About Hubert P. Yockey

Hubert P. Yockey in 2008

Hubert P. Yockey in 2008

Publications by Hubert P. Yockey, Ph.D.

Books

Yockey, Hubert P. (2005) Information Theory, Evolution and the Origin of Life. Cambridge University Press.

Yockey, Hubert P. (1992) Information Theory and Molecular Biology, Cambridge University Press.

Yockey, Hubert P.; Platzman, Robert P.; and Quastler, Henry, eds. (1958) Symposium on Information Theory in Biology, New York, London: Pergamon Press.


Scientific Publications on Information Theory in Molecular Biology and the Origin of Life

Yockey, Hubert P, (2003) Calculating Evolution, Cosmic Pursuit, 3 24-29.

Yockey. Hubert P. (2002) More light on pioneers of electrochemistry Nature 415. 833.

Yockey, Hubert P. (2002) Comment on “Some like it hot, but not the first biomolecules, Science 296, 1982-1983.

Yockey, Hubert P. (2002) Information theory, evolution and the origin of life In: Fundamentals of Life, Gyuala Pályi and  Luciano Caglioti.

Yockey, Hubert P. (2001) Behe’s Irreducible complexity and evolutionary theory, Reports of the National Center for Science Education, 21, 18-20.

Yockey, Hubert P. (2001) Origin Of Life On Earth and Shannon’s Theory Of Communication In: Proceedings Atlantic Symposium on the origin of life: Information Systems & Technology, Cathy C. Wu, Paul P. Wang & Jason T. Wang, editors.

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 was an invited paper.]

Yockey, Hubert P. (1998) Life on Mars From ALH84001? Revisited, Origins & Design 19, 4-5.

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. E. Haeckel, C. Darwin, A. Oparin, Stanley Miller, Walther Löb and the History of the Origin of Life, Invited paper at The Chemistry of Life’s Origins, a two-day symposium on the origins of life with 18 speakers. Part of the Northeast Regional Meeting of the American Chemical Society, June 23-24, 1997.

Yockey, Hubert P. (1997) Life on Mars? Did it Come from Earth? Origins & Design 18, 10-15 (1997).

Yockey, Hubert P. (1995). Comment on “Let There Be Life” by Avshalom C. Elitzur. Journal of Theoretical Biology, 176, 349-355.

Yockey, Hubert P. (1995). Information in bits and bytes. BioEssays, 17, 85-88.

Yockey, Hubert P. (1993) Children of Choice Nature 364, p10.

Yockey, Hubert P. (1992) Big vs. Little Science: A Lesson from Alvarez. Physics Today, 45, p92.

Yockey, Hubert P. (1990) When is random random? Nature 344, p823.

Yockey, Hubert P. (1988) Of Particles, Pyramids and Piper Playing. Physics Today, 41, 129-130.

Yockey, Hubert P. (1986) Materialist Origin of Life Scenarios and Creationism Creation/Evolution Issue XVII, 6, 43-45.

Yockey, Hubert P. (1981). Self-organization origin of life scenarios and information theory. Journal of Theoretical Biology, 91, 13-31.

Yockey, Hubert P. (1979). Do overlapping genes violate molecular biology and the theory of evolution? Journal of Theoretical Biology, 80, 21-26.

Yockey, Hubert P. (1978). Can the Central Dogma be derived from information theory? Journal of Theoretical Biology, 74, 149-152.

Yockey, Hubert P. (1977a). A prescription that predicts functionally equivalent residues at given sites in protein sequences. Journal of Theoretical Biology, 67, 337-343.

Yockey, Hubert P. (1977b). On the information content of cytochrome c. Journal of Theoretical Biology, 67, 345-376.

Yockey, Hubert P. (1977c). A calculation of the probability of spontaneous biogenesis by information theory. Journal of Theoretical Biology, 67, 377-398.

Yockey, Hubert P. (1974). An application of information theory to the Central Dogma and the sequence hypothesis. Journal of Theoretical Biology, 46, 369-406.

Yockey, Hubert P. (1973) Information Theory with Applications to Biogenesis and Evolution In Biogenesis Evolution Homeostasis ed. A. Locker, New York, Heidelberg Berlin: Springer-Verlag.

Yockey, Hubert P. (1960). “The Use of Information Theory in Aging and Radiation Damage,” in The Biology of Aging. American Institute of Biological Sciences, Symposium No. 6 (160), pp338-347.

Yockey, Hubert P. (1958). A study of aging, thermal killing and radiation damage by information theory. In Symposium on Information Theory in Biology. eds. Hubert P. Yockey, Robert Platzman & Henry Quastler, pp. 297-316. New York, London: Pergamon Press.

Yockey, Hubert P. (1956). An application of information theory to the physics of tissue damage. Radiation Research, 5, 146-155.
Condensed Matter Physics

Yockey, Hubert P. & Clifford L. Aseltine. Development of high voltages in potassium dihydrogen phosphate irradiated by g rays. Physical Review B, 11, (1975), 437-438.

Helmut H.A. Krueger, William R. Cook Jr., C.C. Sartain & Hubert P. Yockey. Radiation Damage and the Ferroelectric Effect in Rochelle Salt. Journal of Applied Physics, 34, (1963), 218-224.

C.C. Sartain & H.P. Yockey. Cryostat for Reactor Irradiation. The Review of Scientific Instruments, 29, (1958), 118-121.

M.R. Jeppson, R.L. Mather, A. Andrew & H.P. Yockey. Creep of Aluminum Under Cyclotron Irradiation. Journal of Applied Physics, 26 (1955), 365-376.

Health Physics and Radiation Protection

H.P. Yockey, Symposium on the Effect of the Recommendations of the National Committee on Radiation Protection (NCRP) on National Life, Health Physics, 4, (1961), p205.

H.P. Yockey, Radiation Aging and its Relation to the Principles of Health Physics Health Physics, 1, (1959), 417-426.


Publications on Wilderness Expeditions in Canada

Yockey, Hubert P. The 1918 Expedition of Jim and Maud Watt across the Frozen Wilderness of Labrador-Ungava, The Explorers Journal, Spring 1994.

Yockey, Hubert P. Did the Norsemen Sail from Greenland to Ungava for Timber?, The Explorers Journal 70, 98-100 (1992).

Yockey, Hubert P. Les Voyageur on Québec’s Swampy Bay River, The Explorers Journal 69, 172-176 (1990).

Yockey, Hubert P. Expedition Stress, CANOE 14, p87 (1986).

Yockey, Hubert P. First Down Québec’s Whale River, The Explorers Journal 62, 98-105 (1984). (This was the lead article.)

Yockey, Hubert P. Whitewater on the Youghiogheny, CANOE 6, 16-18 (1978).

Yockey, Hubert P. Scouting a Whitewater Wilderness, CANOE 4, 54-56 (1976).


Scientific Reality vs. Intelligent Design’s False Claims-The Problem Is Getting Caught in Behe’s Tar Baby, Not Darwin’s Black Box

Nuclear physicist and bioinformatician Dr. Hubert P. Yockey shows why Michael Behe and his ilk are wrong in his books, Information Theory, Evolution, and the Origin of Life (Cambridge University Press, 2005) and Information Theory and Molecular Biology (Cambridge University Press, 1992). Dr. Yockey’s publications, going back to the 1950s, were seminal in creating the field of bioinformatics. He also is the only scientist who has defined the distinction between living and non-living matter-his definition is fundamental to the scientific understanding of the origin of life.

Behe’s “tar baby” is a metaphor for his tactic of setting up false premises for his arguments with the intention gaining victory by getting people hopelessly stuck in what is really the wrong debate in the first place.

The points below that annihilate the false assertions of Intelligent Design’s true believers are Points 3, 4 and 5, which address the origin of life, gaps in the fossil record and “irreducible complexity.” The first four points refer to the defendants’ statement of material facts filed 7/13/2005, here.


False assertion by believers in Intelligent Design:

1. The Darwinian theory of evolution, like all scientific theories, is not a fact. (quoting Miller)

The scientific reality:

Scientific theories are explanations of facts. That is why they are not facts.

The clear goal of ID proponents in taking Miller’s true assertion out of context is to mislead readers into concluding that he has said all scientific theories are false, or at least perpetually shaky, because they are not facts. That is a deliberate deception.

False assertion by believers in Intelligent Design:

2. The origin of life is still an unsolved scientific problem. (quoting Miller)

The scientific reality:

The origin of life is unsolvable as a scientific problem.

Proven by Dr. Hubert P. Yockey (Information Theory and Molecular Biology, Cambridge University Press, 1992; Information Theory, Evolution and the Origin of Life, Cambridge University Press, 2005).

Predicted by Nobel laureate Niels Bohr in 1933.

False assertion by believers in Intelligent Design:

3. “Intelligent design is an explanation of the origin of life that differs from Darwin’s view.” (Baksa)

The scientific reality:

If so, that is why Intelligent Design has no place in a science classroom ever, for the following reasons:

1. What should be taught in science classes is why the origin of life is one of science’s unsolvable problems. Information theory and coding theory show why life could not originate proteins first, RNA first, in a pond or ocean, on a rock or on other planets. Life originated, but must be taken as an axiom [something we know to be true, but cannot prove]. For a more detailed explanation, contact Dr. Yockey.

The problem in the origin of life that science is unable to solve is to explain how information began to govern chemical reactions through the means of a code.

One of the reasons that science has not correctly addressed how to solve the problem of the origin of life-and accepted more widely that it is unsolvable-is that it has lacked a definition of the distinction between living and non-living matter.

Dr. Yockey is the first scientist to define the distinction between living and non-living matter, which he does as follows:

“The existence of the genome and the genetic code divides living organisms from non-living matter. There is nothing in the non-living physico-chemical world that remotely resembles the reactions that are determined by a sequence (i.e., the genome) and codes between sequences (i.e., the genetic code) that occur in living matter.”

See definitions below-even many scientists do not understand the distinctions between DNA, which is material, and the genome and the genetic code, which are non-material.

2. Darwin never proposed a theory for the origin of life in his scientific publications. What he wrote about the origin of life in Chapter XV of the sixth edition of The Origin of Species (1872) is as follows:

“It is no valid objection that science as yet throws no light on the far higher problem of the essence or origin of life.”

Darwin’s speculation of life beginning in a “warm little pond” was written in his private correspondence. Private correspondence is intended to be private. If Darwin had truly believed this, he had ample opportunity to include it in his scientific publications. He did not. Also, similar speculations can be dated to the 1840s in both scientific and popular English literature.

Darwin’s real opinion of the origin of life was that life appeared by a “wholly unknown process,” as he wrote in a private letter in 1898:

“But I have long regretted that I truckled to public opinion, and used the Pentateuchal term of ‘creation,’ by which I really meant ‘appeared’ by some wholly unknown process. It is mere rubbish, thinking at present of the origin of life; one might as well think of the origin of matter.”

False assertion by believers in Intelligent Design:

4. Gaps in the fossil record constitute valid objections to Darwin’s theory of evolution because they are spaces for the miraculous appearance of species that have not evolved from any other source.

The scientific reality:

The fundamental consideration in evolution is the genome, not the fossil record. Gaps in the fossil record do not matter. What matters is that there are no gaps in the continuity of the genome from the origin of life to the present. It is the continuity of the genome that shows the connectedness of all life-living, extinct and yet-to-be-evolved. That means there are no gaps in which species miraculously appear, as Intelligent Design falsely claims.

See below for definitions.

False assertion by believers in Intelligent Design:

5. Behe claims biology is “irreducibly complex.”

The scientific reality:

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.

Definitions:

Genome: The genome is the message written in DNA. The genome is information, which is non-material, but measurable, while DNA is a material substance. Thus, “genome” and “DNA” are not synonyms, nor are they synonymous with the term “genetic code.” The units in which information is measured are bits and bytes, which are familiar terms to computer users.

Genetic code: The genetic code is the non-material map of which letter from the 64-letter alphabet in DNA specifies (i.e., puts in place in a sequence) which letter from the 64-letter alphabet in RNA and then which letter from RNA specifies one of 20 amino acids in the formation of a protein. Amino acids are the 20-letter alphabet of proteins. DNA, RNA and protein are sequences.

Complexity and orderliness: In information theory, “complexity” refers to the amount of information required to describe a sequence. “Orderliness” and “complexity” have opposite meanings. The more a sequence is orderly, the less it can be complex because it can be described with a short sequence. The more a sequence is complex, the less it is orderly because it requires a longer sequence to describe.

For more information or to arrange an interview, contact Dr. Yockey at hpyockey@aol.com or Cynthia Yockey at cynthia@cynthiayockey.com. Reviews and more information about Dr. Yockey’s books are also available by searching for “Hubert Yockey” at www.bn.com (Barnes and Noble) and www.amazon.com.

Answers to Scott Minnich’s pre-trial testimony for the defense in Kitzmiller v. Dover Area School District

Quotes from Scott Minnich are taken from his pre-trial expert testimony, titled:

“Federal Rule of Civil Procedure 26, Disclosure of Expert Testimony, Scott Minnich, Ph.D.” in Tammy Kitzmiller, et al. v. Dover Area School District and Dover Area School District Board of Directors, case number 04-CV-2688, available in full at http://www2.ncseweb.org/kvd/experts/minnich.pdf.

Assertion by Scott Minnich in favor of Intelligent Design

1. “Proponents of evolution recognize, as they must, the significant gaps and problems with the theory of evolution. For example, experts in the field acknowledge that we have no phylogenetic history (i.e., inability to historically trace the roots) of a single biochemical pathway or subcellular organelle. … proponents of Darwin’s theory of evolution assume that evolution is true, even though we lack the intermediate structures, we lack fossils, and we do not have adequate knowledge of how natural selection can introduce novel genetic information.” (pages 2 and 3)

Answer from Hubert P. Yockey, bioinformatician and nuclear physicist:

In the nineteenth century and for most of the twentieth, evolution from a common ancestor was demonstrated through morphology and the fossil record. However, what distinguishes living from non-living matter is the genome and the presence of a code. In the twenty-first century, now that we have the ability to sequence genomes, the search for a common ancestor is done by comparing genomes. For example, when we search for a common ancestor of the mouse and the rat, when we compare their genomes, it’s the similarity of their genomes that shows us they have a common ancestor. The greater the similarity of genomes, the more closely related the species are. We know the rate at which changes appear in the genetic message, so by measuring the similarity between the genomes of the mouse and the rat we can compute how long ago they diverged from their common ancestor. Therefore there is no need for records of intermediate structures or a fossil record-because there are no gaps in the genome.

Minnich has it backwards when he asserts “we do not have adequate knowledge of how natural selection can introduce novel genetic information.” “Novel genetic information” comes first through the reshuffling of genetic information in reproduction, then natural selection operates.

I address the specious challenges to evolution by Intelligent Design proponents in my book, Information Theory, Evolution and the Origin of Life (Cambridge University Press, 2005). In Chapter 12, my answer to the question, “Does evolution need an intelligent designer?” concludes as follows:

“I have argued that the origin of life, like the origin of the universe, is unknowable. But once life has appeared, Shannon’s Channel Capacity Theorem (Section 5.3) assures us that genetic messages will not fade away and can indeed survive for 3.85 billion years without assistance from an Intelligent Designer. As I pointed out in Section 5.1.4, there is an enormous redundance in protein families. Although majority logic redundance plays an unimportant role in telecommunications, it is controlling in the genetic communication system. This shows without a doubt that evolution and genetics cannot be understood except by information theory.

“Evolution of the genetic code and of the genome proceeds by a Markov chain or random walk (see the Mathematical Appendix). There are a number of events in this Markov chain, including gene duplication and horizontal gene transfer (Section 5.1.4) through biosynthetic pathways (Chapter 7). The duplicated genes provide redundance protection against mutation to a nonspecific message, but also to the evolution of a new gene (Graure and Li, 2000; Haldane 1932). The slight modifications, as Darwin believed, are supplemented by gene duplication and horizontal gene transfer. Current results in genetic sequencing show that duplicated genes are abundant in most genomes (Lynch 2002; Lynch and Conery, 2000).

“The messages in the DNA sequences are similar to programs used by modern computers. mRNA acts like the reading head on a Turing machine, which moves along the DNA sequence to read off the genetic message to the proteome. The fact that the sequence has been read shows that it is not ‘irreducibly complex’ or random. By the same token, Behe’s mouse trap is not ‘irreducibly complex’ or random.

“The same genetic code, the same DNA, the same amino acids and the genetic message that unites all organisms, independent of morphology, proves that the theory of evolution is as well-established as any in science. There is indeed Aristotle’s ‘Great Chain of Being’ (Lovejoy 1936) that relates all living things. How this happened must be learned by measuring, counting and weighing, as Socrates taught us.

“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.”

Assertion by Scott Minnich in favor of Intelligent Design

“The efficiency of these engines (cellular structures such as the flagellum) is truly remarkable. And we do not have a phylogenetic history of a single such machine.”

Answer from Hubert P. Yockey, bioinformatician and nuclear physicist:

Yes, we do: it’s the genome.

Objections based on morphology are more than 50 years behind the times.

Assertion by Scott Minnich in favor of Intelligent Design

“Irreducible complexity, a term coined by Michael Behe in his scientific argument for intelligent design, essentially states that molecular machines are comprised of a core set of components essential for the function of that machine….

“Most importantly, this concept of irreducible complexity poses a problem for the gradual appearance of such machines. If it is the summation of all the parts that provide function, and the loss of a single component renders the machine useless (much like the ‘invented’ machines we make) then natural selection has nothing upon which to select.”

Answer from Hubert P. Yockey, bioinformatician and nuclear physicist:

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.

Assertion by Scott Minnich in favor of Intelligent Design

“Evolution cannot explain genotype vs. phenotype, the origin of information or even how life initiated.”

Answer from Hubert P. Yockey, bioinformatician and nuclear physicist:

Darwin made it clear, as I show in row 3 of the above table (”False assertions by believers in Intelligent Design vs. The scientific reality”), that he knew that the origin of life was a different problem than evolution. He made it clear that his theory of evolution did not address the origin of life. Darwin’s theory of evolution does not explain genotype vs. phenotype because that is outside its scope-it would be just as logical to complain that Darwin’s theory of evolution doesn’t explain general relativity.

Assertions by Scott Minnich in favor of Intelligent Design

“The very genetic code, what Francis Crick, the co-discoverer of the shape of DNA, referred to as a ‘frozen accident,’ does not appear to have evolved. Yet, it is a true code representing the most efficient information storage system known in the universe. Analysis of this code with the tools of supercomputers now shows us that of all possible codes, assuming ours is arbitrary, the natural code is hands down the best set of amino acid codons optimized to minimize the effects of point mutations. [Minnich's reference for this remark is as follows: Hayes, B. 2004. Ode to the Code. American Scientist. 92(6) Page: 494.]

Answer from Hubert P. Yockey, bioinformatician and nuclear physicist:

Minnich confuses the genome with the genetic code. The genome is the non-material information programmed into DNA. A code is a mapping of one alphabet to another. The genetic code is the mapping of the 64-letter alphabet programmed in DNA to the 64-letter alphabet of RNA to the 20-letter alphabet of protein (i.e., amino acids).

Minnich complains the genetic code has not evolved. It is impossible to tell what he means by this since he obviously confuses the terms “genome” and “genetic code.” It is the genome that evolves, not the genetic code. If the genetic code were to evolve, that would scramble all the genetic messages programmed in the genome because of the changes in mapping between the alphabets of DNA, RNA and protein.

However, Thomas Jukes considered a doublet code as a possible ancestor to the triplet code, but a doublet code can only produce 16 codons and 16 amino acids; since life requires at least 20 amino acids, Jukes dropped this speculation.

[Note: Classically, there are 20 amino acids, but recent research adds two more for a total of 22.]

Assertion by Scott Minnich in favor of Intelligent Design

“I have read and am familiar with the text of Of Pandas and People. This is a good text that critically analyzes various aspects of Darwin’s theory. It asks critical questions in terms of the evidence and mechanism required to drive evolution. Such questions are essential for the advancement of science. Making students aware of the controversy in the science community is good for students and it is good for science. Repressing evidence and ideas has the opposite result.”

Answer from Hubert P. Yockey, bioinformatician and nuclear physicist:

The objections to evolution in Of Pandas and People are invalid, as I have shown in more detail above, and in my books, for the following reasons:

1. The evidence for evolution is in the genome. There are no gaps in the genome from the origin of life to the present and for all life yet-to-be-evolved. Therefore gaps in morphology or the fossil record are not valid objections. Texts objecting to Darwin’s theory of evolution based on morphology and/or gaps in the fossil record are obsolete by several decades.

2. Texts that object to Darwin’s theory of evolution because it does not explain the origin of life are engaging in deliberate deception. Darwin stated clearly (as quoted in my answers to Behe) that his theory of evolution took the origin of life as an axiom and did not attempt to explain it. Texts engaging in deception have no place in the classroom.

3. Life is not irreducibly complex-in the original and correct use of the term-because the program containing the information of the genome starts a task and then stops when it has completed its task. In the case of a mouse, the production of the mouse has a definite beginning and end. Comparisons to non-living examples, such as mousetraps, purporting to show “irreducible complexity” and “intelligent design” are invalid because a mousetrap has no genome and does not produce little mousetraps. While a mousetrap must have a designer to take the place of the genome in order to evolve to better designs, the genome evolves through a random walk and has no need of an Intelligent Designer.

In summary, Darwin’s theory of evolution is as well-established as any theory in science for the following reasons:

1. The engine of evolution is the genome, which is the non-material information programmed in DNA.

2. Introducing a requirement for an Intelligent Designer is ad hoc and invalid. Explanations of the requirement for an Intelligent Designer almost invariably are “inferred” from non-living matter, usually a machine of some kind. Machines require an “Intelligent Designer” to exist-or evolve-because they do not have a genome. Living things do not require an ad hoc “Intelligent Designer” to live and evolve because they DO have a genome.

The crux of Intelligent Design “theory” is therefore to maintain that the Intelligent Designer substitutes for the genome in evolution. However, the genome evolves through a random walk and has no need of an Intelligent Designer.

3. There’s no such thing as “irreducible complexity” in biology because the information programmed in the genome starts tasks and stops when they are completed-the computing process of reading the stored information does not go on indefinitely.

I explain all of these points in detail in my book, Information Theory, Evolution and the Origin of Life.

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