From: kmatsuno@VOSCC.NAGAOKAUT.AC.JP (koichiro matsuno/7129)
Newsgroups: bionet.info-theory
Subject: Re: Yockey Definitions
Date: 18 Feb 1995 05:04:33 -0800
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In article <3i00ti$it0@newsbf02.news.aol.com> hpyockey@aol.com (HPYockey)
wrties:
>What did you think of my comments on the origin of life and the
>self-organization of Manfred Eigen? That is a lot more controversial than
>the Shannon-McMillan Theorem.
May I jump in here? Yockey made the same point almost fifteen years ago
and said that "The argument made in all origin of life scenarios is that one
can trace the origin of life by going back in time along evolutionary
pathways to simpler and yet more simple organisms" (Yockey, H. P., 1981,
J. Theor. Biol. 91, 13). I remember this statement because Sidney Fox and
myself quoted it in our JTB paper (1983, J. Theor. Biol. 101, 321) while
responding to his complaint about all self-organization scenarios. But, I
am not going to repeat the same old stroy again ;-). My intention is quite
the opposite.
Yockey's emphasis on the Shannon-McMillan theorem is sound and
unquestionable. Its corollary, however, is that information thus conceived
is synchronic in the sense that the source matrix of information or how to
partition the probability space, once fixed, remains invariant in time.
This point would become most acute if an evolutionary historical
development is the case. If an invariant ensemble of evolutionary _histories_
is available in a synchronic and time-independent manner, the high
probability sequences would certainly tell us something very significant.
In contrast, if only a single sequence of historical development is
available as the evolutionary process proceeding on our earth, synchronic
information would not be of much use even if it is legitimate. Surely, an
uneasiness with synchronic information is visible in the article <3glqca$pof@
mserv1.dl.ac.uk> of Avi Elitzur <CFELI@WEIZMANN.weizmann.ac.il>:
>The impression of information theory emerging from Yockey's
>book is that of a purely technical tool, hardly interesting for the
>biologist. While offering detailed analyses of DNA sequences, Yockey
>dismisses any attempt to go beyond that.
Information referred to a single sequence of evolutionary development is
diachronic and cannot enjoy the conceptual rigor that synchronic
information takes for granted. What synchronic information is to entropy to
the invariant probability space, that is diachronic information to meaning to
the sequence of experience. Yockey has been most keen in warning against
muddling both synchronic and diachronic information in an unprincipled
manner. We should listen to him at this point. At the same time, diachronic
information waits a new challenge because our experiences in general and
evolutionary processes in particular are simply diachronic, though a lot of
seemingly synchronic pieces could be available if cut arbitrarily.
Regards,
Koichiro
Koichiro Matsuno
Department of BioEngineering
Nagaoka Uniersity of Technology
Nagaoka 940-21, Japan
kmatsuno@voscc.nagaokaut.ac.jp
===reply by Yockey====================================================
From: hpyockey@aol.com (HPYockey)
Newsgroups: bionet.info-theory
Subject: Self- Organization and Information Theory
Date: 23 Feb 1995 10:43:05 -0500
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Subject: Self-organization; Information Theory
kmatsuno@VOSCC.NAGAOKAUT.AC.JP (Koichiro Matsuno/7129)
writes 18 Feb 1995 Message ID:<9502181308.AA00134@voscc.nagaokaut.ac.jp>
com
How nice to hear from Professor Koichiro Matsuno who responds to my
request for comments on self-organization of Manfred Eigen and the origin
of life! He quotes a sentence from my paper in Journal of Theoretical
Biology 91 pages 13-31 (1981).
I reread this paper and I find it one of the best I have ever written. It
began with a quote of George Gaylord Simpson's classic paper Science 143
p769 (1964). "The nonprevalance of humanoids."
Simpson called the search for extra-errestrial life "a gamble of the most
adverse odds in history". We are now 31 years after Simpson's paper and
less is known (sic) than in 1964. Afficionados have lost their cherished
reducing atmosphere and--worst of all-the primeval soup essential to all
"origin of life" scenarios has faded away like a Cheshire cat leaving only
the smile. For justification of that remark see chapter 8 in Information
Theory and Molecular Biology and my reply to Lifson in BioEssays January
1995.
My 1981 paper showed that information theory proves the impossibility that
life originated by a self-organization process, whatever that may be. I
enlarged this argument in Chapter 10 of Information Theory and Molecular
Biology, especially section 10.3 where I discussed the essential fallacies
of Fox's protenoids.
Proteinoids are neither new nor original with Fox. I put the following
epigram at the beginning of Chapter 12.
"I am in point of fact, a particularly haughty and exclusive person, of
pre-Adamic ancestral descent. You will understand this when I tell you
that I can trace my ancestry back to a protoplasmal primordial atomic
globule." Pooh-Bah in The Mikado Act 1 by W. S. Gilbert. Obviously,
Gilbert and his audiences through the years have thought it a huge joke to
put this in the mouth of a comic, pompous, ostentatious official.
After my 1981 paper, professor Sidney Fox and K. Matsuno suffered in
silence until they sent a Letter to the Editor 101 321-323 (1983). It took
some time but in this letter they had at last discovered "some of the
unidentified assumptions in Yockey's (1981) interpretation of information
theory relative to concepts of self-organization in the origin of life".
They continued with the sentence quoted by Matsuno and commented further:
"The essential fallacy of this back-extrapolation for proteins is the
implied dependence upon a one-to-one correspondence in amino acid residues
from one stage to another, especially with respect to information
content."
Sidney Fox was the editor of the Proceedings of the Liberty Fund
Conference on Selforganization held in 1984 at Key Biscayne Florida. He
was careful to see that I was not invited. He does not mention my paper of
1981 in the Proceedings.
He contributed an article to the book Science and Creationism edited by
Ashley Montagu 1984 published by Oxford. In this article he comes up with
these and other bloopers: page 203; "Some recognize that proteins in
modern organisms are nonrandom for the set of molecules as a whole, this
kind of non randomness (or order) being derivative of the action of DNA
and RNA." "The instructions for protobiotic proteins have been explained
experimentally as arising from the amino acids themselves. This novel
experimental fact is crucial to the understanding of the origin of life."
Page 204 "Since the order in the amino acids results from no materials
other than the reactants, mixed amino acids must order themselves." (I
wonder what tRNA is doing!)
Page 214 "Proteinoids are in the main much like proteins, but the very
name indicates they are not proteins." A rose by any other namexx
On page 198 Sidney Fox referred to my 1981 paper and attempted to imply
that I am a creationist: "Many authors, such as Darnbough et al (1981 a,
b) and Yockey (1981), feel they can reconcile scripture and science;
mostly these are not creationists in the sense of the ICR fundamentalists.
Following on page 199 he says: "The self-organizationist theme is accepted
by numerous scientists, e. g. Eigen (1971), Kuhn (1981), Matsuno (1981),
although not by others such as Yockey (1981), whose numerous quotations
from scripture in his critique of self-organization raises a question of
the purity of his scientific premises."
My quotations from scripture and other sources, including Homer and
Jonathan Swift's Gulliver's Travels, available to educated men, are
literary allusions used by all competent authors that illuminate the point
under discussion. Any well-educated and well-read reader would understand
that. Fox's objection is strictly de minimus.
Haldane who, although a communist and an atheist, was an educated man and
a very competent writer, noted in a paper published in 1954 that the idea
that the oceans brought forth life is an old one. Haldane quoted Genesis
1:10 "And God called the dry land Earth; and the gathering of the waters
He called Seas: and God saw that it was good." Genesis 1:20: "And God
said, Let the waters bring forth abundantly the moving creatures that hath
life, and fowl that may fly above the Earth in the open firmament of
Heaven."
In Information Theory and Molecular Biology I made it quite clear that the
role of religion is different from that of science.
Matsuno continues in his posting: "Yockey's emphasis on the
Shannon-McMillan theorem is sound and unquestionable." "Its corollary,
however, is that information thus conceived is synchronic in the sense
that the source matrix of information or how to partition the probability
space, one fixed, remains invariant in time."
This is the old confusion of information and meaning that I discussed in
the book and in my paper in January BioEssays.
In the first place, the Shannon-McMillan Theorem tells us that if the
probability distribution is not all equal we may divide the total number
of the sequences in the ensembles into two groups. The number of sequences
on one group, called the high probability group, is 2^NH where N is the
number of elements in the sequence and H is the Shannon entropy. The
number of sequences in the other group, called the low probability group,
is negligible and may be ignored. Thus the number of sequences in a chain
of 100 amino acids, such as cytochrome c, that one needs to be concerned
with, is not 20^100 but 2^100x3.3966 a number smaller by a factor of about
10^27. See Table 6.4 in my book.
This result is virtually unknown by molecular biologists. Be the first in
your neighborhood to amaze your colleagues!
Problem for the student: calculate these two numbers to see what fraction
of the total possible lie in the high probability group.
Perhaps in another posting Matsuno will tell us what "synchronic
information" is.
I thank Matsuno for pointing out my "keen warning against muddling" the
meaning of words.
A large part of the confusion in Fox's writings lies in the word-traps
random, order, disorder etc. See my explanation in BioEssays January 1995
and in Information Theory and Molecular Biology.
For an explanation of the modern mathematical notion of random see When is
random random? Nature 344 p823 (1990)
Auf wiedersehn, Hubert
=======================================================================
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Brian Harper |
Associate Professor | "It is not certain that all is uncertain,
Applied Mechanics | to the glory of skepticism" -- Pascal
Ohio State University |
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