Too many targets for theories

By: James V. Kohl | Published on: April 1, 2015

Random mutations are the substrates upon which directional natural selection acts.” —  Jay R. Feierman.
Others have claimed that random mutations and natural selection somehow lead to the evolution of morphological phenotypes and behavioral phenotypes. They have not placed their claims into the context of what is known about ecological variation and ecological adaptations manifested as RNA-mediated sex differences in cell types of the human brain and all other cell type differences in all genera?
Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4]. — Foote et al (2013)
For example, see: Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit . It was reported as:

“Too many targets:” Scientists create model to analyze ceRNA regulation, validate results with synthetic gene circuits

This was reported by the same journalist who reported Seeing the (UV) light: Previously undetected difference in human mutation rate unique to Europeans. The differences between what has typically been attributed by theorists to mutations and the reality of facts about the biophysically constrained chemistry of RNA-mediated amino acid substitutions and protein folding can now be compared.
Too many targets” links the viral microRNA / nutrient-dependent microRNA balance from viruses and anti-entropic nutrients to the microRNA/messenger RNA balance and to RNA-mediated amino acid substitutions that enable cell type differentiation of all cells in all individuals of all genera via fixation of the RNA-mediated amino acid substitutions in the context of the physiology of reproduction.
Excerpt 1)  MicroRNA is a small non-coding RNA molecule containing about 22 nucleotides found in plants, animals, and some viruses, which functions in RNA silencing and post-transcriptional regulation of gene expression. Messenger RNA is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression
Excerpt 2) “When the miRNA level is high, the cells need more target transcripts to trigger a ceRNA effect.”
Excerpt 3) “… post-transcriptional regulation can be triggered by only 6-nt” (that is, six-nucleotide) “complementarity of the miRNA 5′-end so-called seed region to the target RNA. When miRNA perfectly matches the target RNA, the miRNA cleaves the target RNA and might be recycled to cleave the next target RNA; when miRNA imperfectly matches the target RNA, the miRNA binds to the target RNA, inhibiting translation or causing RNA destabilizing.”
Excerpt 4 “In addition to an appropriate molecular environment, ceRNA-crosstalk efficiency also positively correlates with the binding strength of miRNA to its MREs, including the number of MREs and the thermodynamic binding stability, while keeping the effective regime unchanged relative to target transcriptional level,”
My comment: Too many viral microRNAs appear to cause genomic instability via uncorrected errors in the stability of protein folding.  Genomic stability is maintained by the epigenetic effects of nutrient-dependent microRNAs and RNA-mediated amino acid substitutions. Parenthetically, that is why nutrient uptake is important to the survival of all ecologically adapted organisms of all genera.
In my atoms to ecosystems model of ecological adaptations, it is the balance of viral microRNAs to nutrient-dependent microRNAs that links nutrient-dependent thermodynamic cycles of protein biosynthesis and degradation to organism-level thermoregulation via everything currently known about the physics, chemistry, and the conserved molecular mechanisms of RNA-mediated cell type differentiation.
See for comparison: NIH’s Collins on Changing the Future of Medicine. See also these RNA society videos and the video representation from my 2013 poster session.
Attempts to compare UV-light induced mutations to what is currently known about the anti-entropic effects of the sun’s biological energy must eliminate the transfer of that energy as information. Not surprisingly, a new theory attempts to do that. See: Photon ‘afterglow’ could transmit information without transmitting energy.
The comments on this article attest to the fact that some theorists are willing to believe in virtually anything they are told until someone tells them something else. Then, only the biologically uniformed theorists will continue to believe in ridiculous untestable theories.
See also: Selective MicroRNA-Offset RNA Expression in Human Embryonic Stem Cells
Abstract excerpt: “…miRNA-offset RNAs (moRNAs) are similar in length to miRNAs…”
My comment: Use of the term moRNAs may prevent others from realizing the connection from the viral microRNA / nutrient-dependent microRNA balance to the microRNA/messenger RNA balance and nutrient-dependent RNA-mediated amino acid substitutions that differentiate the cell types of all genera via fixation of the substitutions in the context of the physiology of reproduction.
For examples of the link from viral microRNAs to amino acid substitutions, see: RNA Genes: Retroelements and Virally Retroposable microRNAs in Human Embryonic Stem Cells

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