Information Theory and Molecular Biology
In rank Theory and Molecular Biology Books
Product Description
This is an introduction to the use of in rank theory in molecular biology. It offers a mathematical foundation approach and provides mathematical definitions for the vocabulary in which basic questions in molecular biology are debated.
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Hubert Yockey, in his book entitled “Information Theory, Evolution, and the Origin of Life”, concludes that the Central Dogma proves that proteins can not have originated prior to the development of DNA/RNA. The Central Dogma originally stated by Crick was intended for the modern, studied living world to explain that information flows from DNA -> DNA, DNA -> RNA, RNA -> DNA, and RNA -> protein. This is based on the known mechanisms of transcription and reverse transcription etc. in modern forms of life that we have characterized to date. Yockey shows that because a codon includes three bases each with four possible types (ACGT) that there are 64 possible codes that represent the 20-22 possible amino acids in a sequence. The genetic code is redundant according to the argument so that it is impossible that DNA may possibly arise from proteins. Yockey’s ultimate conclusion is that DNA/RNA must have come before proteins and that the ultimate origin of life is unknowable. I find the argument naïve, most likely incorrect and essentially a DNA bias. If we can allow that the genetic code is redundant because of codons, we must acknowledge that in fact the genetic code is the product of complexes of proteins and are a consequence of these complexes. Each base is in fact metabolically constructed by sequences of proteins. It is entirely conceivable to hypothesis new codes for unusual amino acids by altering the protein sequences, something that is being done today by biotechnology companies to generate new peptide based therapeutic drugs. So the in rank content of proteins is not just 20 amino acids but the trillions of proteins that can be generated through differing sequences which can yield unique catalytic reactions including generating new codes. In addition, the complexes of the proteins control essential in rank, e.g., changing the sequence of metabolic reactions or the individual proteins. The protein in rank space is essentially unlimited and is much more redundant than the genetic code. It is right that the forms of life we characterize today use a administer that is described by the Central Dogma but it is not right that this is necessarily the way it has everlastingly been especially during the origin of life. It has been shown by other scientists that the components of proteins, aminio acids and peptides are readily formed below the conditions of the early earth. On the other hand the bases, nucleic acids, are not formed in this way and are exceptionally unlikely to have existed before amino acids and peptides existed. I would turn Yockey’s argument on its head and state that the protein space is so much more redundant that it surely originated prior to DNA/RNA.
Rating: 1 / 5
Readers should note that the two reviews below dated 1999 and 1998 are for Yockey’s 1992 book, not this 2005 one. Once Amazon deletes those reviews, Amazon can delete this one as well.
Rating: 3 / 5
This book, which is the long awaited follow-up to In rank Theory and Molecular Biology, is another tour de force in a long history of such insights from Dr. Yockey. As the former head of the U.S. Government’s Aberdeen Proving Grounds, Yockey has a demonstrated history of squashing austensibly scientific thoughts that superficially make sense, but when given the acid test are found entirely wanting. This book is stuffed with such deconstructions and they are much needed as they pertain to the current origin of life debate. Let me cite a few examples:
Perhaps formost among them is the thought that life arose from some Urschleim (primeval slime). Not only does Yockey show that this theory cannot be right, he clarifies just so why, using mathematical certainty. First, he shows, applying In rank theory to Crick’s Central Dogma, that because the flow of in rank can only pass from larger encoding alphabets to smaller ones, but not the other way nearly, it is impossible for the in rank which fills the genetic code to have proceded from proteins (the smaller alphabet) to DNA/RNA (the larger alphabet). Ergo, it is equally impossible for any proteins-first theory of life origin to be right – simply on that basis. Because what matters is not so much the DNA itself, in the scheme of life’s continued existence, but the in rank it contains!
Next, he offers what may be the best summation of evidence in print to show that there simply is no scientific basis whatsoever to conclude that anything like Darwin’s “warm small pond” ever existed. But he goes much further, taking evidence from fossil minutes as to the nature of the earth’s atmosphere during the time the Urschleim was presumed to exist, Yockey shows that it is simply not possible chemically for earth to have had the atmosphere that it did and for those ponds to exist. The upshot being, according to cellular biologist and Nobel Laureate Christian Du Duve, without those ponds, the opportunity of any natural origin of life is zero.
Another strength of the book is the facility with which he ties the procedural activities of the genome to in rank theory, specifically Shannon’s Law. The importance here is his insight into the nature of codes. He starts by demonstrating that the genetic code, in its bestow optimal form, may possibly not have had a natural origin simply because not enough time has existed since the beginning of the universe to allow for it’s actuality strictly in terms of processing.
He furthers this with the following quote from one of his earlier works: “The calculations presented in this paper show that the origin of a rather right genetic code, not necessarily the modern one, is a pons asinorum that must be crossed to pass over the abyss that separates crystallography, high polymer chemistry and physics from biology.(Yockey, 1981, 1992)” Then quoting from the book directly thereafter, “The paradox is seldom mentioned that enzymes are required to define or generate the reaction network, and the network is required to synthesize the enzymes and their component amino acids. There is no trace in physics or chemistry of the control of chemical reactions by a sequence of any sort or of a code between sequences. Thus, when we make the distinction between the origin of the genetic code and its evolution, we find the origin of the genetic code is unknowable.”
But, Yockey is not arguing for some kind of theistic event. In fact, he takes fantastic pains later in the book to exhibit that he does not support any theistic conclusion. From his perspective, even as it is provably right, based on mathematical certainty, that the genetic code did not have a natural origin, because the universe has demonstrated no ability whatsoever to formulate any kind of code, let lonely something as sophisticated as the genome, it cannot be assumed ipso facto that a supernatural event is the only other choice. Because there is no scientific evidence to support that possibility, Yockey is absolutely unwilling to postulate such, even in off-the-record conversations.
To further distance himself from any hint that he supports Intelligent Design (ID) with is work, he takes-on one of the icons of ID, Dr. Michael Behe, and his theory of Irreducible complexity (IR). The way in which he attempts to show that Behe’s theory does not work is to formulate IR as a kind of Gordian Knot that, if Behe is right, is not computable. Because he can show that Behe’s develop is computable, he believes he has shown Behe’s theory to be incorrect in principle.
But, his complete misunderstanding of Behe’s theory leads him to refute something Behe did not theorize. Behe’s IR does not refer to a mathematically unsolvable puzzle, but to a kind of engineering dilemma for which there is no functional step-wise construction. Mechanisms for which there is no gradual, step by step approach to their completion, where every single step is itself a working develop, are termed Irreducibly Complex. In other words, IR refers to any means wherein all the parts necessary for its function are similtaneously extant because no partial iteration of the means will function in any way.
I would use the example of a car engine. There is a net of engine parts required for the engine to run. Below that net assembly of parts, the engine will neither start nor run, even in principle. So even as an engine is constructed sequentially, none of those sequences, small of a complete engine, will function, as is required by Darwinian gradualism.
Behe uses a simpler example, the mouse trap. His theory states that if you remove any one of the simple parts, it is impossible for the trap to function. The net result of Behe’s theory is that IR makes it impossible for any means so possessed to evolve in a gradual way because all the parts have to be there at the start for the means to work. On the other hand, Darwinian Gradualism requires that every step be not only an advancement in function, but a competitive advantage that allows the creature superior ability in the war for continued existence.
Though Yockey confuses Behe’s theory with the mathematical version of irreducibly complexity, to his credit, as the aforementioned quote from his book, regarding the impossibility of a network making enzymes when enzymes themselves must first exist to make the network making enzymes work [a classic Catch 22], he recognizes the irreducibly complex problem to which Behe refers. As such, even as he discusses the it in absolutely different terms, his own example recognizes, as Behe theorizes, that it is impossible for such mechanisms to come into existence by some natural means.
That small flap is but, of no consequence in the panarama of Yockey’s book. Everything he has written on the theme of this book has become a must read for anyone who wants to be absolutely up to speed on the origin of life question. His original insights are powerful correctly because he goes beyond assumption and hypotheses cum theories, to show with the certainty of mathematical law, why some things cannot be. As a consequence, whenever amathematical biologists finally choose to stop arguing about matters that have already been definitively determined, and consult the wisdom and insights of one of a physicist who is one of the 20th century’s fantastic scientific minds, they will obsess this book.
John Tomlinson, MA, CHt
Rating: 5 / 5
Hubert Yockey has long studied life’s programming from the perspective of in rank theory. His sceptical conclusions about origin-of-life theories are often cited by proponents of creationism / intelligent design (ID). But in his new book, Yockey is sceptical about some of their theories, too. For example, hostile to Michael Behe he says that protein sequences cannot be irreducibly complex (p 179).
Regarding ID he comments that, according to in rank theory, “Once life has appeared,… genetic messages will not fade away and can indeed survive for 3.85 billion years without help from an Intelligent Designer” (p 181, 184). Okay, but the most fascinating aspect of evolution is not the survival of ancient genetic programs, but the apparent invention of new ones. Does in rank theory clarify how new genetic programs might be composed de novo? Can the administer be experimental or modeled? An informed discussion of this come forth is truly needed. Yockey’s silence about it surprises and disappoints us.
As he ranges widely through the history of evolutionary theory, Yockey often wants to set the record honest. Specifically, several theories and experiments were known already, before the scientists who got credit for them came by the side of. Furthermore, “Darwin did not judge in a ‘warm small pond’…” (p 120), and “Oparin was very close to Lysenko” (p 153). If you are interested in in rank theory and biology, you will probably be edified by Yockey’s scholarship in this book.
Rating: 4 / 5
This book has the very ambitious task of introducing the general reader to the current thought regarding evolution, the origin of life on Earth, and the question of life on Mars, Europa and elsewhere in the universe.
Dr. Yockey shows that DNA is the genetic in rank system that compares in nearly every aspect with digital data manipulation. DNA represents a code, a program if you will in computer terms that directs life. It also provides for the replication of life, and its evolution into changing forms over time.
The book is aimed at the non-specialist. It is not a text, but a kind of narrative history of significant developments in biology at a fundamental level. There is some mathematics in the book, but it is not a requirement that this be really understood. The math serves as a proof of the statements he is making.
The book includes a chapter ‘Does evolution need an intelligent designer?’ This has caused some ‘intelligent designers’ to use Dr. Yockey’s work in support of their argument.
Dr. Yockey concludes but, that there are some things that we just don’t know and that: ‘The fact that there are many things unavailable to human knowledge and reasoning, even in mathematics, does not mean that there must be an Intelligent Designer.’
This is a very enjoyable book to read. It is well written and clearly shows an intelligent approach to the problem.
Rating: 5 / 5