Re: Information: Brad's reply (was Information: a very

Brian D Harper (
Mon, 29 Jun 1998 22:42:57 -0400

At 08:41 AM 6/25/98 -0700, Greg wrote:
>Brian Harper:
>> I don't know what to say except to repeat what Yockey says in
>> his book. In section 5.1.3 he states that the DNA-mRNA-protein
>> system is discrete, memoryless and unconstrained. These terms
>> are defined as follows:

>Is Yockey talking just about the decoding context, where codons
>are mapped to amino acids? Surely he doesn't mean that there
>are no intersymbol dependencies in DNA when seen as a big part
>of the schematic for a system which has to be alive.

Sorry about my delay. Perhaps this turns out for the best as
I think I understand a little better where your coming from
after reading your recent posts.

Before going on, I better insert my standard disclaimer. When
I wrote "I don't know what to say except to repeat ..." I
really meant this quite literally. I have an amateurs interest
in information theory and its application to molecular biology.
I can relay what Yockey and others have said but I'm really not
proficient enough to defend it.

Having said that it seems to me that Yockey is only concerned
with the decoding context as you suggest above.

Now let me bring up a point that confuses me a great deal.
Awhile back I spent some time looking at the controversy
surrounding "meaning" in information theory. I think its
important to point out that it is not only creationists
who are uncomfortable with this aspect of information theory.
Also, mistakes have been made at the highest levels, so to
speak. For example, according to Yockey anyway, Manfred
Eigen errs in this regard by trying to introduce _ad hoc_
the idea of meaningful information in the development of
his hypercycles. And again, according to Yockey, his
hypercycles self-organize only as a result of this
"meaningful" information in a similar but much more
complicated way that Dawkins typing monkey always seems
to find the target phrase :). Yockey is fond of saying things
like "meaningful to who?" in order to make clear the teleological
nature of "meaningful" information.

Moving on, I gather from your posts that you would side with
Yockey on the point that information theory cannot address
meaning. But here's where I get confused. The analog to
"meaning" in a biological application is functionality or
specificity. So, while Yockey spends a great deal of time
emphasizing the point that information theory cannot address
the meaning of a message, he also spends a great deal of time
later on in his book getting an estimate for the amount of
information needed to specify a molecule of iso 1 cytochrome c (icc).
Here he uses available information on functionally equivalent
sites (sites where more than one amino acid can be present and
retain functionality) in order to significantly reduce the
information content of icc. So, is Yockey contradicting himself?
I really don't think so, however, I think I'll leave this as an
open question for the time being soas to avoid dragging on too

OK, now there were some things about your recent posts that
were bugging me for reasons similar to the above. In
particular your post "More on information, meaning, and
biological application". For example, you talk about all
these things that *we* know and how this reduces *our*
uncertainty and thus the information. But this makes
sense (to me anyway) only if *we* are the receivers. But
isn't it more appropriate to consider ourselves disinterested
observers? The proteins are the receivers, how do all these
things reduce their uncertainty? This doesn't at first sight
seem objectionable wrt what Yockey did. The proteins do
"know" about functionally equaivalent amino acids since
"know" is just a convenient way of talking about the chemistry
involved in the functional equivalence. I think. But I tend
to get more confused the more I think about this.

Brian Harper
Associate Professor
Applied Mechanics
The Ohio State University

"It appears to me that this author is asking
much less than what you are refusing to answer"
-- Galileo (as Simplicio in _The Dialogue_)