Neural systems are manifestations of ecological adaptations
May 21, 2014 | James Kohl
Excerpt: “More than 300 families of transposable elements constitute at least 8.5% of the genome (Supplementary Table 9 and Supplementary Data 2) with numerous examples of diversification of some ancient transposable element classes (for example, transposases and reverse transcriptases). Approximately 1.0% of the genome is methylated. Pleurobrachia also uses DNA demethylation during development, with both 5-hydroxymethyl cytosine (5-hmC) and its synthetic enzyme TET6 (Extended Data Fig. 2). The obtained genome and transcriptome data provide rich resources (http://neurobase.rc.ufl.edu/Pleurobrachia) for investigating both animal phylogeny and evolution of animal innovations including nervous systems2, 3, 7, 8, 9.”
My comment: Since last year, attempts to comment on articles in published in Nature have resulted in the comment: “You are currently not allowed to comment owing to misuse”
Here is what I would have said about the article published earlier today.
“Researchers recently rediscovered a nutrient-dependent epigenetic variant that links vitamin C to what is probably a glucose and glucose dehydrogenase-dependent base pair change. The base pair change results in addition of a methyl group to a cytosine base, which takes on a hydroxyl group to form different 5-hydroxymethylcytosines (5hmCs). Different 5hmCs are associated with differences in cell types that have the same genetic backgrounds. Nutrient-dependent epigenetically-marked bases help to explain how hundreds of cell types in the human body and in the brain  are differentiated and how they maintain their glucose-dependent and other nutrient-dependent receptor-mediated identities .” — Kohl (excerpt from an unpublished invited review) Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (submitted March 13, 2014)
The focus of my model is on ecological adaptations not evolution because no experimental evidence supports the concept of biodiversity that arises from mutations and natural selection. Instead, all experimental evidence, which now includes the evidence in this article, suggests that ecological variation leads to ecological, social, and to neurogenic niche construction manifested in the ecological adaptations of neural systems in different species. Therefore, I wonder if the folks at Nature think ‘misuse’ equates with comments that argue against experimental evidence they publish by using experimental evidence that’s published elsewhere — even when it’s published by the Nature Publishing Group. For example, in the past week, we’ve seen this experimental evidence of ecological adaptations manifested in neural systems in results published by the Nature Publishing Group as Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy, which links the nutrient-dependent development of the neural system and connectome of C. elegans to the human connectome via the conserved molecular mechanisms exemplified in A mechanism for rapid neurosteroidal regulation of parenting behaviour, which was published online by the Royal Society Publishing.
In my model of nutrient-dependent pheromone-controlled ecological adaptations, which was rejected for publication last month because reviewers refused to comment, the mechanism for neurosteroidal regulation of parenting and other behaviors is the same in all vertebrates. The mechanism is also clearly the result of ecological adaptations that can be traced back to the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria. Thus, there is no reason to assume that evolution of the ctenophore genome occurred and somehow resulted in neural systems that arose via molecular mechanisms that are not conserved across all species. The idea that any species might be distinct from other animal genomes in their content of neurogenic, immune and developmental genes is one that is increasingly harder to support given what is known about biophysical constraints on ecological adaptations (see for review: Genes without prominence: a reappraisal of the foundations of biology.)
Instead, Pradhan et al (2014) make this fact clear. Biophysical constraints on the thermodynamics of protein folding and enzyme activity that rapidly modulates social behaviour by influencing neurosteroid production link ecological, social, and neurogenic niche construction across species in the context of ecological variation that is manifested in morphological and behavioral phenotypes in the individuals of all species via cell type differentiation. Clearly, the phenotypes arise in the context of nutrient-dependent biophysical constraints, and recent works now show that the biophysical constraints are pheromone-controlled via the epigenetic effects of species-specific nutrient-dependent pheromone production on System-wide Rewiring [that] Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes.
The system-wide rewiring has its origins in the molecular mechanisms of sensing and signaling common to cell type differentiation in microbial yeasts Signaling Crosstalk: Integrating Nutrient Availability and Sex and mammals Feedback loops link odor and pheromone signaling with reproduction. If not, I could not have modeled cell type differentiation in all species via the conserved molecular mechanisms exemplified in my rejected invited review: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Abstract: This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.