RNA-mediated physics, chemistry, and molecular epigenetics (5)

By: James V. Kohl | Published on: May 10, 2016

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https://whyevolutionistrue.wordpress.com/2016/05/06/researchers-criticize-the-mukherjee-piece-on-epigenetics-part-2/#comment-1342189

Excerpt:

…the organisms that have taught us the most about development – flies (Drosophila) and worms (C. elegans)—do not have the enzymes required for DNA methylation.

My comment:

James V. Kohl

Posted May 9, 2016 at 7:36 pm | Permalink

Please see Structural diversity of supercoiled DNA
Serious scientists have linked the epigenetic landscape to the physical landscape of supercoiled DNA via everything known about the innate immune system and energy-dependent changes in hydrogen-atom transfer in DNA base pairs that link angstroms to ecosystems via metabolic networks and genetic networks.
This report is a problem for pseudoscientists: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Weekend evolution of the bacterial flagellum is not consistent with any theoretical approach. Siddhartha Mukherjee refuses to let neo-Darwinism die without more obfuscation of facts.
See also: The New Yorker screws up big time with science: researchers criticize the Mukherjee piece on epigenetics
Excerpt:

…epigenetic processes analogous to those performed by the Yamanaka factors are performed by bacteria that entirely lack histones and DNA methylation.

My comment: That attests to the need to consider energy-dependent hydrogen-atom transfer in DNA base pairs in solution. Even without the histones and DNA methylation, the physiology of reproduction in bacteria is nutrient energy-dependent and controlled by pheromones. It’s time for everyone to start over in the context of rabbinical debate. Start with: “You fool…” Link Schrodinger’s claims about the anti-entropic energy of sunlight to Dobzhansky’s claims about amino acid substitutions that differentiate all cell types in all individuals of all living genera, and leave the biologically uninformed science idiots with their ridiculous theories. Serious scientists have done that during the past two decades or more.
See also: Dreadful science journalism at Vox: all interpretations of science are equal, but some are cuter than others
Excerpt:

The truth is that Mukherjee didn’t even mention transcription factors (or micro-RNAs that turn gene regulation down or off).

My comment: What have other theorists told us about microRNAs for comparison? Why are his claims being discussed outside the claims of other theorists?
See also: Functional Implications of Human-Specific Changes in Great Ape microRNAs
Conclusion

…miR-299-3p and miR-541-3p are conserved miRNAs with neuronal functions and thus evolutionary changes in these miRNAs may have had an impact in gene regulatory networks ultimately related to the evolution of the nervous system. Conversely, miR-503-3p and miR-508-3p regulate a low number of genes, have a restrictive pattern of expression and, although they seem to be involved in development, their functional role is still very vague. We show that specific nucleotide substitutions in the mature region and/or changes in the length of existing miRNAs may affect miRNA expression and hypothesize that both could be mechanisms by which miRNAs acquire new regulatory functions. Our study addresses for the first time the role that human-specific substitutions in miRNAs could have had in our recent evolutionary history and enlarges our understanding of how the non-coding genome may have contributed to shape human-specific traits.

Reported on 5/9/16 as: Specific changes to non-coding RNA may be part of what makes us human

MicroRNAs are post-transcriptional gene regulators known to be involved in almost every biological function. They are highly conserved among species and, while some differences exist, the effect of the variations is often unclear. The authors of the present study analysed over 1500 microRNAs to identify variations between humans and other great ape species, including orangutans, gorillas, bonobos and chimpanzees, and the possible effect of these variations on function.

The authors found that changes in the sequence and length of four microRNAs may be specific to humans. Two were highly expressed in brain tissue and may exert effects on genes with neural functions, while two exhibit restricted expression patterns that the authors posited implied a role in development. The authors also found that “age” might matter; in an evolutionary sense, “younger” microRNAs had less sequence conservation, expression and disease association, and were more isolated than “older” microRNAs.

My comment: Nutrient energy-dependent changes in microRNA flanking sequences link hydrogen-atom transfer in DNA base pairs in solution from the innate immune system to cell type differentiation via the physiology of reproduction in all living genera. Focus on RNA-mediated events outside the context of DNA methylation in bacteria enables a connection across all species. The physiology of reproduction links chemical ecology from variation in the epigenetic landscape to adaptation, which is manifested in supercoiled DNA. The supercoiled DNA protects all organized genomes from virus-driven energy theft and genomic entropy.
When you read about the criticisms of anyone’s work who has attempted to address what is known to serious scientists about epigenetically effected top-down causation in the context of healthy longevity compared to virus-driven pathology, keep in mind that evolutionary theorists have ignored the role that energy plays in cell type differentiation, which explains their need for a scapegoat. Revisit the claim that “…Mukherjee didn’t even mention transcription factors (or micro-RNAs that turn gene regulation down or off).” When was the first time you saw an evolutionary theorist mention energy-dependent microRNA-mediated gene expression?
For example, see: Mutation-Driven Evolution

MicroRNAs (miRNAs) and other small RNAs encoded by the noncoding regions of DNA are known to control the level of protein production by degrading mRNAs. Changes in these small RNAs may then alter the expression of phenotypic characters. (p. 136)

Conclusion:

…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).

For comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

THIS MODEL DETAILS HOW CHEMICAL ECOLOGY DRIVES ADAPTIVE EVOLUTION VIA: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction. This model exemplifies the epigenetic effects of olfactory/pheromonal conditioning, which alters genetically predisposed, nutrient-dependent, hormone-driven mammalian behavior and choices for pheromones that control reproduction via their effects on luteinizing hormone (LH) and systems biology.

Conclusion:

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

Coyne and others want to make an issue out of Mukherjee‘s ignorance and his failure to mention microRNAs. What are they claiming for comparison, and how does weekend evolution of the bacterial flagellum fit into the context of any theorist’s ridiculous claims? Serious scientists have reached the point where they can discuss human specific microRNAs in the context of healthy longevity or virus-driven pathology.
See also: Evolution of the human-specific microRNA miR-941 reported as: New brain gene gives us edge over apes, study suggests 11/14/12
Excerpt:

…this gene emerged fully functional out of non-coding genetic material, previously termed “junk DNA,” in a startlingly brief interval of evolutionary time.

My comment: The “emergence” of a fully functional gene from non-coding genetic material is a representation that only a neo-Darwinian theorist could make.
Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment

In many experiments, bacteria are exposed to lethal constraints in order to select mutants that happen to have the appropriate trait for surviving. The selective conditions are conceived as an imitation of the environmental action in natural selection. Usually, the effect of one specifc selection factor is tested under uniform and constant conditions. The above-described approach is well developed and provides an efficient test bed for studying issues related to the selection for which they were designed. It is not suitable, however, for revealing the significant continuous role of the environment in bacterial `self-improvement’ between the rare events of selection, due to a large sudden change in a specific factor.

The evolution of gene expression and the transcriptome-phenotype relationship

Evolutionary models are only useful in the extent to which they can accurately predict the biological relationships they supposedly mirror.

Signaling Crosstalk: Integrating Nutrient Availability and Sex

The mechanism by which one signaling pathway regulates a second provides insight into how cells integrate multiple stimuli to produce a coordinated response.

Masculinization of Gene Expression Is Associated with Exaggeration of Male Sexual Dimorphism
Reported as: The Ultimate Wingman
Excerpt:

Behavior and social environment may have an even greater effect on the male turkey’s phenotype than his genes do.

My comment to The Scientist: At the evolutionary advent of sexual reproduction in yeasts, increased nutrient uptake determines “male” morphogenesis and the pheromone-controlled physiology of reproduction. See for example: Signaling Crosstalk: Integrating Nutrient Availability and Sex and our 1996 review for information on the molecular epigenetics of sexual orientation and sex differences in behavior.
“Molecular epigenetics”
Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes…. 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… That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.”
The molecular mechanisms of sex determination via nutrient-dependent alternative splicings do not change in species from microbes to man, which means that sexual dimorphism is also nutrient-dependent and pheromone-controlled in turkeys. (See Bird odour predicts reproductive success.)