The irony and confusion of molecular epigenetics

Science Table of Contents 21 March 2013 Volume 343, Issue 6177

Excerpted in sequence:

Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli Jessica Plucain et al.

The emergence of a stable polymorphism in bacteria involved a multistep process including three specific mutations.

Humans Can Discriminate More than 1 Trillion Olfactory Stimuli C. Bushdid et al.

The number of different odor mixtures people can distinguish is several orders of magnitude larger than anticipated.

————————————————————————————————————————————————————————

My comment: Ecological adaptations occur at the molecular level. They may become more or less obviously manifested in observable species diversity. However, if conserved molecular mechanisms did not link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man,  ecological variation could not result in the ecological adaptations that are manifested in observable species diversity.

The irony:  One report on ecological opportunity and nutrient-dependent pheromone-controlled ecological adaptations in Escherichia coli claims that synergistic interactions among beneficial mutations facilitates the epistasis of the adaptations. The report that follows it attests to the biological fact that the human sense of smell enables nutrient-dependent pheromone-controlled ecological adaptations.

The confusion: The molecular mechanisms of biophysically constrained life do not vary among species. If interactions among beneficial mutations somehow lead to epistasis and ecological adaptations linked to species diversity in microbes like E. coli, interactions among beneficial mutations must also lead to ecological adaptations and species diversity in other species.  If the human sense of smell enables ecological adaptations, the ecological adaptations of E. coli must also be enabled a primitive form of the human sense of smell. That’s why biologists place a high value on experimental evidence that links the molecular mechanisms of cause and effect.

The evidence: No experimental evidence supports ideas about mutations and evolution in species from microbes to man. The stable polymorphisms, which are reported in the context of population genetics, simply cannot arise from mutation perturbed protein folding, and that’s what mutations do — they perturb protein folding.  Thus, no matter how hard some researchers try to convince others that synergistic interactions among beneficial mutations might result in the organization of an organism’s genome, other researchers will continue to correctly represent how olfaction and odor receptors allow the combination of nutrient uptake and pheromone-controlled reproduction to organize the genomes of species from microbes to man. Organization occurs via nutrient-dependent changes in base pairs that lead to amino acid substitutions that stabilize protein folding, which stabilizes the organized genome.

In Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli, selective processes and glucose-dependent metabolism and secretion of by-products that generate negative frequency-dependent selection are placed into the context of mutations.  In Humans Can Discriminate More than 1 Trillion Olfactory Stimuli food odors and pheromones link nutrient uptake to metabolism and secretion of species specific pheromones that control reproduction in species from microbes to man. Removing the irony and confusion suggests that microbes select nutrients that metabolize to pheromones that control their reproduction, which is what all other organisms on this planet do. Nevertheless, it is interesting to see researchers continue to tout the role of mutations in evolution at the same time others are proving that ecological variation results in ecological adaptations via conserved molecular mechanisms in species from microbes to man.