Protein Structure Distribution in Sequence Space

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Seanpit

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Feb 4, 2007, 1:22:04 PM2/4/07
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> On Jan 29, 5:08 pm, "hersheyhv" <hersh...@indiana.edu> wrote:
> > On Jan 27, 12:38 pm, "Seanpit" <seanpitnos...@naturalselection.

> > Once the edge of this "magnetic field" is
> > reached, the minimum threshold is reached and further refinement
> > toward the maximum potential is no problem. It is the reaching of
> > this minimum threshold that is the problem. The island cluster of
> > potentially beneficial sequences represents the entire reach of the
> > potentially attractive "magnetic field". This entire reach is
> > completely isolated from all other island clusters and magnetic fields
> > at higher levels of functional complexity. The biosystem families you
> > speak of just are remotely clustered in one corner of sequence space
> > like you imagine. This notion of yours is way way off base.
>
> Evidence? I keep having to point out the obvious to you. The
> EVIDENCE (see the PNAS article and others that I have presented you)
> actually shows that the biologically useful proteins that *are*
> present in living organisms (and it doesn't matter whether they
> evolved or were created by the creation fairy) are NOT scattered
> throughout total structure space.

Even with regard to single protein systems, they are NOT clustered in
one tiny corner of sequence space. Look up even single protein maps
and you will see that they cover a wide range of sequence space. They
are not all clustered together like you imagine.

"Roughly speaking, however, distances are randomly distributed. This
means that, although only a small fraction of sequence space yields
uniquely folding sequences, sequence space is occupied nearly
uniformly. No "higher order" clustering (i.e., except the trivial case
of the homologous sequences) is visible.

Erich Bornberg-Bauer, "How Are Model Protein Structures Distributed in
Sequence Space?" Biophysical Journal, Volume 73, November 1997,
2393-2403

http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1181141&blobtype=pdf

So, you see, even at very low structural threshold levels, the
distribution of potentially beneficial structures is widespread and
fairly uniform. The clustering effects that are present at lower
levels rapidly decline at higher and higher threshold levels until the
high-level islands are very remotely separated in sequence space.

Sean Pitman
www.DetectingDesign.com

Perplexed in Peoria

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Feb 4, 2007, 2:06:53 PM2/4/07
to

"Seanpit" <seanpi...@naturalselection.0catch.com> wrote in message news:1170613322.7...@v45g2000cwv.googlegroups.com...

Thanks for the link, Sean. I haven't studied it carefully yet, but my
first impression is that they are not looking at (a sample of) real
biological proteins. Instead, they are looking at computer-generated
sets of hypothetical proteins which (based on their structural model)
ought to fold stably and reliably. But I need to read more carefully.

However, I was interested in your parenthetical comment in this:


No "higher order" clustering (i.e., except the trivial case
of the homologous sequences) is visible.

I have mostly responded to your postings as if they were merely a
critique of the evolutionary model rather than positive arguments for
some other model. But I am led to wonder how your favorite model
accounts for all that 'trivial' homology. Take, for example, the
20 or so aminoacyl-tRNA-synthases. Each shows considerable homology
across the entire tree of life (with the trees constructed from any
one of them being consistent with the others, except near the roots).
Furthermore, it seems that they are all homologous with each other -
suggesting that they arose from a common protein ancestor before the
organism-level LUCA. Why would that pattern arise in some other
model besides the evolutionary one?

Furthermore, there are partial homologies between these proteins and
many, many others - especially in the 'nucleotide fold' domain. That
certainly strikes me as a kind of 'clustering'. Do you hypothesize
that this 'nucleotide fold' motif is the only good way to solve the
problem of binding ATP? Isn't it more likely that it is the first
way of binding ATP to be discovered and that it was then copied into
other proteins that needed this fragment of function?

Ron O

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Feb 4, 2007, 2:28:03 PM2/4/07
to
On Feb 4, 12:22 pm, "Seanpit" <seanpitnos...@naturalselection.
> http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1181141&blobtyp...

>
> So, you see, even at very low structural threshold levels, the
> distribution of potentially beneficial structures is widespread and
> fairly uniform. The clustering effects that are present at lower
> levels rapidly decline at higher and higher threshold levels until the
> high-level islands are very remotely separated in sequence space.
>
> Sean Pitmanwww.DetectingDesign.com- Hide quoted text -
>
> - Show quoted text -

My first reading of this paper doesn't seem to indicate any support
for your neutral gaps model being a problem. They are talking about
small peptides that can retain a basic structure with a large number
of "neutral substitutions, but they make no conclusions about the
activity of such structures. It is known from gene families that
basic structure can be retained while function is modified.

So how would studies like this do anything to change the fact that you
don't have a model that you can support in any fashion worth talking
about. What is your alternative explanation for the evolution of
proteins and what is your evidence for it. Recent genome studies
indicate that gene duplication is a lot more frequent than we had been
able to detect before. Gene duplication seems to be a mechanism that
would explain many protein families. Do you have a better
explanation? What is your evidence for your alternative? Claiming
that there is a problem when you don't even have a clue about a
possible viable alternative is pretty bogus don't you think?

Are you ever going to get around to presenting your alternative to
common descent and your evidence for your alternative that you claimed
to have that was better than the current scientific model? You
claimed to have such a model and evidence, so why putz around with
bogus neutral gaps if you have some killer evidence for your beliefs?
Let's see it.

Ron Okimoto


_Arthur

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Feb 4, 2007, 3:07:35 PM2/4/07
to
D. Pitman, are you going to comment the new paper in Nature,
"Empirical fitness landscapes reveal accessible evolutionary paths"
by Frank J. Poelwijk, Daniel J. Kiviet, Daniel M. Weinreich and Sander
J. Tans ?

The paper seems to address your existential fears about hypothetical
barriers.

They studied a particular enzyme which is commonplace in bacteria, and
a "mutant" version, which is 100,000 times more efficient against
antibiotics like penicillin.

The new version of the protein/enzyme happens to be 5 mutations
distant from the canonical version.
Furthermore, the searchers have demonstrated that, in that case,
theres is a mutation pathway where ALL the intermediate forms
conferred increased anti-antibiotic functionality.

So, in that case, we have a smooth pathway to a NEW FUNCTIONALITY, a
100,000-fold improvement in antibiotic resistance.

While you're at it, do comment on the paper in the January issue of
Current Biology: "Continuous molecular evolution of protein-domain
structures by single amino acid changes. " Meier S, Jensen PR, David
CN, Chapman J, Holstein TW, Grzesiek S, Ozbek S. (2007)


Bobby Bryant

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Feb 4, 2007, 3:50:14 PM2/4/07
to
In article <1170619654.9...@p10g2000cwp.googlegroups.com>,
"_Arthur" <Art...@sympatico.ca> writes:

> D. Pitman, are you going to comment the new paper in Nature,
> "Empirical fitness landscapes reveal accessible evolutionary paths"
> by Frank J. Poelwijk, Daniel J. Kiviet, Daniel M. Weinreich and Sander
> J. Tans ?
>
> The paper seems to address your existential fears about hypothetical
> barriers.

s/fears/hopes/


--
Bobby Bryant
Reno, Nevada

Remove your hat to reply by e-mail.

Seanpit

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Feb 4, 2007, 4:23:34 PM2/4/07
to
On Feb 4, 12:07 pm, "_Arthur" <Arth...@sympatico.ca> wrote:
> D.Pitman, are you going to comment the new paper in Nature,

> "Empirical fitness landscapes reveal accessible evolutionary paths"
> by Frank J. Poelwijk, Daniel J. Kiviet, Daniel M. Weinreich and Sander
> J. Tans ?
>
> The paper seems to address your existential fears about hypothetical
> barriers.
>
> They studied a particular enzyme which is commonplace in bacteria, and
> a "mutant" version, which is 100,000 times more efficient against
> antibiotics like penicillin.

The barriers I'm talking about are minimum structural threshold
barriers between what exists in a pool of options and the minimum
structural thresholds of novel potentially beneficial functions. Once
you have any type of function to at least some useful level of
functionality, further refinements, even to the point of 100,000 times
the prior efficiency, aren't a problem. The problem is getting the
particular function, like penicillinase, to even a minimum degree of
usefulness.

The penicillinase function, in particular, has never been shown to
evolve de novo - without this function already existing in the gene
pool to at least some degree of useful activity. This is interesting
partly because the penicillinase function does not have a very high
minimum structural threshold requirement (i.e., no more than 350 or so
specified residues at minimum).

> The new version of the protein/enzyme happens to be 5 mutations
> distant from the canonical version.
> Furthermore, the searchers have demonstrated that, in that case,
> theres is a mutation pathway where ALL the intermediate forms
> conferred increased anti-antibiotic functionality.

Yes, there are a large number of these single-step pathways that have
been identified for refinement of the same type of function where the
minimum threshold requirements have already been reached. The immune
system is another fine example of this sort of thing - of improvement
of the antibody binding function over time.

> So, in that case, we have a smooth pathway to a NEW FUNCTIONALITY, a
> 100,000-fold improvement in antibiotic resistance.

That's right - and there are many more examples of this sort of
refinement activity over time. It's a bit more difficult though when
you haven't reached the minimum threshold requirements for the
function in question at all. Gaining this threshold is the issue
here.

> While you're at it, do comment on the paper in the January issue of
> Current Biology: "Continuous molecular evolution of protein-domain
> structures by single amino acid changes. " Meier S, Jensen PR, David
> CN, Chapman J, Holstein TW, Grzesiek S, Ozbek S. (2007)

Tell me, does this paper talk about the observed evolution of even one
novel function that requires a minimum of more than 1000 specifically
arranged amino acid residues? If not, I'm not interested.

Sean Pitman
www.DetectingDesign.com

Seanpit

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Feb 4, 2007, 4:29:48 PM2/4/07
to
On Feb 4, 11:06 am, "Perplexed in Peoria" <jimmene...@sbcglobal.net>
wrote:

> >http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1181141&blobtyp...


>
> > So, you see, even at very low structural threshold levels, the
> > distribution of potentially beneficial structures is widespread and
> > fairly uniform. The clustering effects that are present at lower
> > levels rapidly decline at higher and higher threshold levels until the
> > high-level islands are very remotely separated in sequence space.
>

> Thanks for the link,Sean. I haven't studied it carefully yet, but my


> first impression is that they are not looking at (a sample of) real
> biological proteins. Instead, they are looking at computer-generated
> sets of hypothetical proteins which (based on their structural model)
> ought to fold stably and reliably. But I need to read more carefully.
>
> However, I was interested in your parenthetical comment in this:
> No "higher order" clustering (i.e., except the trivial case
> of the homologous sequences) is visible.
> I have mostly responded to your postings as if they were merely a
> critique of the evolutionary model rather than positive arguments for
> some other model. But I am led to wonder how your favorite model
> accounts for all that 'trivial' homology. Take, for example, the
> 20 or so aminoacyl-tRNA-synthases. Each shows considerable homology
> across the entire tree of life (with the trees constructed from any
> one of them being consistent with the others, except near the roots).
> Furthermore, it seems that they are all homologous with each other -
> suggesting that they arose from a common protein ancestor before the
> organism-level LUCA. Why would that pattern arise in some other
> model besides the evolutionary one?

What about common design? - Why reinvent the wheel every time a wheel
would work just fine?

> Furthermore, there are partial homologies between these proteins and
> many, many others - especially in the 'nucleotide fold' domain. That
> certainly strikes me as a kind of 'clustering'.

I agree, but it isn't the same thing as the clustering of all types of
protein-based systems into one tiny corner of sequence space. This
limited clustering most certainly produces more closely spaced islands
of beneficial sequences. However, these islands do indeed drift
farther and farther apart as one moves up the ladder of minimum
structural threshold requirements.

> Do you hypothesize
> that this 'nucleotide fold' motif is the only good way to solve the
> problem of binding ATP? Isn't it more likely that it is the first
> way of binding ATP to be discovered and that it was then copied into
> other proteins that needed this fragment of function?

It most certainly isn't the only potentially viable way to achieve
this function. All functions have many possible structural solutions.
However, for ever one possibility that would work, there are trillions
upon trillions that won't work - and this ratio decreases,
exponentially, as one moves up the ladder of minimum structural
threshold requirements. This exponentially declining ratio rapidly
gives rise to the insurmountable non-beneficial gap problem and
evolutionary mechanisms simply stall out.

Sean Pitman
www.DetectingDesign.com


Seanpit

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Feb 4, 2007, 4:41:26 PM2/4/07
to
On Feb 4, 11:28 am, "Ron O" <rokim...@cox.net> wrote:

> >http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1181141&blobtyp...
>
> > So, you see, even at very low structural threshold levels, the
> > distribution of potentially beneficial structures is widespread and
> > fairly uniform. The clustering effects that are present at lower
> > levels rapidly decline at higher and higher threshold levels until the
> > high-level islands are very remotely separated in sequence space.
>

> >SeanPitmanwww.DetectingDesign.com-Hide quoted text -


>
> > - Show quoted text -
>
> My first reading of this paper doesn't seem to indicate any support
> for your neutral gaps model being a problem. They are talking about
> small peptides that can retain a basic structure with a large number
> of "neutral substitutions, but they make no conclusions about the
> activity of such structures. It is known from gene families that
> basic structure can be retained while function is modified.

The question here is one of the likely distribution of potentially
beneficial sequences within sequence space. Is this distribution
tightly clustered in one tiny corner of sequence space? Or, are these
potentially beneficial sequences distributed throughout sequence
space? The author's work and evaluation of existing protein-based
systems strongly support the latter view.

Certainly a structure can be modified with a corresponding
modification in the degree of function of a pre-established system.
However, the likelihood that a novel system of function can be found
in this manner is unlikely and becomes exponentially more and more
unlikely as one considers higher and higher minimum structural
threshold requirements.

> So how would studies like this do anything to change the fact that you
> don't have a model that you can support in any fashion worth talking
> about. What is your alternative explanation for the evolution of
> proteins and what is your evidence for it. Recent genome studies
> indicate that gene duplication is a lot more frequent than we had been
> able to detect before. Gene duplication seems to be a mechanism that
> would explain many protein families. Do you have a better
> explanation? What is your evidence for your alternative? Claiming
> that there is a problem when you don't even have a clue about a
> possible viable alternative is pretty bogus don't you think?

Are you actually trying to argue that a theory cannot be questioned
until one has some other way of explaining a particular phenomenon?
Really? That's a good one!

Beyond the fact that one doesn't have to have an answer before one can
raise questions about a proposed hypothesis or theory, there is indeed
a very good alternative to assuming evolutionary mechanisms did the
job in every case. Intelligent design is quite capable and should at
least be considered in such cases - just as would be proposed if
certain radiosignals were discovered by SETI scientists.

> Are you ever going to get around to presenting your alternative to
> common descent and your evidence for your alternative that you claimed
> to have that was better than the current scientific model? You
> claimed to have such a model and evidence, so why putz around with
> bogus neutral gaps if you have some killer evidence for your beliefs?
> Let's see it.

What do you think SETI scientists are looking for? They are in fact
looking for something that has such a large gap between it and what
non-deliberate processes are capable of achieving that some smart
alien intelligence is the most viable option. A clear demonstration
of non-beneficial gaps does the same thing for demonstrating that
evolutionary mechanisms are most unlikely to have crossed the gap
leaving intelligent deliberate processes as the most likely origin.

> Ron Okimoto

Sean Pitman
www.DetectingDesign.com


Perplexed in Peoria

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Feb 4, 2007, 4:41:55 PM2/4/07
to

"Seanpit" <seanpi...@naturalselection.0catch.com> wrote in message news:1170624588.1...@j27g2000cwj.googlegroups.com...

> On Feb 4, 11:06 am, "Perplexed in Peoria" <jimmene...@sbcglobal.net>
> wrote:
> > However, I was interested in your parenthetical comment in this:
> > No "higher order" clustering (i.e., except the trivial case
> > of the homologous sequences) is visible.
> > I have mostly responded to your postings as if they were merely a
> > critique of the evolutionary model rather than positive arguments for
> > some other model. But I am led to wonder how your favorite model
> > accounts for all that 'trivial' homology. Take, for example, the
> > 20 or so aminoacyl-tRNA-synthases. Each shows considerable homology
> > across the entire tree of life (with the trees constructed from any
> > one of them being consistent with the others, except near the roots).
> > Furthermore, it seems that they are all homologous with each other -
> > suggesting that they arose from a common protein ancestor before the
> > organism-level LUCA. Why would that pattern arise in some other
> > model besides the evolutionary one?
>
> What about common design? - Why reinvent the wheel every time a wheel
> would work just fine?

Well, common design explains the existence of homology. It doesn't
explain why when you construct twenty different phylogenetic trees
for the twenty different enzymes, those trees all agree with each other
on the shape of the crown groups.

Seanpit

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Feb 4, 2007, 5:02:37 PM2/4/07
to
On Feb 4, 1:41 pm, "Perplexed in Peoria" <jimmene...@sbcglobal.net>
wrote:
> "Seanpit" <seanpitnos...@naturalselection.0catch.com> wrote in messagenews:1170624588.1...@j27g2000cwj.googlegroups.com...

It does if the different groups have different by slightly different
functional needs for their slightly different systems and
environments. Nested patterns are often present within human-designed
systems.

Sean Pitman
www.DetectingDesign.com

_Arthur

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Feb 4, 2007, 5:06:25 PM2/4/07
to
On Feb 4, 4:23 pm, "Seanpit" <seanpitnos...@naturalselection.

0catch.com> wrote:
> > So, in that case, we have a smooth pathway to a NEW FUNCTIONALITY, a
> > 100,000-fold improvement in antibiotic resistance.
>
> That's right - and there are many more examples of this sort of
> refinement activity over time. It's a bit more difficult though when
> you haven't reached the minimum threshold requirements for the
> function in question at all. Gaining this threshold is the issue
> here.
>

You miss the point. The enzyme had another use, unrelated to
antibiotic resistance, and offered a negigible protection against
antibiotics.
If you are unwilling to call a 100,000-fold increase in activity A NEW
FUNCTIONALITY, then nothing at all will ever qualify as such, under
your unstated criteria.

> > While you're at it, do comment on the paper in the January issue of
> > Current Biology: "Continuous molecular evolution of protein-domain
> > structures by single amino acid changes. " Meier S, Jensen PR, David
> > CN, Chapman J, Holstein TW, Grzesiek S, Ozbek S. (2007)
>
> Tell me, does this paper talk about the observed evolution of even one
> novel function that requires a minimum of more than 1000 specifically
> arranged amino acid residues? If not, I'm not interested.
>

Yes, the paper makes no mention at all of any barrier linked to 1000,
or 666, or any other arbitray number of mutations. So, of course, you
wouldn't be interrested.

After all, there is no use for you to keep abreast of current
research, since the Pitman Law isn't based on biochemical research.

Biochemist Micheal Behe was so confident in his discovery of the
unevolvability of the immune system, that he didn't bother to follow
the research in the field. That level of confidence made a big
impression on the judge.

Seanpit

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Feb 4, 2007, 5:19:44 PM2/4/07
to
On Feb 4, 2:06 pm, "_Arthur" <Arth...@sympatico.ca> wrote:
> On Feb 4, 4:23 pm, "Seanpit" <seanpitnos...@naturalselection.
>
> 0catch.com> wrote:
> > > So, in that case, we have a smooth pathway to a NEW FUNCTIONALITY, a
> > > 100,000-fold improvement in antibiotic resistance.
>
> > That's right - and there are many more examples of this sort of
> > refinement activity over time. It's a bit more difficult though when
> > you haven't reached the minimum threshold requirements for the
> > function in question at all. Gaining this threshold is the issue
> > here.
>
> You miss the point. The enzyme had another use, unrelated to
> antibiotic resistance, and offered a negigible protection against
> antibiotics.
> If you are unwilling to call a 100,000-fold increase in activity A NEW
> FUNCTIONALITY, then nothing at all will ever qualify as such, under
> your unstated criteria.

And you miss the point, if each single mutation is selectably
beneficial, as you claimed, then the antibiotic activity was not
negligible along the pathway but was selectable during each step in a
positive manner until the final 100,000-fold increase was realized.

Beyond this, even if the original starting point had no selectable
activity for the resulting function, the threshold level in this case
is only a few hundred specified residues - not even close to my
challenge of 1000 specified amino acid residues.

> > > While you're at it, do comment on the paper in the January issue of
> > > Current Biology: "Continuous molecular evolution of protein-domain
> > > structures by single amino acid changes. " Meier S, Jensen PR, David
> > > CN, Chapman J, Holstein TW, Grzesiek S, Ozbek S. (2007)
>
> > Tell me, does this paper talk about the observed evolution of even one
> > novel function that requires a minimum of more than 1000 specifically
> > arranged amino acid residues? If not, I'm not interested.
>
> Yes, the paper makes no mention at all of any barrier linked to 1000,
> or 666, or any other arbitray number of mutations. So, of course, you
> wouldn't be interrested.

What is the size of the evolved sequences? Hmmmm?

> After all, there is no use for you to keep abreast of current
> research, since the Pitman Law isn't based on biochemical research.

There are literally thousands of papers like this that all say pretty
much the same thing. As far as I am aware, not one of them actually
presents the observed evolution any system that requires a minimum
structural threshold of more than 1000 specified residues.

> Biochemist Micheal Behe was so confident in his discovery of the
> unevolvability of the immune system, that he didn't bother to follow
> the research in the field. That level of confidence made a big
> impression on the judge.

Please do present any research that shows any novel function evolving
that requires a minimum structural threshold of more than 1000
specified residues. I'd be most interested. I'm very interested in
following *relevant* research. Otherwise, I read plenty of articles
beyond those that are actually relevant to this discussion. I just
don't have time to read everything that everybody thinks I should
read. So, why not present something that's actually relevant for a
change? - along with a relevant quote for once?

Sean Pitman
www.DetectingDesign.com


Seanpit

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Feb 4, 2007, 6:32:14 PM2/4/07
to
An interesting 3D model for the distribution of existing small single-
protein systems within sequence space is presented in the following
link of the work of Jim Proctor and Andrew Torda (Hamburg University,
last update May, 2004):

http://www.zbh.uni-hamburg.de/wurst/protspace/ECCB_opt.huge.pdf
http://www.zbh.uni-hamburg.de/wurst/protspace/

Sean Pitman
www.DetectingDesign.com

Seanpit

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Feb 4, 2007, 6:43:59 PM2/4/07
to

_Arthur

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Feb 4, 2007, 7:45:08 PM2/4/07
to
On Feb 4, 5:19 pm, "Seanpit" <seanpitnos...@naturalselection.
0catch.com> wrote:

> Please do present any research that shows any novel function evolving
> that requires a minimum structural threshold of more than 1000
> specified residues.

You're the one with the bogus theory. Name me 3 known proteins that
you know for a fact that are 1000 amino-acids away than ANY possible
precursor known or unknown, with ANY possible biologically

And, while you were shifting goalposts, you aknowledged than it
doesn't seems to matter that an enzyme gains or lose a chemical
property by a factor of 100,000 in the process, it is still selectable
-- according to you.

For example, suppose a cell makes an enzyme that has an useful -- and
measurable -- capacity at digesting lactase. And that particular
enzyme has neglible efficiency at breaking down, say, crude oil.
Myself, I see no problem of envisionning a scenario where, after a
certain number of mutations (--does the number really matter? Why --
How ?) the mutated enzyme still presents a marginal lactase activity
but also a faint crude oil degrading functionality. And according to
your newly formulated criteria, the degree of functionality is
immateral, once aquired it can be selected for and improved a
thousandfold, nay, make that 100,000-fold.

Of course in their natural environment, most bacteria have no use for
a lactase-digesting enzyme, there are very few natural sources of
lactase. Or crude oil. Or penicilin.

So name me 3 known human or bacteria proteins that are surrounded by
an impassable moat of unfruited variants utterly devoid of ANY useful
chemical property, 1000 amino-acids deep.

Name me 3 first such proteins that come to your mind.

Robin Levett

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Feb 4, 2007, 11:19:19 PM2/4/07
to
Seanpit wrote:

Sean, before you throw out more references to papers that you can distort to
fit your requirements, isn't it about time you addressed the Choi and Kim
paper that Howard referred you to on 16 October last year? The one which
showed that proteins *in the real world* cluster into 4 families?

www.pnas.org/cgi/content/full/103/38/14056

Oh, and even a layman like me can see that you've got your interpretation of
the Bornberg-Bauer paper wrong. He specifically states that the HP protein
sequences he is examining are not uniformly distributed across sequence
space; see the last couple of paragraphs of the paper; and the RNA
sequences, that he says do "percolate through sequence space", do so in
such a way that "Within a number of mutations small compared to the length
of the sequence, the whole shape-space can be covered".

Even in the abstract he makes clear that "In analogy to protein families,
nets are dense and well-separated in sequence space".

--
Robin Levett
rle...@rlevett.ibmuklunix.net (unmunge by removing big blue - don't yahoo)

Ron O

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Feb 5, 2007, 7:52:51 AM2/5/07
to
On Feb 4, 3:41 pm, "Seanpit" <seanpitnos...@naturalselection.

0catch.com> wrote:
> On Feb 4, 11:28 am, "Ron O" <rokim...@cox.net> wrote:
>
>
>
>
>
> > >http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1181141&blobtyp...
>
> > > So, you see, even at very low structural threshold levels, the
> > > distribution of potentially beneficial structures is widespread and
> > > fairly uniform. The clustering effects that are present at lower
> > > levels rapidly decline at higher and higher threshold levels until the
> > > high-level islands are very remotely separated in sequence space.
>
> > >SeanPitmanwww.DetectingDesign.com-Hidequoted text -

>
> > > - Show quoted text -
>
> > My first reading of this paper doesn't seem to indicate any support
> > for your neutral gaps model being a problem. They are talking about
> > small peptides that can retain a basic structure with a large number
> > of "neutral substitutions, but they make no conclusions about the
> > activity of such structures. It is known from gene families that
> > basic structure can be retained while function is modified.
>
> The question here is one of the likely distribution of potentially
> beneficial sequences within sequence space. Is this distribution
> tightly clustered in one tiny corner of sequence space? Or, are these
> potentially beneficial sequences distributed throughout sequence
> space? The author's work and evaluation of existing protein-based
> systems strongly support the latter view.

No the real question is why you fool around with bogus junk like this,
that even you have to admit doesn't amount to squat in the face of all
the other data that we have, and don't bother to put up or shut up.
"Put up or shut up" is just an expression that you are probably well
aware of. It denotes frustration at the fact that you can obfuscate
the issue a dozen different ways, but you never come out and
demonstrate that you really have anything to discuss. If you aren't
willing to put forward the wonderful stuff that you claim to have
supporting your idea of what happened why do you spend so much time
shooting around the edges and never hitting the target? You make a
lot of noise, but that is all it is. What is your alternative, what
is the evidence for your alternative, and do a real critical analysis
of how it stacks up to the notion that you don't like. That is how an
honest person would approach the issue. They wouldn't keep lying
about what they have and pretending it is just too good to put
forward.

Getting back to this study, why would they have found anything any
different? The distributions donot tell you anything about how much
sequence space has to be searched to do a certain function. Sequence
space is so huge that even if you ran the simulation to check 10E12
sequences where would they all fall? There is also the fact that
their simulation also supports what we see in the molecular record.
Yockey came up with a shaky estimate that based on just what was known
about the various sequences when he made the estimate in the late
1970's that there were over 10E40 different cytochrome c sequences
that would function as cyt c just limiting the sequence to 104 amino
acid residues. These guys demonstrate that in their simulations over
half the amino acids residues can be replaced by mutation and the
internal structure isn't altered that much. They also admit that they
are only using hydrophobicity and we know that disulfide bonds are
very important, and that salt bridges (attraction between acidic and
basic amino acid R groups) are important. We can see that such sites
have changed in concert.

So where does this study leave you in terms of what you think is going
on? How could it possibly help the fact that your model is hopelessly
inadequate to explain the existing data. If you don't think that it
is, put it forward for evaluation. You can't deny that you were the
one that claimed that you had such a model and evidence, so why not
put it forward? Why jerk around with junk like this?

>
> Certainly a structure can be modified with a corresponding
> modification in the degree of function of a pre-established system.
> However, the likelihood that a novel system of function can be found
> in this manner is unlikely and becomes exponentially more and more
> unlikely as one considers higher and higher minimum structural
> threshold requirements.

Where do you get that from this paper? Any limited number of
sequences is going to have large gaps between them in sequence space.
What you need to know is how many of those sequences can provide the
functions that life needs. They do not appear to provide this answer
in the paper. Where is it?

>
> > So how would studies like this do anything to change the fact that you
> > don't have a model that you can support in any fashion worth talking
> > about. What is your alternative explanation for the evolution of
> > proteins and what is your evidence for it. Recent genome studies
> > indicate that gene duplication is a lot more frequent than we had been
> > able to detect before. Gene duplication seems to be a mechanism that
> > would explain many protein families. Do you have a better
> > explanation? What is your evidence for your alternative? Claiming
> > that there is a problem when you don't even have a clue about a
> > possible viable alternative is pretty bogus don't you think?
>
> Are you actually trying to argue that a theory cannot be questioned
> until one has some other way of explaining a particular phenomenon?
> Really? That's a good one!

No, we question our theories all the time, but nothing much changes
until a better explanation comes along that is more useful and
hopefully accurate than the one before. You can't just nit pick in
science. To actually do something you have to actually accomplish
something. No scientific theory is perfect, that is a fact and isn't
any news to anyone involved in science. Obfuscating the issue so that
you can continue to lie to yourself is not only counter productive,
but isn't worth jack in science or the real world except make your
self feel better somehow or to suck money out ot the rubes or make
them bend to your political whims because they really think that you
might have something. Do you still believe that you could do better
than the Ohio rubes and teach the real science of ID? It turned out
that you had been taken in by the IDiot lies and either were clueless
about how bogus ID science was or you were lying about how clueless
you were. Face the facts, you were either scammed by ID or you were
one of the scammers. Pick one and defend it.

>
> Beyond the fact that one doesn't have to have an answer before one can
> raise questions about a proposed hypothesis or theory, there is indeed
> a very good alternative to assuming evolutionary mechanisms did the
> job in every case. Intelligent design is quite capable and should at
> least be considered in such cases - just as would be proposed if
> certain radiosignals were discovered by SETI scientists.

Raise questions and then figure out how to do the research to solve
the problem. That is how science works. If we knew everything there
would be no science just technicians and librarians. You can't just
nay say because we all know (even you in your more lucid moments) that
your alternative is so much worse than the one that you don't like
that you don't even try to put it forward. Why not put it forward and
nit pick it? It would be much more fruitful and you can get definite
answers about what is wrong with it. That is the difference between
your nit picking and what happened to your notion. This sequence
space junk is at the limits of our understanding and we are far from
understanding it. Your model failed long ago based on well known and
accepted principles. A better alternative came along and it was
demonstrated to be better in so many ways that you don't stand a
chance. All you can do is obfuscate the issue and pretend that your
nit picking really matters, when if you did the same thing to your
alternative it would be no contest on which idea came up short.

>
> > Are you ever going to get around to presenting your alternative to
> > common descent and your evidence for your alternative that you claimed
> > to have that was better than the current scientific model? You
> > claimed to have such a model and evidence, so why putz around with
> > bogus neutral gaps if you have some killer evidence for your beliefs?
> > Let's see it.
>
> What do you think SETI scientists are looking for? They are in fact
> looking for something that has such a large gap between it and what
> non-deliberate processes are capable of achieving that some smart
> alien intelligence is the most viable option. A clear demonstration
> of non-beneficial gaps does the same thing for demonstrating that
> evolutionary mechanisms are most unlikely to have crossed the gap
> leaving intelligent deliberate processes as the most likely origin.

This is a stupid analogy because SETI is looking for a signal that
they can differentiate from a natural occurring signal. If all they
were looking for is something far away from what is known, three
pulsars in close proximity would be considered a SETI signal because
if it did occur only once in the Universe that would be as far away as
they could get. Get a clue. There are certain criteria that they
have to look for, and if and when they ever detect something the
debate will be one as to what that something is. If all they had was
looking at the different proteins and claiming that there was
intelligent signal there they would be doomed because we see those
protein sequences evolving even today.

Just demonstrate that your gaps exist, and then look at your
demonstration and compare it to what is wrong with your model and tell
us which one comes up short. Why keep obfuscating when you could nail
everyone with your model and evidence? Why can you see all that is
wrong with what you don't like, but you aren't willing to do the same
thing to your own model? Your methodology not only sounds bogus it is
bogus and you know it at some level, but insanity could be a defense.
You weren't too coherant when you were blathering about how you could
do better about teaching ID than the Ohio rubes, and I've pretty much
left your alone because of that mental break, but before you put up
your wonderful science of ID I'd like to see your alternative and the
evidence to back it up. Why claim that you have it if you aren't
willing to put it forward?

Your obfuscation tactics aren't just a little problem are they?
Obfuscation is all you have for the simple reason that you have
nothing else worth putting into the argument. If this isn't true, put
your junk forward and evaluate it for everyone. Someone that can talk
about problems in sequence space should be able to tell us why your
alternative comes up short compared to common descent, right?

Ron Okimoto

>
> > Ron Okimoto
>
> Sean Pitmanwww.DetectingDesign.com- Hide quoted text -

Seanpit

unread,
Feb 5, 2007, 1:39:07 PM2/5/07
to
On Feb 4, 4:45 pm, "_Arthur" <Arth...@sympatico.ca> wrote:
> On Feb 4, 5:19 pm, "Seanpit" <seanpitnos...@naturalselection.
>
> 0catch.com> wrote:
> > Please do present any research that shows any novel function evolving
> > that requires a minimum structural threshold of more than 1000
> > specified residues.
>
> You're the one with the bogus theory. Name me 3 known proteins that
> you know for a fact that are 1000 amino-acids away than ANY possible
> precursor known or unknown, with ANY possible biologically.

You don't seem to understand the challenge. I'm not asking you to
present a case of a function evolving that was 1000aa away from any
possible precursor. I'm asking you to present a case of a function
evolve that requires of minimum of 1000 specifically arranged amino
acid residues to work - regardless of how far or close it may or may
not be from what came before.

Again, the gap distance is not the same thing as the minimum
structural threshold requirement. They are related, but they are not
the same. The likely gap distance is always much smaller than the
minimum threshold size.

> And, while you were shifting goalposts, you aknowledged than it
> doesn't seems to matter that an enzyme gains or lose a chemical
> property by a factor of 100,000 in the process, it is still selectable
> -- according to you.

That's what you claimed the author's of the paper your referenced said
- that each step along the pathway was functionally selectable. If
that is true, there is really no problem at all since there is no
functionally neutral gap. You started with an intact functional
system that already had, to a selectable degree, the function in
question - or isn't that really what the author's claimed?

> For example, suppose a cell makes an enzyme that has an useful -- and
> measurable -- capacity at digesting lactase. And that particular
> enzyme has neglible efficiency at breaking down, say, crude oil.
> Myself, I see no problem of envisionning a scenario where, after a
> certain number of mutations (--does the number really matter? Why --
> How ?) the mutated enzyme still presents a marginal lactase activity
> but also a faint crude oil degrading functionality. And according to
> your newly formulated criteria, the degree of functionality is
> immateral, once aquired it can be selected for and improved a
> thousandfold, nay, make that 100,000-fold.

That's right. Once the threshold requirements of the new function are
acquired to a selectable degree, further refinements aren't a problem.

> Of course in their natural environment, most bacteria have no use for
> a lactase-digesting enzyme, there are very few natural sources of
> lactase. Or crude oil. Or penicilin.

Right - -

> So name me 3 known human or bacteria proteins that are surrounded by
> an impassable moat of unfruited variants utterly devoid of ANY useful
> chemical property, 1000 amino-acids deep.
> Name me 3 first such proteins that come to your mind.

Again, that's not my claim for my 1000aa threshold (see above
explanation). There are many types of functions that require far more
than 1000 specifically arranged residues to work at all - even a
little bit. The flagellar motility system is a classic example,
requiring well over 10,000 specified residues. Ameboid motility,
exocitosis, pinocytosis, photosynthesis, eye-spot vision systems, etc.
all require thousands of specifically arranged amino acid residues
working together at the same time.

Sean Pitman
www.DetectingDesign.com

Seanpit

unread,
Feb 5, 2007, 1:45:11 PM2/5/07
to
On Feb 5, 4:52 am, "Ron O" <rokim...@cox.net> wrote:

< snip >

> > What do you think SETI scientists are looking for? They are in fact
> > looking for something that has such a large gap between it and what
> > non-deliberate processes are capable of achieving that some smart
> > alien intelligence is the most viable option. A clear demonstration
> > of non-beneficial gaps does the same thing for demonstrating that
> > evolutionary mechanisms are most unlikely to have crossed the gap
> > leaving intelligent deliberate processes as the most likely origin.
>
> This is a stupid analogy because SETI is looking for a signal that
> they can differentiate from a natural occurring signal. If all they
> were looking for is something far away from what is known, three
> pulsars in close proximity would be considered a SETI signal because
> if it did occur only once in the Universe that would be as far away as
> they could get. Get a clue. There are certain criteria that they
> have to look for, and if and when they ever detect something the
> debate will be one as to what that something is. If all they had was
> looking at the different proteins and claiming that there was
> intelligent signal there they would be doomed because we see those
> protein sequences evolving even today.

Not true. We do not see protien sequences evolving even today at all
beyond very low levels of functional complexity - not a single example
goes beyond the 1000 specified amino acid residue structural threshold
requirement. Therefore, finding such a functional system significantly
beyond this threshold is most certainly the same thing as "a signal
that they [SETI] can differentiate from a natural occurring signal."
Why? Because it does not occur naturally at all and statistically it
cannot occur this side of a practical eternity of time.

< snip >

Sean Pitman
www.DetectingDesign.com

Seanpit

unread,
Feb 5, 2007, 2:00:50 PM2/5/07
to
On Feb 4, 8:19 pm, Robin Levett <rnlev...@yahoo.co.uk> wrote:
> Seanpit wrote:
> > An interesting 3D model for the distribution of existing small single-
> > protein systems within sequence space is presented in the following
> > link of the work of Jim Proctor and Andrew Torda (Hamburg University,
> > last update May, 2004):
>
> >http://www.zbh.uni-hamburg.de/wurst/protspace/ECCB_opt.huge.pdf
> >http://www.zbh.uni-hamburg.de/wurst/protspace/
>
> Sean, before you throw out more references to papers that you can distort to
> fit your requirements, isn't it about time you addressed the Choi and Kim
> paper that Howard referred you to on 16 October last year? The one which
> showed that proteins *in the real world* cluster into 4 families?
>
> www.pnas.org/cgi/content/full/103/38/14056

If you read the paper carefully, Choi and Kim do not say that proteins
form four families. Rather, they argue that protein folds can be
roughly categorized into four families. That's a big difference.
Also, consider the actual 3D model of their sequence space:

http://www.lbl.gov/Science-Articles/Archive/PBD-Universe-map-Kim.html

Notice in this model that even when it comes to very low-level protein
folding sequence space, the viable folds do not all overlap. Sure,
they are close together, but this is only to be expected at this very
low level of sequence space. It's kinda like the sequence space of 3-
letter words. They are all very closely clustered together like
this. However, this closeness of the potential steppingstones rapidly
expands as one moves up the ladder of minimum structural threshold
requirements.

> Oh, and even a layman like me can see that you've got your interpretation of


> the Bornberg-Bauer paper wrong. He specifically states that the HP protein
> sequences he is examining are not uniformly distributed across sequence
> space; see the last couple of paragraphs of the paper; and the RNA
> sequences, that he says do "percolate through sequence space", do so in
> such a way that "Within a number of mutations small compared to the length
> of the sequence, the whole shape-space can be covered".

That's right! The *whole* shape-space can be covered via relatively
small steps. This in fact means that the steppingstones here are
indeed distributed throughout sequence space. They are not clustered
together in one tiny corner. The fact that one can get across the
whole of sequence space without having to step very far from one to
the next steppingstone simply means that the ratio of steppingstones
vs. the non-viable "gap" options is rather high at this level of
minimum structural threshold requirements - as in the case of 3-letter
words. However, as you move up the ladder of threshold requirements,
this ratio drops off exponentially. As this happens, the
steppingstones drift apart rapidly. Pretty soon, it becomes very
difficult to take the same short steps and hit any steppingstone at
all.

> Even in the abstract he makes clear that "In analogy to protein families,
> nets are dense and well-separated in sequence space".

Exactly! And they cover the entire space! The nets are dense because
of the relatively high ratio that exists at such low levels of minimum
structural threshold requirements.

> Robin Levett

Sean Pitman
www.DetectingDesign.com


_Arthur

unread,
Feb 5, 2007, 3:00:25 PM2/5/07
to
Remind me again what's a "specified residue", and how one is supposed
to count them ?

Also, the flagellar motility system is not a single protein, but an
assembly of approximatively 42 unique proteins.

Are you telling me that nothing prevents any single of those proteins
to be evolved individually by the cell, but that the whole *flagella*
is surrounded by some invisible "Pitman Gap" with the magic number
"1000aa" thrown in somewhere ?

I must know where you place your goalposts, you seem to be hiding them
begind a screen of fuzzy and ever-changing non-definitions and weasel-
concepts.

richardal...@googlemail.com

unread,
Feb 5, 2007, 3:48:29 PM2/5/07
to
On Feb 5, 6:45 pm, "Seanpit" <seanpitnos...@naturalselection.

WHO specified the "1000 specified amino acid residue structural
threshold" and WHY is it relevant?

You have given no reason to think that it is anything other than an
arbitrary number you have pulled out of the air to falsify an
inaccurate model of evolution you have devised for no reason other
than to "falsify" it.

Novel functions can evolve without the need to cross your "1000
specified amino acid residue structural threshold".

There is no mechanism which prevents further evolution.

You may be able to fool the creationists with this sort of drivel, but
it is very clear that you can't fool anyone who knows anything about
the subject. Evidently your motive is to impress the creationists, not
to persuade the scientists, but as your whole argument is built on a
fabric of misrepresentation, distortion and outright falsehoods it is
deeply dishonest.

Evidently you are happy to use such dishonest methods to support your
case. You present your arguments here, and on your web sites knowing
perfectly well that they are bogus, based on unfounded assertion at
best and on outright falsehoods at worst, and would be utterly
demolished by any scientist with any knowledge of the subject were
they submitted to any form of academic review.

If you had a scrap of honesty you would submit your ideas to review.

I'm totally confident that you won't.

RF

Seanpit

unread,
Feb 5, 2007, 6:47:08 PM2/5/07
to
On Feb 5, 12:00 pm, "_Arthur" <Arth...@sympatico.ca> wrote:

> Remind me again what's a "specified residue", and how one is supposed
> to count them ?

All protein-based systems of function require a certain number of
specifically arranged amino acid residues. While flexibility of
arrangement can be tolerated, the degree of flexibility is often
fairly restricted. Several papers have been published about this sort
of thing to include papers by Sauer, Olsen, and Yockey. Estimates of
flexibility produce ratios for fairly specified 100aa systems of
around 1e-35 to 1e-65 or so.

> Also, the flagellar motility system is not a single protein, but an
> assembly of approximatively 42 unique proteins.

Actually, the number is a bit less than 42, but that's not the point.
The point is that all of the proteins (which are each made up of two
or three hundred fairly specified amino acid residues) in the
flagellar motility system have to be specifically arranged for the
overall system to work.

> Are you telling me that nothing prevents any single of those proteins
> to be evolved individually by the cell, but that the whole *flagella*

> is surrounded by some invisible "PitmanGap" with the magic number


> "1000aa" thrown in somewhere ?

The relatively small single proteins aren't a problem. What is a
problem is the assembly of many single proteins to produce a system
that requires a total of many thousands of amino acid residues to be
specifically arranged with each other at the same time. You just
can't add one protein together to gain the flagellar motility system
because of a lack of beneficial steppingstones that are actually that
close together.

The gaps between steppingstones at this level may not seem very big,
only a few dozen character changes in places along the pathway, but
these seemingly small gaps would require evolutionary mechanisms
trillions upon trillions of years to cross.

> I must know where you place your goalposts, you seem to be hiding them
> begind a screen of fuzzy and ever-changing non-definitions and weasel-
> concepts.

LOL - My goalposts have been just were they are now for many years.
My definitions have not changed. You just don't seem to understand
concepts that really are quite simple and intuitively obvious.

Sean Pitman
www.DetectingDesign.com


_Arthur

unread,
Feb 5, 2007, 7:55:37 PM2/5/07
to
On Feb 5, 6:47 pm, "Seanpit" <seanpitnos...@naturalselection.

0catch.com> wrote:
> The relatively small single proteins aren't a problem. What is a
> problem is the assembly of many single proteins to produce a system
> that requires a total of many thousands of amino acid residues to be
> specifically arranged with each other at the same time. You just
> can't add one protein together to gain the flagellar motility system
> because of a lack of beneficial steppingstones that are actually that
> close together.

Why the blather about *protein* structures, why all along you really
meant the total combination of all the genes necessary for a multi-
protein structure ?

Ron O

unread,
Feb 5, 2007, 8:15:25 PM2/5/07
to
On Feb 5, 12:45 pm, "Seanpit" <seanpitnos...@naturalselection.

Pathetic evasion. Sean what is good enough? Show us what is good
enough for you. Put up your alternative and the evidence for it so
that we can see just how much your bullpucky of only low level changes
in functional complexity really matters. If what we have is so bad,
what does that tell you about the pathetic junk that you have to
believe means anything? Really, show us what you think is good
enough.

Ron Okimoto

>
> < snip >

Seanpit

unread,
Feb 5, 2007, 8:56:46 PM2/5/07
to
On Feb 5, 12:48 pm, richardalanforr...@googlemail.com wrote:

> > Not true. We do not see protein sequences evolving even today at all


> > beyond very low levels of functional complexity - not a single example
> > goes beyond the 1000 specified amino acid residue structural threshold
> > requirement.
>
> WHO specified the "1000 specified amino acid residue structural
> threshold" and WHY is it relevant?

If you look in scientific literature you will see something very
interesting. There are many examples of novel protein-based systems
evolving. However, all of these systems require significantly less
than 1000 specified amino acid residues. There isn't a single
example, in all of literature, of any real time evolution in action
that produces any novel function that requires at least 1000
specifically arranged residues working at the same time. Beyond this,
the number of examples drops off dramatically as one approaches this
1000aa mark.

If you don't understand why that is relevant, you must be deliberately
blind.

> You have given no reason to think that it is anything other than an
> arbitrary number you have pulled out of the air to falsify an
> inaccurate model of evolution you have devised for no reason other
> than to "falsify" it.

Show me just one example then of observed evolution in action beyond
this structural threshold.

> Novel functions can evolve without the need to cross your "1000
> specified amino acid residue structural threshold".

Novel functions that require at least 1000 specifically arranged
residues have never been observed to evolve. There are no real time
examples - period. Not one. Those functions that do evolve require
only a few hundred specified residues - like your cockroach milk
evolution example (only about 200 or so loosely specified residues
needed), which isn't even an observed example.

> There is no mechanism which prevents further evolution.

Then why doesn't evolution happen beyond the 1000aa threshold? What
makes evolution so common at levels below the 1000aa threshold, but
completely absent beyond this level?

> You may be able to fool the creationists with this sort of drivel, but
> it is very clear that you can't fool anyone who knows anything about
> the subject. Evidently your motive is to impress the creationists, not
> to persuade the scientists, but as your whole argument is built on a
> fabric of misrepresentation, distortion and outright falsehoods it is
> deeply dishonest.

You don't have the first clue what you are talking about here. You
don't understand your own proposed evolutionary mechanism and are
oblivious to the fact that this mechanism only works at levels well
below the 1000aa threshold.

> Evidently you are happy to use such dishonest methods to support your
> case. You present your arguments here, and on your web sites knowing
> perfectly well that they are bogus, based on unfounded assertion at
> best and on outright falsehoods at worst, and would be utterly
> demolished by any scientist with any knowledge of the subject were
> they submitted to any form of academic review.

Have at it then. Where are your devastating arguments? Hmmmm? Just
one example is all you need. Where is it?

> If you had a scrap of honesty you would submit your ideas to review.

What do you think I'm doing here? Don't you have a real argument of
your own?

> I'm totally confident that you won't.

LOL - whatever . . .

> RF

Sean Pitman
www.DetectingDesign.com


Seanpit

unread,
Feb 5, 2007, 9:03:10 PM2/5/07
to
On Feb 5, 5:15 pm, "Ron O" <rokim...@cox.net> wrote:

> > > This is a stupid analogy because SETI is looking for a signal that
> > > they can differentiate from a natural occurring signal. If all they
> > > were looking for is something far away from what is known, three
> > > pulsars in close proximity would be considered a SETI signal because
> > > if it did occur only once in the Universe that would be as far away as
> > > they could get. Get a clue. There are certain criteria that they
> > > have to look for, and if and when they ever detect something the
> > > debate will be one as to what that something is. If all they had was
> > > looking at the different proteins and claiming that there was
> > > intelligent signal there they would be doomed because we see those
> > > protein sequences evolving even today.
>

> > Not true. We do not see protein sequences evolving even today at all


> > beyond very low levels of functional complexity - not a single example
> > goes beyond the 1000 specified amino acid residue structural threshold
> > requirement. Therefore, finding such a functional system significantly
> > beyond this threshold is most certainly the same thing as "a signal
> > that they [SETI] can differentiate from a natural occurring signal."
> > Why? Because it does not occur naturally at all and statistically it
> > cannot occur this side of a practical eternity of time.
>

> Pathetic evasion. Sean, what is good enough? Show us what is good
> enough for you.

Do you have problems with reading comprehension Ron? I just pointed
out to you that no functional system that requires a minimum of more
than 1000 specified amino acid residues evolves. Why not go about
showing some examples beyond this threshold limitation? Why not
explain why there are no current examples of evolution in action
beyond this level? Why not explain why evolutionary mechanisms stall
out very rapidly as this threshold is approached?

> Put up your alternative and the evidence for it so
> that we can see just how much your bullpucky of only low level changes
> in functional complexity really matters. If what we have is so bad,
> what does that tell you about the pathetic junk that you have to
> believe means anything? Really, show us what you think is good
> enough.

Just one example would be fine Ron.

Seanpit

unread,
Feb 5, 2007, 9:05:53 PM2/5/07
to

It really doesn't matter either way - a single or a multi-protein
structure would work just fine. What really matters is the total
number of specifically arranged amino acid residues that are
required. Those functions beyond the 1000aa level usually are made up
of independently coded proteins that are linked together in specific
arrangements with each other.

Sean Pitman
www.DetectingDesign.com


richardal...@googlemail.com

unread,
Feb 6, 2007, 2:46:38 AM2/6/07
to
On Feb 6, 1:56 am, "Seanpit" <seanpitnos...@naturalselection.

0catch.com> wrote:
> On Feb 5, 12:48 pm, richardalanforr...@googlemail.com wrote:
>
> > > Not true. We do not see protein sequences evolving even today at all
> > > beyond very low levels of functional complexity - not a single example
> > > goes beyond the 1000 specified amino acid residue structural threshold
> > > requirement.
>
> > WHO specified the "1000 specified amino acid residue structural
> > threshold" and WHY is it relevant?
>
> If you look in scientific literature you will see something very
> interesting. There are many examples of novel protein-based systems
> evolving. However, all of these systems require significantly less
> than 1000 specified amino acid residues. There isn't a single
> example, in all of literature, of any real time evolution in action
> that produces any novel function that requires at least 1000
> specifically arranged residues working at the same time. Beyond this,
> the number of examples drops off dramatically as one approaches this
> 1000aa mark.

So freaking what?
Evolution does not proceed by saltational leaps.


>
> If you don't understand why that is relevant, you must be deliberately
> blind.


>
> > You have given no reason to think that it is anything other than an
> > arbitrary number you have pulled out of the air to falsify an
> > inaccurate model of evolution you have devised for no reason other
> > than to "falsify" it.
>
> Show me just one example then of observed evolution in action beyond
> this structural threshold.

No, YOU need give a reason to think that it is anything other than an


arbitrary number you have pulled out of the air to falsify an
inaccurate model of evolution you have devised for no reason other
than to "falsify" it.

>


> > Novel functions can evolve without the need to cross your "1000
> > specified amino acid residue structural threshold".
>
> Novel functions that require at least 1000 specifically arranged
> residues have never been observed to evolve.

SO freaking what? Evolutionary theory does not require such
saltational leaps.

> There are no real time
> examples - period. Not one. Those functions that do evolve require
> only a few hundred specified residues - like your cockroach milk
> evolution example (only about 200 or so loosely specified residues
> needed), which isn't even an observed example.

What utter nonsense! If you have a better explanation for the evidence
presented by the authors of the paper, feel free to offer it. Their
conclusions are firmly based on that evidence.

>
> > There is no mechanism which prevents further evolution.
>
> Then why doesn't evolution happen beyond the 1000aa threshold? What
> makes evolution so common at levels below the 1000aa threshold, but
> completely absent beyond this level?

The fact that evolution does not proceed by saltational leaps.
The fact that your model is grossly and deliberately inacurate.
The fact that your models is not supported by a scrap of evidence.
The fact that your 1000aa threshold is completely arbitrary and not
founded on any evidence.

Your argument is no different from the facile creationist demand that
they will not "believe in" evolution unless they see a dog giving
birth to a cat. It is both ignorant and dishonest.

>
> > You may be able to fool the creationists with this sort of drivel, but
> > it is very clear that you can't fool anyone who knows anything about
> > the subject. Evidently your motive is to impress the creationists, not
> > to persuade the scientists, but as your whole argument is built on a
> > fabric of misrepresentation, distortion and outright falsehoods it is
> > deeply dishonest.
>
> You don't have the first clue what you are talking about here. You
> don't understand your own proposed evolutionary mechanism and are
> oblivious to the fact that this mechanism only works at levels well
> below the 1000aa threshold.

You have provided no evidence or argument whatsover to support your
assertion that it should. Your "1000aa threshold" is no more than an
arbitrary number you have pulled out of the air to falsify your own
personal model of evolution which you have devised for no reason other
than to falsify it.

>


> > Evidently you are happy to use such dishonest methods to support your
> > case. You present your arguments here, and on your web sites knowing
> > perfectly well that they are bogus, based on unfounded assertion at
> > best and on outright falsehoods at worst, and would be utterly
> > demolished by any scientist with any knowledge of the subject were
> > they submitted to any form of academic review.
>
> Have at it then. Where are your devastating arguments? Hmmmm? Just
> one example is all you need. Where is it?
>

No, what *YOU* need to do is to justify your assertion that such a
demand is reasonable based on evolutionary theory.

> > If you had a scrap of honesty you would submit your ideas to review.
>
> What do you think I'm doing here? Don't you have a real argument of
> your own?
>

What you are doing here is persisting in an utterly discredited
argunment which is based on nothing other than your unfounded
assertions and ignoring any evidence which demonstrates that it is
false. You mispresent and distort the words of the authors of the
papers you cite in support of your "theory", and ignore those parts of
the papers which don't suit you.

You are not submitting your ideas to review, something which I know
you won't because you are an intellectual coward who prefers to
pontificate on subjects about which you know very little to boost your
status in the creationist community rather than to learn about them
and make any genuine contribution to science.


> > I'm totally confident that you won't.
>
> LOL - whatever . . .
>

Which confirms that you are a moral and intellectual coward.

RF


> > RF
>
> Sean Pitmanwww.DetectingDesign.com


Ron O

unread,
Feb 6, 2007, 7:51:02 AM2/6/07
to
On Feb 5, 8:03 pm, "Seanpit" <seanpitnos...@naturalselection.

You seem to have a comprehension problem. This whole schtick of yours
is just evasion. Where did you get the 1000 specified amino acids
junk? The average protein size is only 300 and you can't even explain
the evolutionary data of short proteins like cyt c that are only
around 100.

What is your alternative to common descent and the evidence for it?
We have reams of data using your "impossible" protein sequences that
tell us something that your model can't explain worth beans. If it
could you would have put it up years ago.

Lurkers should not be confused by Sean's evasion tactics. Any regular
knows what Sean has been up to for years. He made his common descent
claim a couple of years before Ohio hit the fan. He claimed that he
had an alternative model and evidence to back it up, what? Seven
years ago? He never backed up that claim. Right after the Ohio State
school board fiasco where the ID scam artists had to run the bait and
switch scam on the Ohio rubes in 2002 Sean claimed that he could do
better and that he had some real science to teach about ID, but he
never put it forward. The Ohio rubes were conned by the ID scam and
wanted to teach the science of ID, but all they got from the guys that
had perpetrated the ID scam was a replacement obfuscation scam that
didn't even mention that ID had ever existed. Sean claimed that there
was ID science to teach, but where is it? Why didn't it show up in
Dover when they needed it? Why hasn't Sean ever presented what he
claims exists?

Why dishonestly obfuscate about 1000 specified amino acids when you
know that you don't have jack as an alternative to the real science?
Sean has to explain the protein data that we have before he tries to
claim something about what we (and he) doesn't know. Sean knows for a
fact that he can't do what he claims or he wouldn't be waffling about
it for 7 years. We aren't talking about a few months or a couple of
years, but over half a decade of denial. It isn't that people are
being mean to Sean, it is that Sean is either incompetent or
dishonest. I've pretty much left him alone for several years because
I lean towards mental incompetence, but he seems to claim otherwise so
who is to argue?

>
> > Put up your alternative and the evidence for it so
> > that we can see just how much your bullpucky of only low level changes
> > in functional complexity really matters. If what we have is so bad,
> > what does that tell you about the pathetic junk that you have to
> > believe means anything? Really, show us what you think is good
> > enough.
>
> Just one example would be fine Ron.

Why the evasion Sean? After you make good on your common descent
claim may be we can get around to you demonstrating that your 1000
junk is biologically relevant. Of course the point would be moot
after you demonstrate that you are just a blowhard incompetent. I
didn't make your claim, you did that, so put up. How long will you be
in denial? 10 years? 20? More?

Why not be more honest and call your site creationistobfuscation101?

Ron Okimoto

>
> > Ron Okimoto

Vend

unread,
Feb 6, 2007, 9:06:19 AM2/6/07
to
On 4 Feb, 23:02, "Seanpit" <seanpitnos...@naturalselection.0catch.com>
wrote:

> > Well, common design explains the existence of homology. It doesn't
> > explain why when you construct twenty different phylogenetic trees
> > for the twenty different enzymes, those trees all agree with each other
> > on the shape of the crown groups.
>
> It does if the different groups have different by slightly different
> functional needs for their slightly different systems and
> environments.

But why trees? and why the trees are consistent?

> Nested patterns are often present within human-designed
> systems.

You mean like a cd-player in a car?
Human designed object form generic graphs, not trees.

_Arthur

unread,
Feb 6, 2007, 9:05:44 AM2/6/07
to
On Feb 5, 9:05 pm, "Seanpit" <seanpitnos...@naturalselection.
0catch.com> wrote:

Blather.

Seanpit

unread,
Feb 6, 2007, 10:50:10 AM2/6/07
to
On Feb 6, 6:05 am, "_Arthur" <Arth...@sympatico.ca> wrote:

> > > Why the blather about *protein* structures, why all along you really
> > > meant the total combination of all the genes necessary for a multi-
> > > protein structure ?
>
> > It really doesn't matter either way - a single or a multi-protein
> > structure would work just fine. What really matters is the total
> > number of specifically arranged amino acid residues that are
> > required. Those functions beyond the 1000aa level usually are made up
> > of independently coded proteins that are linked together in specific
> > arrangements with each other.
>
> >SeanPitmanwww.DetectingDesign.com
>
> Blather.

You can lead a horse to water . . .

_Arthur

unread,
Feb 6, 2007, 10:58:39 AM2/6/07
to
On Feb 6, 10:50 am, "Seanpit" <seanpitnos...@naturalselection.
0catch.com> wrote:

>
> > > It really doesn't matter either way - a single or a multi-protein
> > > structure would work just fine. What really matters is the total
> > > number of specifically arranged amino acid residues that are
> > > required. Those functions beyond the 1000aa level usually are made up
> > > of independently coded proteins that are linked together in specific
> > > arrangements with each other.
>
>

> > Blather.
>
> You can lead a horse to water . . .

So the Pitman Gap you invented extends not around proteins, but rather
around biological structures, now ?

Seanpit

unread,
Feb 6, 2007, 11:12:22 AM2/6/07
to
> > > On Feb 5, 11:46 pm, richardalanforr...@googlemail.com wrote:
> > On Feb 6, 1:56 am, "Seanpit" <seanpitnos...@naturalselection.

> > > WHO specified the "1000 specified amino acid residue structural


> > > threshold" and WHY is it relevant?
>
> > If you look in scientific literature you will see something very
> > interesting. There are many examples of novel protein-based systems
> > evolving. However, all of these systems require significantly less
> > than 1000 specified amino acid residues. There isn't a single
> > example, in all of literature, of any real time evolution in action
> > that produces any novel function that requires at least 1000
> > specifically arranged residues working at the same time. Beyond this,
> > the number of examples drops off dramatically as one approaches this
> > 1000aa mark.
>
> So freaking what?
> Evolution does not proceed by saltational leaps.

You do understand, by now hopefully, that the 1000aa structural
threshold is not a measure of the step or "leap" size. It is a
measure of the minimum part requirement and degree of arrangement
needed to achieve a particular type of function regardless of how that
1000aa+ structure is produced. It is *possible* for such a functional
system to be just one point mutation away from something that already
exists within a population's gene pool. It is just that this
possibility is extremely *unlikely* at this level.

It is far far more likely that such a functional system would be
several dozen mutational steps away from anything that exists within a
population's gene pool - even if the population under consideration
consists of all living things on Earth (the likely distribution
follows a Poisson curve). Finding any novel beneficial function beyond
the 1000aa threshold, given the most likely minimum gap size, would
most certainly require a great many random mutation steps or "leaps";
exponentially more mutational steps and/or leaps than were needed
below this threshold. Of course, that means that exponentially more
time is required to achieve higher and higher minimum structural
threshold requirements - and that's a big big problem.

Small mutational steps simply do not add up to move a population up
the ladder of minimum structural threshold requirements. There just
aren't any examples of such evolution in action in all of literature -
not one. Your cockroach milk evolution example isn't even a real time
example and it doesn't cross a structural threshold of more than 200
or so loosely specified amino acid residues.

There are a great many such examples because the odds that such a
potentially beneficial function will be very close (within one or two
mutational steps) to what already exists within a gene pool are pretty
good, relatively speaking. However, the odds that this short distance
will also be a reality as one move up the ladder of minimum structural
threshold requirements drop exponentially.

> > If you don't understand why that is relevant, you must be deliberately
> > blind.
>
> > > You have given no reason to think that it is anything other than an
> > > arbitrary number you have pulled out of the air to falsify an
> > > inaccurate model of evolution you have devised for no reason other
> > > than to "falsify" it.
>
> > Show me just one example then of observed evolution in action beyond
> > this structural threshold.
>
> No, YOU need give a reason to think that it is anything other than an
> arbitrary number you have pulled out of the air to falsify an
> inaccurate model of evolution you have devised for no reason other
> than to "falsify" it.

I've already told you the reason. Don't tell me you still don't grasp
the significance of the fact that all examples of evolution "in
action" fall well below the 1000aa threshold. There is not a single
example beyond this level in all of literature. This threshold level
is not pulled out of thin air. It is presented in scientific
literature as the threshold that is never crossed. Please do explain
that - - if you can.

> > > Novel functions can evolve without the need to cross your "1000
> > > specified amino acid residue structural threshold".
>
> > Novel functions that require at least 1000 specifically arranged
> > residues have never been observed to evolve.
>
> SO freaking what? Evolutionary theory does not require such
> saltational leaps.

The 1000aa threshold has never been crossed by any series of
evolutionary steps, short or long, small or large. Small little steps
simply do not progress up the ladder of minimum structural threshold
requirements like you imagine. They only produce novel functions that
are below the 1000aa threshold. There is no progression up the ladder
- not one example.

> > There are no real time
> > examples - period. Not one. Those functions that do evolve require
> > only a few hundred specified residues - like your cockroach milk
> > evolution example (only about 200 or so loosely specified residues
> > needed), which isn't even an observed example.
>
> What utter nonsense! If you have a better explanation for the evidence
> presented by the authors of the paper, feel free to offer it. Their
> conclusions are firmly based on that evidence.

It doesn't matter Richard. Even if this example were actually
observed in real time, it is an example of crossing a threshold that
is far below the 1000aa threshold. The threshold crossed here is a
200aa threshold of loosely specified residues. That's not even
close! Even Barry Hall's lactase evolution example crosses a much
higher threshold of about 380aa that are much more specified.

There are much much better examples than your roach-milk example.
It's just that none of them come close to the 1000aa threshold.

< snip >

> RF

Sean Pitman
www.DetectingDesign.com

Seanpit

unread,
Feb 6, 2007, 11:15:23 AM2/6/07
to
On Feb 6, 7:58 am, "_Arthur" <Arth...@sympatico.ca> wrote:

> So thePitmanGap you invented extends not around proteins, but rather


> around biological structures, now ?

Both. It is just that the gap is much smaller for smaller protein-
based functional structures (which usually include single proteins).
The larger the minimum structural size and specificity requirement the
larger the gap size. It's really very simple and downright intuitive.

Sean Pitman
www.DetectingDesign.com


Seanpit

unread,
Feb 6, 2007, 11:24:50 AM2/6/07
to
On Feb 6, 6:06 am, "Vend" <ven...@virgilio.it> wrote:
> On 4 Feb, 23:02, "Seanpit" <seanpitnos...@naturalselection.0catch.com>
> wrote:
>
> > > Well, common design explains the existence of homology. It doesn't
> > > explain why when you construct twenty different phylogenetic trees
> > > for the twenty different enzymes, those trees all agree with each other
> > > on the shape of the crown groups.
>
> > It does if the different groups have different by slightly different
> > functional needs for their slightly different systems and
> > environments.
>
> But why trees? and why the trees are consistent?

Does an artists or designer of any kind have to have a reason that
appeals to you before you can detect design? This is the whole "No
intelligent designer would have done it that way" argument. Some
might say that about a Picasso painting if they were from an alien
planet. Yet, it is easy to detect a great deal of deliberate
intelligence behind a Picasso.

Beyond this, the nested hierarchy in nature makes a lot of creative
sense and is even beautifully elegant. The pattern is very similar to
patterns observed in highly technical human designs of integrated
systems - especially if a single designer or a small group of
designers were at work.

And, beyond this, the detection of design isn't about the detection of
a pattern that a mindless process is likely to produce. It is about
the detection of something that mindless processes are very unlikely
to produce. One cannot simply focus on one aspect of a phenomenon and
make a conclusive hypothesis about mindless or mindful origin. One
must consider all aspects of the phenomenon before a reliable
hypothesis can be established. While the nested pattern observed in
living things can indeed be explained by mindless evolutionary
processes, the functional aspects of living things, as they move
beyond very low levels of minimum structural threshold requirements,
are exponentially harder and harder to explain via mindless
evolutionary processes.

> > Nested patterns are often present within human-designed
> > systems.
>
> You mean like a cd-player in a car?
> Human designed object form generic graphs, not trees.

Not always . . . nested patterns can also be seen in human design.

Sean Pitman
www.DetectingDesign.com


richardal...@googlemail.com

unread,
Feb 6, 2007, 12:59:11 PM2/6/07
to
On Feb 6, 4:12 pm, "Seanpit" <seanpitnos...@naturalselection.

0catch.com> wrote:
> > > > On Feb 5, 11:46 pm, richardalanforr...@googlemail.com wrote:
> > > On Feb 6, 1:56 am, "Seanpit" <seanpitnos...@naturalselection.
> > > > WHO specified the "1000 specified amino acid residue structural
> > > > threshold" and WHY is it relevant?
>
> > > If you look in scientific literature you will see something very
> > > interesting. There are many examples of novel protein-based systems
> > > evolving. However, all of these systems require significantly less
> > > than 1000 specified amino acid residues. There isn't a single
> > > example, in all of literature, of any real time evolution in action
> > > that produces any novel function that requires at least 1000
> > > specifically arranged residues working at the same time. Beyond this,
> > > the number of examples drops off dramatically as one approaches this
> > > 1000aa mark.
>
> > So freaking what?
> > Evolution does not proceed by saltational leaps.
>
> You do understand, by now hopefully, that the 1000aa structural
> threshold is not a measure of the step or "leap" size. It is a
> measure of the minimum part requirement and degree of arrangement
> needed to achieve a particular type of function regardless of how that
> 1000aa+ structure is produced. It is *possible* for such a functional
> system to be just one point mutation away from something that already
> exists within a population's gene pool. It is just that this
> possibility is extremely *unlikely* at this level.
>

So what?

> It is far far more likely that such a functional system would be
> several dozen mutational steps away from anything that exists within a
> population's gene pool - even if the population under consideration
> consists of all living things on Earth (the likely distribution
> follows a Poisson curve). Finding any novel beneficial function beyond
> the 1000aa threshold,

You have yet to explain why your "1000aa threshold" is of any
significance. Novel beneficial functions evolved with changes well
below this threshold.

What is so special about novel beneficial functions above this
arbitrary threshold?

> given the most likely minimum gap size, would
> most certainly require a great many random mutation steps or "leaps";
> exponentially more mutational steps and/or leaps than were needed
> below this threshold. Of course, that means that exponentially more
> time is required to achieve higher and higher minimum structural
> threshold requirements - and that's a big big problem.

Only in your model of evolution, which is formulated only so that you
can falsify it.

What mechanism prevents the accumulation of beneficial functions at
levels of change well below your arbitrary threshold?

>
> Small mutational steps simply do not add up to move a population up
> the ladder of minimum structural threshold requirements.

Why not?

> There just
> aren't any examples of such evolution in action in all of literature -
> not one.

There are very large numbers of papers which present of evidence for
evolution as a series of mutational steps in the literature.
Dismissing them as "not convincing", as is your habit, will not make
them go away.

> Your cockroach milk evolution example isn't even a real time
> example

So freaking what? Since when has observation in "real time" been a
requirement in science? You'll be insisting that I'm using the
"judicial method" next.

> and it doesn't cross a structural threshold of more than 200
> or so loosely specified amino acid residues.
>

Which demonstrates that novel functions can evolve at levels of change
well below your arbitrary threshold.
What mechanism prevents further changes to the genomenes of these
cockroaches?

> There are a great many such examples because the odds that such a
> potentially beneficial function will be very close (within one or two
> mutational steps) to what already exists within a gene pool are pretty
> good, relatively speaking. However, the odds that this short distance
> will also be a reality as one move up the ladder of minimum structural
> threshold requirements drop exponentially.

Once such a novel function has been acquired, what mechanism prevents
the acquisiting of another novel function? Or the loss of the acquired
function? This is, after all how evolutionary theory models the
evolution of more complex functions.


>
> > > If you don't understand why that is relevant, you must be deliberately
> > > blind.
>
> > > > You have given no reason to think that it is anything other than an
> > > > arbitrary number you have pulled out of the air to falsify an
> > > > inaccurate model of evolution you have devised for no reason other
> > > > than to "falsify" it.
>
> > > Show me just one example then of observed evolution in action beyond
> > > this structural threshold.
>
> > No, YOU need give a reason to think that it is anything other than an
> > arbitrary number you have pulled out of the air to falsify an
> > inaccurate model of evolution you have devised for no reason other
> > than to "falsify" it.
>
> I've already told you the reason.

No you haven't.
You have asserted over and over again that this is requirement, but
provided no evidence whatsoever to suggest that it has any meaning in
the real world.

> Don't tell me you still don't grasp
> the significance of the fact that all examples of evolution "in
> action" fall well below the 1000aa threshold.

The signifiance is that there is no requirement for changes above the
arbitrary threshold you have invented to evolution to carry on quite
happily.

> There is not a single
> example beyond this level in all of literature.

There are numerous example in the literature. The fact that you ignore
them, or pretend that they don't exist, or dismiss them without even
reading them as "unconvincing" is irrelevant. If you have a better
explanation for the evidence, or a better predictive model than
evolutionary theory, feel free to offer it.

> This threshold level
> is not pulled out of thin air. It is presented in scientific
> literature as the threshold that is never crossed.

Where?

> Please do explain
> that - - if you can.
>

The explanation is that you are persitently mispresenting the words of
a paper written over 30 years ago when our knowledge of the way in
which proteins function in genes was in its infancy.

> > > > Novel functions can evolve without the need to cross your "1000
> > > > specified amino acid residue structural threshold".
>
> > > Novel functions that require at least 1000 specifically arranged
> > > residues have never been observed to evolve.
>
> > SO freaking what? Evolutionary theory does not require such
> > saltational leaps.
>
> The 1000aa threshold has never been crossed by any series of
> evolutionary steps, short or long, small or large.

Why does it need to?

> Small little steps
> simply do not progress up the ladder of minimum structural threshold
> requirements like you imagine.

Why not?
Is there a mechanism which prevents the acquisition of further novel
functions once one has been acquired?

> They only produce novel functions that
> are below the 1000aa threshold. There is no progression up the ladder
> - not one example.

So what?


>
> > > There are no real time
> > > examples - period. Not one. Those functions that do evolve require
> > > only a few hundred specified residues - like your cockroach milk
> > > evolution example (only about 200 or so loosely specified residues
> > > needed), which isn't even an observed example.
>
> > What utter nonsense! If you have a better explanation for the evidence
> > presented by the authors of the paper, feel free to offer it. Their
> > conclusions are firmly based on that evidence.
>
> It doesn't matter Richard. Even if this example were actually
> observed in real time, it is an example of crossing a threshold that
> is far below the 1000aa threshold. The threshold crossed here is a
> 200aa threshold of loosely specified residues.

Quite so. It means that evolution can proceed perfectly well at levels
of change well below the arbitrary limit you have set.

What mechanism prevents the evolution of further novel functions?

> That's not even
> close! Even Barry Hall's lactase evolution example crosses a much
> higher threshold of about 380aa that are much more specified.
>

So what?

> There are much much better examples than your roach-milk example.
> It's just that none of them come close to the 1000aa threshold.

You have not explained why they need to.
Novel functions can evolve without any need to approach your arbitrary
threshold.
There is no mechanism to prevent further novel functions evolving.

>
> < snip >


Lets restore some of those snips, shall we?

> Then why doesn't evolution happen beyond the 1000aa threshold? What
> makes evolution so common at levels below the 1000aa threshold, but
> completely absent beyond this level?

The fact that evolution does not proceed by saltational leaps.
The fact that your model is grossly and deliberately inacurate.
The fact that your models is not supported by a scrap of evidence.
The fact that your 1000aa threshold is completely arbitrary and not
founded on any evidence.

Your argument is no different from the facile creationist demand that
they will not "believe in" evolution unless they see a dog giving
birth to a cat. It is both ignorant and dishonest.

> You don't have the first clue what you are talking about here. You


> don't understand your own proposed evolutionary mechanism and are

> oblivious to the fact that this mechanism only works at levels well
> below the 1000aa threshold.

You have provided no evidence or argument whatsover to support your


assertion that it should. Your "1000aa threshold" is no more than an
arbitrary number you have pulled out of the air to falsify your own

personal model of evolution which you have devised for no reason other
than to falsify it.

> Have at it then. Where are your devastating arguments? Hmmmm? Just


> one example is all you need. Where is it?

No, what *YOU* need to do is to justify your assertion that such a
demand is reasonable based on evolutionary theory.

> What do you think I'm doing here? Don't you have a real argument of
> your own?

What you are doing here is persisting in an utterly discredited
argunment which is based on nothing other than your unfounded
assertions and ignoring any evidence which demonstrates that it is
false. You mispresent and distort the words of the authors of the
papers you cite in support of your "theory", and ignore those parts of
the papers which don't suit you.

You are not submitting your ideas to review, something which I know
you won't because you are an intellectual coward who prefers to
pontificate on subjects about which you know very little to boost your
status in the creationist community rather than to learn about them
and make any genuine contribution to science.

> LOL - whatever . . .

richardal...@googlemail.com

unread,
Feb 6, 2007, 1:02:28 PM2/6/07
to
On Feb 6, 4:15 pm, "Seanpit" <seanpitnos...@naturalselection.

....and not supported by a shred of evidence.

How do you explain that, Sean?

>
> Sean Pitmanwww.DetectingDesign.com


John Wilkins

unread,
Feb 6, 2007, 1:41:46 PM2/6/07
to
<richardal...@googlemail.com> wrote:

I want to ask Sean a question. Do you think a 999aa change is possible?
--
John S. Wilkins, Postdoctoral Research Fellow, Biohumanities Project
University of Queensland - Blog: scienceblogs.com/evolvingthoughts
"He used... sarcasm. He knew all the tricks, dramatic irony, metaphor,
bathos, puns, parody, litotes and... satire. He was vicious."

_Arthur

unread,
Feb 6, 2007, 1:47:47 PM2/6/07
to
On Feb 6, 11:15 am, "Seanpit" <seanpitnos...@naturalselection.

Wat are the precise structural size and complete specificity
requirements of the bacterial flagellae ?

Seanpit

unread,
Feb 6, 2007, 2:32:08 PM2/6/07
to

Greater than 10,000 fairly specified (1e-25 per 100aa) residues. If
you can come up with a threshold significantly less than this, I'd be
most interested.

Sean Pitman
www.DetectingDesign.com

Seanpit

unread,
Feb 6, 2007, 2:46:41 PM2/6/07
to
On Feb 6, 9:59 am, richardalanforr...@googlemail.com wrote:

> > > So freaking what?
> > > Evolution does not proceed by saltational leaps.
>
> > You do understand, by now hopefully, that the 1000aa structural
> > threshold is not a measure of the step or "leap" size. It is a
> > measure of the minimum part requirement and degree of arrangement
> > needed to achieve a particular type of function regardless of how that
> > 1000aa+ structure is produced. It is *possible* for such a functional
> > system to be just one point mutation away from something that already
> > exists within a population's gene pool. It is just that this
> > possibility is extremely *unlikely* at this level.
>
> So what?

Oh come on now! Think about it. If the odds that a short gap distance
actually exist decline exponentially with each increase in the minimum
structural threshold requirements, odds are that the actual minimum
gap distance will be greater. This means that the time it takes to
cross the gap is likely to be equivalently greater. Since the odds
change exponentially here, odds are that an exponentially greater
amount of time will be required to find a novel beneficial sequence at
a higher structural threshold level.

> > It is far far more likely that such a functional system would be
> > several dozen mutational steps away from anything that exists within a
> > population's gene pool - even if the population under consideration
> > consists of all living things on Earth (the likely distribution
> > follows a Poisson curve). Finding any novel beneficial function beyond
> > the 1000aa threshold,
>
> You have yet to explain why your "1000aa threshold" is of any
> significance. Novel beneficial functions evolved with changes well
> below this threshold.

How many times do I have to repeat myself? Novel beneficial functions
have evolved with the use of one or two or even three or four
mutational steps. However, and try and catch this point, the
resulting functional system did not require more than a few hundred
fairly specified residues in order to work to some selective
advantage.

It is because the resulting function was a low-level function that the
gaps size was so small. Odds are that no functional systems that have
higher minimum structural threshold requirements will be as close to
anything in any member of any population. These odds are
exponentially reduced with each step up the ladder. By the time the
1000aa level is considered, the odds that any gap will exist that is
only one or two mutations wide or even one or two dozen mutations wide
are extremely poor.

The odds follow a Poisson-type distribution. As one considers higher
and higher structural threshold requirements, the odds of a narrow gap
existing drop in such a way as to produce a Poisson distribution
pattern.

That is why the likely minimum gap distance is always much smaller
than the threshold level. However, a gap distance of just a few dozen
would require evolutionary mechanisms in a huge population of, say,
all living things on Earth, trillions upon trillions of years to
cross.

With each step up the ladder the ratio of potentially beneficial
steppingstone targets decreases exponentially. That's a fact. What
results is a widening of the gap between steppingstone targets as one
moves higher and higher up the ladder.

< snip rest - repetitive (both me and you) >

Sean Pitman
www.DetectingDesign.com


richardal...@googlemail.com

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Feb 6, 2007, 3:08:20 PM2/6/07
to
On Feb 6, 7:46 pm, "Seanpit" <seanpitnos...@naturalselection.

You don't.
You just have to provide an explanation for your assertion which is
supported by evidence.
Repeating the same assertion ad nauseam does not make it true.

> Novel beneficial functions
> have evolved with the use of one or two or even three or four
> mutational steps. However, and try and catch this point, the
> resulting functional system did not require more than a few hundred
> fairly specified residues in order to work to some selective
> advantage.

And the evidence you have to back this assertion is.......?

There is plenty of evidence both from studies of the genemones of
existing organisms and the fossil record that novel beneficial
functions *have* evolved involving a far greater number of
evolutionary steps that your arbitrary limit suggests.

Just to repeat a question I have asked many times and which you have
not answered:
What mechanism prevents the acquisition of more novel functions once
one has been acquired?

>


> It is because the resulting function was a low-level function that the
> gaps size was so small. Odds are that no functional systems that have
> higher minimum structural threshold requirements will be as close to
> anything in any member of any population. These odds are
> exponentially reduced with each step up the ladder. By the time the
> 1000aa level is considered, the odds that any gap will exist that is
> only one or two mutations wide or even one or two dozen mutations wide
> are extremely poor.

The evidence from the real world shows that this is not the case.
There is no evidence whatsoever to suggest that evolution stalls out
at any level.

So even though you deny the evidence from the real world, that
evidence shows that your model of evolution is wrong.

>
> The odds follow a Poisson-type distribution. As one considers higher
> and higher structural threshold requirements, the odds of a narrow gap
> existing drop in such a way as to produce a Poisson distribution
> pattern.

What mechanism prevents the acquisition of further novel functions


once one has been acquired?

Each time such novel function is acquired, we are back to square one.
Evolution, contrary to the model on which you insist, is not goal-
oriented.

>
> That is why the likely minimum gap distance is always much smaller
> than the threshold level. However, a gap distance of just a few dozen
> would require evolutionary mechanisms in a huge population of, say,
> all living things on Earth, trillions upon trillions of years to
> cross.

And how have you calculated "trillions upon trillions of years?
Surely this is not another number you have pulled out of the air?

>
> With each step up the ladder the ratio of potentially beneficial
> steppingstone targets decreases exponentially. That's a fact. What
> results is a widening of the gap between steppingstone targets as one
> moves higher and higher up the ladder.

"Higher and higher" eh?
This may come as news to you, but the idea of evolution as a great
chain of being was discredited about 200 years ago.
I suggest that you come to terms with the fact that you have
substantial gaps in your knowledge of evolutionary theory.

>
> < snip rest - repetitive (both me and you) >

Ah well.
I'll just put back all the questions you refuse to answer:

> Small mutational steps simply do not add up to move a population up
> the ladder of minimum structural threshold requirements.

Why not?

> There just
> aren't any examples of such evolution in action in all of literature -
> not one.

There are very large numbers of papers which present of evidence for
evolution as a series of mutational steps in the literature.
Dismissing them as "not convincing", as is your habit, will not make
them go away.

So where are the conclusions drawn by the authors of papers presenting
evidence for evolution as a series of mutational steps flawed?
You need to address the evidence, not simply ignore it.

> Your cockroach milk evolution example isn't even a real time
> example

Since when has observation in "real time" been a requirement in
science?

What mechanism prevents further changes to the genomenes of these
cockroaches?

Once such a novel function has been acquired, what mechanism prevents


the acquisiting of another novel function?
Or the loss of the acquired function?
This is, after all how evolutionary theory models the evolution of
more complex functions.

> > > If you don't understand why that is relevant, you must be deliberately
> > > blind.

> > > > You have given no reason to think that it is anything other than an
> > > > arbitrary number you have pulled out of the air to falsify an
> > > > inaccurate model of evolution you have devised for no reason other
> > > > than to "falsify" it.

> > > Show me just one example then of observed evolution in action beyond
> > > this structural threshold.

> > No, YOU need give a reason to think that it is anything other than an
> > arbitrary number you have pulled out of the air to falsify an
> > inaccurate model of evolution you have devised for no reason other
> > than to "falsify" it.

> I've already told you the reason.

No you haven't.
You have asserted over and over again that this is requirement, but
provided no evidence whatsoever to suggest that it has any meaning in
the real world.

So YOU need give a reason to think that it is anything other than an


arbitrary number you have pulled out of the air to falsify an
inaccurate model of evolution you have devised for no reason other
than to "falsify" it.

There are numerous example in the literature. The fact that you ignore


them, or pretend that they don't exist, or dismiss them without even
reading them as "unconvincing" is irrelevant. If you have a better
explanation for the evidence, or a better predictive model than
evolutionary theory, feel free to offer it.

> The 1000aa threshold has never been crossed by any series of
> evolutionary steps, short or long, small or large.

Why does it need to?

> Small little steps
> simply do not progress up the ladder of minimum structural threshold
> requirements like you imagine.

Why not?
Is there a mechanism which prevents the acquisition of further novel
functions once one has been acquired?

> They only produce novel functions that
> are below the 1000aa threshold. There is no progression up the ladder
> - not one example.

So what?

What mechanism prevents the evolution of further novel functions?

You have provided no evidence or argument whatsover to support your

RF

>
> Sean Pitmanwww.DetectingDesign.com


_Arthur

unread,
Feb 6, 2007, 3:19:52 PM2/6/07
to
On Feb 6, 2:32 pm, "Seanpit" <seanpitnos...@naturalselection.

In other words, you have no clue how to measure the key value dictated
by your own quack theory that no one can make heads or tail of.

You cite the bacterial flagellae as a prime example of your theory,
but you miserably fail to measure is "fairly specified residues".

But we have your good word that it is certainly greater than 10,000
quatloos, from your own authority. By how much ? You cannot tell.
Any margin of error ? No margin necessary, because your whole concept
is an egregious error.


Vend

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Feb 6, 2007, 4:11:53 PM2/6/07
to
On 6 Feb, 17:24, "Seanpit" <seanpitnos...@naturalselection.0catch.com>
wrote:

> On Feb 6, 6:06 am, "Vend" <ven...@virgilio.it> wrote:
>
> > On 4 Feb, 23:02, "Seanpit" <seanpitnos...@naturalselection.0catch.com>
> > wrote:
>
> > > > Well, common design explains the existence of homology. It doesn't
> > > > explain why when you construct twenty different phylogenetic trees
> > > > for the twenty different enzymes, those trees all agree with each other
> > > > on the shape of the crown groups.
>
> > > It does if the different groups have different by slightly different
> > > functional needs for their slightly different systems and
> > > environments.
>
> > But why trees? and why the trees are consistent?
>
> Does an artists or designer of any kind have to have a reason that
> appeals to you before you can detect design? This is the whole "No
> intelligent designer would have done it that way" argument. Some
> might say that about a Picasso painting if they were from an alien
> planet. Yet, it is easy to detect a great deal of deliberate
> intelligence behind a Picasso.

Well, an unspecified designer could produce anything. That's why
asserting design without specifying anything about the designer is
unfalsifiable and therefore unscientific.

> Beyond this, the nested hierarchy in nature makes a lot of creative
> sense and is even beautifully elegant.

You mean like dolphins with non-functional elbow joints and without
gills?

> The pattern is very similar to
> patterns observed in highly technical human designs of integrated
> systems - especially if a single designer or a small group of
> designers were at work.

For instance?

> And, beyond this, the detection of design isn't about the detection of
> a pattern that a mindless process is likely to produce. It is about
> the detection of something that mindless processes are very unlikely
> to produce.

If I toss 1000 coins the specific sequence I obtain had an a priori
probability of 2^-1000: very unlikely. Do you detect that it wasn't
produced by a mindless process?

> One cannot simply focus on one aspect of a phenomenon and
> make a conclusive hypothesis about mindless or mindful origin. One
> must consider all aspects of the phenomenon before a reliable
> hypothesis can be established. While the nested pattern observed in
> living things can indeed be explained by mindless evolutionary
> processes, the functional aspects of living things, as they move
> beyond very low levels of minimum structural threshold requirements,
> are exponentially harder and harder to explain via mindless
> evolutionary processes.

You keep repeating this, but what is this exponential structural
threshold requirement and how do you know that it exists in biological
systems?

> > You mean like a cd-player in a car?
> > Human designed object form generic graphs, not trees.
>
> Not always . . . nested patterns can also be seen in human design.

Perhaps in some, but they are not the norm. Human designers constantly
mix technologies developed for unrelated applications.
This is what I would expect from an "intelligent" designer for any
reasonable meaning of the word "intelligent".
And we don't see this in biological systems.


Robin Levett

unread,
Feb 7, 2007, 12:17:54 AM2/7/07
to
Seanpit wrote:

> On Feb 4, 8:19 pm, Robin Levett <rnlev...@yahoo.co.uk> wrote:
>> Seanpit wrote:
>> > An interesting 3D model for the distribution of existing small single-
>> > protein systems within sequence space is presented in the following
>> > link of the work of Jim Proctor and Andrew Torda (Hamburg University,
>> > last update May, 2004):
>>
>> >http://www.zbh.uni-hamburg.de/wurst/protspace/ECCB_opt.huge.pdf
>> >http://www.zbh.uni-hamburg.de/wurst/protspace/
>>
>> Sean, before you throw out more references to papers that you can distort
>> to fit your requirements, isn't it about time you addressed the Choi and
>> Kim
>> paper that Howard referred you to on 16 October last year? The one which
>> showed that proteins *in the real world* cluster into 4 families?
>>
>> www.pnas.org/cgi/content/full/103/38/14056
>
> If you read the paper carefully, Choi and Kim do not say that proteins
> form four families. Rather, they argue that protein folds can be
> roughly categorized into four families. That's a big difference.

I have read the paper carefully; you appear not to have done. Try this:

"Protein structures are more conserved than sequences in evolution, thus
most proteins in a given sequence family have similar or related molecular
structures."

Note, by the way, that Choi and Kim are dealing with real, not modelled,
proteins.

It is true that it is the protein structures that fall into 4 classes - but
it is also true that the many protein sequence families fall within those
same 4 classes.

> Also, consider the actual 3D model of their sequence space:
>
> http://www.lbl.gov/Science-Articles/Archive/PBD-Universe-map-Kim.html
>
> Notice in this model that even when it comes to very low-level protein
> folding sequence space, the viable folds do not all overlap. Sure,
> they are close together, but this is only to be expected at this very
> low level of sequence space. It's kinda like the sequence space of 3-
> letter words. They are all very closely clustered together like
> this. However, this closeness of the potential steppingstones rapidly
> expands as one moves up the ladder of minimum structural threshold
> requirements.

Interesting assertion. Any backup for it - it's not in the papers discussed
here.

>> Oh, and even a layman like me can see that you've got your interpretation
>> of
>> the Bornberg-Bauer paper wrong. He specifically states that the HP
>> protein sequences he is examining are not uniformly distributed across
>> sequence space; see the last couple of paragraphs of the paper; and the
>> RNA sequences, that he says do "percolate through sequence space", do so
>> in such a way that "Within a number of mutations small compared to the
>> length of the sequence, the whole shape-space can be covered".
>
> That's right! The *whole* shape-space can be covered via relatively
> small steps. This in fact means that the steppingstones here are
> indeed distributed throughout sequence space. They are not clustered
> together in one tiny corner. The fact that one can get across the
> whole of sequence space without having to step very far from one to
> the next steppingstone simply means that the ratio of steppingstones
> vs. the non-viable "gap" options is rather high at this level of
> minimum structural threshold requirements - as in the case of 3-letter
> words. However, as you move up the ladder of threshold requirements,
> this ratio drops off exponentially. As this happens, the
> steppingstones drift apart rapidly. Pretty soon, it becomes very
> difficult to take the same short steps and hit any steppingstone at
> all.
>
>> Even in the abstract he makes clear that "In analogy to protein families,
>> nets are dense and well-separated in sequence space".
>
> Exactly! And they cover the entire space! The nets are dense because
> of the relatively high ratio that exists at such low levels of minimum
> structural threshold requirements.

No they don't; neither Bornberg-Bauer nor Choi say this. Bornberg is
referring to RNA sequences as percolating through sequence space; the HP
protein sequences he is examining did *not* do so. "Dense and
well-separated in sequence space" does *not* mean "distributed throughout
sequence-space".

When you appreciate this you will realise that your comments above are
misconceived.

Choi, by the way, says this:

"The fact that most of proteins are structured and that the protein
structure space is very sparsely populated and restricted mostly to the
four elongated regions suggest that mutations in genes encoding proteins
have been constrained to those resulting in a structurally viable protein
occupying one of the four allowed regions of the protein structure space:
structural selection or ??designability?? (17, 18)."

which, if read "carefully", should tell you something.

--
Robin Levett
rle...@rlevett.ibmuklunix.net (unmunge by removing big blue - don't yahoo)

richardal...@googlemail.com

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Feb 7, 2007, 6:35:09 AM2/7/07
to
On Feb 6, 6:41 pm, j.wilki...@uq.edu.au (John Wilkins) wrote:

> <richardalanforr...@googlemail.com> wrote:
> > On Feb 6, 4:15 pm, "Seanpit" <seanpitnos...@naturalselection.
> > 0catch.com> wrote:
> > > On Feb 6, 7:58 am, "_Arthur" <Arth...@sympatico.ca> wrote:
>
> > > > So thePitmanGap you invented extends not around proteins, but rather
> > > > around biological structures, now ?
>
> > > Both. It is just that the gap is much smaller for smaller protein-
> > > based functional structures (which usually include single proteins).
> > > The larger the minimum structural size and specificity requirement the
> > > larger the gap size. It's really very simple and downright intuitive.
>
> > ....and not supported by a shred of evidence.
>
> > How do you explain that, Sean?
>
> I want to ask Sean a question.

No point. Sean doesn't answer questions. It's against his religion,
whatever that may be.

RF

John Wilkins

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Feb 7, 2007, 6:51:17 AM2/7/07
to
<richardal...@googlemail.com> wrote:

> On Feb 6, 6:41 pm, j.wilki...@uq.edu.au (John Wilkins) wrote:
> > <richardalanforr...@googlemail.com> wrote:
> > > On Feb 6, 4:15 pm, "Seanpit" <seanpitnos...@naturalselection.
> > > 0catch.com> wrote:
> > > > On Feb 6, 7:58 am, "_Arthur" <Arth...@sympatico.ca> wrote:
> >
> > > > > So thePitmanGap you invented extends not around proteins, but rather
> > > > > around biological structures, now ?
> >
> > > > Both. It is just that the gap is much smaller for smaller protein-
> > > > based functional structures (which usually include single proteins).
> > > > The larger the minimum structural size and specificity requirement the
> > > > larger the gap size. It's really very simple and downright intuitive.
> >
> > > ....and not supported by a shred of evidence.
> >
> > > How do you explain that, Sean?
> >
> > I want to ask Sean a question.
>
> No point. Sean doesn't answer questions. It's against his religion,
> whatever that may be.
>
> RF
>
> >Do you think a 999aa change is possible?

So I see. I wonder why he won't answer.

Seanpit

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Feb 7, 2007, 2:50:08 PM2/7/07
to

The calculation is based on the likely minimum number of specifically
arranged proteins needed to achieve flagellar motility. Each protein
part also has a likely minimum number of residues. Given this
information, the total likely minimum can be roughly estimated to at
least a useful degree.

If you think this estimate is significnatly off based, then by all
means, do present your own estimate of the likely minimum structural
requirements. I'd be most interested.

Sean Pitman
www.DetectingDesign.com

_Arthur

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Feb 7, 2007, 4:28:49 PM2/7/07