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Category Archive for 'Evolutionary biology'

  An article published online at the Nature web site on November 24 (Chou et al., 2014) presents a fascinating study of examples in which bacterial genes have found their way to a number of distinct eukaryotic lineages including ticks and mites, gastropod (e.g., snails and slugs) and bivalve mollusks (e.g. clams and oysters), and […]

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  Recently, I heard the latter portions of the radio version of a play, “Lucy” by Damien Atkins, relating to autism and produced by L.A. Theatre Works.  “Lucy” was originally performed and reviewed as long ago as November of 2007, but I was not aware of it until I encountered the production for radio about […]

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After posting my last commentary on the ongoing Ebola outbreak in West Africa, I listened to the netcast, This Week in Virology (www.twiv.tv), for September 14, 2014.  TWiV sessions, hosted by Vincent Racaniello, a well-known virologist at Columbia University, are generally highly informative, typically offering thoughtful discussions about recently published studies pertaining to viruses or […]

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Over the past several weeks the health news has been dominated by the outbreak of infections by Ebola virus (EBOV) in several West African nations: Guinea, Sierra Leone, Liberia, and Nigeria.  A study (Gire et al., 2014) published online at the end of August and now in print by a large collaborative group based in […]

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Epistasis refers to the influence of one genomic mutation or variant on the phenotypic effects of another mutation or variant.  Based on available evidence and theory, this phenomenon has a major influence on evolutionary trajectories for organisms of all sorts.  The role of epistasis has been studied primarily in the context of adaptive evolutionary change.  […]

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Toxoplasma gondii is an intracellular protozoan parasite that infects many different vertebrate species asexually and undergoes a sexual cycle after infecting cats (http://www.cdc.gov/parasites/toxoplasmosis/, 2013).  Parasite oocysts are potentially introduced into the human environment in cat feces.  T. gondii is of interest in clinical medicine because humans can serve as accidental intermediate hosts when they ingest […]

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A prion is a protein that can adopt a conformation other than the ‘standard’ functional conformation and this alternative conformation favors self-association. The aggregation-associated conformation can then be imposed on additional copies of the protein in the original conformation.  This self-templating mechanism for propagation is known primarily for causing neurodegenerative conditions in humans and in […]

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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 […]

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Biomedical scientists and biologists routinely consider how selection shapes the structure and function of proteins of interest.  Less commonly, I suspect, do we consider how selection for attributes other than protein structure and function can favor or disfavor nucleotide sequences that encode particular amino acid sequences.   A new study (Stergachis et al., 2013) published in […]

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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 […]

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In his 1987 book, “The Evolution of Individuality,” Leo Buss addressed a fundamental biological question: “How could individual multicellular animals (known as metazoans), like sea anemones, insects, frogs, and humans arise?”  Buss focused on a key challenge confronting any multicellular animal with differentiated cell types performing different functions: the potential conflict between selection on the […]

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A central focus of recent research aimed at developing a vaccine for HIV-1 is the identification of potent broadly-neutralizing antibodies (bNAbs).  Due to work from several laboratories, many such antibodies have now been identified, produced in quantity as monoclonal antibodies, and characterized with respect to key properties such as epitope specificity, affinity for the corresponding […]

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Currently, I am on vacation near the beach in South Carolina.  Consequently, I have opted for a topic that is bit different than the majority of my monthly commentaries in that it focuses not on a recent original report but instead on a conceptual point made in a book over thirty years ago.  Nevertheless, after […]

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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.  […]

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The consortium of investigators known as ENCODE (ENCyclopedia Of DNA Elements) published, with much publicity, a series of about thirty papers last fall purporting to “identify all functional elements in the human genome sequence” (https://www.genome.gov/ENCODE/).  Dan Graur, an evolutionary geneticist at the University of Houston, and his associates have published a paper in Genome Biology […]

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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: […]

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  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 […]

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In 1996, Dean et al. (Science), demonstrated that a loss-of-function allele (CCR5Δ32) encoding a version of the chemokine receptor, CCR5, confers very substantial resistance to infection with HIV-1 in the homozygous state and slows progression in the heterozygous state.  Given the relatively recent origin of HIV-1, this finding raised the question of what source of […]

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A major problem confronting physicians, nurses, and other hospital personnel is transmission of pathogens among inpatients or between medical personnel and inpatients (in either direction).  A crucial component in efforts to control such infectious outbreaks in hospital wards is determining whether particular cases are linked by instances of person-to-person transmission.  Standard methods of analysis involve […]

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A paper recently appearing in Science (Näsvall et al. 2012) offers a new insights into the mechanisms by which gene duplication can lead to new genes, gene products, and functions.  The new scheme is termed the innovation-amplification-divergence (IAD) model. 

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