Molecular evolution and Michael Behe

Michael Behe, in his October 2005 testimony in support of Intelligent Design as science, confidently stated under oath that there is no research on molecular evolution published in scientific journals. Here are his own words as recorded on Page 20 of the court transcript (PDF) (italics mine):

Michael Behe“Molecular evolution is not based on scientific authority. There is no publication in the scientific literature, in prestigious journals, speciality journals, or books that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occurred. There are assertions that such evolution occurred, but absolutely none are supported by pertinent experiments or calculations. Since no one knows molecular evolution by direct experience, and since there is no authority on which to base claims of knowledge, it can truly be said that… the assertion of Darwinian molecular evolution is merely bluster.”

Is it flat-out perjury or is it just wilfully blind stupidity? I am not a scientist. Unlike Behe, I don’t have access to any academic Web subscriptions for research results. But my quick Web search gives the lie to his statement. It’s ignorance squared, first of the history of molecular evolution research and then of the results. Out in the real world of science:

He could read about the science and history of Molecular Evolution:

  • Perspectives on Molecular Evolution (from MIT’s Web pages on the History of Recent Science and Technology): “Beginning in the 1960s, evolutionary biology was significantly transformed by the incorporation of ideas and techniques from molecular biology. This led to many novel views (and as many controversies) about phylogenetic relationships, rates and mechanisms of evolutionary change, and standards of inference and hypothesis testing.”
  • Michael R. Dietrich’s article, The Origins of the Neutral Theory of Molecular Evolution, in the Journal of the History of Biology, 27 (1994), 21-59. “The first major conferences on molecular evolution were held in 1964.” (PDF)

He could read peer-reviewed papers about molecular evolution:

International Journal of Systematic and Evolutionary Microbiology Molecular evolution of the Chlamydiaceae —Bush and Everett 51 in the International Journal of Systematic and Evolutionary Microbiology, Vol 51, 203-220, Copyright © 2001 by Society for General Microbiology
Journal Toxicon Regional and accelerated molecular evolution in group I snake venom gland phospholipase A2 isozymes–Chuman Y, Nobuhisa, et al. in the Toxicon 2000 Mar;38(3):449-62, Copyright © 2000 by International Society on Toxinology

He could find more scientific papers about molecular evolution in any of these journals:

Journal of Molecular Evolution (published for 30 years, 8 of them available online). The Journal of Molecular Evolution (JME) covers experimental and theoretical work aimed at deciphering features of molecular evolution and the processes bearing on these features, from the initial formation of macromolecular systems onward. Topics addressed in the Journal include the evolution of informational macromolecules and their relation to more complex levels of biological organization, up to populations and taxa. This coverage accommodates well such subfields as comparative structural and functional genomics, population genetics, the molecular evolution of development, the evolution of gene regulation and gene interaction networks, and in vitro evolution of DNA and RNA.
Journal of Molecular Biology and Evolution Molecular Biology and Evolution, founded in 1984, publishes research at the interface between molecular and evolutionary biology. The journal publishes investigations of molecular evolutionary patterns and processes, tests of evolutionary hypotheses that use molecular data, and studies that use molecular evolutionary information to address questions about biological function at all levels of organization. Reports of work on comparative and evolutionary genomics and the evolution of molecular structure and function are particularly welcome. It is published by the Society for Molecular Biology and Evolution, an international society of molecular evolutionists.
Genetics journal Genetics publishes contributions that present the results of original research in genetics and related scientific disciplines.
Nucleic Acids Research journal Nucleic Acids Research (NAR) publishes the results of leading edge research into physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic acid metabolism or interactions… under the following categories: chemistry, computational biology, genomics, molecular biology, nucleic acid enzymes, RNA and structural biology…. The first issue of each year is devoted to biological databases, and an issue in July is devoted to papers describing web-based software resources of value to the biological community. NAR Methods Online provides a forum for the online publication of methods papers.
Journal of Applied and Environmental Microbiology Applied and Environmental Microbiology publishes a substantial share of the most significant current research in the areas of biotechnology, microbial ecology, food microbiology, and industrial microbiology. Sections include “Genetics and Molecular Biology” and “Evolutionary and Genomic Microbiology.”
Journal of Virology Journal of Virology is a source of broad-based, high-quality, original research concerning viruses.The journal provides fundamental new information obtained in studies using cross-disciplinary approaches of biochemistry, biophysics, cell biology, genetics, immunology, molecular biology, morphology, physiology, and pathogenesis and immunity. Sections include “Recombination and Evolution.”
Mathematical Medicine and Biology Mathematical Medicine and Biology publishes original articles with a significant mathematical content addressing topics in medicine and biology. Papers exploiting modern developments in applied mathematics are particularly welcome.The biomedical relevance of mathematical models should be demonstrated clearly and validation by comparison against experiment is strongly encouraged.
Bioinformatics Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers.
Its main focus is on new developments in genome bioinformatics and computational biology.
Protein Science journal Protein Science is dedicated to research on all scientific aspects of protein molecules. The journal publishes papers by leading scientists from all over the world that report advances in the understanding of proteins in the broadest sense.
Glycobiology journal Glycobiology provides a unique forum dedicated to research into the biological functions of glycans, including glycoproteins, glycolipids, proteoglycans and free oligosaccharides, and on proteins that specifically interact with glycans (including lectins, glycosyltransferases, and glycosidases).
FEBS Journal FEBS Journal is an international journal devoted to the rapid publication of full-length papers describing original research in all areas of the molecular life sciences, including the subdiscipline of “Molecular evolution.” Preference is given to papers that advance new concepts or develop new experimental techniques. It is published by The Federation of European Biochemical Societies.
journal of Molecular Endocrinology Journal of Molecular Endocrinology provides a wide coverage of research in all aspects of endocrinology. It is in the top ranks of global endocrine journals and publishes high quality, leading-edge research from all over the world.
Physiological Genomics Physiological Genomics publishes results of a wide variety of studies from human and from informative model systems with techniques linking genes and pathways to physiology, from prokaryotes to eukaryotes. The Journal encourages the submission of research that links genes to cell replication, development, metabolic function, cell signal transduction and intracellular signaling pathways, tissue and organ function, and whole organism function.

Physiological Genomics encourages the utilization of approaches ranging from expression profiling, assays for molecular interactions, natural and directed gene alteration, selective breeding studies, gene identification, and the assessment of gene/environment interaction.

The Journal welcomes important new technologies and concepts that enhance the study of functional genomics. The Journal encourages publication of new computational approaches, integrative models, and image analysis predictive of gene function.

PNAS - Proceedings of the National Academy of Sciences of the U.S. PNAS (Proceedings of the National Academy of Sciences of the U.S.) is one of the world’s most-cited multidisciplinary scientific serials. Since its establishment in 1914, it continues to publish cutting-edge research reports, commentaries, reviews, perspectives, colloquium papers, and actions of the Academy. Coverage in PNAS spans the biological, physical, and social sciences. It is published by the U.S. National Academy of Sciences.
Annals of Botany Annals of Botany is an international plant science journal with at least one extra issue each year that focuses on a particular theme in plant biology. Areas of plant science include those applying molecular, analytical, mathematical and statistical techniques to examine topical questions at any level of biological organization ranging from cell to community, from tissue culture to crop production, and from microclimate to ecosystem. Its scope extends to all flowering and non-flowering taxa, and to taxonomic and evolutionary questions particularly when these are addressed using molecular tools. The journal is managed by the Annals of Botany Company, a not-for-profit educational charity established to promote plant science worldwide.
Biological Bulletin The Biological Bulletin publishes outstanding experimental research on a wide range of organisms and biological topics from the fields of Neurobiology and Behavior, Physiology and Biomechanics, Ecology and Evolution, Development and Reproduction, Cell Biology, Symbiosis, and Systematics. Published since 1897 by the Marine Biological Laboratory (MBL) in Woods Hole, Massachusetts, The Biological Bulletin is one of America’s oldest peer-reviewed scientific journals.
FASEB Journal The FASEB Journal is a multi-disciplinary resource for the life sciences published by The Federation of American Societies for Experimental Biology.
Journal of Clinical Microbiology Journal of Clinical Microbiology publishes the most current research on the microbiological aspects of human and animal infections and infestations, with emphasis on their etiologic agents, diagnosis, and epidemiology. It is published by the American Society for Microbiology. Its Epidemiology section includes papers on molecular evolution. Sample paper from the current (Oct. 2005) issue:

cov-journal-humanmolecualrgenetics.gif Human Molecular Genetics. concentrates on full-length research papers covering a wide range of topics in all aspects of human molecular genetics. These include the molecular basis of human genetic disease, developmental genetics, cancer genetics, neurogenetics, chromosome and genome structure and function, gene therapy, mouse and other models of human diseases, functional genomics, and computational genomics. HMG also publishes research on other model systems for the analysis of genes, especially when there is an obvious relevance to human genetics.
Journal of Biological Chemistry Journal of Biological Chemistry. JBC publishes more than 55,000 pages per year of original research reports on biochemistry and molecular biology. It is published by the American Society for Biochemistry and Molecular Biology.
Journal of Bacteriology Journal of Bacteriology, established in 1916, keeps pace with the times by advancing and disseminating fundamental knowledge of bacteria and other microorganisms. Sample paper from the current issue:

Journal of Biochemistry Journal of Biochemistry. It is published by the Japanese Biochemical Society.
Biophysical journal Biophysical Journal. It is published by the Biophysical Society. Sample paper from the current issue:

QJM (Quarterly Journal of Medicine) QJM (QJM: An International Journal of Medicine) focuses on internal medicine. It publishes articles in clinical medicine and in molecular/cell science relevant to medicine. Sample article:

Protein Engineering Design and Selection journal Protein Engineering Design and Selection (formerly Protein Engineering). Sample paper from the current issue:

  • “An evolution-based analysis scheme to identify CO2/O2 specificity-determining factors for ribulose 1,5-bisphosphate carboxylase/oxygenase.”
journal of General Virology Journal of General Virology includes topics on all aspects of animal, plant, insect, bacterial and fungal viruses, transmissible spongiform encephalopathies, molecular biology and immunology, virus–host interactions, and antiviral compounds. It is published by the Society for General Microbiology. Sample paper from the current issue:

  • “Recombination in circulating Human enterovirus B: independent evolution of structural and non-structural genome regions.”
Microbiology and Molecular Biology Reviews Microbiology and Molecular Biology Reviews is the definitive, broad-based review journal in the disciplines of microbiology, immunology, and molecular and cellular biology, keeping readers abreast of the latest findings about bacteria, viruses, parasites, fungi, and other higher eukaryotes. It is published by the American Society for Microbiology.
  • Science calls itself the world’s leading journal of original scientific research, global news, and commentary. It is published by the American Association for the Advancement of Science. Sample papers from the current issue:
    • Xinquan Wang et al. “Structure of the Quaternary Complex of Interleukin-2 with Its , ß, and c Receptors ” (A hormone activates immune cells by sequentially recruiting two specific receptors and then a common third receptor, forming a high-affinity signaling complex)
    • J. Kirsty Millar et al. “DISC1 and PDE4B Are Interacting Genetic Factors in Schizophrenia That Regulate cAMP Signaling” (Two genes associated with schizophrenia code for interacting proteins that modulate cyclic AMP metabolism, suggesting that this signaling pathway may contribute to the disorder).
  •  Nature Nature. This journal was founded by, among others, Charles Darwin. Sample paper:

    He could visit or join any of these organizations:

    He can attend meetings and conferences on Molecular Evolution:

    He could find and read books about it:

    He could keep up with regular science news, which frequently covers evolution, biochemistry, and genome discoveries:

    There are literally dozens more links that I could add, to

    • conferences,
    • university departments,
    • peer-reviewed research papers,
    • scientists,
    • scientific organizations,
    • university courses, and
    • more journals.

    But my typing fingers are getting tired. Whom are you going to believe? Michael Behe, with his flat statement that there is no research on molecular evolution? Or hundreds, thousands, of workers in the search for a real and complex truth? There’s one good thing about it: it was a Behe blunder of great importance in the Kitzmiller vs. Dover trial.

    Finally, here’s a review of Behe’s book, Darwin’s Black Box (and a Wikipedia article).

    16 Responses to “Molecular evolution and Michael Behe”

    1. Rhetorical tactics: the Behe Blunder « Science Notes Says:

      […] Molecular evolution and Michael Behe […]

    2. sauerkraut Says:

      In answer (late as it is) to your question, Michael Behe is a liar.

      Which is why his side in the Dover case LOST!

    3. monado Says:

      I originally wrote this in November, 2005, after hearing of Behe’s incredibly stupid testimony at Kitzmiller v. Dover: “Is there good research in molecular evolution?

    4. ssoi Says:

      i hope this behe guy is not right… otherwise i have been imagining all the papers i have been reading for the past few weeks for my rotation in a human population genetics lab. i should go seek mental help!

    5. themayan Says:

      I dont think poster understands Behes statement and is assuming that just because a book is entitled Micro biology or Protein Science etc. that it somehow explains the evolution of complex biological systems when in reality this is inferred and words like might, maybe, perhaps, or could have are very common. In fact one of the books cited is about protein engineering by an intelligent agent or agents, and a couple of others cited do not even deal with evolution but with present day systems. Out of all the Journals cited, poster could not even point out one specific example. Maybe it would be better to understand what is actually being stated in these books rather than just rely on a title of a Journal to explain these deeper questions that Behe speaks of.

    6. monado Says:

      Oh, I understand. I understand that Behe claimed there was no research in Molecular Evolution when the first major conferences were held in the 1960s. He swore under oath that there was no possible explanation and then admitted that he hadn’t bothered to read the plausible explanations that had been published in basic Molecular Evolution textbooks. He demands endless further detail, ignoring the fact that thermodynamically and chemically sound hypotheses have been proposed and are being tested and perfected. But when asked to provide an explanation for his calculations, such as why he insists on assuming that all mutations must happen at once, he replies, “I’m not going to give your pathetic level of detail.” His calculations are the equivalent of that old joke of proving that bumblebees can’t fly by assuming that they are fixed-wing aircraft. His own calculations depend on similar invalid assumptions and consistently show that he is ignorant of biological facts. His big argument in The Edge of Evolution is based on his own errors. To quote reviewer Nicholas Matzke:

      Behe begins by trying to shore up his argument that “irreducibly complex” multiprotein systems, such as flagella, are unevolvable. He claims that the bacterial flagellum is now known to be even more complex than previously thought, trumpeting the extra complexity of four regulatory proteins—apparently unaware they are absent in various flagella. Similarly, he claims that the unrelated eukaryotic flagellum (or cilium) represents “irreducible complexity squared” because intraflagellar transport (IFT) is required for assembly. But Behe somehow missed the fact, mentioned even in literature that he cites, that the malaria parasite Plasmodium assembles its flagellum without IFT.

      Quoted from here, where there are lots more examples and references: The Edge of Creationism.

    7. themayan Says:

      “He swore under oath that there was no possible explanation and then admitted that he hadn’t bothered to read the plausible explanations that had been published in basic Molecular Evolution textbooks”

      Behe didn’t use this language. He has always said that it was highly unlikely or very improbable that the BF could have evolved in a Darwinian fashion which is the current and accepted synthesis also referred to as the modern synthesis. Most scientist stay away from language and words like “impossible”.
      Can you please give citation for this supposed saying or at least give original quotations of Behe?

      Nicholas Matzke who you quoted, blogs and write under many different pseudonyms which people sometimes do to protect them from critique and not ruin the reputation of their real name when and if they embarrass themselves. This in itself tells a lot about a person.

      Matzke proposes that the T3SS is ancestral to the BF yet he ignores the scientific literature himself and often leaves out the fact that the ten proteins in common with the BF are not the same, homologous yes, but not the same, and they have a different amino acid sequence. The wings of a Sparrow are supposed to be homologues to the wings of an Eagle but try to interchange them and you will have a big problem. Again as for the ancestral argument…………

      The T3SS is closely related to the bacterial flagellum. It is unresolved, however, exactly how the two are related. There are three competing hypotheses : first, that the flagellum evolved first and the T3SS is derived from that structure, second, that the T3SS evolved first and the flagellum is derived from it, and third, that the two structures are derived from a common ancestor. Current opinion tends to favor the first option, where the T3SS is derived from an early flagellum.

      ^ Medini D, Covacci, A, Donati, C (2006). “Protein homology network families reveal step-wise diversification of type III

      ^ Saier, M (2004). “Evolution of bacterial type III protein secretion systems”. Trends in Microbiology 12 (3): 113–115

      I would urge you to consider both sides and take a look a Behes response at…..

    8. monado Says:

      Did you look at the links I posted? Your guy is a luzer who refuses to look at the evidence and proposes no mechanism for any alternative to evolution and twists out his desired conclusion by making assumptions which are false to fact. The evolution of bacterial flagella from the Type III secretin system is back on the table; your research has been superseded.

      Variants of at least seven T3SS proteins are also found in the flagellum, within a subsystem called the protein export system. This sits within the basal body and funnels replacement flagellin subunits to the filament, using a mechanism remarkably similar to the T3SS. In fact, the two systems are so similar that the flagellar protein export system is now considered to be a subclass of the T3SS (Trends in Microbiology, vol 14, p 157).

      Such similarities, or “homologies”, are strong evidence that the two systems evolved from a common ancestor – analogous to the way that the arrangement of bones in the limbs of horses, bats and whales reveal their common ancestry despite their very different outward appearance and function. Similar homologies can be seen in the DNA sequences of genes, and in the amino acid sequences and 3D structures of proteins – all are clear evidence of shared descent.

    9. themayan Says:

      If you had read my reply, common ancestry between the BF and T3SS is already one of several competing hypothesis as I cited before. Please read again if you missed it. The most prevailing view as cited, is that the BF is ancestral to T3SS not the other way around. Even if they shared a common ancestor it still does not answer what the intermediate stages would have been like, or why there would be any intermediates stages since there would be no known use for them until entire unit was in place, besides the fact that there is no known common ancestor. It has to be imagined, wich happens a lot in evolutionary theory.

      I also said that a few proteins were homologues between BF and T3SS, maybe you missed that part also. However homologous they are not the same, and have a different amino acid sequence wich are extremely specific and are not haphazard or random. The article you cited also gave an example of wings and other body parts wich Darwinist use as evidence for common ancestry. The problem with this homology paradigm is that there is no way to falsify it. For example, the wings of a sparrow are homologous to the wings of an eagle, hawk, humming bird or any other avian including chickens.

      There is one big problem with this paradigm. If the wings of birds indicate common ancestry, then how do explain the wings of insects, or wings of mammals such as bats that have no congruent common ancestry within genus. In this case, the Darwinist simply uses the wild card and calls it analogous, meaning convergent evolution. The extinct Tazmanian tiger/wolf had the same morphological and anatomically homologues structures as the North American Timber wolf, yet these two different mammals (one a marsupial and one a placental) have been separated by 65 million years. They share no recent common ancestor but yet on the anatomic level are extremely homologous.

      As I have mentioned before, the hypothesis that the BF and T3SS had a common ancestor is one of many competing propositions. It is nothing new as I cited in my previous thread. Nothing has been superseded. Your citation is tentative and not empirical.

      James Shapiro an evolutionist said this…….”There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations.

      This is exactly what Behe has been saying along.

      • monado Says:

        Let’s see now… the wings of a bird are not homologous to the wings of a butterfly. The wings of all birds are homologous because they are relatively closely related and share a common ancestor. The wings of bats are homologous in the sense that they are developed from the same body structure, the forelimb. The Tasmanian marsupial “wolf” and the mammalian wolf look similar because they have similar ways of foraging, etc., but there are plenty of differences in detail, as pointed out by Kevin Padian in his testimony at Kitzmiller vs. Dover, that show they are not closely related.

        Whether the TSS developed into a part of the bacterial flagellum rotor or the flagellum rotor developed into a transport system, it’s still common ancestry and evidence for evolution. It is also false that there would be no other uses for them… that is the point. Behe’s blunder is assuming that there would be no other uses. In evolution, parts are in use at all times. Or are you going to tell me that seals can’t exist because they aren’t whales yet? There are parts in some rotors that are missing from other fully functioning rotors. Reality proves that Behe is wrong.

    10. themayan Says:

      “The wings of bats are homologous in the sense that they are developed from the same body structure, the forelimb”

      “mammalian wolf look similar because they have similar ways of foraging, etc., but there are plenty of differences in detail, as pointed out by Kevin Padian in his testimony at Kitzmiller vs. Dover, that show they are not closely related.”

      Many non related animals have similar ways of foraging. This means nothing. Of course there are detailed differences. One is a placental, and the other is a marsupial. Of course they are not closely related, but they still have similar anatomical structures, and for all intensive proposes those structures are homologous, this was my point, buts since there is no direct ancestor, the wild card of convergent evolution is played and are then considered analogous. This is exactly what I meant when I said there is no way to falsify this paradigm, and falsifiability is required for any scientific theory.

      I’m sorry but you are wrong about bat wings being homologous with wings of birds, again they are considered analogous.
      Bird and bat wings are analogous—that is, they have separate evolutionary origins, but are superficially similar because they evolved to serve the same function. Analogies are the result of convergent evolution.

      Darwinist want to have it both ways and say that the the forelimbs are from a common ancestor, but no one has been able to produce this supposed common ancestor. Again, great leaps of faith and imagination have to be incorporated. If you know of such ancestor, then please provide information. I would be very interested in this, as I’m sure many others would be also.

      I have already stated my case for the BF. I’m not going to repeat myself and I am not interested in non existing hypotheticals. I am interested in empirical science.

      “are you going to tell me that seals can’t exist because they aren’t whales yet?”
      I have never heard anyone make the claim that seals evolve into whales. I’m not even sure how to answer that. I don’t want to be rude so Ill pass on that one.

      • monado Says:

        I didn’t suggest that bat wings evolved from bird wings. OK, I see our problem. I was thinking “forelimb of a tetrapod” and you were thinking “wings.” The wings are not homologous as wings: they evolved separately and use different mechanisms to fly (feathers vs. skin membranes). But they evolved from the same forelimb. The bones are homologous. If you’ll go here and look in the textbook Human Biology by Daniel Chiras, Page 429, you’ll see a diagram of the bones of various forelimbs. The bones of the bird wing, the mammalian arm, and the whale’s flipper, and so on are homologous: the corresponding bones in each structure are coloured the same.

        I think you indulged in a bit of quote-mining, quotation incomplete and deceptive, to support your argument. The next sentence after what you quoted says,

        Interestingly, though bird and bat wings are analogous as wings, as forelimbs they are homologous. Birds and bats did not inherit wings from a common ancestor with wings, but they did inherit forelimbs from a common ancestor with forelimbs.

        We have a lot of common ancestors: Tiktaalik, the common ancestor of amphibians, reptiles, dinosaurs, and mammals; Trichoplax, likely the common ancestor of metazoans, a common ancestor of all frogs and salamanders, and so on. There is no intrinsic mystery to the explanation. Fossils are just the icing on the cake, like the heirloom picture of your great-grandfather standing in front of a barn in the 1800s. Even if you don’t know who your great-great-grandfather was, or have no picture of him, you know that you had one.

        I explain the wings of butterflies, beetles, and bats by saying that flight is useful and it evolved independently several times. No evolutionary scientist claims differently.

    11. themayan Says:

      I did not quote mine anything. I corrected you when you said wings of bats and birds were homologous and even cited source. I didn’t try to hide anything, and I mentioned forelimbs in the same thread and told you that Darwinist imagine a common ancestor that has yet to be provided by anyone much less any intermediate sequence.

      As I said before, the anatomy of the taz wolf and timber wolf are almost identical yet separated by 65 million years. In the first sentence of the second paragraph in Wikipedia it states that Tiktaalik is suggested to be an ancestral form. A suggestion is not empirical. They said the same about coelacanth and called it an extinct ancestor.

      The only problem is, we have found several of them since the thirties. I am a little busy right now, but after the holidays I will be free. If you want to have a serious debate on this subject I will be more than happy to oblige.

    12. jarleko Says:

      M. Behe´s point is that nobody has yet presented a good theory for evolution. But that does not mean that evolution has not taken place.

      • monado Says:

        Yes; I realize that his view of evolution is a straw man and that he even gets his facts wrong when describing organisms, thus cutting his arguments off at the knees.

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