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To: StJacques; betty boop; PatrickHenry; tortoise; Doctor Stochastic; All
This is a reply post to a message on another thread which is also applicable to the discussion here:

Review of Yockey’s book, Information Theory and Molecular Biology (1st printing)

IMHO, this review illustrates the reviewer’s failure to understand the difference between the message and the communication of the message – as he ignores much to reduce the entire process to “decoding”. Most of his concerns center on his suspicion that Yockey is an intelligent design theorist or creationist.

On the handy side though, the webpage includes a graphic which illustrates and compares the Shannon communication model in normal engineering v biological systems (though he ignores both the communication and the rise of symbolization in his review).

Yockey responded to the above review in an email dated Nov 13, 2000:

Dear Gert:

Thank for your review of my book Information Theory and Molecular Biology. This book is now out of print but I am working on the second edition.

You seem puzzled by my quotations of the Bible. Please note that I also quote Robert Frost, Homer's Iliad, the Mikado, Charles Darwin, Machiavelli''s The Prince, Plato, The Rubaiyat and other sources. When something was said 2000 years ago, it is plagiarism to say it again without quotation.

It is a viscous circle indeed! (*) But that is what we find by experiment. We are the product of nature not its judge. As Hamlet said to his friend: "There are many things, Horatio, between Heaven and Earth unknown in your philosophy."

See Gregory Chaitin's books "The Limits of Mathematics",1998 and "The Unknowable",1999 both Springer-Verlag. See also my comments on unknowability in Epilogue. We will never know what caused the Big Bang and we will never know what caused life.

By the way, I am indeed an anti-creationist becaue I believe that the origin of life is, like the Big Bang, a part of nature but is unknowable to man.

Taken all in all, especially for those who finished reading the review, it is very favorable.

Here is a list of my recent publications. If you send me your postal address I shall send you the Computers & Chemistry paper. That will explain why the recent data on the genomes of human and other organisms provide a mathematical proof of "Darwinism" beyond a reasonable doubt. (**) I suggest you read the paper in Perspectives in Biology and Medicine. Perhaps you would then like to read some of Walther Löb's papers. Stanley Miller was not the first to find amino acids in the silent electrical discharge.

Yours very sincerely, Hubert P. Yockey

Yockey, Hubert P. (2000) "Origin Of Life On Earth and Shannon's Theory Of Communication", in: "Open Problems of computational molecular biology", Computers & Chemistry 24 issue 1 pp105-123 [This is an invited paper.]

Yockey, Hubert P. (1997) Walther Löb, Stanley L. Miller and "Prebiotic Building Blocks" in the Silent Electrical Discharge Perspectives. in: Biology and Medicine 41, Autumn pp1125-131.

Yockey, Hubert P. (1990) "When is random random?", Nature Vol 344 p823. (scientific correspondence).

A great source on the web (most of Yockey’s work is printed but not on the web) is: Biological Information Theory and Chowder Society

Here’s a helpful tidbit to get one’s “arms around” the question:

If someone says that information = uncertainty = entropy, then they are confused, or something was not stated that should have been. Those equalities lead to a contradiction, since entropy of a system increases as the system becomes more disordered. So information corresponds to disorder according to this confusion.

If you always take information to be a decrease in uncertainty at the receiver and you will get straightened out:

R = Hbefore - Hafter.

where H is the Shannon uncertainty:

H = - sum (from i = 1 to number of symbols) Pi log2 Pi (bits per symbol)

and Pi is the probability of the ith symbol. If you don't understand this, please refer to "Is There a Quick Introduction to Information Theory Somewhere?".

Imagine that we are in communication and that we have agreed on an alphabet. Before I send you a bunch of characters, you are uncertain (Hbefore) as to what I'm about to send. After you receive a character, your uncertainty goes down (to Hafter). Hafter is never zero because of noise in the communication system. Your decrease in uncertainty is the information (R) that you gain.

Since Hbefore and Hafter are state functions, this makes R a function of state. It allows you to lose information (it's called forgetting). You can put information into a computer and then remove it in a cycle.

Many of the statements in the early literature assumed a noiseless channel, so the uncertainty after receipt is zero (Hafter=0). This leads to the SPECIAL CASE where R = Hbefore. But Hbefore is NOT "the uncertainty", it is the uncertainty of the receiver BEFORE RECEIVING THE MESSAGE.

The post continues with an example in DNA binding sites.

And here is a message posted by Yockey on the Chowder Society in response to abiogenesis: Yockey #7

To: Brian D. Harper:

I have been lurking in this newsgroup for some time. You have understood my articles and my book. Congratulations. I directed the book to molecular biologists, applied mathematicians and theoretical physicists. It is nice to have someone from Applied Mechanics. Has there been any conversation about this at the faculty club?

"Your book gets discussed here every now and then. I am hoping that people will take this opportunity to pose their questions to the author himself, rather than get second-hand interpretations. I will list below what I feel are some of your more controversial views that should be of interest to this group. Please feel free to modify these if I mis-represent your views in any way ;-)"

You asked three questions:

a) the primeval soup probably never existed

b) even if it did, the various self-organizational schemes proposed to "explain" the origin of life still don't work

c) life must be accepted as an axiom

You get an A!

Response to a) The correct way to pose that statement is: There is no evidence that a primeval soup ever existed. If one looks for geological evidence that a primeval soup existed one comes up empty. See discussion in Information in Bits and Bytes in BioEssays v17 85-88 1995.

There is a more thorough discussion in Information Theory and Molecular Biology. Dialectical materialists are atheists. Their belief in a primeval soup without evidence puts them in bed with theologians. In science the "Absence of evidence IS evidence of absence." One does not believe unless and until one has overwhelming evidence. You will note of course that this is a twist from the usual declaration of faith by SETI disciples. Forgive me if I think this incongruous situation is very funny.

Response to b) All dialectical materialist origin of life scenarios require in extremis a primeval soup. There is no path from this mythical soup to the generation of a genome and a genetic code. John von Neumann showed that fact in his Theory of Self-Reproducing Automata U of Ill. Press 1966. One must begin with a genetic message of a rather large information content. Manfred Eigen and his disciples argue that all it takes is one self-catalytic molecule to generate a genome. This self-catalytic molecule must have a very small information content. By that token, there must be very few of them [Section 2.4.1] As they self-reproduce and evolve the descendants get lost in the enormous number of possible sequences in which the specific messages of biological are buried. From the Shannon-McMillan theorem I have shown that a small protein, cytochrome c is only 2 x 10^-44 of the possible sequences. It takes religious faith to believe that would happen. Of course the minimum information content of the simplest organism is much larger than the information content of cytochrome c.

c) Niels Bohr in his Light and Life [Nature 1933 v131 p421-423; 457-459] lecture is the author of the suggestion that life must be taken as an axiom inasmuch as we take the quantum of action in quantum theory as an axiom. There are many other examples in relativity and quantum mechanics. Prominent among these is the wave-particle dualism. How can an electron, clearly a matter particle, be at once a wave and a particle?

Pose this proposition to your enemies (not your friends): Given any two theories, an experiment will decide between them and prove one true and one false. This is the philosophy of Sir Karl Popper. When a physicist does an experiment to prove that an electron is a particle, it behaves as a particle. When another physicist does an experiment to show an electron is a wave, it behaves as a wave. In some diffraction experiments ray tracing shows the electron or neutron was in two places at once. Thus these experiments prove the wave-particle dualism. Einstein was extremely annoyed by this and suggested experiments to explain what he regarded as a dilemma. He exclaimed: Der lieber Gott wuerfelt nicht mit der Welt! Bohr's reply was: "Einstein, stop telling God what to do!"

Faced with what physicstis and chemists have had to accept from relativity and quantum mechanics, taking the origin of life as an axiom seems rather tame.

In the book I discussed other mathematically deeper questions, for example undecidability. Until the work of Goedel and Turing it was assummed that a mathematical proposition was either true of false. They proved that some questions are undecidable. For example, given any computer program it is undecidable whether it will ever stop. One can check it empirically. But suppose it doesn't stop in one year, no one can be sure it wouldn't stop in another five minutes. So it is with the origin of life.

The dialectical materialist lumpen-intelligentsia are extremely annoyed that God didn't take their advice when He made the universe.

Incidentially my suggestion that biologists follow particle physicsts in doing enormously expensive experiments was intended as a joke.

This is enough for now. Refer to what I have posted on other newsgroups. Best regards , Hubert

150 posted on 12/15/2004 9:22:21 AM PST by Alamo-Girl
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To: Alamo-Girl
a) the primeval soup probably never existed

Nonsense. Hydrothermal systems that exhibit complex organic chemistry bootstrapping are known to exist today in some corners of the world.

b) even if it did, the various self-organizational schemes proposed to "explain" the origin of life still don't work

Nonsense. Significant biochemistry substructures are observed to be generated in the systems referenced above. However, the chemistry of this catalytic self-assembly is not fully understood.

c) life must be accepted as an axiom

Nonsense. Life is not even well-defined, and becomes very fuzzy under scrutiny in practice -- there is no such thing as a closed system. Regardless, "life" is an arbitrary categorization based on a set of system properties, not an axiom. (In a sense, this makes the above argument a circular definition.)

151 posted on 12/15/2004 9:53:58 AM PST by tortoise (All these moments lost in time, like tears in the rain.)
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