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Nasty feelings in the OOL community toward Hubert Yockey?

Notable Book Reviews (by Jason Rosenhouse) shows that attempts are being made to discredit Hubert Yockey’s work, particularly his last book on the origin of life published in 2004:

reviewer Chris Adami:

many derivations in this book (all of them already present in the 1992 version) are deeply flawed either mathematically, or by the use of inappropriate biological assumptions, or both.

What is most surprising is that such a volume could pass an impartial peer review process. Cambridge University Press would do well to examine the circumstances of this and the previous book’s approval and editing process.

Adami is recommeding an investigation into Yockey’s 1992 book, Information Theory and Molecular Biology? Come on guys, why wait this long?

Now it turns out Yockey’s peer-reviewed work has been cited by many creationists and some IDists. Is that the real reason? Is there a move now, 14 years after the fact, to discredit him and his literature?

Well, if I may offer a speculation, in addition to giving inadvertent aid and comfort to the enemy (IDists and creationists) with his writings, Yockey’s last book managed to ruffle a lot of feathers, particularly in the origin of life community. And the fact his ideas have been peer-reviewed in mainstream theoretical biology journals, and then cited by creationists and IDists after acceptance makes him a good target I suppose.

First of all, I have Yockey’s book, and being a student of the information sciences I can say his ideas and literature are far superior to any of Adami’s literature that I’ve seen. (Adami by the way is an author of the make-believe world of Avida which we IDists routinely take sport in bashing because it’s so filled with bugs, misconceptions, and circular reasoning. Adami should be one to talk about the use of inappropriate biological assumptions. )

How about a cursory look of claims by Adami:

The sequence data for much of the presentation in Chapter 6—unchanged since its 1992 inception—is ostensibly from the Protein Information Resource 2003, but checking with the 1992 book reveals that the source is a 1986 paper.

Oh really, what does Yockey really say in his 2004 book:

for example page 80:

Found by Data from Protein Information Resource (2003)…
phage T4 Lyxozyme 157 from Alber et al. (1987). Nature 330…..
phage k from Reidharr-Olson & Sauer (1988). Science 241…
phage lambda sites 84-91 from Reidharr-Olson & Sauer (1988)…

Uh, Adami, did you fail to read the the data source notes?

And what did Yockey actually say about the Protein Information Rescource (2003)

page 68:

The Protein Information Resource (2003) has provided an alignment of iso-1-cytochrome c sites from a number of organisms, together with replacements from other studies, that were found to be either functionally equivalent at that site or not functionally equivalent http://pir.georgetown.edu

That’s right, he even provides in his book the website the reader can visit to check the data for himself. I went to the pir.georgetown.edu site and fumbled through some of the cytochrome sequences. The site was impressive.

One thing to consider, even if the principal source is a 1986 paper, some data points will appear exactly as in the 2003 database as they did in the 1986 papers. Uh, gee, the kind of amino acid in sequence position 4 of human cytochrome-c in 1986 would probably be the same kind of amino acid in sequence position 4 in human cytochrome-c in 2003. As Adami points out: “The sequence data for much of the presentation in Chapter 6—unchanged since its 1992 inception.” Well Duh!

Yockey was listing the number of variants in each position. But here is something to consider in comparing 1986 to 2003 data: would we expect that there would be any radical changes, especially if a lot of these positions are “conserved”? No. For example we may have more data for cytochrome-c in primates, but would we expect the number of variants in position 4 to change simply because we’ve added more primate sequences to the database? No.

Furthermore, could Adami point to one deeply flawed calculation or concept? He could have been more specific and said, “Oh Yockey incorrectly applies the Shannon-McMillan-Breiman Theorem in his analysis of sequence space…..” or “Yockey is inccorect that evolution requires an increase in Kolmogorov-Chaitin algorithmic entropy”. But, no, just vague generalizations.

Ok, what was it that possibly got Yockey in hot water? Yockey summarizes the conclusion of his book, which if true, would show why OOL money (like Harvard’s multi million dollar initiative) will be good only for keeping scientists employed, not for solving any scientific questions:

from his website www.hubertpyockey.com:

The origin of life is unsolvable as a scientific problem…..

To give flavor of the jabs he takes at OOL researchers in his book, here is his criticism of Stanley Miller who once said, “We believe that there must have been a period when the Earth’s atmosphere was reducing”

Yockey responds:

The reverent words “we believe” are clearly based on faith and a qausi-religiosity will to believe. They are appropriate to apologetics but not in scientific literature.

And Yockey has harsh words for NASA:

These facts do not discourage faith in the official NASA policy for the origin of life (Morrison, 2001). That policy is based on the Marxist dialectical materialism of Engels and Oparin. NASA policy follows Engels “proteins first” from dialectical materialism….

Most origin of life projects supported by NASA and other funding agencies are “proteins first” and are due to to go the way of perpetual motion machines

And then takes shots at self-organizational theorists:

the thrust of many origin of life scenarios has been to attempt to show how to generate “order” out of “chaos” (Morowitz et al., 2000). Those who pursue this approach are caught up by the Tar Baby, like Br’er Rabbit, and get into more and more trouble…

I must admit, I rather enjoyed the irreverent tone he conveyed toward the origin of life industry. He shows why the life work of many and the tens of millions of dollars spent will ultimately be for naught.

I concede, all this is a speculation, but I’m sensing Yockey’s very fine work will be subject to some harsh criticism and rejection by the scientific community. I presume, Dr. Yockey is effectively retired, and this was his parting shot. Good for him….

Salvador
PS

Yockey’s also lashed out at IDists as pointed out by Bill here A Pox on all your houses except mine. (Yockey loves Darwin).

Amusingly, I learned something from reading Yockey, “Irreducible Complexity” was apparently a term coined by Alan Turing to describe a computation that runs indefinitely.

Yockey equivocates Turing’s definition with Behe’s definition of “Irreducible Complexity” and forms a consequently fallacious based on the equivocation. Yockey was wrong about ID, but was correct about the eventual failure of OOL….

(thank you to Jason Rosenhouse for breaking the news of the review)

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11 Responses to Nasty feelings in the OOL community toward Hubert Yockey?

  1. Scordova,
    Thanks for this fine post & it’s unraveling of a long-standing controversy. Your speculations seem right-on.

    Can you say more about Turing’s coining of “Irreducible Complexity” and any analog it has with Behe’s term? I can imagine an irreducibly complex computer program that is the minimum goto-loop. But it sounds like Turing had a different meaning in mind.

  2. Is this Adami of Avida fame? I hardly think that Adami is in a position to criticise, considering the claims of his group are so mathematically untenable – see here:
    http://exilefromgroggs.blogspo.....avida.html

    Avida also protects against random mutation the code the digital “organisms” require for replication. In real living things nothing is protected against deleterious mutation, not the replication machinery and not even the environment. But I’ve said before that Avida really does emulate the theory of evolution which is to say it demonstrates a mechanism producing the laughably simple and extrapolates that into being able to produce the hideously complex. -ds

  3. The website is:

    http://www.hubertpyockey.com

    with a P between Hubert and Yockey

    All the best.

    hbenkeshet

  4. Thank you benkeshet, I made the correction!

    Sal

  5. Hi dougmoran,

    You asked:

    “Can you say more about Turing’s coining of “Irreducible Complexity” and any analog it has with Behe’s term? I can imagine an irreducibly complex computer program that is the minimum goto-loop. But it sounds like Turing had a different meaning in mind. ”

    Indeed Turing had something completely different in mind. Take a look at:
    Irreducible Complexity in Pure Mathematics and compare that with Behe!

    Yockey, argued against Behe’s IC using Turing’s definition of IC. A classic equivocation. I kept thinking when I read Yockey’s book, “huh?, how does that show biology does not have IC?”. It was when Yockey posted on his website that it made sense when he mentioned Turing.

    Anyway, Yockey only gave 2 paragraphs regarding ID in his book….The following is about as much as you’ll find in his book regarding ID. His website actually has more about ID.

    http://www.hubertpyockey.com:

    First, Behe did NOT coin the term “irreducible complexity,” he hijacked it from Alan Turing and stole its identity. Turing defined “irreducible complexity” as a computation that runs indefinitely. Cellular processes start and stop, therefore they do not run indefinitely, therefore they are not irreducibly complex.

    The correct definition of “irreducible complexity” in information science is a computation whose result can be computed for eternity and never reach its final answer. Behe cannot appropriate this term and substitute his own intuitive understanding of the words.

    Biology is not irreducibly complex because the bit string in the genome that describes a protein is finite and stops after it produces the protein (so the computation does not run indefinitely).

    A summary of another proof of why biology is not “irreducibly complex” is as follows:

    As Dr. Yockey’s work shows, the genome is digital, linear and segregated. “Digits” in this case means the letters of an alphabet, each one different from the other. The letters of the alphabet of the genome are the 64 codons of DNA and RNA. The letters are in a sequence in DNA and RNA, so they are linear. And they are separate and distinct from one another, so they are segregated.

    Claude Shannon showed that information can be measured in any sequence that is digital, linear and segregated. Therefore the information in the genome can be measured. Therefore the genome—the critical element for evolution in biology—is not “irreducibly complex.” Therefore, there is no requirement in evolution for an Intelligent Designer.

  6. If a problem has a solution, a Turing machine will halt. If not it will go into a loop and continue forever. In mathematics “irreducible” refers to something uncomputable, like a fact that has no reason, as something that must be taken as an axiom itself (if it the universe was truly random, every phenomena would be “irreducible”). A Godel formula is such an irreducible statement – and I hold that the origin of life is such an “irreducible phenomenon”.

    Irreducible complexity refers to something different, but it could be that the flagellum is an “irreducible” phenomenon in the sense that it does not follow from natural law or some genetic algorithm, but by design inference.

  7. This is too stupid of an error for someone like Yockey to make, unless he was simply assuming that Behe was using Turing’s definition without reading Behe’s book. My (wild, unsubstantiated) guess is that he felt the need to attack ID in order to protect his own criticisms of the establishment.

  8. Yockey says

    Behe cannot appropriate this term and substitute his own intuitive understanding of the words.

    Behe certainly can define the words according to his understanding, as long as he tells his reader how he is defining them – which he does.
    This is a perfectly legitimate practice, as Dawkins, for instance, tells us when he defines “gene” for his own purposes.

  9. “This is too stupid of an error for someone like Yockey to make, unless he was simply assuming that Behe was using Turing’s definition without reading Behe’s book. My (wild, unsubstantiated) guess is that he felt the need to attack ID in order to protect his own criticisms of the establishment. ”

    Well, maybe he’s really a secret Wedgie agent. He realized the only way to infiltrate the establishment is to use token criticisms of ID as cover while sneaking Wedge literature into the mainstream in attempt to subvert all of science and public education, and establish a theocracy just like Barbara Forrest said. (just kidding)

    Glad to hear form you johnnyb.

    Sal

  10. Welcome Albert Voie!!!

    Thank you for visiting our weblog, and congratulations on the acceptance of your paper.

    Salvador

  11. Dr. Yockey is an evolutionist, he just departs with his fellow colleagues on the matter of the origin of life. At any rate, he states that the fossil record doesn’t matter as far as evolution is concerned. Instead, what matters, is the continuity and similarity of biological genomes. This is quite laughable, has he not heard of common design. Obviously, when we see real world designers, we see a lot of similarities between what the designer has created. Sorry Mr. Yockey, you need to use your head on this one!

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