Flaws emerge in RNA method to build tree of life

Excerpt 1:  “…some pieces of RNA are only expressed at particular moments in an animal’s lifetime, whereas genes in the genome are steady.”
Excerpt 2): “…microRNAs cannot alone unveil species relationships.”

My comment: Until earlier today, I was not aware that anyone had been touting the evolution of microRNA (miRNA) or that that the role of miRNAs was being examined outside the context of the miRNA/messenger RNA (mRNA) balance. This report simply characterized the statistical behavior and phylogenetic utility of miRNA data. The researchers have not linked biologically-based cause and effect to biodiversity or exposed any flaws in works that do link the epigenetic landscape to the physical landscape of DNA in organized genomes via nutrient-dependent changes in miRNAs.

Journal article excerpt: “MicroRNAs originate from random hairpin sequences in intronic or intergenic regions (typically 60–80 bp in length) of the genome that become transcribed into RNA (14, 15).”

Some of the miRNAs found in human cell types, appear to come from plants. If the origin of miRNAs is placed into the context of random hairpin sequences, everything known about biophysical constraints on the carbon-hydrogen bonds essential to nutrient-dependent protein folding is removed from consideration. Thus, in this journal article, the evolution of biodiversity appears to begin sometime after the theromodynamics of protein folding  and organism-level thermoregulation have been dismissed — as if the Laws of Physics were nothing more than suggestions.

I’m not sure what any evolutionary theorists think about the required link from physics to chemistry and molecular biology, but I’ve seen no experimental evidence that suggests miRNAs originate from random hairpin sequences in intronic or intergenic regions of the genome.

“Consistently, plant miRNAs were detected in various tissues, including liver, intestine and lung. Different plant miRNAs accumulated at different levels, which also varied from one tissue to another, but their levels could reach up to one tenth of the most abundant human miRNA.”

Plant miRNAs do not seem to automagically appear in the cell types of different tissues, however. Thus, what is currently known about the gene-cell-tissue-organ-organ system pathway and the interactome points to functional miRNA/mRNA targets across genes in networks of genes that interact and link our nutrient-dependent metabolism via the circulatory system to miRNA functions in brain.  Changes in the nutrient-dependent miRNA/mRNA balance can therefore be linked via conserved molecular mechanisms of the nutrient-dependent pheromone-controlled physiology of reproduction to behavior in species with circulatory systems.

In my model, for example, nutrient-dependent pheromone-controlled ecological adaptations link ecological variation to pieces of RNA that are only expressed in some individuals of some species at particular moments in their lifetime.  The miRNA/mRNA balance changes with nutrient uptake in invertebrates and vertebrates which is how intercellular links the base pair changes and amino acid substitutions to cell type differentiation and ecological adaptations.

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.

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Reports that characterize the statistical behavior and phylogenetic utility of miRNA data may make it appear that random hairpin sequences in intronic or intergenic regions of the genome that become transcribed into RNA are somehow linked to biodiversity. However, serious scientists know that nutrient-dependent changes in the miRNA/mRNA balance link ecological variation to ecological adaptations via conserved molecular mechanisms of alternative splicings, amino acid substitutions, and cell type differentiation in species from microbes to man.