The Future of the “Selfish Gene” Metaphor

This past December, science writer David Dobbs published an essay (2013) in the online magazine Aeon (aeon.co/magazine/) that purports to explain why the ‘selfish gene’ concept is outmoded and should be retired.  It elicited a good deal of commentary, and in early March, Aeon published responses (Sapolsky et al., 2014) to the original article from four individuals (two scientists, a genetic counselor, and a philosopher) as well as additional comments by Dobbs.  For those who are interested in this controversy, responses to the original Dobbs article were also posted elsewhere by Richard Dawkins (2013) and Jerry Coyne (2013a, b).  Below, I provide a sense of the arguments of Dobbs, the tenor of the criticisms of Dobbs’s piece, and selected other critiques of the gene-centric approach to evolution. (more…)

Human Phenotypic Differences and the Blurring Boundary Between Genetic and Epigenetic Variation

Three new papers (Kilpinen et al., 2013; McVickers et al., 2013; Kasowski et al., 2013) published earlier this month in Science all address the effects on human patterns of gene expression and other phenotypes of 1) genetic variation in non-protein coding regions of the genome and 2) covalent modifications of chromatin, the complex of DNA and proteins that facilitates the packaging and organization of DNA in the limited volume of the cell nucleus.  Regulation of gene expression is known to involve enzymes that covalently modify the chromatin proteins, known as histones, by attaching such moieties as methyl, acetyl, or phosphate groups to the so-called histone tails.  These post-translational modifications are commonly known as epigenetic marks and different marks, distinguished by both the chemical structure of the added substituent and the particular histone and precise amino acid modified, are associated with consistent and distinct effects on gene expression. (more…)

Phenotypic and Genotypic Variation of a Fungal Pathogen Powered by Codon Ambiguity and Degenerate Translation

The term “genetic code” is associated with a measure of ambiguity.  For molecular biologists, “genetic code” has historically referred to a table that provides for each messenger RNA ribonucleotide triplet the corresponding amino acid that is incorporated into the growing end of a nascent polypeptide chain, i.e. the translation from RNA sequence to protein sequence.  In colloquial parlance, “genetic code” is frequently used to refer to all or part of the deoxribonucleotide sequence of a genome.  A recent paper, published online ahead of print in Proceedings of the National Academy of Sciences (Bezerra et al., PNAS, 2013) demonstrates that this semantic ambiguity can have a counterpart in the ribosomal interpretation of the genetic code, using the technical molecular biological meaning of the latter term. (more…)

Intelligent Design, the Resurfacing of a Pseudo-Theory

In the past six months, I have encountered a review, by Thomas Nagel in The New York Review of Books (2012), of Alvin Plantinga’s latest book (Where the Conflict Really Lies: Science, Religion, and Naturalism, 2011 ) and a review, by Alvin Plantinga in The New Republic (2012), of Thomas Nagel’s latest book (Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False, 2012).  Both authors are regarded as distinguished philosophers.  In their respective books, they both criticize what may be called the materialist neo-Darwinian approach to explaining life.  Plantinga and Nagel both discuss as a putative alternative to evolutionary explanations, the framework known as intelligent design (ID).  Whereas Plantinga appears to support ID, Nagel does not endorse ID but criticizes proponents of evolution for being overly disparaging of ID theorists. (more…)

Are Viruses Alive?

 

Recently, a valued friend and scientific colleague of mine (Jonathan Yewdell of the NIAID in Bethesda) made me aware of a netcast (http://www.twiv.tv/) and associated blog (http://www.virology.ws/) relating to virology.  The originator of both is Vincent Racaniello, a well-known and highly regarded virologist and professor of microbiology at Columbia University.  Dr. Racaniello currently happens to be curating a survey (http://www.virology.ws/are-viruses-alive/) asking people to answer the question: “Are viruses living?” (more…)

History of the Immunological Thread in the Fabric of Evolutionary Medicine

In his essay (2011) on the history of Darwinian (or evolutionary) medicine, Jonathan Fuller describes potentially relevant interests and insights that preceded the famous paper by Nesse and Williams (1991) that is widely regarded as having catalyzed the resurgence of interest in applying evolutionary concepts and principles to medicine.  For example, the author describes aspects of Aristotle’s biological thinking as well as elements of the medical concepts of Hippocrates that anticipated some features of evolutionary medicine while possibly also impeding full acceptance of the evolutionary perspective on medical phenomena.  Fuller also mentions the writings of individuals such as A. C. Allison and Paul Ewald relating to infectious disease as relevant examples of pre-1991 applications of evolutionary thinking to medically-relevant problems.
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There is, however, another medical field with a relatively long history (going back at least a century) of applying evolutionary principles and concepts to understanding phenomena of interest, immunology (Silverstein, 2003), which Fuller mentions only in passing. (more…)