Michael J. Behe A (R)evolutionary Biologist

Articles

In addition to his books and academic writings, Michael Behe writes regularly at Evolution News. Of note, Behe and his colleagues have written at great length in response to objections to his arguments and expanded on many of his key concepts, such as irreducible complexity and the edge of evolution.  
Academic Writing

Academic Writing

Getting There First: An Evolutionary Rate Advantage for Adaptive Loss-of-Function Mutations

Michael J. Behe

Biological Information: New Perspectives, edited by R. J. Marks II, M. J. Behe, W. A. Dembski, and B. L. Gordon. World Scientific Publishing, Hong Kong, 450-473.

Abstract: Over the course of evolution organisms have adapted to their environments by mutating to gain new functions or to lose pre-existing ones. Because adaptation can occur by either of these modes, it is of basic interest to assess under what, if any, evolutionary circumstances one of them may predominate. Since mutation occurs at the molecular level, one must look there to discern if an adaptation involves gain- or loss-of-function. Here I present a simple, deterministic model for the occurrence and spread of adaptive gain-of-function versus loss-of-function mutations, and compare the results to laboratory evolution experiments and studies of evolution in nature. The results demonstrate that loss-of-function mutations generally have an intrinsic evolutionary rate advantage over gain-of-function mutations, but that the advantage depends radically on population size, ratio of selection coefficients of competing adaptive mutations, and ratio of the mutation rates to the adaptive states.

Experimental evolution, loss-of-function mutations, and “the first rule of adaptive evolution”

Michael J. Behe

The Quarterly Review of Biology 85(4) (December 2010), pp. 419-45.

Abstract: Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function, and I discuss the possible reasons for the prominence of such mutations.

Simulating evolution by gene duplication of protein features that require multiple amino acid residues

Michael J. Behe, David W. Snoke

Protein Science, Volume 13, Issue 10 (October 2004), pp. 2651-2664.

Abstract: Gene duplication is thought to be a major source of evolutionary innovation because it allows one copy of a gene to mutate and explore genetic space while the other copy continues to fulfill the original function. Models of the process often implicitly assume that a single mutation to the duplicated gene can confer a new selectable property. Yet some protein features, such as disulfide bonds or ligand binding sites, require the participation of two or more amino acid residues, which could require several mutations. Here we model the evolution of such protein features by what we consider to be the conceptually simplest route—point mutation in duplicated genes. We show that for very large population sizes N, where at steady state in the absence of selection the population would be expected to contain one or more duplicated alleles coding for the feature, the time to fixation in the population hovers near the inverse of the point mutation rate, and varies sluggishly with the λth root of 1/N, where λ is the number of nucleotide positions that must be mutated to produce the feature. At smaller population sizes, the time to fixation varies linearly with 1/N and exceeds the inverse of the point mutation rate. We conclude that, in general, to be fixed in 108 generations, the production of novel protein features that require the participation of two or more amino acid residues simply by multiple point mutations in duplicated genes would entail population sizes of no less than 109.

Irreducible Complexity: Obstacle to Darwinian Evolution

Michael J. Behe, David W. Snoke

In Debating Design: from Darwin to DNA, Ruse, M. and Dembski, W.A., eds. (Cambridge University Press: 2004), pp. 352-370.

Reply to My Critics: A Response to Reviews of Darwin’s Black Box: The Biochemical Challenge to Evolution

Michael J. Behe

Biology and Philosophy, Volume 16, (2001) pp. 683–707.

Abstract: In Darwin’s Black Box: The Biochemical Challenge to Evolution I argued that purposeful intelligent design, rather thanDarwinian natural selection, better explains some aspects of the complexity that modern science has discovered at the molecular foundation of life. In the five years since itspublication the book has been widely discussedand has received considerable criticism. Here Irespond to what I deem to be the mostfundamental objections. In the first part of the article I address empirical criticisms based on experimental studies alleging either that biochemical systems I discussed are not irreducibly complex or that similar systems have been demonstrated to be able to evolve byDarwinian processes. In the remainder of the article I address methodological concerns, including whether a claim of intelligent design is falsifiable and whether intelligent design is a permissible scientific conclusion.

Self-Organization and Irreducibly Complex Systems: A Reply to Shanks and Joplin

Michael J. Behe

Philosophy of Science 67, (2000) 155-162.

Abstract:

Some biochemical systems require multiple, well-matched parts in order to function, and the removal of any of the parts eliminates the function. I have previously labeled such systems “irreducibly complex,” and argued that they are stumbling blocks for Darwinian theory. Instead I proposed that they are best explained as the result of deliberate intelligent design. In a recent article Shanks and Joplin analyze and find wanting the use of irreducible complexity as a marker for intelligent design. Their primary counterexample is the Belousov-Zhabotinsky reaction, a self-organizing system in which competing reaction pathways result in a chemical oscillator. In place of irreducible complexity they offer the idea of “redundant complexity,” meaning that biochemical pathways overlap so that a loss of one or even several components can be accommodated without complete loss of function. Here I note that complexity is a quantitative property, so that conclusions we draw will be affected by how well-matched the components of a system are. I also show that not all biochemical systems are redundant. The origin of non-redundant systems requires a different explanation than redundant ones.

An overabundance of long oligopurine tracts occurs in the genome of simple and complex eukaryotes

Michael J. Behe

Nucleic Acids Research, Volume 23, Issue 4 (February 25, 1995), pp. 689–695.

Abstract: A search of sequence information in the GenBank flies shows that tracts of 15–30 contiguous purines are greatly overrepresented in all eukaryotlc species examined, ranging from yeast to human. Such an overabundance does not occur in prokaryotlc sequences. The large Increase in the number of oligopurine tracts cannot be explained as a simple consequence of base composition, nearest-neighbor frequencies, or the occurrence of an overabundance of oligoadenosine tracts. Oligopurine sequences have previously been shown to be versatile structural elements in DNA, capable of occuring in several alternate conformations. Thus the bias toward long oligopurine tracts in eukaryotic DNA may reflect the usefulness of these structurally versatile sequences in cell function.

The protein-folding problem: the native fold determines packing, but does packing determine the native fold?

Michael J. Behe, E E Lattman, and G D Rose

Proceedings of the National Academy of Sciences (PNAS), (May 15, 1991)

Abstract: A globular protein adopts its native three-dimensional structure spontaneously under physiological conditions. This structure is specified by a stereochemical code embedded within the amino acid sequence of that protein. Elucidation of this code is a major, unsolved challenge, known as the protein-folding problem. A critical aspect of the code is thought to involve molecular packing. Globular proteins have high packing densities, a consequence of the fact that residue side chains within the molecular interior fit together with an exquisite complementarity, like pieces of a three-dimensional jigsaw puzzle [Richards, F. M. (1977) Annu. Rev. Biophys. Bioeng. 6, 151]. Such packing interactions are widely viewed as the principal determinant of the native structure. To test this view, we analyzed proteins of known structure for the presence of preferred interactions, reasoning that if side-chain complementarity is an important source of structural specificity, then sets of residues that interact favorably should be apparent. Our analysis leads to the surprising conclusion that high packing densities–so characteristic of globular proteins–are readily attainable among clusters of the naturally occurring hydrophobic amino acid residues. It is anticipated that this realization will simplify approaches to the protein-folding problem.

Binding of p-Nitrophenyl Phosphate and Other Aromatic Compounds by β-Lactoglobulin

Harold M.Farrell Jr., Michael J.Behe, Judith A. Enyeart

Journal of Dairy Science, Volume 70, Issue 2 (February 1987), pp 252-258

Abstract: Results obtained from gel filtration showed that β-lactoglobulin binds p-nitrophenyl phosphate with a stoichiometry of 1 mol of ligand per 18,360 monomer. Circular dichroic spectra confirmed the binding and implicated tryptophan and phenylalanine residues in the interaction. Fluorescence of the protein was quenched on binding also supporting complex formation; analysis of these data indicates that p-nitrophenyl phosphate binds to β-lactoglobulin A with a dissociation constant of 31 μM. The B and C genetic variants of β-lactoglobulin bind p-nitrophenyl phosphate with dissociation constants of 63 and 70 μM, respectively. In addition, a series of other nitrophenyl compounds and pyridoxal phosphate were also investigated by fluorescence analysis and found to bind to the protein. These results are discussed with respect to a recent hypothesis that β-lactoglobulin binds retinol and is structurally related to serum retinol binding protein.

Temperature‐dependent conformational transitions in poly(dG‐dC) and poly(dG‐m5dC)

Michael J. Behe, Gary Felsenfeld, Shousun Chen Szu, Elliot Charney

Biopolymers, Volume 24, Issue2 (February 1985), pp. 289-300

Abstract: The double‐stranded helical complexes of poly(dG‐dC) and of poly(dG‐m5dC) are shown to convert from B‐ to Z‐DNA‐type conformations at moderate or low ionic strengths, lower for the 5‐methyl than for the non‐methyl species, in a highly cooperative temperature‐dependent equilibrium. In the presence of low concentrations of divalent ion, e.g., Mg2+, the temperature at which the B → Z transition occurs is virtually independent of the salt concentration and the B‐conformation is favored at lower temperature, while the Z‐conformation is favored at higher temperature. Since the Debye‐Hückel screening parameter changes rapidly with ionic strength in this region, electrostatic interaction with the free ions appears to be only a small factor in the forces that promote the transition; the temperature dependence must derive principally from effects on the solvent. The temperature dependence at high salt concentrations is also reported.

Evolution News

Evolution News

Citrate Death Spiral

Michigan State University biologist Richard Lenski and collaborators have just published a terrific new paper.

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Featured Articles

Citrate Death Spiral

Michigan State University biologist Richard Lenski and collaborators have just published a terrific new paper.

A Response to My Lehigh Colleagues

Recently in the journal Evolution, two of my colleagues in the Lehigh University Department of Biological Sciences published a seven-page critical review of Darwin Devolves. As I’ll show below, it pretty much completely misses the mark. Nonetheless, it is a good illustration of how sincere-yet-perplexed professional evolutionary biologists view the data, as well as how they see opposition to their Read More ›

Here’s How to Tell if Scientists are Exaggerating

How much can the public trust confident claims by scientists? Especially about morally or politically or philosophically charged topics? Alas, not so much, as the New York Times Magazine reminds us once again in a recent article, “How Beauty Is Making Scientists Rethink Evolution.” The subtitle asks, “The extravagant splendor of the animal kingdom can’t be explained by natural selection alone — ...

Waiting Longer for Two Mutations

A roll-up of "Waiting Longer for Two Mutations", Parts 1-5
An interesting paper appeared recently in an issue of the journal Genetics, “Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution” (Durrett, R & Schmidt, D. 2008. Genetics 180: 1501-1509). As the title implies, it concerns the time one would have to wait for Darwinian processes to produce some helpful biological feature (here, Read More ›

Science, E. coli, and the Edge of Evolution

Dear Readers, As I wrote in The Edge of Evolution, Darwinism is a multifaceted theory, and to properly evaluate the theory one has to be very careful not to confuse its different aspects. Unfortunately, stories in the news and on the internet regularly confuse the facets of Darwinism, ignore distinctions made in The Edge of Evolution, or misstate the arguments of intelligent Read More ›

Whether Intelligent Design is Science

A Response to the Opinion of the Court in Kitzmiller vs Dover Area School District
Senior Fellow, Dr. Michael Behe, testified as an expert witness in the Kitzmiller v. Dover Area School Board intelligent design trial in 2005. Judge Jones issued a ruling against the school board and in so doing asserted that intelligent design was not based on science. Dr. Behe disagrees, and here we publish his direct responses to many claims of the Court.

Michael Behe on Molecular Exploitation and the Theory of Irreducible Complexity

The bottom line of the study is this: the authors started with a protein which already had the ability to strongly interact with three kinds of steroid hormones (aldosterone, cortisol, and “DOC” [11-deoxycorticosterone]). After introducing several simple mutations the protein interacted much more weakly with all of those steroids. In other words, a pre-existing ability was decreased.

Design for Living

The Basis for a Design Theory of Origins
Bethlehem, Pa. |— IN the wake of the recent lawsuits over the teaching of Darwinian evolution, there has been a rush to debate the merits of the rival theory of intelligent design. As one of the scientists who have proposed design as an explanation for biological systems, I have found widespread confusion about what intelligent design is and what it Read More ›

In Defense of the Irreducibility of the Blood Clotting Cascade

Response to Russell Doolittle, Ken Miller and Keith Robison
Darwin's Black Box: The Biochemical Challenge to Evolution I devoted a chapter to the mechanism of blood clotting, arguing that it is irreducibly complex and therefore a big problem for Darwinian evolution. Since my book came out, as far as I am aware there have been no papers published in the scientific literature giving a detailed scenario or experiments to show how natural selection could have built the system. However three scientists publishing outside science journals have attempted to respond.

A Mousetrap Defended

Response to Critics
In Darwin's Black Box: The Biochemical Challenge to Evolution I coined the term "irreducible complexity" in order to point out an apparent problem for the Darwinian evolution of some biochemical and cellular systems. In brief, an irreducibly complex system is one that needs several well-matched parts, all working together, to perform its function.

“A True Acid Test”

Response to Ken Miller
In this essay I reply to what I consider to be the most important claim made by any critic of intelligent design: that direct experimental evidence has shown that evolution can indeed generate irreducibly complex biochemical systems. As I will show below, the claim is false.

Teach Evolution

And Ask Hard Questions
BETHLEHEM, Pa. — The debate leading the Kansas Board of Education to abolish the requirement for teaching evolution has about the same connection to reality as the play ‘Inherit the Wind’ had to the actual Scopes trial. In both cases complex historical, scientific and philosophical issues gave way to the simplifying demands of the morality play. If the schoolchildren of Read More ›

The Sterility of Darwinism

As it struggles to comprehend nature, science sometimes has to completely re-think how the world works. For example, Newton’s laws apply to everyday objects but can’t handle nature’s tiny building blocks. Propelled by this discovery, quantum mechanics overthrew Newton’s theory. Revolutions in biology have included the cell theory of life in the 19th century, as well as the slow realization Read More ›

Darwin Under the Microscope

In his statement, the Pope was careful to point out that it is better to talk about "theories of evolution" rather than a single theory. The distinction is crucial. Indeed, until I completed my doctoral studies in biochemistry, I believed that Darwin's mechanism — random mutation paired with natural selection — was the correct explanation for the diversity of life. Yet I now find that theory incomplete.

Molecular Machines

Experimental Support for the Design Inference
This article presents an overview of the key ideas in biochemist Michael Behe's book Darwin's Black Box: The Biochemical Challenge to Evolution. A more detailed discussion of these ideas can be found in the book itself. Those interested in the debate over intelligent design in biology should also check out Michael Behe's extensive responses to various critics.

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