The MicroRNAome Strikes Back: A Sokalian hoax (5)

By: James V. Kohl | Published on: January 25, 2018

Premise: Sunlight is the quantized energy as information that is required to link endogenous RNA interference to healthy longevity (The energy-dependent creation of microRNAs links the physiology of reproduction from changes in electrons to ecosystems in all living genera via the creation of ATP, RNA, and supercoiled DNA in organized genomes.)
Counter claim:  The Quantum Thermodynamics Revolution: Information theory
Understanding entropy as a subjective measure allows the universe as a whole to evolve without ever losing information.
See, for comparison: On causal roles and selected effects: our genome is mostly junk 

The title is misleading, but this claim is not.

Selection is involved in such a story, but it is purifying selection against the loss of a component or activity (the chaperone), not positive selection for its presence.

Natural selection for food energy-dependent reproduction is purifying selection. I’ve already cited Frohlich (1968) in that regard. his proposals are no longer speculative. Purifying selection links the speed of light on contact with water to the creation of microRNAs that biophysically constrain the epigenetic effects of  food odors and pheromones via the creation of enzymes.

The epigenetic effects of food odor and pheromones on the creation of energy-dependent microRNAs and enzymes prevent the virus-driven degradation of messenger RNA in all living genera. The virus-driven theft of quantized energy degrades the enzymes linked to the degradation of messenger RNA and gene losses.

I am not the only one who knows that, but few others seem willing to admit that energy is required to create new genes. For example, here the authors make a claim about de novo assemblies of genomes.

See: The phylogenetic utility and functional constraint of microRNA flanking sequences

Both miRNAs and their flanking sequences provide phylogenetic signals suitable for the inference of phylogeny with high levels of accuracy, when sufficient numbers of this type are concatenated. As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

De novo assemblies of geneomes and inferred phylogeny are linked to the slow evolution of microRNAs and microRNA flanking sequences. If I thought the authors were not serious about that ridiculous claim, I would have reported their work in the context of another Sokalian hoax. They eliminated the need for the energy-dependent creation of the microRNAs and the biophysical constraints on viral latency, but I think they seriously considered the de novo assembly of genomes to be possible. Indeed, to some theorists, the creation of new genes is like the magic of evolution.

Instead, I wrote: My comment to Science published at 2:54 pm on 1/29/15 

The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made since the 2013 ecological epigenetics symposium. For example, since then authors claimed “…ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” 

Six months later, other authors traced signaling factors found in vertebrates to the origin of nerve cell centralization via the diffuse nerve net of animals like the sea anemone.  That fact suggests ecological variation is linked to ecological adaptations in morphological and behavioral phenotypes via signaling protein concentrations that differentiate various cell types in body axes and the central nervous system.

Links across species from the epigenetic landscape to the physical landscape of DNA in organized genomes appear to have their origins in the conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated protein folding. Two weeks after the publication that refuted ideas about independently evolved neural systems or muscle specification — and perhaps refuted the independent evolution of anything else, SICB presenters linked crustaceans to insects.

Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.

Why were they left with any questions about how crustaceans and insects could all be part of one big family? They linked RNA-mediated cell type differentiation to what we described in our section on molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior 

Instead of natural selection for the food energy-dependent protection of RNA and supercoiled DNA, this gene-centric pseudoscientific nonsense emerged on January 25, 2018, from the depths of theorist’s ignorance. (At times it seems that a conspiracy theory is linked from the insane ignorance of biologically uninformed theorists, to my insane obsession with disseminating facts.)

The new findings are in agreement with recent genetic studies that show changes in genes related to brain development in our lineage since the population split between Homo sapiens and Neandertals. They add to the accumulating archeological and paleoanthropological evidence demonstrating that Homo sapiens is an evolving species with deep African roots and long-lasting gradual changes in behavioral modernity, brain organization, and potentially brain function.

For comparison to experimentally established fact about selection for energy-dependent reproduction, archeological and paleoanthropological evidence suggests that genes emerged and that they automagically led to “…long-lasting gradual changes in behavioral modernity, brain organization, and potentially brain function.”

I have consistently failed to grasp the logic of  claims that fail to link what is known to serious scientists about the microRNAome to food energy-dependent “…long-lasting gradual changes in behavioral modernity, brain organization…” and biophysically constrained viral latency linked to brain function.

For instance, all organisms can find food without the energy-dependent creation of G protein-coupled photoreceptors. But the energy as information-dependent de novo creation of microRNAs, enzymes and  G protein-coupled receptors is required to linke for food odors and pheromones from pH-taxis to chemotaxis in all species that must forage to find food and reproduce.
All individuals of all species must also enzymatically metabolize the food to species-specific pheromones, which have consistently been linked, since the time of our 1996 review: From Fertilization to Adult Sexual Behavior, to epigenetically-effected sex differences in behavior in species from yeasts to mammals via the conserved molecular mechanisms of chromosomal rearrangements and the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes.
It is time to watch very closely for more Sokalian hoaxes as the Inter-kingdom communication mechanisms mediated by non-coding RNAs (e.g, pre-mRNAs or microRNAs) are placed back into the context of claims about what supposedly has not been known to all serious scientists for more than 25 years.

The Expressed MicroRNA—mRNA Interactions of Toxoplasma gondii 4 Jan 2018

MicroRNAs-Based Inter-Domain Communication between the Host and Members of the Gut Microbiome 27 Sep 2017

Microbiota-Derived Extracellular Vesicles as New Systemic Regulators 24 Aug 2017

HIV-1 Nef Signaling in Intestinal Mucosa Epithelium Suggests the Existence of an Active Inter-kingdom Crosstalk Mediated by Exosomes 08 June 2017

Viruses and miRNAs: More Friends than Foes 15 May 2017

In summary, we are far from fully understanding the molecular mechanisms underlying the complex crosstalks between miRNA pathways and viral infections.

New Insight into Inter-kingdom Communication: Horizontal Transfer of Mobile Small RNAs 01 May 2017

The Role of HCMV and HIV-1 MicroRNAs: Processing, and Mechanisms of Action during Viral Infection 21 April 2017

Gut Microbiota as a Trigger of Accelerated Directional Adaptive Evolution: Acquisition of Herbivory in the Context of Extracellular Vesicles, MicroRNAs and Inter-Kingdom Crosstalk 20 April 2017

Linking Diet to Colorectal Cancer: The Emerging Role of MicroRNA in the Communication between Plant and Animal Kingdoms 05 April 2017

Non-coding RNAs in Host–Pathogen Interactions: Subversion of Mammalian Cell Functions by Protozoan Parasites 21 March 2017

Small Luggage for a Long Journey: Transfer of Vesicle-Enclosed Small RNA in Interspecies Communication 16 March 2017

Exo-miRExplorer: A Comprehensive Resource for Exploring and Comparatively Analyzing Exogenous MicroRNAs 01 February 2017

The Development of Our Organ of Other Kinds—The Gut Microbiota 23 Dec 16

See for comparison: Big Strides in Cellular MicroRNA Expression

A lack of knowledge of the cellular origin of miRNAs has greatly confounded functional and biomarkers studies. Recently, three studies characterized miRNA expression patterns across >78 human cell types. These combined data expand our knowledge of miRNA expression localization and confirm that many miRNAs show cell type-specific expression patterns.

There is no lack of knowledge about the quantized energy-dependent creation of microRNAs, which are now used as biomarkers of healthy longevity for comparison the the number of viral microRNAs, which is linked to pathology in species from bacteria that become archaea and humans that become non-human primates in the context of one or more base pair changes and fixation, or not, of one RNA-mediated amino acid substitution.
Here’s the problem: Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull
See for comparison: Energy as information and constrained endogenous RNA interference (4)
Watch what happens when so-called science journalists wake up and recognize the Sokalian hoax.

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