman
www.DetectingDesign.com
wf3h
prove it. go ahead. prove that our intelligence was produced as you
say.
we'll wait.
>
> It is the informational complexity of a system that is in question
> here. This informational complexity must be pre-established on a very
> high level before it can produce true "artifacts" that are clearly
> identifiable as true artifacts.
babbling creationist doubletalk without scientific meaning.
how does 'informational complexity' rule out natural processes
creating intelligence?
answer: it doesnt.
what is a 'high level'? answer: it's meaningless
this is garbage. theo-trash. it's biblical trailer park nonsense.
>
> Sean Pitmanwww.DetectingDesign.com- Hide quoted text -
>
> - Show quoted text -
John Stockwell
> On Apr 26, 3:00 pm, "Steven L." <sdlit...@earthlink.net> wrote:
>
>
>
> > Kent Paul Dolan wrote:
> > > Someone URLed this link a day or two ago,
> > > I've forgotten who, but thanks, in any case.
>
> > > Lo and behold, the document is _not_ behind a pay
> > > wall!!
>
> > > It is a very nice document, since the authors went
> > > to the trouble completely to debunk what might be
> > > called "SeanPitmanmath", with the explicit
> > > conclusion that the use of such math to "prove" the
> > > need for divine intervention in creating the tree of
> > > life is a bogus enterprise.
>
> > I just read the paper.
>
> > Yes, it answers Pitman nicely.
>
> How is that? It doesn't even address my argument of levels of
> functional complexity and the exponential stalling out effect as
> higher and higher levels are attempted by the mechanism of RM/NS.
> This paper only deals with functional systems that are extremely low
> level - much much lower level than even 100 fsaar systems. That's
> complete nonsense when it comes to explaining the origin of truly
> complex systems of function via RM/NS.
Maybe they didn't address your arguments, because, unless you publish
them, they doesn't really exist, scientifically. You never have
addressed
the issue of duplication. It's obvious that duplication of existing
structures
can go easily over your alleged 1000aa "barrier".
>
>
>
> > But it also answers Gould and Sagan too--on a different subject:
>
> > "Protein sequence space is often viewed as a limitless desert of
> > maladjusted sequences with only a few oases of working sequences linked
> > by narrow pathways (Axe 2000, 2004). The navigation over this space by
> > natural selection is difficult and could take many different routes thus
> > resulting in organisms with largely different protein compositions. This
> > idea of contingency, if taken at the level of species, led Gould to
> > suggest that if one was to rerun the ‘tape of life’ then evolution would
> > take a totally different path and we, as a species, would only appear as
> > a highly improbable accident (Gould 1991; Luisi 2003; de Duve 2007a,b).
> > However, if there is any merit to our simple calculation then protein
> > sequence analysis provides no support for the idea of contingency at a
> > molecular level and it provides strong support for the ideas of
> > convergence (Conway Morris 2000, 2004; Dawkins 2005; Vermeij 2006; de
> > Duve 2007a,b). If one was to rerun the tape, then the protein
> > composition of organisms would be similar. "
>
> > That has implications for SETI too. We know that amino acids exist in
> > outer space. If "convergence" is true, then life forms elsewhere in the
> > Universe should be protein-based, and maybe even nucleic-acid-based.
>
> > Good paper!
>
> > --
> > Steven L.
> > Email: sdlit...@earthlinkNOSPAM.net
Perplexed in Peoria
You're thinking about this wrong. The question is, what is the
minimum specificity requirement needed to produce the system in
question. In this case, even given our characters in the alphabet,
the minimum specificity needed is in fact 1 in 2^22.
You see, the alphabet doesn't really matter. It is the minimum
requirements of the system that matter. You assume that the system
would have to use all the letters of the alphabet. That is an
incorrect assumption. The system in question, at minimum, may not
need to use all the letters of the alphabet. It is therefore the
system that dictates the level of complexity, not the alphabet.
...
Again, the size of the alphabet that can be worked with is irrelevant
to the problem. Levels of functional complexity are not defined by the
alphabet, but by the minimum structural threshold requirement of the
system in question - a minimum requirement that is not bound to use
all the characters that are available.
------------------------------
PiP:
Sean, your response is just bizarre. You seem to be trying to insert
some kind of Kolmogorov-style definition of functional complexity
into a straightforward sequence-space computation.
Think about it some more. You are dead wrong here.
'Rev Dr' Lenny Flank
Blah blah blah. Dude, this "747's can't form by chance in a tornado"
BS died decades ago.
Give it up already.
'Rev Dr' Lenny Flank
> Why not actually go back and try to read what I've written for years
> in this forum for comprehension?
Gee, Sean, this seems to be a pretty common problem for you --- seems
that EVERYONE who reads your mathy sciencey stuf, "doesn't understand
it" -- or, as that means in the real world, they think it's full of
shit.
Why is that, Sean? Why is that NOBODY, absolutely NOBODY, without any
exception, seems to, uh, "understand" your wonderful mathy sciency
arguments?
Is it because everyone on earth is stupid except you?
Is it because YOU'RE the one who's too stupid to explain his stunning
science in a way that people can understand it?
Or is it because everyone really DOES understand it -- and thinks it's
a load of horse shit?
Which is it, Sean?
(snicker) (giggle) <--- yes, Sean, I am laughing at you. Again.
'Rev Dr' Lenny Flank
The problem here is that if the gaps between what is already
> there and the next closest beneficial sequence are too large
Says you. (shrug)
Of course, there is no law of nature that says large gaps have to be
crossed all at once. They can be crossed in several steps. Complex
747's don't form all at once by chance. They come from simpler
airplanes -- and airplanes came from bicycles.
Which makes your entire argument . . . well . . bullshit. (shrug)
'Rev Dr' Lenny Flank
So now you're an atheist again . . . ?
Ray !!!!!!!!!!! I have someone over here who is denying the
necessity for God !!!!!!!!!!!!
'Rev Dr' Lenny Flank
>
> It is the informational complexity of a system that is in question
> here.
And how do we measure that, again . . . . . . .?
You're just bullshitting everyone.
pol...@msx.dept-med.pitt.edu
> On Apr 27, 9:09 am, pol...@msx.dept-med.pitt.edu wrote:
>
> > On Apr 27, 11:14 am, Seanpit <sean...@gmail.com> wrote:
>
> > > On Apr 26, 10:20 pm, unrestrained_h...@hotmail.com wrote:
>
> > > > You haven't established that your 1000aa sequences have to be started
> > > > from scratch.
>
> > > That's because they aren't started from scratch. They are never
> > > maximally distant from a given genome.
>
> > > > This is, on the face of it, counter intuitive. It is
> > > > also refuted buy the evidence.
>
> > > Exactly. The evidence shows that the distances between higher and
> > > higher level beneficial sequences with novel functions increases in a
> > > linear manner.
>
> > Golly ! All these years BEFORE, you were bellowing it was an
> > EXPONENTIAL increase !
>
> > Now you stepped it down to merely linear. Why ? Reality slapping you
> > so hard it generated a tiny crack in your belief shield, and a small
> > glimmer of light got in ?
>
> Why not actually go back and try to read what I've written for years
> in this forum for comprehension? The increase in gap distance is
> linear. The increase in the average time needed to cross the gap is
> exponential. Therefore, the average time to success increases
> exponentially as the gap distance increases linearly.
And, since your 'model' is GIGO-numerology, no further effort need be
wasted on thinking about it.
Examination of ACTUAL sequences from ACTUAL organisms refutes the
silly-arsed 'single-target' delusion needed to make your 'math' even
look valid.
> > > > You haven't established that the sequences we do have which are that
> > > > long were the goal of evolution in any meaningful way.
>
> > > The goal of the evolutionary mechanism of RM/NS is to find new
> > > beneficial sequences. If it only finds neutral or detrimental
> > > sequences, Darwinian-style evolution doesn't happen. While there is
> > > no specific target to be sure, since the mechanism is mindless, there
> > > are in fact targets upon which success or failure of the search
> > > process is based.
>
> > Good thing that neutral and beneficial sequences can be found by
> > 'Darwinian-style' evolution.
>
> > In REALITY, success is defined NOT as 'how closely does this sequence
> > conform to one of Lord Pitman's delusional, teleological endpoints',
> > but rather 'does this sequence grant an advantage over OTHER existing
> > sequences in this environ ?'
No response that that Lord Pitman ?
> > > > You haven't established that *you have looked at all of the possible
> > > > useful mutations, and know the odds of them happening.
>
> > > You don't have to look at all possible sequences in sequence space
> > > before you can have a very good idea as to the ratio of beneficial vs.
> > > non-beneficial.
>
> > Too bad your silly 'ratio' ignores the effects of selection, and
> > retains ALL sequences (beneficial AND deleterious) each generation -
> > only by retaining all sequences does your silly ratio bloating happen.
>
> > Since you desperately NEED the ratio to bloat (so you have an excuse
> > to invoke the unknowable whim of an unknown external intelligence that
> > somehow did something sometime in the past), you ignore selection at
> > every step.
No response to that Lord Pitman ?
> > > That's why it is a science. If you actually knew all
> > > about all possible sequences, you wouldn't need science. Science is
> > > about working with limited information. It isn't about producing
> > > perfection.
>
> > > > You haven't established that you know the evolutionary precursor to
> > > > any 1000aa genetic sequence.
>
> > > That's because an evolutionary precursor is statistically unlikely to
> > > have ever existed.
>
> > By your 'model', the 'odds' of a 100 amino acid sequence having a
> > useful fold is about :
>
> > 20^ln(100)/20^100, or about 1 in 10^174.
>
> That's the number of viable folds - not the number of beneficial
> sequences. You haven't yet grasped the difference between folds and
> sequences nor have you grasped the concept of minimum specificity
> requirements.
Because you can't define them in any objective or rational way - your
'requirements' are whatever Lord Pitman NEEDS them to be so he can
invoke the whim of an External Intelligence (that somehow did stuff
sometime in the past).
Given that folds ARE FROM SEQUENCES, the RELEVANT DIFFERENCE between a
'beneficial fold' and a 'beneficial sequence' is what again ?
YOUR math doesn't make that distinction; why should anyone else ?
You've used that math to 'prove' a 300aa precursor to a 1000 aa
precursor is too improbable to exist; now, when the idiocy of that
position is shown, you run away from your own calcuations ?
> > REAL WORLD experiments show the odds of a 100 amino acid sequence
> > having a selectable function is :
>
> > 1 in 10^9 to 1in 10^15.
>
> > Given that your 'model' is off by over 100 orders of magnitude for
> > even the SMALLEST protein, why, EXACTLY, should anyone take your
> > claims about anything seriously ?
>
> This published number deals with all systems smaller than 100aa
> regardless of type or minimum sequence specificity requirements. It
> does not deal with systems that require at least 100aa that are
> "fairly specified" as I've defined this term.
The term defined as : 'whatever Lord Pitman DECREES it to
be !!!!!!!' ?
The researchers took RANDOM SEQUENCE peptides about 100 amino acids
long and figured out how many had a SELECTABLE FUNCTION. They - nor
any sane or rational person - 'demands' or expect the sequences
conform to some externally derived, silly-arsed blitherings about
'fairly specified' residues. The RELEVANT question is not : 'how well
do these sequences conform to Lord Pitman's delusional targets ?', but
rather 'HOW WELL DO THEY DO THE JOB ?'
For one experiment (generation of an ATP biding protein), the
experiments yielded a zinc-finger protein. NO ATP-BINDING PROTEIN
before that experiment was a zinc finger protein. It takes a few
'fairly specified' residues to form a stable zinc finger.
> For example, some of
> the functional systems used in this calculation are only proteins that
> simply bind to other proteins or sequences. Simple binding to at
> least some useful level isn't a very complex function and doesn't
> require very much sequence specificity.
BY YOUR MATH - the SAME blithering gibbertwittery you 'use' to 'prove'
that even a 300 aa protein is IMPOSSIBLE !!11!!!! to form this side of
'zillions and zillions of years', the odds that a useful fold (needed
for useful protein functions), the 'odds' that a 100aa protein should
have a beneficial fold/selectable function (kinda hard to have
selectable functions without 'beneficial folds') is 1 in 10^174;
REALITY shows the odds of a selectable function (which kinda requires
useful folds) show up 1 in 10^9 to 1 in 10^15.
Given that your 'model' is off by over 100 orders of magnitude, WHY
should anyone take your sanctimonious posturing seriously ?
> My calculations, on the other hand, are right in line with published
> estimates of those like Yockey, Sauer, Max, and Olsen which do deal
> more with higher levels of sequence specificity and minimum size
> requirements.
You are aware that cytochrome c is ONLY ABOUT 100 amino acids long -
the same size as the random sequences you are trying so hard to
urinate all over ?
They did the experiments in reverse - they took a functional protein
and mutated it until it lost ONE DEFINED FUNCTION.
A slightly different question than 'what are the odds that a random
sequence 100 amino acids long would have a SELECTABLE function'.
> > In your 'model', chimeric genes should not exist, since you
> > 'determined' the 'odds' of one existing are too small.
>
> > Examination of REALITY reveals that several chimeric genes exist.
>
> Of course they exist. They just don't produce novel beneficial
> functional systems beyond 1000 fsaars. There's not a single example
> of the production of any chimeric gene or protein that crosses this
> threshold level.
Sorry simpleton - you've BLITHERED that the 'odds' of a functional
chimeric gene forming are so low that it should take 'zillions and
zillions of years' for one OF ANY SIZE to form.
Nature is under no obligation to conform to your silly-arsed 'limits'
or 'definitions'. By your 'logic', the fact that turtles have not
developed stainless steel shells 'proves' that an External
Intelligence somehow did something sometime in the past to create
flagellum.
The ONLY relevant criteria for beneficial sequences is 'how beneficial
are they ?' and NOT 'how big is it ?'
About 90% or so of all proteins are BELOW 1000 amino acids; those few
bigger than that are easily explainable as domain duplications and
other KNOWN processes.
> > Given that reality conflicts with your 'model', will you claim that
> > REALITY is at fault, and it is 'obvious' than an unknown intelligence
> > somehow did something to generate chimeric genes for some reason ?
>
> > > If you think otherwise, were is your statistical
> > > analysis that shows that such a precursor is actually likely to have
> > > existed and that your proposed mechanism is remotely likely to have
> > > done the job this side of trillions of years of time? All I see from
> > > your end are fairytale just-so stories and bravado - no real science
> > > or statistical analysis of any kind.
>
> > >SeanPitmanwww.DetectingDesign.com
>
> > Where is your statistical analysis that shows the odds an external
> > intelligence that could create DNA sequences existed billions of years
> > ago ? Your willful incredulity is evidence of nothing except the fact
> > you are willfully incredulous.
So, Lord Pitman, where IS your statistical analysis that shows the
I do. Your gibbering numerology is based on several ludicrous
assumptions - that there is no selection, that everything MUST fall
together all at once PURELY by chance EXACTLY as we see it today, that
functions cannot change, that proteins have one AND ONLY ONE function,
that islands of 'useful function' are scattered randomly throughout
all of sequence space, that ALL of sequence space is available to
search, that nature MUST conform to your silly-arsed delusions of
adequacy, that it is IMPOSSIBLE for a beneficial sequence to be
smaller than 1000 amino acids, that your gibbering about 'fairly
specified residues' is worth listening to, that your 'calculations'
are even close to being biologically relevant ...
Three ways to get a royal flush :
1. blind chance.
2. search through deck and pull out needed cards (Pitman/IDiot
scenario)
3. process : draw five cards, [keep highest cards of the same suit,
discard rest, draw back to five cards] Repeat until get royal flush.
You see that I have a royal flush. WHICH METHOD DID I USE TO GET IT ?
In your megalomania, you note that since the pure chance method is
unlikely, you IMMEDIATELY jump to option #2 (after declaring option #3
IMPOSSIBLE !!1!1!!!!11!! because it does not conform to your silly
little models)
If something like a flagellum can ONLY be explained by the direct
intervention of an unknown External Intelligence, where did the
External Intelligence come from ? After all, an Intelligence capable
of designing a flagellum from scratch MUST be pretty complex, and if
the less complex flagellum MUST have a designer, then the External
Intelligence that designed it can only be explained by the action of a
Designer of Designers. And so on ad infinitum.
Unless, of course, you invoke special bleating : 'but, but - EVERY
complex things MUST have a designer. EXCEPT my particular even-more-
complex-than-everything-else-that-exists-External Intelligence that
somehow did stuff !!!!'
In cards, since we KNOW the odds of an event happening, cheating is
easy to detect (too many royal flushes shows something is up), and we
KNOW what agents are involved (that shifty looking guy at the end of
the table).
Your 'math' presumes that protein sequence formation is purely random
- examination of REALITY shows it isn't.
You insist on continuously making the AND-multiplication error :
http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/AND-multiplication-error.html
"It is inappropriate to multiply probabilities unless the two events
are independent. One must account for all of the events (in other
words, honor the dead). The functional amino acids in a protein are
not obtained independently since many organisms die for the few that
survive to reproduce. Each change to an amino acid occurs in the
context of the current protein and therefore depends on the previous
history of the protein. Although the amino acids may be functionally
independent (allowing, for example, the computation of a sequence
logo), the appearance of the selected amino acids is sequential during
evolution and is, therefore, dependent on previous steps. It is
invalid to directly apply the multiplication rule to computing the
probability that proteins came into existence.
Documents that make the AND-multiplication error and use it to draw
conclusions are flawed to the core and their conclusions can be
immediately dismissed as invalid."
(now I suppose you'll assert that you know more about bioinformatics
than someone that does it for a living !)
Stephen
> On Apr 27, 11:21 am, Kent Paul Dolan <xanth...@well.com> wrote:
> > Seanpit wrote:
> >
> > > The goal of the evolutionary mechanism of RM/NS is
> > > to find new beneficial sequences.
> >
> > What part of "evolution is not teleological" do you
> > remain too pig ignorant to accept?
>
> What part of evolution doesn't happen unless novel beneficial
> sequences are found don't you understand? Evolution doesn't have to
> happen - that's for sure. But, for evolution to actually be realized,
> novel beneficial sequences must be found.
>
It seems to me that
-- if evolution is "change in allele frequency within a population"
then "finding novel beneficial sequences" does not have to happen; all
that must happen is "change in allele frequency".
-- even if "evolution" does find "novel beneficial sequences", that
does not mean "finding novel beneficial sequences" is the *goal* of
evolution; it's a *byproduct* of the activity, not a *goal*.
Regards,
Stephen
--
Dan Luke
"TomS" wrote:
> Let's see if I understand you correctly.
>
No one understands Sean correctly, according to him. He's too smart,
don'cha know. He's a revolutionary mathematical genius.
The funny thing is, Sean doesn't understand Sean, either.
--
Dan
"How can an idiot be a policeman? Answer me that!"
-Chief Inspector Dreyfus
R. Baldwin
news:47ced67d-841e-49da...@v23g2000pro.googlegroups.com:
> On Apr 26, 8:40�pm, "R. Baldwin" <res0k...@nozirevBACKWARDS.net>
> wrote:
>>
>> Sean is correct that the paper does not address his argument about
>> levels of functional complexity. The authors explicitly accept the
>> prevailing idea that protein evolution depends on simpler folds. This
>> is an idea that Sean simply ignores. The paper does not address the
>> idea that "levels of functional complexity" even exist, because they
>> have never been demonstrated to exist, and that concept is
>> inconsistent with a hierarchy based on families of protein sequences,
>> protein structures, and fold domains.
>
> You're mistaken. Sure proteins are based on relatively simple folds.
> I do in fact address this idea very clearly in my essay on the
> flagellar motility system.
I looked at your article again
http://www.detectingdesign.com/flagellum.htm
and see that you now at least address the idea. Last time I looked at
your article you didn't address it period. That was just a couple of
months ago.
I do not agree that you address it, or anything else, clearly.
> The problem is that higher level systems
> require many of these simple folds at minimum - many many more
> compared to the simple systems discussed in your paper here. In fact,
> the minimum structural threshold for a system like the flagellar
> motility system requires over 10,000 fairly specified amino acid
> residues working together at the same time. The number of unique
> folds is relatively few, but that is irrelevant to the problem of
> levels of functional complexity.
How do you know there is any such thing as a "minimum structural
threshold"?
>
>> I doubt that any serious scientific article ever would address Sean's
>> "levels of functional complexity" because it has no basis in fact.
>> There is no reason to give it serious consideration.
>
> Oh come on. It is obvious that some systems are far more complex and
> have a far greater minimum structural requirement than do other
> systems. Don't tell me that you cannot tell which systems are more or
> less functionally complex. That's just nonsense.
If it is so obvious, can you cite the relavant scientific literature
about "levels of functional complexity" and "minimum structural
requirements"?
>
>> As for the "exponential stalling out effect", for this to
>> established, not only would Sean would have to demonstrate why the
>> prevailing paradigm for protein evolution is erroneous, but that all
>> conceivable paradigms for protein evolution are erroneous. I doubt
>> that he will even attempt this, since he doesn't appear to understand
>> the prevailing paradigm at all.
>
> It is easy to show that the prevailing paradigm for protein evolution
> is erroneous beyond very very low levels of functional complexity.
> First off, it just doesn't happen beyond levels that require more than
> a few hundred fairly specified residues at minimum. There isn't one
> example of evolution in action in all of literature beyond the 1000aa
> level - not one. And, statistically, it is very unlikely to ever be
> realized this side of trillions of years of time.
Only if you use a bogus model and bogus math.
>
> If you think otherwise, by all means, produce some real statistical
> analysis, some real science, to prove me wrong. So far, the very best
> you guys have come up with are these endless examples of low level
> evolution and your fairytale stories about how higher level evolution
> could have happened without any consideration of the likelihood of
> your stories. Without at least some statistical analysis, they have no
> predictive value and therefore simply are not "science". They are
> just-so stories. That's it.
You already lost the argument that statistical analysis is necessary for
science. Hadn't you noticed? Or did you run away from those threads
without reading the responses?
>
>> Of course, if Sean believes I am not doing him justice, he could
>> counter my argument here, by completing the following:
>>
>> "The prevailing paradigm for protein evolution is:"
>
> Evolution works on what came before. That is the prevailing paradigm
> for protein evolution. The problem is that the gaps between what came
> before or what already exists in a given genome and the next
> potentially beneficial sequence in sequence space (with a novel
> function) grows linearly with each increase in the functional
> complexity of the systems in question. That is why evolutionary
> progress is so limited to very very low levels of functional
> complexity and why it has never ever been observed beyond the 1000
> fsaar level.
>
No, the prevailing paradigm for protein evolution is not "evolution
works on what came before." Of course, I am not surprised that you are
unable to articulate what the prevailing paradigm is.
Mark Isaak
> [...]
> The goal of the evolutionary mechanism of RM/NS is to find new
> beneficial sequences.
"Goal"? Go back to a remedial biology class. Don't come back until you
learn what evolutionary mechanisms are.
And you have the nerve to complain that Dryden et al. don't know biology.
Your own ignorance is profound.
--
Mark Isaak eciton (at) earthlink (dot) net
"It is certain, from experience, that the smallest grain of natural
honesty and benevolence has more effect on men's conduct, than the most
pompous views suggested by theological theories and systems." - D. Hume
Kent Paul Dolan
> Sure proteins are based on relatively simple
> folds. ...
You perhaps let your eyes glaze over each place the
referenced paper debunked your idiocy. In this case,
it was suggested that the folding patterns were not
dependent on particular proteins being encoded, but
only on whether those proteins were among the
hydrophilic group or among the hydrophobic group,
thus limiting the "folding alphabet" size to _two_.
> I do in fact address this idea very clearly in my
> essay on the flagellar motility system.
One of the many papers you make available so that
readers can confirm your membership in the
creationist cadre of innumerate dunces.
I've read it, and laughed so much it hurt, in
response.
> The problem is that higher level systems require
> many of these simple folds at minimum - many many
> more compared to the simple systems discussed in
> your paper here.
Again your eyes apparently glazed over when this
idiocy was debunked in that paper.
> In fact, the minimum structural threshold for a
> system like the flagellar motility system requires
> over 10,000 fairly specified amino acid residues
> working together at the same time.
So what?
Working together at the same time in the current
version has nothing to do with a contention that the
string had to be built all at once, or even in
anything larger that single easy mutation steps.
You contend, with total lack of proof, what amounts
to the already refuted "irreducible complexity"
argument, that there is _no_ evolutionary path to
that long sequence in a series of small sized steps.
That's just you lying some more, trying to push
forward that for which you have not a shred of
evidence, just your naked assertions.
Under a gradualist view of evolution, how long the
eventual encoding is doesn't mean squat as long as
there is _some_ path of building it, _and if
necessary building intermediate scaffolding leading
to it but omitted in the final result_, that
consists of short easy changes that are at least not
lethal to the offspring.
[It has been proved, by computer modeling that
tracked every intermediate "organism" of
computer "genetic algorithm" evolution, that
evolution works just fine taking advantage of
fitness diminishing pathways that lead directly
to fitness enhancing pathways. Strangely enough,
this is all just part of a proper statistical
modeling of evolution, something you wouldn't
recognize if it were a tiger fish hanging from
your butt by its many long, sharp teeth.]
> The number of unique folds is relatively few, but
> that is irrelevant to the problem of levels of
> functional complexity.
Your entire argument is irrelevant to evolution,
since it is based on the debunked concept of
irreducible complexity. "747/tornado/junkyard" math
need not apply in attempts to explain how evolution
works, since evolution is _observed_ to work by an
accumulation of small changes.
>> I doubt that any serious scientific article ever
>> would address Sean's "levels of functional
>> complexity" because it has no basis in fact.
>> There is no reason to give it serious
>> consideration.
> Oh come on.
"Oh, come on" is not an argument functional when
addressing questions of scientific fact.
> It is obvious
"It is obvious" is not an argument functional when
addressing questions of scientific fact. If you
think this is _so obvious_, why have you so totally
failed to document that "obviousness" from credible
sources?
> that some systems are far more complex and have a
> far greater minimum structural requirement than do
> other systems.
> Don't tell me that you cannot tell which systems
> are more or less functionally complex.
Arguments from incredulity are not functional when
addressing questions of scientific fact. You are the
one making the claim, you are the one who is
obligated to support that claim with citations to
credible sources.
> That's just nonsense.
Arguments by naked ASSertion are not functional when
addressing questions of scientific fact.
Quite apparently, you have no clue whatever how
science is conducted. This is a surprise to no one
who is familiar with your posted eructions.
>> As for the "exponential stalling out effect", for
>> this to established, not only would Sean would
>> have to demonstrate why the prevailing paradigm
>> for protein evolution is erroneous, but that all
>> conceivable paradigms for protein evolution are
>> erroneous. I doubt that he will even attempt
>> this, since he doesn't appear to understand the
>> prevailing paradigm at all.
> It is easy to show that the prevailing paradigm
> for protein evolution is erroneous beyond very
> very low levels of functional complexity.
But of course, you are lying, you can't do this at
all, you just wave your hands _really_ fast and hope
to find someone dull enough to accept what you offer
as a demonstration.
Instead, you just go back to reciting your pig
ignorant litany of idiocy.
Arguments based, as are yours here, on profusely
repeating unsupported lies early and often are not
functional when addressing questions of scientific
fact.
> First off, it just doesn't happen beyond levels
> that require more than a few hundred fairly
> specified residues at minimum.
Your literature search confirming this meaningless
word salad contention has been published by you in
what peer reviewed journal, once again?
> There isn't one example of evolution in action in
> all of literature beyond the 1000aa level - not
> one.
So what?
No sane person believes that your butt-pulled
mumbo-jumbo "1000aa" limit has warm spit to do with
how evolution works in nature.
Evolution is under no compulsion to work as you want
it to work in make your bogus math "meaningful",
which it will never be.
Evolution works in gradual steps, has been described
to do so since Darwin, and it is observed to work
just fine in small easy steps, always going for the
low hanging fruit in the "fitness improvement" game.
Your teleological contentions to the contrary are
without merit or evidence in their favor.
> And, statistically, it is very unlikely to ever be
> realized this side of trillions of years of time.
And yet you were just pointed to a paper explicitly
debunking this idiocy of yours, on the bounce and by
the numbers.
Given the facts, by recognized experts in the field,
in profuse detail, to counter which you have so far
offered nothing but your usual blind assertions, you
refuse to incorporate those facts into modifying
your opinions, the opinions of a known incompetent
in the field of evolutionary science.
Invincible ignorance is not an attractive mental
illness in you.
> If you think otherwise, by all means, produce some
> real statistical analysis, some real science, to
> prove me wrong.
That's not how science works.
Nobody is required to prove you wrong until you do
the work necessary to prove yourself at least
potentially right.
So far, all you've managed to do is to prove
yourself to be an innumerate, scientifically
illiterate buffoon.
> So far, the very best you guys have come up with
> are these endless examples of low level evolution
> and your fairytale stories about how higher level
> evolution could have happened without any
> consideration of the likelihood of your stories.
It really isn't necessary to do a statistical
analysis to prove that things observed to happen are
capable of occurring.
Your contention to the contrary is idiocy.
Again, your arguments have nothing to do with
science, everything to do with portraying yourself
as a buffoon.
> Without at least some statistical analysis, they
> have no predictive value and therefore simply are
> not "science".
This idiocy by you has been rebutted countless
times, yet you refuse to pay attention to those
rebuttals.
Observational science does _not_ require statistical
analysis to prove that what _is_ observed is
_capable of being_ observed.
Your contention to the contrary is the babbling of a
buffoon.
Invincible ignorance is not an attractive mental
illness in you.
> They are just-so stories.
On the basis of that argument, Kepler's astronomical
observations were "just so stories".
Once again, you prove yourself to be an imbecile.
No one is surprised by this habitual behavior of
yours.
> That's it.
What, you've run out of lies to tell?
>> Of course, if Sean believes I am not doing him
>> justice, he could counter my argument here, by
>> completing the following:
>> "The prevailing paradigm for protein evolution
>> is:"
> Evolution works on what came before. That is the
> prevailing paradigm for protein evolution.
Funny how you miss the "and extends it in small,
easy steps" part of how evolution works.
> The problem
...is that you reject the _observations_ of hundreds
of thosands of trained scientists working in their
fields of expertise, who have contributed to the
literature supporting the theory of evolution, and
try to promote your opinion, based on no pertinent
technical education and unsuppported by any
legitimate observation -- for you evolution can't
work "because I don't like it" -- to some undeserved
level of authority superseding all of science.
Want to guess what your chances are of ever
succeeding at that ploy?
Try a statistical analysis of your chances, and
report back what you find, showing all your work.
> is that the gaps between what came before or what
> already exists in a given genome and the next
> potentially beneficial sequence in sequence space
> (with a novel function) grows linearly with each
> increase in the functional complexity of the
> systems in question.
1) You have not defined "functional complexity". For
certain, it is not "length of genome string", as the
existence of junk DNA so easily demonstrates.
2) You pretend that _you_ get to choose which
beneficial sequence in sequence space evolution must
achieve, and want it to achieve one that is far
isolated from other viable sequences, but evolution
just sticks out it tongue and waggles its fingers
from its ears at you, and makes its own choices
independent of your idiotic teleology.
> That is why evolutionary progress is so limited to
> very very low levels of functional complexity and
> why it has never ever been observed beyond the
> 1000 fsaar level.
Bafflegab which does nothing to counter the expert
disproof of your inexpert, innumerate idiocy already
cited to you.
> Sean Pitman www.DetectingDesign.com
I'm so glad you keep citing your web site in your
signature. That way anyone reading here who cannot
believe that you could *possibly* be the idiot which
you present yourself to be here, can go to your web
site and view in all its splendor the length, width,
and depth of your scientific incompetence, and the
pervasive and crippling contamination you apply to
discussions of science in support of your fanatic
cult religion's agenda.
xanthian.
Kent Paul Dolan
> The flagellar motility system is a classic
> example.
Yes, it is a classic example of why your arguments
are completely bogus.
> It requires a minimum of around 10,000 fairly
> specified amino acid residues (fsaars).
So what?
There absolutely is no evidence that it had to be
created in a single evolutionary step from nothing
more organized than a soup of naked codons, so your
math is meaningless.
> And, it is remotely isolated from the next closest
> beneficial system at the same level or lower
> levels of functional complexity by gaps that are
> far too large to cross this side of many trillions
> of years of time.
That "remotely isolated" is an "irreducible
complexity" argument by you
1) for which you have precisely zero evidence,
2) which trys to use an already debunked creatinist
argument whose own author, Behe, has abandoned it,
3) which is simply untrue.
The step from "rotor" and "flagellum" to "flagellum
+ roter == propulsion mechanism" is very likely a
single copy and paste mutation: stick the encoding
for a flagellum somewhere into the encoding for a
rotor. Flagella and rotors are both known to exist
separately, having fitness-promoting functions other
than propulsion, in nature.
Even if what is produced at first is an extremely
awkward propulsion mechanism, because the "paste"
missed the optimum location, evolution can then go
right ahead and tune the encoding for that
propulsion mechanism for better performance, so
there's no need that the currently seen version in
nature is the version initially produced by
mutation.
There's nothing difficult at all about a single cut
and paste mutation, here one that joins two large
chunks of "sequence" to make one bigger one the size
of the two combined, yet you ground your entire
bogus argument on the falsehood of there being no
way to build the final product from simpler
components in an easy step.
How obviously wrong you are, since just such cut and
paste mutations are frequently seen in nature.
Sucks to be you.
xanthian.
Kent Paul Dolan
> Science is based on what is currently known - not
> on what might become known in the future. And,
> based on what is currently known, right now,
That is a typical creationist "god of the gaps"
argument from ignorance: "if you don't know the
answer in complete detail, then my _entirely
unsupported_ opinion must be correct, there is no
third alternative".
Well, no.
> it is in fact statistically impossible for the
> mechanism of RM/NS to do what you guys claim it
> did.
That is not merely unsupported idiocy, it is
intellectually dishonest, a flat lie.
You know no such thing.
Evolution is an observed fact of nature.
You don't overturn observed facts with statistical
analysis insisting those observations cannot have
been made.
That is the error of the engineers who claimed their
analysis showed that bumblebees "could not fly"
while watching bumblebees fly.
They at least had made an honest error, eventually
overturned, and, in the face of contrary reality,
they did not claim their analysis to be "correct",
but to be "puzzling".
You, on the other hand, flogging a septic cult
agenda, _know_ your analysis is utterly false, but
dishonestly claim it to be sound despite that
knowledge.
You just want to contend that such a falsehood is
true to support your rabid cult religion agenda
denying that evolution, though observed everywhere
in the nature of living things, happens.
It will be no surprise to anyone but you that
arguments from ignorance and arguments based on lies
are not how the business of science is conducted.
But then, you are not conducting science, you are
shilling propaganda.
xanthian.
Kent Paul Dolan
> What part of evolution doesn't happen unless novel
> beneficial sequences are found don't you
> understand?
The parts where those sequences have to be novel, or
beneficial, and where you pretend to understand what
evolution even _is_.
Evolution is well documented to work with recycled
sequences; that's almost all sexual crossover is
about, for example.
Evolution is well documented to be able to bridge
mild detrimental changes for several generations so
long as overcompensating beneficial changes are
eventually added.
> Evolution doesn't have to happen - that's for
> sure.
Sadly for your already vanished reputation, this
also is an entirely false statement.
Given its precursor -- continuous introduction of
fitness-modifying inheritable variation -- evolution
cannot be _prevented_ from happening.
Not to mention that genetic drift is also
"evolution", and again cannot be avoided.
> But, for evolution to actually be realized, novel
> beneficial sequences must be found.
Your definition of "evolution" seems to be unique to
you, and unrelated to the one scientists conversant
with the theory of evolution use.
Probably that is because your usage of "evolution"
is teleological in intent ("must be found") and
assumes that evolution _must_ accomplish goals _you_
set for it, a double falsehood.
This is just more pig ignorant BS from Sean Pitman.
What else is new?
It sucks to be an intellectual slave to a rabid cult
religion actively promoting ignorance among both
its followers and the wider public, to no good
purpose, only its evil power-hungry and greedy ones.
Id est: it sucks to be you.
xanthian.
richardal...@googlemail.com
> On Apr 27, 8:52 am, "richardalanforr...@googlemail.com"
>
>
>
> <richardalanforr...@googlemail.com> wrote:
>
> > > On Apr 26, 7:37 pm, "'Rev Dr' Lenny Flank" <lfl...@yahoo.com> wrote:
>
> > > > On Apr 26, 7:24 pm, Seanpit <sean...@gmail.com> wrote:
>
> > > > > How is that? It doesn't even address my argument
>
> > > > That's because your argument is just the same tired old "747 in a
> > > > tornado" bullshit that everyone laughed at 40 years ago.
>
> > > > Everyone but you seems to realize that evolution doesn't make things
> > > > all at once intact in one fell sdwoop by randomly assembling pieces.
> > > > Evolution works by modifying what is already there.
>
> > > there. The problem here is that if the gaps between what is already
> > > there and the next closest beneficial sequence are too large, a
> > > years of time - on average.
>
> > So,Sean.
> > Identify *ANY* protein used in *ANY* biological system which is
> > isolated from its nearest neighbours in the sequence space of proteins
> > by a gap too large to be crossed other than by a large number of
> > intermediate steps which would take "trillions of years".
>
> > If you can't, it demonstrates that your whole argument is utterly
> > bogus.
>
> Yep, that would be true if in fact there were no examples of higher
> level systems that are in fact remotely isolated. But, alas, there
> example. It requires a minimum of around 10,000 fairly specified
> amino acid residues (fsaars). And, it is remotely isolated from the
> next closest beneficial system at the same level or lower levels of
> functional complexity by gaps that are far too large to cross this
> side of many trillions of years of time.
Sean, this is a flat lie. You know perfectly well that the flagellar
motility system can be derived from other systems with only minor
modifications - you've even referred to this in recent posts. You
claimed there that there is a cluster of functional systems isolated
in sequence space. Of course, that claim is a bogus as the one you are
making here.
>
> > Of course, we know that you can't, you know that you can't, and that
> > the only reason why you continue to promote your silly "theory" is
> > that you want to impress the creationists who you can count on for
> > uncritical acceptance of anything couched in scientific-sounding
> > language which appears to support their cause.
>
> Think again. The evidence is overwhelmingly on my side of this
> issue.
Sean, you haven't produced a shred of evidence to support your
"theory".
> You're the one, on the other hand, who has absolutely no
> statistical basis to believe that the mechanism of RM/NS can do much
> of anything beyond levels of complexity that are far lower than the
> 1000 fsaar level.
The evidence shows that humans have evolved from lobe-finned fish, and
there is a vast amount of evidence - morphological, palaeontological
and genetic - which supports this conclusion. This involves far more
changes than your "1000 fsar level". There is a vast amount of
statistical support for evolutionary theory - much of modern
statistics was developed by evolutionary biologists!
>
> > You won't write it up as an academic paper and submit it for
> > publication because you know perfectly well that no editor of any
> > academic journal would treat it as anything other than a joke. Your
> > excuse that *NO* editor of *ANY* academic journal has a "candid mind"
> > and *ALL* are brainwashed by the evolutionist elite is so
> > transparently facile - not to say dishonest - that only a creationist
> > could accept it. You know that you have nothing of any scientific
> > value to offer, which is why you just post the same old nonsense over
> > and over again in forums such as this rather than demonstrating the
> > strength of your convictions by actually *trying* to get it published.
>
> Try to counter it yourself, using something other than fairytale just-
> so stories and bravado, for a change . . .
Why on earth should I bother? You have nothing to offer but a bunch of
distortion and lies.
Of course, you could prove me and all your other critics wrong by
writing your "theory" up as a scientific paper and submitting it for
publication, but you won't because you know perfectly well that no
editor of any academic journal would treat it as anything other than a
joke.
You have nothing but lies and bluster, Sean, and you know it.
RF
>
> > RF
>
> Sean Pitmanwww.DetectingDesign.com
Kent Paul Dolan
Wow, did that swish as the goalposts went
rushing by muss _your_ hair?
Once again, you have refused to accept the very
information you demanded.
That disqualifies you from ever demanding that
information again.
Sorry, you don't get to attempt to win your argument
with word salad.
None of those tossed greens have had any
demonstration that they are in any way related to
evolution _as it happens in nature_.
Until you publish such a demonstration in a
reputable, pertinent peer reviewed journal of
science, and it is accepted by peer review, you are
ineligible to use that word salad definition of what
it means to be "sufficiently interesting evolution"
or whatever in hades it is you are trying with your
limited word skills to convey.
Your earlier challenge was that no "big functional
change" had ever been documented to occur as a
result of evolution, where again you left "big"
undefined.
That is now certainly a falsehood,
Some E. coli eat vitamin C.
So, you are *compelled* to change your contentions
to cater for that new human knowledge.
Or, you can choose to continue to be the butt of
ridicule.
Probably your cult would strongly prefer you take
that path on their behalf, and thrown yourself on
the conceptual gernade for them.
> These low-level examples
Changing the chemistry of a single celled organism
to accomodate an enhanced metabolic pathway to cater
for a new form of nourishment is by no means a "low
level example".
You contend, elsewhere, that even the single celled
organism is an immensely complex organism.
You don't get to have things both ways.
Just because an instance of evolution occurs in a
single celled organism doesn't make that instance
"low level".
Sorry, you blather, you obfuscate, you lie, you
lose.
The situation remains the sams as always.
> are the very same as those presented by the
> authors of the paper you've just listed here in
> this thread.
Your eyes just glazed right over as you skimmed that
document, didn't they?
Why should you bother to learn anything, when your
religion presents you with an agenda it insists you
accept as correct with no regard for mere facts?
The above is just one more falsehood from Sean
Pitman -- go read that paper until you comprehend it
even with your disconnect from reality, limited
grasp of science, and nonexistent grasp of
mathematics.
> The fact remains that the mechanism of RM/NS can
> only explain these low-level examples and no
> further.
False.
You insist, incorrectly, that evolution be what you
want it to be, for the purpose of you debunking it.
Unfortunately for your agenda, evolution is what it
is, which works quite splendidly despite your and
your cult's hostility to it.
Evolution proceeds by "grabbing the low hanging
fruit", where that may be, incredibly infrequently,
a saltation level change that just happens to be an
easily accomplished change (say, polyploidy), but is
in the massively prevalent case a long series of
gradual (at least) fitness enhancing changes across
a broad frontier of directions of change to the
species' organism's features, adding up in the end
to a lot of large changes.
> It cannot explain higher levels of functional
> complexity.
And yet it does. You just chose to throw a lot of
bogus math and word salad at it, pretending that the
existing explanation does not suffice.
Sadly for your agenda, the gradualist explanation of
evolution entirely suffices to explain large
additions of functionality over time.
[Notice that Dembski's "functional/specified
complexity" is still not satisfactorily defined,
and is thus a meaningless noise. Neither you nor
any other creationist has produced an acceptable
way of measuring "functional complexity".]
> That's where the rub comes in. That's where the
> evolutionary mechanism stalls out.
Such a shame for your agenda that, even after around
4.2 billion years of continuous operation, evolution
just keeps on chugging along with nary a sign of
"stalling out".
Evolutionary processes go on evolving incredibly
complicated organisms like aspen groves and whale
sharks and tree shrews from the modest beginning of
something extremely simple at abiogenesis, that
eventually evolved over generations to be a single
celled organism.
Your vapors and delusions affect only your own
questionable sanity, not the operation of evolution
in nature, which doesn't care about you even enough
to have contempt for you.
xanthian.
wf3h
> On Apr 27, 9:10 am, wf3h <w...@vsswireless.net> wrote:
>
> >
> > and how does 'design' handle this? the fact is, it doesn't. it doesn't
> > at all. it's completely unable to specify ANY method which can
> > confront a problem you yourself have generated.
>
> Not true. Human-level technology can produce such sequences and is
> even getting very close to producing novel information at this level
> beyond simply copying it from what already exists on the nano-scale.
do you see the word 'technology' there? that's the word that's missing
from your argument. even YOU can't conceive of a system without
TECHNOLOGY. yet you rule out any natural processes.
you have worked yourself into a trap. you yourself can't conceive of a
production system that is not TECHNOLOGY based. thus even you
implicitly admit your creationist view of the development of DNA is
wrong.
> > and, without a mechanism of knowing how amino acid chains
> > develop....apart from evolution...we simply do not know WHAT causes
> > them to change. it's an unknown. so to say that the change is
> > statistically impossible is nonsense. the mechanism may be very simple
> > indeed. we just haven't found it.
>
> Science is based on what is currently known - not on what might become
> known in the future. And, based on what is currently known, right
> now, it is in fact statistically impossible for the mechanism of RM/NS
> to do what you guys claim it did.
uh...no. science is not based on what is 'currently known'. if that
were the case, no one would do research. science is based on the
assumption that there are NATURAL processes based on NATURAL laws
which can be explored and understood
that's why your creationism is wrong. it kills such an observation
with the claim 'god did it' and thus closes off further investigation.
and i dont care about RM/NS. it's irrelevant to me whether it's
correct or not. CREATIONISM...your mechanism...is, however, wrong.
>
> > THEN to reject the LOGICAL assumption...an unknown process...in favor
> > of one that has FAILED....creationism...is mind blowing. this type of
> > reasoning stopped science dead in its tracks for the last 2000 years.
>
> Human-level intelligence has not failed.
intelligence can do nothing as even you admitted above. your
psychology betrayed you when you used the term 'technology'. you
creationists want to insert magic where even you admit TECHNOLOGY must
be involved
IOW you do not have a coherent argument.
>
> > care to cite a SINGLE example of a success in THAT area?
>
> Human-level intelligence and technology? - lots of examples.
ah. there's that nasty word again...technology....
>
>
>
> > oh. you can't. after using this argument for TWO MILLENIA....you still
> > can't point to a single success.
>
> You're confusing an attempt to prove God with an attempt to
> demonstrate at least human-level intelligence and creativity - big
> difference.
and you are confusing your own use of the concept of
magic...creationism...with the idea of 'technology'.
>
> > and as you admit, creationism has never been observed anywhere at any
> > time under any circumstances.
>
> > yet you think it's right. IOW evidence be damned, your church has the
> > answer.
>
> > thanks,sean. after seeing your 2000 year history of failure, i think
> > i'll take my business elsewhere.
>
> You are again confusing beliefs in God with beliefs in that at least
> human-level intelligence is required to explain certain phenomena.
> They aren't the same argument Bob - not at all.
your argument is that
1. natural processes (technology) must be excluded since we do not see
it producing complexity
2.therefore god did it
and how did god do it if technology is excluded? you don't say. you
wander back and forth, contradicting yourself, on one hand saying
'technology', on the other saying 'god did it'.
no wonder creationism made no progress in 2000 years. you're a prime
example of its thinking.
Paul Ciszek
In article <gt6b00$jmu$1...@news.albasani.net>,
Kent Paul Dolan <xant...@well.com> wrote:
>
>That is the error of the engineers who claimed their
>analysis showed that bumblebees "could not fly"
>while watching bumblebees fly.
Sigh. It was a long time ago, when much less computing power was
available, and a program written to simulate fixed-wing aircraft
was inappropriately appied to bumblebees, which are not "fixed
wing aircraft", and found that they are unstable. Meaning, at
most, that a dead bumblebee will tumble if you try to make it
glide.
--
Please reply to: | "Any sufficiently advanced incompetence is
pciszek at panix dot com | indistinguishable from malice."
Autoreply is disabled |
Kent Paul Dolan
> Kent Paul Dolan <xant...@well.com> wrote:
>> That is the error of the engineers who claimed
>> their analysis showed that bumblebees "could not
>> fly" while watching bumblebees fly.
> Sigh.
> It was a long time ago, when much less computing
> power was available,
Not pertinent.
> and a program written to simulate fixed-wing
> aircraft was inappropriately appied
As is Sean Pitman's model, which denies that
evolution even of large changes happens in small
steps, inappropriately applied, since evolution
doesn't operate the way he insists it must.
> to bumblebees, which are not "fixed wing
> aircraft",
Nor are the large observed changes of evolution
"saltationist steps" that must be done in a single
genome modification.
> and found that they are unstable.
Sean Pitman finds that the single large steps which
he incorrectly insists are the only way evolution is
able to operate, are probablistically impossible.
> Meaning, at most, that a dead bumblebee will
> tumble if you try to make it glide.
Meaning, at most, that in some other universe where
the laws of physic and chemistry work differently
than they do in this one, so that evolution by
one-large-step saltation is the only allowable
mechanism, evolution couldn't work.
All of that accepted, the analogy to Sean Pitman
claiming that his "statistical analysis" disproves
that evolution can happen, while evolution, despite
his analysis, still happens and is observed to
happen, remains appropriate.
xanthian.
Seanpit
> Seanpit wrote:
> > On Apr 27, 11:21 am, Kent Paul Dolan <xanth...@well.com> wrote:
> > > Seanpit wrote:
>
> > > > The goal of the evolutionary mechanism of RM/NS is
> > > > to find new beneficial sequences.
>
> > > What part of "evolution is not teleological" do you
> > > remain too pig ignorant to accept?
>
> > What part of evolution doesn't happen unless novel beneficial
> > sequences are found don't you understand? Evolution doesn't have to
> > happen - that's for sure. But, for evolution to actually be realized,
> > novel beneficial sequences must be found.
>
> It seems to me that
>
> -- if evolution is "change in allele frequency within a population"
> then "finding novel beneficial sequences" does not have to happen; all
> that must happen is "change in allele frequency".
That's not the definition of Darwinian-style evolution where lizards
are able to turn into birds and fish into land animals, etc. What
you've just described is Mendelian variation, not Darwinian-style
evolution.
> -- even if "evolution" does find "novel beneficial sequences", that
> does not mean "finding novel beneficial sequences" is the *goal* of
> evolution; it's a *byproduct* of the activity, not a *goal*.
Whatever. This is just semantics. The point is that for real
evolution to happen, novel beneficial sequences must be found. It
doesn't matter if you call that process the "goal" or the "byproduct",
the basic concept is still the same.
> Regards,
> Stephen
Sean Pitman
www.DetectingDesign.com
Seanpit
wrote:
Not at all. This has nothing to do with Kolmogorov complexity. The
definition of functional complexity includes the minimum specificity
requirements of a system or structure. If a structure with a given
minimum size requirement can be produced with just two characters
instead of 20 different ones, that reduces that structure's minimum
specificity requirement.
For example, say that you have a 1000-character system that is fully
specified. If the system requires a 20-character alphabet to produce,
the sequence space will be 20^1000 (1e1301). And, if a system with
the same minimum size requirement is only required to use a 2-
character alphabet, the sequence space size will be 2^1000 (1e301).
I bet by now you are thinking, "See, this proves my whole point!" -
right?
While it is true that this difference is an enormous difference, it
really doesn't solve the expanding non-beneficial gap problem. All
that would have to happen for the 2-character alphabet system to end
up with a sequence space size equivalent to the 20-character system is
for the minimum size of the system in question to be increased less
than 4.4 fold to a 4,400 character minimum size requirment. This
really doesn't solve the problem. Consider that having a larger
alphabet would likely reduce the minimum size requirement for certain
systems vs. a smaller alphabet. Fewer basic characters could be used
since a single additional unique character may be able to do the job
that would take more characters from a smaller alphabet to produce.
For example, it would probably take a lot more characters to code for
a flagellar motility system given a 2-character alphabet compared to a
20 character alphabet. So, the overall minimum complexity and sizes
of sequence space of the system remains essentially unchanged. And,
like I said originally, the alphabet that is used really has little
effect on the level of functional complexity of a system. The system
itself defines its own level - not the alphabet.
I think you need to go back and think about this a bit more. I'm
afraid you're the one who is "dead wrong" here.
Sean Pitman
www.DetectingDesign.com
'Rev Dr' Lenny Flank
> I'm
> afraid you're the one who is "dead wrong" here.
Hey Sean, why is it that everyone you explain your wonderful mathy
sciency stuff to --- absolutely everyone without exception -- thinks
it's a load of horse shit?
Why is that, Sean?
Why does NOBODY seem to, uh, understand your paradigm-shattering world-
chaning scientific discovery of the millenium? Why doe EVERYBODY
think it's a load of horse shit?
Is it because everyone but you is engaged in a vast international
conspiracy against you?
Is it because you arfe too stupid and incompetent to explain your
earth-shattering discovery in such a way that people can understand it
and grasp its utter genius?
Or is it because your mathy sciency stuff really is jsut full of shit?
Which is it, Sean?
(snicker) (giggle) <---- yes, Sean, I am laughing at you. Again.
hersheyh
> On Apr 27, 4:25 pm, "Stephen" <ssan...@austin.rr.com> wrote:
>
>
>
> > Seanpit wrote:
> > > On Apr 27, 11:21 am, Kent Paul Dolan <xanth...@well.com> wrote:
> > > > Seanpit wrote:
>
> > > > > The goal of the evolutionary mechanism of RM/NS is
> > > > > to find new beneficial sequences.
>
> > > > What part of "evolution is not teleological" do you
> > > > remain too pig ignorant to accept?
>
> > > What part of evolution doesn't happen unless novel beneficial
> > > sequences are found don't you understand? Evolution doesn't have to
> > > happen - that's for sure. But, for evolution to actually be realized,
> > > novel beneficial sequences must be found.
>
> > It seems to me that
>
> > -- if evolution is "change in allele frequency within a population"
> > then "finding novel beneficial sequences" does not have to happen; all
> > that must happen is "change in allele frequency".
>
> That's not the definition of Darwinian-style evolution where lizards
> are able to turn into birds and fish into land animals, etc. What
> you've just described is Mendelian variation, not Darwinian-style
> evolution.
Semantics. Giving the process a different name (Mendelian variation)
does not mean that evolution does not happen within species. What,
besides lots more time in isolation or changes that favor reproductive
isolation, is required to produce speciation. Once you have
speciation, all you need is repeated speciation. Birds, of course,
are largely land animals (penguins excepted). And ancestral fish did
not turn into dogs in one swell foop via some large functionless goo
of a gap.
>
> > -- even if "evolution" does find "novel beneficial sequences", that
> > does not mean "finding novel beneficial sequences" is the *goal* of
> > evolution; it's a *byproduct* of the activity, not a *goal*.
>
> Whatever. This is just semantics. The point is that for real
> evolution to happen, novel beneficial sequences must be found.
Why does evolution have to find *novel* beneficial sequences? What
differentiates a *novel* beneficial sequence from a sequence that has
a modified, additional, emergent, or increase in secondary function?
As far as I know, evolution only has to occasionally produce examples
of the latter.
richardal...@googlemail.com
> On Apr 27, 4:25 pm, "Stephen" <ssan...@austin.rr.com> wrote:
>
>
>
> > Seanpit wrote:
> > > On Apr 27, 11:21 am, Kent Paul Dolan <xanth...@well.com> wrote:
> > > > Seanpit wrote:
>
> > > > > The goal of the evolutionary mechanism of RM/NS is
> > > > > to find new beneficial sequences.
>
> > > > What part of "evolution is not teleological" do you
> > > > remain too pig ignorant to accept?
>
> > > What part of evolution doesn't happen unless novel beneficial
> > > sequences are found don't you understand? Evolution doesn't have to
> > > happen - that's for sure. But, for evolution to actually be realized,
> > > novel beneficial sequences must be found.
>
> > It seems to me that
>
> > -- if evolution is "change in allele frequency within a population"
> > then "finding novel beneficial sequences" does not have to happen; all
> > that must happen is "change in allele frequency".
>
> That's not the definition of Darwinian-style evolution where lizards
> are able to turn into birds and fish into land animals, etc.
Actually, it is - or rather, it's a definition of modern evolutionary
theory.
Inventing your private meanings for concepts merely demonstrates how
intellectually bankrupt your position is.
> What
> you've just described is Mendelian variation,
Actually, it isn't. In "Mendelian variation" the frequencies of
alleles in a population don't change, they just get expressed in
different patterns. It was the discovery of mutations by de Vries and
others in the early part of the 20th century which provided a source
for the variation needed to drive the evolutionary process.
> not Darwinian-style
> evolution.
As modern evolutionary theory has moved on considerably from
"Darwinian-style evolution" - something of which you *must* be aware -
yet again you are dishonestly attempting to obfusticate.
>
> > -- even if "evolution" does find "novel beneficial sequences", that
> > does not mean "finding novel beneficial sequences" is the *goal* of
> > evolution; it's a *byproduct* of the activity, not a *goal*.
>
> Whatever. This is just semantics. The point is that for real
> evolution to happen, novel beneficial sequences must be found. It
> doesn't matter if you call that process the "goal" or the "byproduct",
> the basic concept is still the same.
It does when you imply that the evolution of proteins is directed at a
goal isolated in sequence space with no intervening functionality at
all.
RF
>
> > Regards,
> > Stephen
>
> Sean Pitmanwww.DetectingDesign.com
Kent Paul Dolan
> [...] real evolution [...]
Astonishingly (to you), redefining what the common
terms for your subject matter mean, into your own
idiosyncratic definitions, then arguing against the
definitions _you_ have created, rather than the ones
in technical use [that is, erecting then arguing
against strawmen], is going to gain your ideas no
acceptance whatever among rational humans.
Not so amazingly, that is exactly what has been
happening in your attempts to sell you spew of cult
religion sewage as if it were science.
It seems like a person with a high school education
would already know that sort of stuff.
Just how did _you_ avoid ever learning in all these
years how reasoned discourse is done?
xanthian.
hersheyh
What impossible-to-evolve "novel beneficial sequence" caused the
speciation (actually several speciation iterations) difference between
humans and chimps? Are all the differences between humans and chimps
"Mendelian variation, not Darwinan-style evolution"?
Both genomes have been sequenced. Surely you can find the sites which
cannot have evolved by a simple search.
david....@ed.ac.uk
generated all of this discussion. Steven Litvintchouk has asked me to
comment on the analysis of my paper performed by Sean Pitman and this
is appended at the end of this text. I must say that I am a bit
surprised at the amount of interest and discussion that has arisen
from the little paper by myself and two colleagues. However, I am
pleased that it has done so and that my decision to pay for it to be
an “open access” paper has been justified. It is my hope that within
10 years all professional peer-reviewed science will be freely
available.
I have skimmed through many of the other comments and noted one
disparaging comment concerning our acknowledgement of discussion with
Simon Conway Morris. I would like to briefly explain why we did this.
I attended a lecture by him in which he discussed convergence at
length and briefly mentioned the big numbers problem. I started
corresponding with him and have met him on numerous occasions now for
further discussions on these two topics. (Inevitably we have also
talked about his religious views plus his view of creationism/ID. His
negative views on creationism and ID fully concur with my own.) He is
a highly respected biologist and palaeontologist and his ideas on
convergence in organisms would appear to tally with many ideas on
convergence at the molecular level, my area of interest. He was
essentially a catalyst in getting me to seriously research the big
numbers issue so it is perfectly normal practice in science for him to
be acknowledged. The comment also assumed we were chemists but in
addition to having worked in chemistry and physics, we have many years
of practical experience in genetics, molecular biology and
biochemistry. Not obvious from our address of course.
I am probably going to write far too much but if you want the
conclusion, it is that Sean Pitman is completely and utterly wrong in
everything he says in his comments and displays a great ignorance of
proteins and their structure and function. However, I do hope he will
read on.
He has failed to recognise that we wished to establish limits on the
amount of sequence space explored. Defining limits is a standard
scientific procedure, though often forgotten, and prevents a lot of
time wasting as long as one does not initially restrict the
calculation unnecessarily. Hence, these upper and lower limits are as
generous as possible based upon current knowledge. They may be out by
a few powers of ten but this is negligible and as research proceeds
the limits are likely to come closer together narrowing the range of
possibilities. In our graph, we overlaid the limits on top of the
number of different sequences possible for a given pool of letters.
The letters may total up to 20 in number but it’s just a number. If
these letters are considered to be amino acids, then we can group the
20 amino acids into a smaller number of categories related to their
physical chemical properties. As soon as you state that the symbols
you use in the calculation of these big numbers represent physical
entities then you cannot ignore their physical properties. Such
groupings are well known to be valid in experiment and are the basis
for computer-driven sequence analysis. It is unfortunate that such
computer analysis has been carried too far by some people especially
those who wish to push the ID complexity agenda and that sight has
been lost of the fact that proteins do not exist in silico.
What follows below is a “lecture” on protein structure for Sean
Pitman’s benefit. He could of course read a book such as the excellent
“Introduction to protein structure” by Branden and Tooze and
accessible to all audiences. I apologise to the rest of you if it gets
boring but it will eventually lead back to discussing Pitman’s
comments. Also please do not feel that I am talking “down” to you
expecting you to believe the expert, I just wish to bring some of the
latest research and some well established data to you. Also, the
formality in the writing is just to keep it precise and to exclude, if
possible, more than one interpretation though given the haste in which
I have had to write this, it is not perfect.
In the real world of protein structure and function, it is well
established that many amino acids can be changed with little or no
effect on function (there are only two “functions” for a protein: to
bind and control another object or to bind another object and catalyse
a reaction on that object-and this latter includes proton pumping to
rotate a flagellum). The catalytic chemical mechanisms performed by
enzymes and ribozymes fall into only 6 categories of well understood
chemical reactions (a rather small reaction space). All of
biochemistry is built upon them. Those mutations that do change
function usually define an active site (for function) or a crucial
folding region. It is known that proteins are built up from the
repetitive use of smaller peptide sequences being joined together by
gene duplication and recombination in the DNA coding. A general
consensus seems to be that amino acid sequences of length about 20 or
30 really start to get interesting in terms of function but even
smaller folding units are being proposed as progenitors (see work if
possible by Edward N Trifonov and also note that even single amino
acids are capable of catalysing reactions). The joining of these
20-30mers (via the gene), which fold into “super-secondary” structure
units, rapidly leads to a folded “domain” of 50-150 amino acids. These
domains are small folded units. This domain size is essentially
universal. You do not find examples of a 1000 amino acid domain but it
will instead comprise around 10 smaller domains. It is very important
to note that in many cases such folding does not require complete
specification of the sequence but only maintenance of the pattern of
amino acid categories (polar, non-polar etc). Many domains do
interesting things but a recurring theme is to then bring collections
of the domains together either as separate subunits to form quaternary
structure or to string them together into one single chain by making
them via a single gene. This latter process is how one makes a 1000
amino acid protein. Nature takes the domain modules and puts them
together to make novel structures and functions. (Note that very few
long protein chains are found as their synthesis is tricky due to
increasing chances of errors in gene replication, transcription or
translation. These problems were recognised by Francis Crick if I
recall correctly in the 1960’s. The average protein size is around 500
amino acids.) The number of domains with unique folds appears to be
limited to around 1000 to 10,000 (certainly less than a million) and
it is becoming rare for science to find new ones. This means that
whatever sequence you have, you get one of these folds (but note that
there is a relatively new discovery of “natively-unfolded” proteins
which are unfolded until they bind to their target molecule at which
point they fold up. How much of sequence space is occupied by these
fully functional proteins is unknown). The number of protein types in
any organism also appears to be very limited from several hundred in
the bacteria with very small genomes to perhaps of the order of 10,000
in multicellular organisms. These proteins still contain the same
domains. These limited numbers of proteins perform a limited number of
reactions (again totalling hundreds to thousands of such reactions as
detailed in standard biochemistry textbooks). The important thing to
produce different species is how all these reactions are controlled
(mostly) by proteins each built using the same structural principles
as already detailed. This area of control is often referred to as part
of EvoDevo or evolutionary development and it is where the real
discussions of complexity are going on. That’s not my speciality so I
will return now to proteins.
Hopefully it is clear that we have considerable understanding of
protein structure and how they function and that they are not so
complex that we cannot possibly explain them (and even design them
ourselves. David S Goodsell has published an excellent book on
“Bionanotechnology” showing what Nature has achieved and how our
understanding of it lets us design new experiments). We could if we
wished define a structural space and a functional space in the same
way as a sequence space. From the foregoing, it should be clear that
neither of these spaces is particularly large when compared to the
possible size of sequence space.
Given the small sizes of the spaces of domain structure, chemical
reactivity, and biochemical function, or perhaps I could refer to them
as toolboxes, it does not seem to be too much of a guess that the last
common ancestor of all life on earth would be equipped with all of
these toolboxes. This is why we decided to determine the limits of use
of these toolboxes and calculate the upper and lower limits starting
from way back in time. The tools may not have been fully utilised or
explored by that stage (or even by bacteria today), but later when
multicellular organisms appeared, these tools were ready to be used
and even reconfigured.
So we return to the problem of how big is sequence space? It is not 20
raised to the power of the number of amino acids in the sequence but
much less as we discussed in our paper. There is no need to have 20
different types of amino acid each with unique properties or sequence
lengths greater than around 100. This is due to the physical
similarities between amino acids and the limited range of folded
structures. Only a few amino acids in any protein are crucial for its
function. Changing these ones will sometimes do almost nothing to the
function. However, some will change the function to something new
while maintaining structure, and a very few will change the protein
structure (and hence its original function) altogether but in all
probability still confer a new function. Even if the original
structure is destroyed by a mutation and the protein does not fold,
the possibility of a new function is not lost as evidenced by the
discovery of natively unfolded proteins which acquire fold and
function upon binding to a target.
Sequence space when proposed was quickly recognised as a silly
“paradox” by protein scientists (though not unfortunately by some
other scientists) rather like the silly Levinthal “paradox” of protein
folding. Sequence space may be large but that does not mean it is
complex. I hope the above short essay on protein structure and
function is useful even to Sean Pitman who needs to stop being
obsessed with computer-based numerology and do some reading and talk
to some practical protein scientists. I also hope that he will realise
that proteins are not relevant to religion and that they as well as
other macromolecules provide absolutely no foundation for ID.
Some short specific replies to the critique by Sean Pitman
"The authors argue that because some types of functional proteins are
smaller than 100aa [amino acids], and because some types of proteins
have very low sequence specificity requirements, that pretty much all
of sequence space could have been searched in just a few billion
years.
"What these authors fail to realize is that not all protein-based
systems are created equal. Some systems do indeed require very few
amino acid building blocks and little sequence specificity. These, of
course, are on very low levels of functional complexity. Other
systems, however, require far more than the 100aa systems discussed by
the authors - at minimum. And, many of these systems require a
significant degree of specificity. These systems are on a much higher
level of functional complexity and therefore occupy much much larger
sequence spaces and also have exponentially lower ratios of
potentially beneficial vs. non-beneficial at these higher levels.”
Reply: With nearly 50 years of biological and chemical research shared
between the authors, we really do understand that not all molecules
are the same. We are not saying only a few specified amino acids are
available but a few types of amino acids- polar, non-polar, negative,
positive and so on. For example, any one of the polar ones might do at
a particular site. All you need to specify is polarity. Since this is
the entire basis of using sequence comparisons to group proteins into
functional families and these computer methods are used by supporters
of ID, they should know this. Small proteins are not necessarily
functionally simple nor are big proteins necessarily complex in
function (in fact some a remarkably boring).
"The authors of this paper do not even address the concept of
different levels of functional complexity. They only point out the
obvious that some types of functional systems are very very low level
systems. Well duh! What about those systems that are on much much
higher levels of minimum size and/or specificity requirements?...”
Reply:These increasing degrees of functional complexity are a mirage.
Just because a flagellum spins and looks fancy does not mean it is
more complex than something smaller. The much smaller wonderful
machines involved in manipulating DNA, making cell walls or
cytoskeletons during the cell’s lifecycle do far more complex and
varied things including switching between functions. Even a small
serine protease has a much harder job than the flagellum. The
flagellum just spins and spins and yawn…
"The evidence shows that the distances [in sequence space] between
higher and higher level beneficial sequences with novel functions
increases in a linear manner."
Reply: What evidence? And if importance of function scales with
sequence length and the scaling is linear then I am afraid that 20^100
is essentially identical to 2 x 20^100. Also a novel function is not a
new function but just one we stumble upon in doing the hard work in
the lab. It’s been there a long time…
richardal...@googlemail.com
Many thanks for this fascinating post.
RF
'Rev Dr' Lenny Flank
(snip)
> if you want the
> conclusion, it is that Sean Pitman is completely and utterly wrong in
> everything he says in his comments and displays a great ignorance of
> proteins and their structure and function.
(snip)
OK, Sean, here is the part where you tell the author of this paper
that he doesn't understand his own paper, and that YOU do. . . . .
My my my, Sean, you always seem to have the very same problem ---
every time you show your wonderful mathy sciencey stuff to someone who
knows the subject, they quickly conclude that you are full of shit.
Why is that, Sean? Is it because everyone who knows the subject is
part of the international atheist plot to get you, Sean? Is it
because you are too stupid and incompetent to either explain your
wonderful paradigm-shattering discovery to people in such a way that
they can grasp its genius, or to explain to those who think it's horse
shit why it's really NOT horse shit, in such a way that they can grasp
their wrong-headedness and your genius?
Or is it because all your arguments really are just bullshit,
Sean . . . ?
Which of those is the more probable explanation, Sean? Which occupies
more sequence space?
(snicker) (giggle) <------- yes, Sean, I am laughing at you. Again.
Kent Paul Dolan
[...]
> I am probably going to write far too much but if
> you want the conclusion, it is that Sean Pitman is
> completely and utterly wrong in everything he says
> in his comments and displays a great ignorance of
> proteins and their structure and function.
[...]
The degree of warm fuzzy feelings that generates is
hard to quantify. Let's just say that it would cure
an ice age.
Anyone taking bets on how long it will take Sean
Pitman to come back, powered by the insane opinions
of his creationist cult religion, bringing the full
foetid force of his massive ignorance of mathematics
and biogenomics to bear on this issue again, yet
again invincibly ignorant, ignoring all invitations
to acquire first an education in the topics on which
he spews endless nonsense?
I give it a week.
xanthian.
'Rev Dr' Lenny Flank
Everyone here should save Dr Dry's paragraph as a text file on their
hard drive, and simply cut-and-paste it in response to every single
post Sean ever makes here again.
Kent Paul Dolan
long blocks of text had become eye glazing, replaced
some non-ASCII characters with my best guess at
their intents, and re-flowed the paragraphs to cater
to my astygmatism.
All that said, it is plenty of time to start the
Posting of the Month candiodate list for May 2009.
Nominated.
xanthian.
david....@ed.ac.uk wrote:
> _Introduction to protein structure_ by Branden and
> excellent book on _Bionanotechnology_ showing what
> and yawn...
> "The evidence shows that the distances [in
> sequence space] between higher and higher level
> beneficial sequences with novel functions
> increases in a linear manner."
> Reply: What evidence? And if importance of
> function scales with sequence length and the
> scaling is linear then I am afraid that 20^100 is
> essentially identical to 2 x 20^100. Also a novel
> function is not a new function but just one we
> stumble upon in doing the hard work in the lab.
> It’s been there a long time.
Friar Broccoli
> In the below, I have added some white space where
> long blocks of text had become eye glazing, replaced
> some non-ASCII characters with my best guess at
> their intents, and re-flowed the paragraphs to cater
> to my astygmatism.
>
> All that said, it is plenty of time to start the
> Posting of the Month candiodate list for May 2009.
>
> Nominated.
Seconded.
And I hope the author will come back toward the middle of
next month so he can correct (or refuse) my edits of
his very informative post, assuming he wins the vote.
richardal...@googlemail.com
Is there any possibility that he won't?
RF
Ye Old One
"richardal...@googlemail.com"
<richardal...@googlemail.com> enriched this group when s/he
wrote:
I think there would have to be something really fantastic to beat it.
--
Bob.
'Rev Dr' Lenny Flank
> <richardalanforr...@googlemail.com> enriched this group when s/he
Sean could write a devestating response that shatters the entire
modern scientific paradigm, destroys atheistic darwinistic materialism
forever, and ruins all our lives.
(snicker) (giggle) <---- yes, Sean, I am laughing at you. Again.
Richard Harter
<xant...@well.com> wrote:
>In the below, I have added some white space where
>long blocks of text had become eye glazing, replaced
>some non-ASCII characters with my best guess at
>their intents, and re-flowed the paragraphs to cater
>to my astygmatism.
>
>All that said, it is plenty of time to start the
>Posting of the Month candiodate list for May 2009.
>
>Nominated.
>
>xanthian.
[snip]
Nominated, of course. Thank you for the reformatting.
I never could quite bring myself to slog through Sean's
effusions. The article makes clear where Sean goes wrong; he
assumes that genes for long proteins arise by one at a time point
changes whereas in fact they arise by composition.
In short, he show that that which is not done is impossible and
argues thereby that that which happened did not happen.
Richard Harter, c...@tiac.net
http://home.tiac.net/~cri, http://www.varinoma.com
If I do not see as far as others, it is because
I stand in the footprints of giants.
Ye Old One
You know, you are so funny, you should be on telly :)
--
Bob.
Steven L.
> david....@ed.ac.uk wrote:
>
> [...]
>
> > I am probably going to write far too much but if
> > you want the conclusion, it is that Sean Pitman is
> > completely and utterly wrong in everything he says
> > in his comments and displays a great ignorance of
> > proteins and their structure and function.
>
> [...]
>
> The degree of warm fuzzy feelings that generates is
> hard to quantify. Let's just say that it would cure
> an ice age.
But that much heat may make it impossible to solve the global warming
problem!
Dr. Dryden has doomed us all!
--
Steven L.
Email: sdli...@earthlinkNOSPAM.net
Remove the NOSPAM before replying to me.
Steven L.
> Someone URLed this link a day or two ago,
> I've forgotten who, but thanks, in any case.
>
> Lo and behold, the document is _not_ behind a pay
> wall!!
>
> It is a very nice document, since the authors went
> to the trouble completely to debunk what might be
> called "Sean Pitman math", with the explicit
> conclusion that the use of such math to "prove" the
> need for divine intervention in creating the tree of
> life is a bogus enterprise.
>
> How much of protein sequence space
> has been explored by life on Earth?
>
> [...]
>
> To further support this idea of a reduced alphabet
> of amino acids, there are also very plausible
> suggestions that the original amino acid repertoire
> consisted of only four or five amino acids like
> those found in the Miller--Urey experiments and the
> Murchison meteorite (Miller et al. 1976), and that
> the genetic code was initially limited to these few
> amino acids that still predominate in proteins to
> the current day (e.g. Trifonov 2000; Brooks et al.
> 2002; Ikehara 2002). Proteins with reduced amino
> acid repertoires can fold and function successfully
> (e.g. Cordes et al. 1996; Riddle et al. 1997; Plaxco
> et al. 1998; Guo et al. 2004; Doi et al. 2005; López
> de la Osa et al. 2007).
>
> [...]
>
> Finally, we conclude that the number 20^100 and
> similar large numbers (e.g. Salisbury 1969; Maynard
> Smith 1970; Mandecki 1998; Luisi 2003; Carrier 2004;
> de Duve 2005) are simply ‘straw men’ advanced to
> initiate discussion in the same spirit as the
> ‘Levinthal paradox’ of protein folding rates
> (Levinthal 1969; Zwanzig et al. 1992). 20^100 is now
> no more useful than the approximate 2×10^1834097
> books present in Borges' (1999) fantastical ‘Library
> of Babel’ and has no connection with the real world
> of amino acids and proteins. Hence, we hope that our
> calculation will also rule out any possible use of
> this big numbers ‘game’ to provide justification for
> postulating divine intervention (Bradley 2004;
> Dembski 2004)
>
> http://rsif.royalsocietypublishing.org/content/5/25/953.long
>
> I can only add that after this analysis has been
> cited into a discussion, any such attempt to use
> "Sean Pitman math" to attempt "to provide
> justification for postulating divine intervention"
> is a dishonest enterprise, as well.
>
> Life is, as usual when drop-kicking creationist
> loons, good.
Dr. Pitman has been browsing this NG, and he emailed me with his
responses to Seanpit's criticisms. (Remember? I had offered to email
Dr. Dryden with Seanpit's more temperate criticisms, in hopes of getting
a reply. Well, I did!)
I have posted Dr. Dryden's reply separately.
Steven L.
> On May 2, 7:16 pm, Kent Paul Dolan <xanth...@well.com> wrote:
>> In the below, I have added some white space where
>> long blocks of text had become eye glazing, replaced
>> some non-ASCII characters with my best guess at
>> their intents, and re-flowed the paragraphs to cater
>> to my astygmatism.
>>
>> All that said, it is plenty of time to start the
>> Posting of the Month candiodate list for May 2009.
>>
>> Nominated.
>
> Seconded.
No need for a vote this month.
Dr. Dryden's post(s) should win by acclamation.
Rodjk #613
> Remove the NOSPAM before replying to me.
Did you mean to say "Dr. Dryden has been browsing this NG"?
Rodjk #613
Kent Paul Dolan
>>>>> In the below, I have added some white space
>>>>> where long blocks of text had become eye
>>>>> glazing, replaced some non-ASCII characters
>>>>> with my best guess at their intents, and
>>>>> re-flowed the paragraphs to cater to my
>>>>> astygmatism.
>>>>> All that said, it is plenty of time to start
>>>>> the Posting of the Month candiodate list for
>>>>> May 2009.
>>>>> Nominated.
>>>> Seconded.
>>>> And I hope the author will come back toward the
>>>> middle of next month so he can correct (or
>>>> refuse) my edits of his very informative post,
>>>> assuming he wins the vote.
>>> Is there any possibility that he won't?
Sure. There are some really good postings written
here some months, usually from members of a small
group of calm, well educated, well spoken authors.
So far, we just have one excellent posting.
That shouldn't discourage other author from a
reach for excellence.
See also my comments below, re: Ray Ray.
>> I think there would have to be something really
>> fantastic to beat it.
> Sean could write a devastating response that
> shatters the entire modern scientific paradigm,
> destroys atheistic darwinistic materialism
> forever, and ruins all our lives.
Surely that should have been aimed at Ray Martinez?
Sean Pitman is never, ever, going to do anything
memorable, but will just continue to wave his hands
frantically in the air and mouth arrant nonsense, a
puppet dangling on the strings pulled by his cult
religion church. He doesn't have the makings of
greatness, or even of mediocrity. He has the mindset
of someone whose lifework is instantly forgettable.
Ray Martinez, mad as a hatter, on the other hand,
surely could prance off with the posting of the
month votes simply by publishing his long delayed
paper this month and having it meet every single one
of his over the top claims for its upcoming
contents -- using an argument of pure science based
on reliable and repeatable factual observations, all
while never counter-productively arguing based upon
the unsubstantiated claims of Holy Scripture --
thereby crushing atheism, demolishing Darwinism,
falsifying the Theory of Evolution, and establishing
the One True Church of (only) Ray.
It could happen.
Right about the same time, flying pigs will achieve
Mach 2.5 on sheer evolved supersonic wing-power.
xanthian.
R. Baldwin
@s16g2000vbp.googlegroups.com:
[snip]
Thank you for the very thoughtful and informative post.
Seanpit
> Hello, I’m David Dryden, the main author of the paper which has
> generated all of this discussion. Steven Litvintchouk has asked me to
> comment on the analysis of my paper performed by Sean Pitman and this
> is appended at the end of this text. I must say that I am a bit
> surprised at the amount of interest and discussion that has arisen
> from the little paper by myself and two colleagues. However, I am
> pleased that it has done so and that my decision to pay for it to be
> an “open access” paper has been justified. It is my hope that within
> 10 years all professional peer-reviewed science will be freely
> available.
That would be a huge step forward indeed!
> I have skimmed through many of the other comments and noted one
> disparaging comment concerning our acknowledgement of discussion with
> Simon Conway Morris. I would like to briefly explain why we did this.
> I attended a lecture by him in which he discussed convergence at
> length and briefly mentioned the big numbers problem. I started
> corresponding with him and have met him on numerous occasions now for
> further discussions on these two topics. (Inevitably we have also
> talked about his religious views plus his view of creationism/ID. His
> negative views on creationism and ID fully concur with my own.) He is
> a highly respected biologist and palaeontologist and his ideas on
> convergence in organisms would appear to tally with many ideas on
> convergence at the molecular level, my area of interest. He was
> essentially a catalyst in getting me to seriously research the big
> numbers issue so it is perfectly normal practice in science for him to
> be acknowledged. The comment also assumed we were chemists but in
> addition to having worked in chemistry and physics, we have many years
> of practical experience in genetics, molecular biology and
> biochemistry. Not obvious from our address of course.
>
> I am probably going to write far too much but if you want the
> conclusion, it is that Sean Pitman is completely and utterly wrong in
> everything he says in his comments and displays a great ignorance of
> proteins and their structure and function. However, I do hope he will
> read on.
I think you simply don't understand my argument, or the nature of the
concept of increasing levels of functional complexity. It seems like
your understanding of functional complexity is based on how
interesting you think the function in question is. My definition of
functional complexity, in comparison, is not based on how interesting
various systems may or may not be, but in the minimum structural
threshold requirements needed to build a system so that it will work
to at a selectable level of usefulness.
> He has failed to recognise that we wished to establish limits on the
> amount of sequence space explored.
But I do recognize and even agree with your estimates on the limits of
the amount of sequence space that can be explored over a given time
limit. But that isn't the main problem here. The main problem is how
much time it takes to actually find novel beneficial sequences that go
beyond the very very low levels of minimum structural threshold
requirements noted in your paper. You only deal with systems that
have, at minimum, very very low level structural thershold
requirements - less than 100aa or "characters" at minimum.
> Defining limits is a standard
> scientific procedure, though often forgotten, and prevents a lot of
> time wasting as long as one does not initially restrict the
> calculation unnecessarily. Hence, these upper and lower limits are as
> generous as possible based upon current knowledge. They may be out by
> a few powers of ten but this is negligible and as research proceeds
> the limits are likely to come closer together narrowing the range of
> possibilities.
I agree . . .
> In our graph, we overlaid the limits on top of the
> number of different sequences possible for a given pool of letters.
> The letters may total up to 20 in number but it’s just a number. If
> these letters are considered to be amino acids, then we can group the
> 20 amino acids into a smaller number of categories related to their
> physical chemical properties. As soon as you state that the symbols
> you use in the calculation of these big numbers represent physical
> entities then you cannot ignore their physical properties. Such
> groupings are well known to be valid in experiment and are the basis
> for computer-driven sequence analysis. It is unfortunate that such
> computer analysis has been carried too far by some people especially
> those who wish to push the ID complexity agenda and that sight has
> been lost of the fact that proteins do not exist in silico.
I'm not sure I know anyone who is prominent within the ID camp who
would argue otherwise. Of course protein-based systems "do not exist
in silico".
> What follows below is a “lecture” on protein structure for Sean
> Pitman’s benefit. He could of course read a book such as the excellent
> “Introduction to protein structure” by Branden and Tooze and
> accessible to all audiences. I apologise to the rest of you if it gets
> boring but it will eventually lead back to discussing Pitman’s
> comments. Also please do not feel that I am talking “down” to you
> expecting you to believe the expert, I just wish to bring some of the
> latest research and some well established data to you. Also, the
> formality in the writing is just to keep it precise and to exclude, if
> possible, more than one interpretation though given the haste in which
> I have had to write this, it is not perfect.
>
> In the real world of protein structure and function, it is well
> established that many amino acids can be changed with little or no
> effect on function
This is only true if you are talking about changing amino acids one at
a time. It becomes exponentially less and less true when you start
talking about changing more and more amino acids at the same time.
Consider the following quotes from Bloom et al:
"Our theory predicts that for large numbers of substitutions the
probability that a protein retains its structure will decline
exponentially with the number of substitutions, with the severity of
this decline determined by properties of the structure. . . Our work
unifies observations about the clustering of functional proteins in
sequence space. . . " 1
Bloom goes on to point out:
"Experiments have demonstrated that proteins can be extremely
tolerant to single substitutions; for example, 84% of single-residue
mutants of T4 lysozyme and 65% of single-residue mutants of lac
repressor were scored as functional. For multiple substitutions, the
fraction of functional proteins decreases roughly exponentially with
the number of substitutions, although the severity of this decline
varies among proteins." 2
1. Jesse D. Bloom, Alpan Raval, and Claus O. Wilke, Thermodynamics of
Neutral Protein Evolution, Genetics. 2007 January; 175(1): ( Link -
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1775007)
2. Jesse D. Bloom, Jonathan J. Silberg, Claus O. Wilke, D. Allan
Drummond, Christoph Adami, and Frances H. Arnold, Thermodynamic
prediction of protein neutrality, Proc Natl Acad Sci U S A. 2005
January 18; 102(3): 606-611. ( Link -
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15644440)
> (there are only two “functions” for a protein: to
> bind and control another object or to bind another object and catalyse
> a reaction on that object-and this latter includes proton pumping to
> rotate a flagellum). The catalytic chemical mechanisms performed by
> enzymes and ribozymes fall into only 6 categories of well understood
> chemical reactions (a rather small reaction space). All of
> biochemistry is built upon them. Those mutations that do change
> function usually define an active site (for function) or a crucial
> folding region. It is known that proteins are built up from the
> repetitive use of smaller peptide sequences being joined together by
> gene duplication and recombination in the DNA coding. A general
> consensus seems to be that amino acid sequences of length about 20 or
> 30 really start to get interesting in terms of function but even
> smaller folding units are being proposed as progenitors (see work if
> possible by Edward N Trifonov and also note that even single amino
> acids are capable of catalysing reactions). The joining of these
> 20-30mers (via the gene), which fold into “super-secondary” structure
> units, rapidly leads to a folded “domain” of 50-150 amino acids. These
> domains are small folded units. This domain size is essentially
> universal. You do not find examples of a 1000 amino acid domain but it
> will instead comprise around 10 smaller domains.
Correct.
> It is very important
> to note that in many cases such folding does not require complete
> specification of the sequence but only maintenance of the pattern of
> amino acid categories (polar, non-polar etc). Many domains do
> interesting things but a recurring theme is to then bring collections
> of the domains together either as separate subunits to form quaternary
> structure or to string them together into one single chain by making
> them via a single gene. This latter process is how one makes a 1000
> amino acid protein. Nature takes the domain modules and puts them
> together to make novel structures and functions. (Note that very few
> long protein chains are found as their synthesis is tricky due to
> increasing chances of errors in gene replication, transcription or
> translation. These problems were recognised by Francis Crick if I
> recall correctly in the 1960’s. The average protein size is around 500
> amino acids.) The number of domains with unique folds appears to be
> limited to around 1000 to 10,000 (certainly less than a million) and
> it is becoming rare for science to find new ones. This means that
> whatever sequence you have, you get one of these folds
Good so far.
> (but note that
> there is a relatively new discovery of “natively-unfolded” proteins
> which are unfolded until they bind to their target molecule at which
> point they fold up. How much of sequence space is occupied by these
> fully functional proteins is unknown).
While it is true that the exact ratio of functional vs. non-functional
proteins is not known, an upper limit on the ratio can be determined
to a useful degree of certainty based on the idea that the vast
majority of potential protein folds are not stable and therefore would
not make viable proteins. This ratio of potentially viable vs. non-
viable folds decreases exponentially with each increase in the size of
the protein sequence under consideration.
> The number of protein types in
> any organism also appears to be very limited from several hundred in
> the bacteria with very small genomes to perhaps of the order of 10,000
> in multicellular organisms. These proteins still contain the same
> domains. These limited numbers of proteins perform a limited number of
> reactions (again totalling hundreds to thousands of such reactions as
> detailed in standard biochemistry textbooks). The important thing to
> produce different species is how all these reactions are controlled
> (mostly) by proteins each built using the same structural principles
> as already detailed. This area of control is often referred to as part
> of EvoDevo or evolutionary development and it is where the real
> discussions of complexity are going on. That’s not my speciality so I
> will return now to proteins.
So far so good . . .
> Hopefully it is clear that we have considerable understanding of
> protein structure and how they function and that they are not so
> complex that we cannot possibly explain them (and even design them
> ourselves. David S Goodsell has published an excellent book on
> “Bionanotechnology” showing what Nature has achieved and how our
> understanding of it lets us design new experiments). We could if we
> wished define a structural space and a functional space in the same
> way as a sequence space. From the foregoing, it should be clear that
> neither of these spaces is particularly large when compared to the
> possible size of sequence space.
This is because you are only dealing with sequence spaces for protein-
based systems that are made up of single proteins - and small ones at
that. The real problems come when you start considering multi-protein
systems where all the protein parts, and therefore all of their
individual residues, are required to be in a fairly specific
arrangement relative to each other at the same time for the function
in question to be realized.
It is very clear that protein-based systems do indeed contain a degree
of flexibility where many mutations can be tolerated without a
significant loss of the function in question. It is also agreed that
a smaller alphabet of amino acids would be able to do the job.
However, there are several problems with the assumptions behind this
argument. One problem is the assumption that the minimum size
requirement for a system would not increase given a smaller alphabet.
One might be able to build a flagellar motility system with an
alphabet of only two characters, but most likely the system would
require far more characters, at minimum, than if a 20-character
alphabet were used.
It is like the difference between the English language system of 28-
characters (letters, spaces and periods) and a computer language that
is based on just two characters. Given these two systems, consider a
problem of transmitting the information on a blueprint to build a
particular kind of house. Do you really think it would take the same
number of characters in both language systems to code for the same
particular structure? I don't think so. A few more characters would
be needed, at minimum, for the two-character system vs. the 28-
character system.
> Sequence space when proposed was quickly recognised as a silly
> “paradox” by protein scientists (though not unfortunately by some
> other scientists) rather like the silly Levinthal “paradox” of protein
> folding. Sequence space may be large but that does not mean it is
> complex. I hope the above short essay on protein structure and
> function is useful even to Sean Pitman who needs to stop being
> obsessed with computer-based numerology and do some reading and talk
> to some practical protein scientists. I also hope that he will realise
> that proteins are not relevant to religion and that they as well as
> other macromolecules provide absolutely no foundation for ID.
This has nothing to do with any particular "religion" - unless you
want to call science a form of religion.
> Some short specific replies to the critique by Sean Pitman
>
> "The authors argue that because some types of functional proteins are
> smaller than 100aa [amino acids], and because some types of proteins
> have very low sequence specificity requirements, that pretty much all
> of sequence space could have been searched in just a few billion
> years.
>
> "What these authors fail to realize is that not all protein-based
> systems are created equal. Some systems do indeed require very few
> amino acid building blocks and little sequence specificity. These, of
> course, are on very low levels of functional complexity. Other
> systems, however, require far more than the 100aa systems discussed by
> the authors - at minimum. And, many of these systems require a
> significant degree of specificity. These systems are on a much higher
> level of functional complexity and therefore occupy much much larger
> sequence spaces and also have exponentially lower ratios of
> potentially beneficial vs. non-beneficial at these higher levels.”
>
> Reply: With nearly 50 years of biological and chemical research shared
> between the authors, we really do understand that not all molecules
> are the same.
Great! ; )
> We are not saying only a few specified amino acids are
> available but a few types of amino acids- polar, non-polar, negative,
> positive and so on. For example, any one of the polar ones might do at
> a particular site. All you need to specify is polarity.
That's correct. That's what makes protein-based systems fairly
flexible with regard to tolerance of mutations - especially those that
occur one at a time.
It is much like the English language system where pretty much any
letter in this paragraph could be mutated, one at a time, without a
significant loss of meaning of the paragraph as a whole. The very
same thing is true of protein-based systems. There is a degree of
mutational tolerance. However, reducing the number of characters
doesn't help solve the problem of searching sequence space for higher
and higher level systems. This is because a reduction in the number
of characters would only increase the overall specificity requirements
of the system in question in line the the reduction of the number of
character options in the alphabet. In short, the larger sequence
space only means that the functional islands within that space are
larger. Reducing the overall size of sequence space doesn't change
the ratio of potentially beneficial vs. non-beneficial since the size
of the beneficial islands is also reduced to the same degree as the
reduction of sequence space.
> Since this is
> the entire basis of using sequence comparisons to group proteins into
> functional families and these computer methods are used by supporters
> of ID, they should know this. Small proteins are not necessarily
> functionally simple nor are big proteins necessarily complex in
> function (in fact some a remarkably boring).
This is also correct. I think you are not understanding my argument
here. I'm not talking about just any large protein-based system. Not
all large proteins are created equal either. Some require more
specificity than do other proteins. My argument is that given a
specific degree of required sequence specificity, increasing the
minimum size requirement ends up producing a exponential decrease in
the ratio of sequences in sequence space able to produce a beneficial
function at that level of minimum structural threshold requirements.
So, you see, I'm not just talking about any large protein here. Many
large proteins have very little specificity requirements and therefore
their attached functionality can be achieved by a great many more
proteins in sequence space. In other words, the ratio of these types
of functions is relatively high in sequence space.
> "The authors of this paper do not even address the concept of
> different levels of functional complexity. They only point out the
> obvious that some types of functional systems are very very low level
> systems. Well duh! What about those systems that are on much much
> higher levels of minimum size and/or specificity requirements?...”
>
> Reply:These increasing degrees of functional complexity are a mirage.
> Just because a flagellum spins and looks fancy does not mean it is
> more complex than something smaller. The much smaller wonderful
> machines involved in manipulating DNA, making cell walls or
> cytoskeletons during the cell’s lifecycle do far more complex and
> varied things including switching between functions. Even a small
> serine protease has a much harder job than the flagellum. The
> flagellum just spins and spins and yawn…
You're mistaken here. You have to consider the minimum structural
threshold requirement needed to produce a particular type of
functionality. A serine protease is a single protein enzyme that
requires no more than a few hundred fairly specified amino acid
residues, at minimum, to work to a useful level of activity. This is
simply not true of a multiprotein system like a rotary flagellar
motility system. There is no way that you could produce such a system
with only a few hundred coded residue positions regardless of their
arrangement in sequence space. At minimum such a system requires
several thousand amino acid residues working together at the same time
in a fairly specified arrangement.
I'm sorry, but your attempt to argue that a single-protein enzyme is
just as functionally complex as a flagellar motility system is simply
ludicrous. The fact that you are bored with the functionality of the
flagellar system, arguing that it does nothing more than go round and
round, "yawn", has nothing to do with what it takes to make this
"boring" function actually work - at minimum.
> "The evidence shows that the distances [in sequence space] between
> higher and higher level beneficial sequences with novel functions
> increases in a linear manner."
>
> Reply: What evidence? And if importance of function scales with
> sequence length and the scaling is linear then I am afraid that 20^100
> is essentially identical to 2 x 20^100. Also a novel function is not a
> new function but just one we stumble upon in doing the hard work in
> the lab. It’s been there a long time…
The functional island has been there all along in sequence space. It
is just as matter of discovering it - as you note. The very same
thing is true of the evolutionary mechanism of RM/NS for a living
organism or population of organisms. The average time needed for the
mechanism of evolution to find a novel functional system in sequence
space depends on the average distance between potentially beneficial
islands of sequences in overall sequence space. It is this ratio that
determines the likely minimum distance between anything in the
existing gene pool of options and the closet potential target (i.e.,
beneficial sequence with a novel beneficial function) in sequence
space.
As it turns out, as the minimum size and/or specificity requirements
of systems under consideration increase in a linear manner, the ratio
of potentially beneficial vs. non-beneficial systems decrease in an
exponential manner. This is true regardless of the size of your
alphabet. As the ratio decreases exponentially, the average distance
between potentially beneficial islands in sequence space increases in
a linear manner. And, with each linear increase in the distance to
the closest potentially beneficial island the average number of
mutations needed to reach that island (or any other beneficial island)
increases exponentially as well.
That is the problem for the mechanism of RM/NS in a nutshell. And, it
is this very problem that your paper does not address - and neither
does any other paper in mainstream literature.
For a more detailed review of this problem see:
http://www.detectingdesign.com/flagellum.html#Calculation
In any case, I do thank you for the time you took to present your
thoughts. I don't think you actually understand my position, however,
or the problem of exponentially decreasing ratios of beneficial vs.
non-beneficial with increasing levels of functional complexity. Your
paper basically treats all protein-based systems as if they were on
the same level - a very very low level of functional complexity that,
by definition, has a relatively high ratio of potentially beneficial
vs. non-beneficial systems. Certainly searching out practically all
of such low levels of functional complexity is no problem for the
mechanism of RM/NS within a few billion years. That's a no brainer.
The problems come when you move up the ladder a few steps to consider
systems that require at least 1000 fairly specified amino acid
residues (or characters in whatever alphabet you want to consider)
working together at the same time (as in systems that require multiple
specified proteins to work - not just single-protein systems).
Sean Pitman
www.DetectingDesign.com
Seanpit
> In the below, I have added some white space where
> long blocks of text had become eye glazing, replaced
> some non-ASCII characters with my best guess at
> their intents, and re-flowed the paragraphs to cater
> to my astygmatism.
>
> All that said, it is plenty of time to start the
> Posting of the Month candiodate list for May 2009.
>
> Nominated.
I agree. I second or third the nomination - with a link to my reply:
http://groups.google.com/group/talk.origins/msg/5506c671e7437e38?hl=en
> xanthian.
Sean Pitman
www.DetectingDesign.com
wf3h
> On May 2, 7:54 am, david.dry...@ed.ac.uk wrote:
>
> > Hello, I’m David Dryden, the main author of the paper which has
> > generated all of this discussion.
>
>
> > I am probably going to write far too much but if you want the
> > conclusion, it is that Sean Pitman is completely and utterly wrong in
> > everything he says in his comments and displays a great ignorance of
> > proteins and their structure and function. However, I do hope he will
> > read on.
>
> I think you simply don't understand my argument, or the nature of the
> concept of increasing levels of functional complexity
jesus. is there ANYONE sean DOESN"T say this to? it's a cliche.
sean's argument is wrong. the people sean HIMSELF relies to to make
HIS arguments say he's wrong. yet he says THEY don't understand their
own work...
>
> > In the real world of protein structure and function, it is well
> > established that many amino acids can be changed with little or no
> > effect on function
>
> This is only true if you are talking about changing amino acids one at
> a time. It becomes exponentially less and less true when you start
> talking about changing more and more amino acids at the same time.
> Consider the following quotes from Bloom et al:
looks to me like sean doesn't understand bloom. sean is very selective
in who he says does/doesn't understand their own work!
sean's argument has failed one test: the ability to explain a feature
of nature. creationism never has.
but it's amazing how EVERYONE misunderstands their own work...and how
well sean corrects them. it's a wonder anyone did anything before sean
showed up
Kent Paul Dolan
> looks to me like sean doesn't understand bloom.
You are correct. The parts of Bloom which Sean
quotes are about changes _within_ an existing,
unchanging length sequence, but Sean is attempting
to use them as commentaries on the difficulty of
_extending_ a genome sequence, codon by codon, or
perhaps gene by gene, not at all the same problem.
Moreover, so far as I can see, Bloom is also in
error, demonstrating the "multiply AND" error
recently cited here, ignoring that evolution works
by discarding lots of unviable sequences and fixing
viable ones, applying natural selection change by
change. not by making all the changes first, and
then only at the end applying fitness selection, as
their math would imply.
xanthian.