Trevors and Abel paper

I have read the paper in more detail and found its claims to be even
more wanting than I had initially imagined.

They discuss the code optimization and redundancy in the genetic code
and claim that

<quote>
Such optimization makes it all the more difficult to explain the
molecular evolution of such exquisite non-human genetic algorithms.
Random walks (Markov Processes) (Holland, 2003
<http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WCB-4DTKB55-1&_coverDate=11%2F01%2F2004&_alid=318995320&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=6734&_sort=d&view=c&_acct=C000047944&_version=1&_urlVersion=0&_userid=918210&md5=2ada792f9d3a8545cf4a4bbd7939b320#bib75>)
will never provide an adequate explanation for the generation of such a
highly refined translative coding system. Nor will it provide an
explanation for the codonic operating system and specific programs
generated through selection of each nucleotide in a strand.
</quote>

But the argument is not that random walks are an adequate explanation of
the 'refined coding system', on the contrary, the argument is that this
presents a selective refinement after a more simple code had arisen via
stereochemical relationships between codons and their binding sites.
While the Holland paper addresses a Markovian process, it does not
address the selection part. In fact, little or none of the paper deals
with the origin of the genetic code as far as I can tell

A Derived Markov Process for Modeling Reaction Networks Author: Holland
J.H. Evolutionary Computation, Volume 11, Number 4, 1 November 2003, pp.
339-362(24)

Why the authors focus on a mostly irrelevant paper and seem to ignore
the relevant ones is regrettable.

When scientists do work in this area the complaint is that these
examples are 'artificial' as they involve human engineering. This is a
common and fallacious objection from ID creationists against such
experiments, namely that these experiments should somehow be rejected
because they are 'artificial'.

The paper continues its random walk through scientific knowledge never
really addressing the existing scenarios other than by ignoring them or
rejecting them out of hand.

The paper reads like a typical ID paper to me. Many words, little content.

They even use the term "prescriptive information", not unlike the term
"specified information; combined with the concept of irreducible
complexity "All necessary structures/functions for protein synthesis
would have had to be in place, and a predetermined specific
correspondence between codon sequence and amino acid sequence had to
have predated translation."

They make the fallacious claim, not unlike Dembski's that

"Natural mechanisms are all highly self-ordering. Reams of data can be
reduced to very simple compression algorithms called the laws of physics
and chemistry. No natural mechanism of nature reducible to law can
explain the high information content of genomes. This is a mathematical
truism, not a matter subject to overturning by future empirical data."

And yet we know how information content can arise under fully natural
processes of chance and regularity (Schneider, Adami, Lenski and others)

They then continue to confuse Shannon uncertainty with Shannon
information. As Schneider has shown, people seem to often confuse
Shannon information with the log2 P. It's the reduction in Shannon
uncertainty which generates high information content. In other words, an
initial random distribution will have high entropic values, the
reduction in entropy when certain solutions are constrained or selected
for, increases the information content of the genome.

In my opinion, and others may surely disagree, the arguments proposed
against chance and regularity, while mimicking ID's arguments, also fail
because of the failure of these ID arguments. ID, doomed to present
evolution in its worst light, seems unable to envision why less strawmen
like processes could not explain the "high information content" of the
genome nor the irreducibly complex nature. Failure to understand
evolutionary explanations leads one to suggest that since DNA appears to
resistant to change (in other words, IC) it cannot have evolved.
That goes against all the arguments and examples presented which
indicate strong evidence not only that the genetic code has evolved but
also how it may have evolved.

What does ID have to offer?

It's time to explore in more depth this paper and address its failings
in more detail. A cursory evaluation already shows that it relies on
many of the flawed ID arguments.
Received on Sun Oct 2 16:51:40 2005