Autism, the Evolution of Homo sapiens sapiens, and the Definition of “Human”

Autism, the Evolution of Homo sapiens sapiens, and the Definition of “Human”

There is reason to believe that among the key traits that distinguish humans from the primates that are phylogenetically closest to us are cognitive and social abilities as exemplified by language and diverse aspects of social interaction and cultural expression. It is reasonable to speculate that these characteristic human phenotypes are based on differences from closely related species in neural development, which in turn ought to reflect differences in the nucleotide sequences of the genes that encode proteins or RNA molecules involved in this process. A study (1) published in Cell in October of this year by Christopher A. Walsh of Harvard Medical School, his associates, and collaborators from numerous institutions focuses on so-called human accelerated regions (HARs), portions of the human genome that have diverged more rapidly than other regions from the genomes of the species most closely related to humans. Doan et al. sought to identify mutations in HARs that are associated with abnormal cognition and social behavior of the sort that can be found in autism. (more…)

Social evolution in microbes, with Dr. Kevin Foster

Social evolution in microbes, with Dr. Kevin Foster

Biologist Kevin FosterDr. Kevin Foster, from the University of Oxford, visited the Center for Evolution and Medicine at Arizona State University last week to talk about competition and sociability among a variety of bacteria, some of which call our guts home. Using humorous descriptions of psychedelic broccoli, tiger and lion fights, and breathing on hornet’s nests, he walked us through the complexity of sociality found in microbes, which ranges from competition among specific bacterial cells to between-species cooperation. Foster used to study social insects, but now he applies his expertise of social behavior (and kin selection) to microbes. While kin selection provides an evolutionary explanation for many complex social behaviors in eukaryotic organisms, it may also be a good model to use in understanding the behavior of genetically similar microbes and how such behavior may affect human health.

(more…)

The Challenge of Breaking the Meta-Code: Context and the Meaning of the Genome

In lay publications, it is commonplace for writers to refer to the deoxynucleotide sequence of an individual’s nuclear genome as that individual’s “code” and to the determination of that sequence as “deciphering the code.”   Molecular biologists mean by the “genetic code,” not a DNA sequence but the relationships between RNA (or DNA) nucleotide triplets and particular amino acids.  For those interested in clinical genetics, the real code-deciphering challenge is much more daunting than determining nucleotide sequences; it is the mapping of genotypes to medically-relevant phenotypes, i.e. predicting diseases from the totality of sequences in a genome.

The somewhat cryptic paradox at the heart of genome-based personalized medicine at the present state of our understanding is easily put: (more…)

Possible Degeneracy in Genotype-Phenotype Relationships due to DNA-RNA Sequence Disparity

An assumption fundamental to medical genetics is that the DNA sequence of an allele at a particular locus will (in the vast majority of instances) be faithfully transcribed into RNA and translated into protein.  This assumption has been largely accepted in spite of known rates of transcriptional and translational errors as well as special cases of RNA editing, in which enzymes alter the RNA sequence post-transcriptionally in ways that can influence translation.  If DNA-RNA-peptide sequence fidelity were reduced to zero, it would not be worth attempting to correlate genotype and phenotype.  More fundamentally, traits would not be heritable, thereby abrogating a necessary condition for Darwinian evolution.

 Therefore, the recent study by Li et al., in Science (2011) is of substantial interest.  The authors document numerous differences (still a minority) between DNA sequences and the putatively corresponding RNA sequences (referred to by the authors as RNA-DNA differenes or RDDs). (more…)

Man, Machine, and Metaphorical Misdirection

The imitation of living and sentient beings by machines is recently much on the minds of many Americans.  A computer designed and built by scientists and engineers at IBM, “Watson,” convincingly defeated two former “Jeopardy” champions in a televised competition on the long-running game show.  This triumph of a machine over humans has stimulated both recollections of the last hallmark event in this series, the defeat (in six games in May of 1997) of chess grand master Garry Kasparov by another IBM computer, “Deep Blue,” and speculation about the future of artificial intelligence.  

Interest in the ability of computers to simulate human thought and intelligence persists in parallel with the tendency of many biologists and biomedical scientists to think of biochemical entities, (such as transcription, splicing, and signaling complexes), cells, and whole organisms as analogous to machines.  For example, the hijacking of cellular processes by viruses often invokes a phrase referring to the exploitation, by the virus, of cellular “machinery.”  Biologists frequently refer to cellular structures, like ribosomes, as “molecular machines.”  (more…)