Re: DNA sequence space

Cornelius Hunter wrote:

> Terry:
>
>
>> Cornelius,
>>
>> #1 is disputable. By no means a clear picture. Pim provided some
>> recent work in the area. ID folks claim that "science is giving us a
>> clear picture", but it's mere assertion.
>
>
> So, speculation about how (not whether) the code evolved from people
> who presuppose that it must have evolved constitutes "work in the
> area" but our knowledge from biochemistry and empirical evidence that
> the code is difficult to evolve is "mere assertion." Funny how things
> get spun. Here is a paper that actually does address the question at
> hand:
>
>
Indeed, funny how things get spun. Remember your claim was that science
shows that

" it is unlikely that the DNA code evolved via unguided naturalistic
processes as evolutionists maintain is true."

All we have done is shown that your presentation of science is incorrect.

You also continue to confuse the resistance to evolution of the present
day code versus the evolution of said genetic code.
Do some reading, the researchers have gone beyond speculations and are
focusing on ways to test their hypotheses. Perhaps you want to present
your hypotheses to the mix and see how well they do?

Whether or not you like what the papers I provided have to say, they
undermine your #1 premise.

> I've read the papers Pim cites. They do little to address the question
> of how the evidence bears on whether or not the code evolved, for the
> simple reason that they are doing normal science where evolution is
> presupposed.

There we go again with the continued confusion of Cornelius part. What
is wrong about accepting the fact of evolution? Surely they do not limit
their explanations to selection alone so it's hard to argue that they
have presupposed Darwinian Evolution. They are merely taking the
evidence and see where it leads them. Surely their work disagrees with
your #1 premise. Time to drop it.

> It doesn't matter how absurd the proposition is, they keep hammering
> away at it regardless. Quite frankly, it is remarkable that
> evolutionists continue to maintain that there is, somewhere, some
> strong evidence for the code evolving.
>
That's because the evidence is extremely strong for this. I thought you
had read the papers....

> However, be that as it may. My point does not hinge on whether or not
> #1 is in dispute. My point is merely that evolution skeptics and IDs
> hold to #1, or the equivalent for other biological wonders.

There go those goalposts again... So skeptic: Why do you not present
YOUR best explanation of the genetic code? "Poof"...?

As far as the paper quoted by Cornelius, let me provide a fuller
overview of the arguments, including the title and the authors involved

Chance and necessity do not explain the origin of life Cell Biology
International *Volume 28, Issue 11, Pages 729-833 (November 2004) *Pages
729-739 J.T. Trevors and D.L. Abel

Referenced by three papers

2005 Thermosynthesis as energy source for the RNA World: A model
for the bioenergetics of the origin of life Muller, A.W.J.
BioSystems 82 (1), pp. 93-102

2005 Hypothesis: The origin of life in a hydrogel environment
Trevors, J.T., Pollack, G.H. Progress in Biophysics and Molecular
Biology 89 (1), pp. 1-8
Abstract: A hypothesis is proposed that the first cell(s) on the Earth
assembled in a hydrogel environment. Gel environments are capable of
retaining water, oily hydrocarbons, solutes, and gas bubbles, and are
capable of carrying out many functions, even in the absence of a
membrane. Thus, the gel-like environment may have conferred distinct
advantages for the assembly of the first cell(s).

2005 Origin of genetic instructions is presently unknowable and
undecidable and requires scientific experimentation that is not readily
possible Trevors, J.T. Rivista di Biologia - Biology Forum 98 (1),
pp. 23-31
The last one is one that got me more interested since Rivista di
Biologia is not only a strongly anti-Darwinian publication but also the
title suggests that the origin of genetic instructions is presently
unknowable/undecidable and requires experimentation that is not readily
possible. They are not arguing that science is without explanations,
just that deciding which of these explanations is better, cannot
presently be resolved.

Abstract: What was the origin of genetic instructions? The answer to
this question remains both unknowable and undecidable at this time from
a scientific perspective ***if*** genetic instructions did not arise by
a combination of necessity, chance or random events, long periods of
time and prebiotic chemistry. Moreover, the origin of genetic
instructions may have been by events that humans have not discovered at
this time, but possibly will discover in the future.
The paper reads like something ID proponents could have written: Deny
that chance and necessity can explain X, thus ID becomes a viable
possibility. But science presents viable chance/necessity pathways and
supports this with evidence. What does ID have to offer here?

Trevors and Abel argue that ***if*** genetic instructions did not arrive
by a combination of chance or necessity... But that's begging the
question given the state of research in this area, one cannot reject
this strong possibility.

So now we have yet another detail added

Thermosynthesis as energy source for the RNA World: A model for the
bioenergetics of the origin of life
 Biosystems Volume 82, Issue 1 , October 2005, Pages 93-102 by Anthonie
W.J. Muller which addresses Trevor and Abel's assertions

The possibility of at least a theoretical solution to the problem of the
origin of life has been doubted and the need for an overall model or
concept has been stressed (Woese, 1980 and Medawar and Medawar, 1985).
The emergence of the genetic machinery especially is considered hard to
explain (Trevors and Abel, 2004). The presented model accounts for the
self-organization, the thermodynamics and the emergence of the genetic
machinery including the genetic code. The key remaining unsolved issue,
the primordial synthesis of a protein library that contains pF1s with
the proposed general substrate condensing ability, will have to be
solved by experiment.

So given the countless examples contradicting the Trevors and Abel
paper, why should we suddenly reject these hypotheses just because this
paper makes some critical statements?
After all, various plausible and yes even testable claims exist about
the origin of the genetic code.

Such as stereochemistry for instance

It hase been found that there is strong association between the codons
which code for arginine and arginine binding sites. Research found that
more codons showed such association such as Tyr, Lle, Gln, Leu and Phe.
See http://bayes.colorado.edu/
Received on Sun Oct 2 14:41:46 2005