Design Theory, Critiques and Protein Folding
Sat, 29 May 1999 17:58:43 EDT

Greetings to One and All:

As part of my background reading for the review paper I am writing, I ran
across the following quotation. I applies to any scientific model, but I
believe it applies especially to intelligent design theory:

"Models are evaluated against...criteria by means of critiques, published or
unpublished. ('Critique' as used here is broadly defined as the cognizance
of potential flaws in a model.) If based on theoretical [or in the case of
ID theory philosophical] grounds only, critiques do little more than alert to
possible weaknesses in the model, or merely place doubt on the model. To
prove that a model is faulty, or to show that an alternative model is more
valid, the theoretical basis of the critique must itself be tested and
verified by experiment or by observation." Duane L. Rohlfing 1974, from
"Evolution of Models for Evolution" in K Dose, SW Fox, GA Deborin, TE
Pavlovskaya, eds., _The Origin of Life and Evolutionary Biochemistry_, Plenum
Publishing Corp., New York, pg. 399.

This could simply be dismissed as another form of the anti-creationism "if
you criticize an established theory you have to prove you are right" dodge,
but it still emphasizes the point that it is the responsibility of the people
who challenge a model -- established or not -- to prove their own critique
rather than the responsibility of those who defend the model to refute the
critique. It seems to me that ID theorists are ignoring this simple
scientific truth. Nearly all I have seen of any ID argument consists of
philosphical and some few theoretical critiques of the evolutionary model,
with virtually no experimental evidence to back it up. The recent attemt to
use the peppered moth scenario by the Discovery Institute is a case in point.
The argument presented consists entirely of several critiques of the
scenario, but no actual evidence to show either that the critiques are right
or even significant, or that a revised scenario presents any particular
problem for the evolutionary model.

I have tried to find specific experimental or observational evidence that
would support one particular ID critique of evolution -- irreducible
complexity -- and found only one case. I had heard on another discussion
group that Jay Richards of the Discovery Institute had advised someone on how
to find articles on how the protein folding problem contradicted evolution
that were published in recent journals. So I e-mailed Mr. Richards to ask
for a couple of references and perhaps the names and contact information of
any scientists who had evidence that protein folding contradicted evolution.
For those of you who do not know, the protein folding problem amounts to the
fact that we protein chemists cannot yet predict the three-dimensional shape
of a protein from its amino acid sequence. As a protein chemist the idea
that protein folding might contradict evolution intrigued me.

At first Mr. Richards refused, stating that he was worried I would attack the
scientists. When I assured him that I would not, he then said to look in the
March issue of the Journal of Molecular Biology of this year. I did so and
discovered not only that there were four issues for that month (the journal
is published weekly) but that every one had at least one article of protein
folding, sometimes more. So I e-mailed him again and asked for a specific
reference. Again he refused. Fortunately Paul Nelson gave me the name of
the primary author -- Douglas Axe, who was also listed as a postdoctoral
fellow at the Discovery Institute -- and thus I was able to find the article
in question (Axe DD, Foster NW, Fersht AR. "An Irregular beta-Bulge Common
to a Group of Bacterial RNases is an Important Determinant of Stability and
Function in Barnase." _Journal of Molecular Biology_ 1999; 286:1471-85) plus
two more (Axe DD, Foster NW, Fersht AR. "A Search for Single Substitutions
That Eliminate Enzymatic Function in a Bacterial Ribonuclease."
_Biochemistry_ 1998; 37:7157-66; Axe DD, Foster NW, Fersht AR. "Active
barnase variants with completely random hydrophobic cores." _Proceedings of
the National Academy of Sciences USA_ May 1996; 93:5590-4). By the way, I
have PDF file copies of these articles for anyone who wants one.

Paul recommended that I not "pester" Dr. Axe, otherwise it would only prove
to Mr. Richards that my aim was to cause trouble, but I began an e-mail
conversation with Dr. Axe in any event, sending blind copies of my
correspondence to Paul to show that I would not "pester" him. To make a long
story short, Dr. Axe denied that his work had any relevance on intelligent
design. It was also soon after that that I noticed his name had been removed
from the Discovery Institute website as a postdoctoral fellow. (By the way,
the Discovery Institute had provided funds for Dr. Axe to do his research;
the JMB paper acknowledges the financial contribution.)

So the one case (that I know of) of "real" evidence that supports the ID
critique of evolution turns out to be either a deliberate misrepresentation
or an honest error that was never checked out and so never corrected. The
question then becomes, does ID theory in fact have ANY evidence to support
its critiques, or is the only thing it can do is caste unsubstantiated doubts?

Kevin L. O'Brien