Nutrient-dependent RNA interference

By: James V. Kohl | Published on: April 14, 2015

This David Sloan Wilson interview of Eva Jablonka reflects the desperation of evolutionary theorists. Jablonka claims there is no need to re-define “evolution.” She also places all prior claims about evolution into the context of “symbolic evolution.” She attests to the fact that “evolution” (e.g., change over time) will probably be re-defined to fit whatever anyone was taught to believe it might be. See: Beyond Genetic Evolution. A Conversation With Eva Jablonka
Excerpt: “This is a good opportunity to move to the second dimension of evolution, epigenetics. Now we do have mechanisms, and we can begin to understand how epigenetics counts as an inheritance system.”
My comment: Epigenetics is not the “second dimension of evolution.” Epigenetic effects of the sensory environment link ecological variation to ecological adaptation via the biophysically constrained chemistry of nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate cell types in all genera. Fixation of the amino acid substitutions occurs in the context of the physiology of reproduction, which limits the detrimental effects of mutations that might otherwise accumulate and extend to all individuals across all generations. Instead, amino acid substitutions link the organized genomes of all genera to all other genera via the physiology of their nutrient-dependent reproduction.
My comment on the article in “This View of Life”
Sabatini’s group appears to have just linked “Nutrient-Sensing Mechanisms across Evolution” from the light-induced de novo creation of amino acids to the RNA-mediated stability of all organized vertebrate genomes via insertion of glycine in the GnRH decapetide. See “SHMT2 drives glioma cell survival in ischaemia but imposes a dependence on glycine clearance
An additional comment was not published. Others may also want to see for information that integrates physics, chemistry, and molecular epigenetics.
Feedback loops link the nutrient-dependent physiology of reproduction to chromatin loops in the context of nutrient-dependent pheromone-controlled epigenetically-effected biodiversity. See also:
Addendum: In our 1996 Hormones and Behavior review article we linked RNA-mediated events to cell type differentiation and epigenetically-effected biodiversity in species from yeasts to mammals via the physiology of their reproduction.
From Fertilization to Adult Sexual Behavior (see the section on molecular epigenetics)
Excerpt (1996):  “Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…”
Eight years later, more details about RNA-mediated events that differentiate all cell types were revealed. See: Revealing the world of RNA interference
Conclusion (2004): “The past ten years have seen an explosion in the number of noncoding RNAs found to orchestrate remarkably diverse functions63, 64. These functions include: sequence-specific modification of cellular RNAs guided by small nucleolar RNAs65; induction of chromosome-wide domains of chromatin condensation by the mammalian noncoding RNA Xist (X-inactive specific transcript)66; autosomal gene imprinting and silencing by noncoding mammalian Air (antisense IgF2r RNA)67; and finally sequence-directed cleavage and/or repression of target mRNAs and genes by miRNAs and siRNAs, discussed here and in the accompanying reviews. Some have likened this period to an RNA revolution. But considering the potential role of RNA as a primordial biopolymer of life, it is perhaps more apt to call it an RNA ‘revelation’. RNA is not taking over the cell — it has been in control all along. We just didn’t realize it until now.”
One year later, Jablonka and Lamb published their textbook: Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life (2005) The pdf opens here
Excerpt: “…where there were networks of RNA-mediated interactions, natural selection could have led to some RNA molecules responding to changes in conditions in a way that inhibited the activities of other molecules with a similar sequence. They might have modified the structure of these molecules by base-pairing with them, for example. Later in evolutionary history, as the division of labor between nucleic acids (eventually DNA) as information carriers and proteins as the main enzymes and regulatory molecules increased, vestiges of earlier RNA control systems may have remained. These could have become modified to fit the new information system and defend it against foreign RNA and DNA sequences.
What we have just said is very vague and speculative, and based on no evidence whatsoever. The reality is that biologists know so little about how the RNAi system works that it is premature to speculate at all about its origins. However, as with the chromatin-marking EISs, we are reluctant to accept the view that RNAi evolved primarily for genome defense, simply because we see no good reason why it should not have been selected as an epigenetic control system that contributed to cell heredity right from the beginning” (p. 333).
My comment: Textbooks typically contain large amount of dated material. However, the ‘dated’ claim (above) is repeated on 327 of the 2014 paperback edition. What, if anything, are textbook author’s reading about cell type differentiation. In 2011, Denis Noble wrote:  “If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based” (p 1014).
In his 2013 textbook: Mutation-Driven Evolution, Masatoshi Nei concluded: “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements” (p. 199).
In my 2013 review,  Nutrient-dependent/pheromone-controlled adaptive evolution: a model, I concluded:

Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

The 2013 conclusion from Mutation-Driven Evolution and 2014 excerpt from Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life can be placed into the context of my invited review on nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems, which “…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.”
Actually, the 2013 conclusion from Mutation-Driven Evolution and 2014 excerpt from Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life can be placed into the context of everything known about how viral microRNAs and nutrient-dependent microRNAs link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man.  See: Force for ancient and recent life: viral and stem-loop RNA consortia promote life (Villarreal, 2014) Evolution: viruses are key players (Witzany and Baluška, 2014) and the 2015 interviews of Villarreal and of Baluška by Suzan Mazur.

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