Eliminating correlations from evolutionary ecology

By: James V. Kohl | Published on: November 18, 2014

De novo creation of olfactory receptor genes clearly links food odors via amino acid substitutions to cell type differentiation in mosquitoes, and in nematodes, flies, honeybees, etc. It would be surprising if cause and effect did not extend to vertebrates from invertebrates. Indeed, Elekonich and Robinson (2000) linked our 1996 model of RNA-mediated cell type differentiation to hormone-organized and hormone-activated behavior in insects more than a decade ago.
Since then, Vosshall’s lab has established the role that amino acid substitutions play in the de novo creation of olfactory receptor genes.
See: Amino Acid Residues Contributing to Function of the Heteromeric Insect Olfactory Receptor Complex . Extension of the conserved molecular mechanisms that link cell type differentiation in species from microbes to man also links the amino acid substitutions to Behavioral Responses to Mammalian Blood Odor and a Blood Odor Component in Four Species of Large Carnivores. The pattern that links metabolic networks and networks of genes is clear. It has been extended to humans via testing associated with nutrigenomics and with pharmacogenomics testing available from Alpha genomix.
Moving forward means we must rapidly distance ourselves from the practice of evolutionary medicine. Ridiculous theories about mutations that supposedly can be linked from cell type differentiation to increasing organismal complexity via the evolution of bio-physically constrained nutrient-dependent pheromone-controlled biodiversity can be eliminated from any further consideration. Serious scientists can compare silly theories to facts in the context of Experimental Food Restriction Reveals Individual Differences in Corticosterone Reaction Norms with No Oxidative Costs.
Excerpt: “A central goal in evolutionary ecology is to characterize patterns of selection on the optimal phenotype for a given environment.”
My comment: That fact places what is known about sex differences in cell types into the context of: Dobzhansky (1972) “Reproductive isolation evidently can arise with little or no morphological differentiation.” (p. 665)
Those who are familiar with the effects of food restriction present a valid complaint associated with comparisons between what is known about ecological adaptation and what is suspected about the evolution of sex via cell type differentiation. For example, changes in levels of hormones are often reported in the context of cause and effect. The changes are more likely to be correlations.

A number of studies have identified strong phenotypic correlations between plasma hormone concentrations and fitness measures and conclude that these correlations are evidence of natural selection [5]–[8]. However, these trait-fitness correlations and selection coefficients may be confounded or overestimated because of individual plasticity [9].

That nutrient-dependent plasticity is readily apparent in yeasts. “Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus…” Epigenetic modifications of cell types is also apparent during the life history transitions of honeybees. See: Honey bees as a model for understanding mechanisms of life history transitions.
Altering the diet of sparrows leads to accurate representations of cause and effect via the conserved molecular mechanisms that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via the honeybee model organism. This links nutrient-dependent changes in labile hormone levels to behaviors in organisms that must quickly adapt to an ecological challenge. A series of already published works have linked nutrient-dependent hormone organization and hormone activation to the pheromone-controlled behavior of birds via the innate immune system of species from microbes to man.
See, for examples:
Preen secretions encode information on MHC similarity in certain sex-dyads in a monogamous seabird
Excerpt: “At the molecular level, the link between MHC and non-peptide odours may stem from excreted odorants becoming conjugated with amino acids…”
Bird odour predicts reproductive success
Excerpt: “Our results show that the abundance and relative proportion of the volatile compounds that make up bird odour may predict genetic and social reproductive success in dark-eyed juncos.”
Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes Excerpt: “The ZAL2 and ZAL2m alleles code for 597 amino acids, with two fixed differences driving a Val73Ile and Ala552Thr polymorphism in ZAL2m. valine to alanine substitution.”
New insights into the hormonal and behavioural correlates of polymorphism in white-throated sparrows, Zonotrichia albicollis
Excerpt: “…behaviour and endocrine function may be linked to a chromosomal rearrangement that determines plumage colour.”
My comment: Unpublished works presented yesterday and today at the annual meeting of the Society for Neuroscience extend a model of nutrient-dependent pheromone-controlled ecological adaptions from birds to rodents. See:
Gene co-expression network analysis in a free-living, behaviorally polymorphic species
The effect of histone deacetylase inhibitors on the behavioral responses to social defeat in Syrian hamsters
The links to the two poster presentation abstracts may make it easier to grasp the link between nutrient-dependent RNA-directed DNA methylation in birds and pheromone-controlled histone acetylation in hamsters. Methylation and acetylation are linked to human behavioral development by the single amino acid substitution detailed in the context of Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults. Nutrient-dependent amino acid fixations obviously via the physiology of reproduction and are linked to behavioral diversity.
It may be important to connect the amino acid substitutions to a light-induced amino acid substitution in plants that links light energy as a nutrient source to nutrient-dependent amino acid substitutions in plants and animals that differentiate the cell types and animal behaviors associated with mobility.
See: Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins
Excerpt: “This strong connection between structural biology and physics means that ultrafast light-harvesting functions are under genetic and evolutionary control.”
My comment: Unfortunately, others often place their experimental results into the context of evolutionary theory, as stated above. They defy what is known about links from the laws of physics to the chemistry of protein folding and to the conserved molecular mechanisms that link amino acid substitutions from viruses to living organisms via cell type differentiation.
See the report on the “single-residue insertion”: Quantum biology: Algae evolved to switch quantum coherence on and off
Excerpt: “They found that in two species a genetic mutation has led to the insertion of an extra amino acid that changes the structure of the protein complex, disrupting coherence.”
My comment: Similarly, see: Amino Acid Substitutions in Polymerase Basic Protein 2 Gene Contribute to the Pathogenicity of the Novel A/H7N9 Influenza Virus in Mammalian Hosts If you are not too frightened to do so, also see: Identification of two amino acid residues on Ebola virus glycoprotein 1 critical for cell entry.
Facts about cell type differentiation via amino acid substitutions can then be compared in the context of social science is pseudoscience: Richard Feynman and Pseudoscience, which is an excerpt from: Richard P. Feynman – The Pleasure of finding things out [national bestseller]
What pseudoscientists never found out about quantum mechanics and quantum biology has been addressed several times. See, for example, works by Luca Turin, which include Molecular Vibration-Sensing Component in Human Olfaction. It was reported as ‘Quantum smell’ idea gains ground. Turin’s work has gained ground very slowly. Chandler Burr helped to explain why in a book that I reviewed here:The Emperor of Scent: A Story of Perfume, Obsession and the Last Mystery of the Senses. I erred by claiming that: “… Turin never attempted to work within the system.” He contacted me to let me know that his first publication was in a highly ranked journal Nature: see Carbon dioxide reversibly abolishes ionic communication between cells of early amphibian embryo.

Luca Turin has since recently published Electron spin changes during general anesthesia in Drosophila, which may link Dose-Dependent Effects of the Clinical Anesthetic Isoflurane on Octopus vulgaris: A Contribution to Cephalopod Welfare to what is currently known about the molecular mechanisms of nutrient-dependent RNA-mediated amino acid substitutions and neurotransmission exemplified in Excitatory amino acid transporters: recent insights into molecular mechanisms, novel modes of modulation and new therapeutic possibilities. In my book review, I also wrote: “Perhaps a future proponent of molecular vibration theory will manage better than Dyson, Wright and, most recently, Turin. Truly this theory may be years ahead of its time. It also may be a theory that cannot be sufficiently supported by scientific fact.’ Obviously, the theory was way ahead of its time and it has since been supported with scientific facts.

Suppression of scientific facts by pseudoscientists is addressed in: Solving Biology’s Mysteries Using Quantum Mechanics: The new field of quantum biology applies the craziness of quantum physics to biology’s most fundamental processes.
Excerpt: “In the case of the fast-adapting E. coli, that would correspond to its DNA being primed to both enable the bacteria to eat lactose and also not be able to eat lactose.”
My comment: Claims that Richard Lenski is The Man Who Bottled Evolution can now be addressed in the context of physics, chemistry, and molecular biology. Clearly the ability to eat or not eat lactose did not evolve.
Indeed, as Vosshall’s group has now shown, the ability to eat is experience-dependent, nutrient-dependent, and the ability involves the de novo creation of olfactory receptor genes. De novo creation occurs via RNA-mediated events in species from microbes to man.
That explains why Humans Can Discriminate More than 1 Trillion Olfactory Stimuli. Simply put, we are extremely well ecologically adapted in the context of RNA-directed DNA methylation and histone acetylation.
We did not evolve via mutations that perturb protein folding. That idea exemplifies the pseudoscientific nonsense of population geneticists.
Any who are interested in moving forward may want to see my comment from March, 2014, on yet another article from Leslie Vosshall’s group. The comment was published earlier today (more than 7 months later) to the Science Magazine site: Humans Can Discriminate More than 1 Trillion Olfactory Stimuli.
It was submitted and published immediately to The Scientist Magazine site: The Nose Knows.
See also: The Nose Knows: Pheromones and Human Sexuality (1995) and listen for Leslie Vosshall’s comments to Avery Gilbert, a human pheromone-denier who believes in strippers.

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