Naturally, I immediately went to see if Yockey had responded to that particular article in one of the messages I read so that Lurkers could have both sides. He did.
Here is Yockey’s response to the article you mentioned, along with his response to various other reviews:
"In several places the author (Hubert P. Yockey) states that although molecular biology must be consistent with chemical and physical processes, biological principles cannot be derived from physics and chemistry alone. This statement holds still more for the relationship between mathematics and molecular biology (or any other branch of science)."
Haken then makes a coy remark attempting to leave the impression that the Huns are assaulting the battlements of molecular biology: "But Yockey repeatedly conveys the impression that the laws of molecular biology can be derived from mathematics."
Haken's remark is non sense. What I actually stressed is that the laws of molecular biology lie in the axioms from which one reasons, specifically the sequence hypothesis and the genetic code. Mathematics is the highest form of human reasoning about the consequences of those axioms. Nevertheless, mathematics has limitations pointed out by Goedel and Turing that lead to undecidability. For example, it is impossible to determine whether a given computer program will halt.
Haken now makes an emotional accusation of heresy and lese majesty:x "So the author's polemic against the seminal work of Manfred Eigen, who clearly recognized and formulated the fundamental role of these dynamics, is not only unfounded but misleading."
As Haken wrote in his first paragraph: "Quite often the word 'information' is used with different meanings but from the very beginning he (Yockey) sticks to a single interpretation-Shannon information." So far well and good, but, rather subtlety, in his last paragraph, hoping the reader will not notice, Haken uses 'information' in the sense of 'meaning' or 'knowledge'. "Yockey makes wild extrapolations in a futile attempt to show how the classical concept of information theory can be applied to problems in generating information."
Haken has missed Section 12.1.2 where my "wild extrapolations" are related to the well established concepts of Kolmogorov-Chaitin algorithmic entropy. I asked Professor Haken for a list of his publications. He gracefully complied and proved to be an expert in lasers, quantum field theory of solids and synergetics. The only publication I found on his list pertaining to biology is: Entstehung von Biologischer Information undOrdnung von Haken und Haken-Krell, herausgegegen Wissenschaftliche Buchgesellschaft Darmstadt (1989). In English: Origin of Biological Information and Order published by Scientific Book Company, Darmstadt (1989).
A quotation from Chapter 8 will support the point I wish to make: First in the original German; "Der Shannonische Informationbegriff sagt aber nichts aus darueber, ob eine Nachricht sinnvoll oder sinnlos, wertvoll oder wertlos ist, das heist, es geht ihm jeder Sinngehalt ab, oder, in anderen Worten, es fehlt ihm die Semantik. Gerade in biologischen Bereich kann dieses Fehlen ein wesentliches Manko bedeuten."
My English translation: "The Shannon information concept says nothing about whether the message is meaningful or meaningless, valuable or valueless, that is, it goes in every sense of the words, or in other words semantics is lacking. In the field of biology this fault means a substantial deficiency."
Early in the history of information theory, philosophers traded on the word information and thought they had a mathematical means for dealing with semantics, in spite of the Shannon's denial in the second paragraph of his 1948 paper. See Bar-Hillel (1955) Philosophy of Science vol.22 pp86-105 and Bar-Hillel and Carnap (1953) British Journal of the Philosophy of Scince volume 22 pp147-157. The reason this cannot be done is that there is no mathematical measure for 'value' or 'meaning'. The meaning of words depends on the language and the context. 'Meaning' cannot be measured. As I pointed out in my book if you send a package labeled Gift to Professors Eigen or Haken, you will violate German postal regulations. Gift means poison in German.
As R. V. L. Hartley pointed out in 1928: "What I hope to accomplish in this direction is to set up a quantitative measure whereby the capacities of various systems to transmit information may be compared." Bell System Technical Journal volume 7 pp535-563, (1928). Shannon carried Hartley's plan forward and found the fundamental theorems of information theory and coding theory and the quantitative measure in bits and bytes as we have it today.
My 'polemic against the seminal work of Manfred Eigen' exposes his confusion of philosophical notions of semantics and information measured in bits as well as a number of other basic faults. Eigen feels free to introduce conjectures cooked up ad hoc to suit each problem. One can solve (sic) any problem with enough ad hoc conjectures. To remedy what he sees as an inadequacy in "classical information theory" he calls for a purely empirical "value parameter" that is characteristic of "valued information". He states that this "valued information" is reflected by increased "order". On the contrary, it is well known in information theory that 'increased order' decreases the information content of a message. Anyone who is computer literate knows that, in the context of computer technology, the word information does not mean knowledge. Along with many other authors, Eigen makes a play on words by using information in the sense of knowledge, meaning and specificity. For example, in Naturwissenschaften (1971) volume 58 465-523 (in English) he states with reference to sequences in DNA that: "Such sequences cannot yet contain any appreciable amount of information." He means knowledge or specificy.
Eigen uses the word 'information' in two different senses in one sentence: "Information theory as we understand it today is more a communication theory. It deals with problems of processing information rather than of "generating" information."
Eigen purports to reinvent Shannon's Channel Capacity Theorem in order to deal with an "error catastrophe" He does this by dealing with the errors themselves rather than with information mutual entropy that Shannon proved to be the correct concept. Eigen and all the Goettingen school are also completely unaware of the Shannon-McMillan-Breiman theorem. Had anyone in the Goettingen school finished reading Shannon's 1948 paper they would have found both theorems.
Notice that Haken did not challenge my Chapter 10 on self-organization directly but appealed to emotional charges of heresy and lese majesty. When distinguished scientists are wrong they are just as wrong as the restof us. The principle that the king can do no wrong does not apply in science. Idols have feet of clay.
Hmm, I see only one side posted :) The reviews, which I'm not going to post are generally favorable with respect to the math and IT, and neutral to negative on the biology.