The MicroRNAome Strikes Back: A Sokalian hoax (2)

(click to enlarge)

The problem with -omics has repeatedly been detailed in articles from social scientists and other theorists who fail to link what is known to serious scientists about the microRNAome to their theories. Pseudoscientists continue to create bricks that clutter the metaphorical physical landscape and prevent the epigenetic landscape from being linked from the physiology of nutrient energy-dependent pheromone-controlled reproduction to all cell type differentiation via energy-dependent changes in atoms to ecosystems in all living genera.
On 1/22/18, I discussed this with a plumber and his assistant, who is –like me– a veteran of the US Military. The plumber, prefaced the discussion with a comment about adaptations for comparison to evolution. The veteran provided supportive comments from his expertise in history, which he hopes will not repeat itself in the context of the 1918 Spanish flu, smallpox, or the bubonic plague.
I learned the value of social science because he believes that vultures put an end to the bubonic plague in the context of their unique ability to thermoregulate their organized genome by spreading their wings to create what most people would refer to as a virus-killing fever. I may not be so critical of other social scientists after meeting one that was not biologically uninformed.
There may be others, but I doubt it.
See: Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay

We identified and confirmed orthologous gene pairs with 3′-UTR SINEs that independently function in SMD control of myoblast metabolism. Expanding to other species, we demonstrated that SINE-directed SMD likely emerged in both primate and rodent lineages >20-25 million years ago. Our work reveals a mechanism for the convergent evolution of posttranscriptional gene regulatory networks in mammals by species-specific SINE transposition and SMD.

No mechanism for convergent evolution was revealed. All posttranscriptional gene regulatory networks require the energy-dependent creation of microRNAs that biophysically constrain viral latency. That fact was not mentioned.
See for comparison: microRNA  
For example: Genetic polymorphism in Hsp90AA1 gene is associated with the thermotolerance in Chinese Holstein cows

…one SNP in the promoter, three SNPs in the coding region, and one in 3′-UTR were novel and reported for the first time in this study.

[…]The expression of Hsp90AA1 in cow bearing mutant allele C was higher (4.18 +/- 0.928) than cows bearing wild-type allele G (1.008 +/- 0.0.129) in stress season. In summary, there was an association between genetic variations in the Hsp90AA1 and thermoresistance. This association could be used as a marker in genetic selection for heat tolerance in Chinese Holstein cattle breeds.

There is no such thing as genetic selection for heat tolerance. The limits of food energy-dependent thermotolerance are biophysically constrained in the context of food energy that biophysically constrains viral latency,which typically limits or prevents activation of the death gene.
Preventing activation of the death gene was reported as: Study finds convergent evolution of gene regulation in humans and mice January 18, 2018

Organisms that aren’t closely related may evolve similar traits as they adapt to similar challenges. It’s called convergent evolution, and familiar examples include the wings of birds, bats, and insects, and echolocation in bats and dolphins. Now, molecular biologists have found evidence of convergent evolution in an important mechanism of gene regulation in humans and mice.

Serious scientists do not call ecological adaptation convergent evolution, and serious scientists do not claim to discover important mechanisms of gene regulation. All the mechanisms are biophysically constrained by ecological variation in the availability of food and the physiology of pheromone-controlled reproduction in species from mice to humans (and from microbes to humans).
But see for comparison: A simple explanation of Born’s rule

…the agreement between quantum theory and experiments follows from a one-to-one correspondence between the logical possibilities and the physical possibilities and, in particular, implies that the outcomes of quantum measurements are not constrained by any physical reason.

Thanks to so-called science journalist Philip C. Ball for calling this to my attention. In my first blog post about Nonomura’s Sokalian hoax, I mentioned Frohlich (1968). Long-range coherence and energy storage in biological systems. I do not expect pseudoscientists or so-called science journalists to accept the facts about constrained energy storage. The facts are neo-Darwinian theory killers.  Once again, the theorists have a problem understanding how the creation of energy must be linked from energy storage to biophysically constrained viral latency and all biodiversity.
Nonomura’s hoax links the energy-dependent epigenetic silencing of transposable elements to the central events of germline transmission via the creation of sunlight, the creation of ATP, and the creation of microRNAs. The light energy-dependent creation of microRNAS must be linked to RNA-mediated DNA repair and to the relatively error-free genome of the next generation via the pheromone-controlled physiology of reproduction that biophysically constrains viral latency.
Unanswered questions about viral latency and transcriptional quiescence (aka gene silencing), which is a hallmark of the biophysically constrained germ cell lineage in many organisms, are the clear link to my claim that Nonomura has published a Sokalian hoax as Small RNA pathways responsible for non-cell-autonomous regulation of plant reproduction — as a peer-reviewed monograph.
The unanswered questions allow biologically uninformed peers to accept the claims of non-cell-autonomous regulation as if they could be part of an evolutionary approach to energy-dependent reproduction. For comparison, the first question a serious scientist would ask is about how non-cell-autonomous pathways compensate for ecological variation, which must be linked to energy-dependent ecological adaptation via the availability of some nutrients, materials and signals. Most serious scientists will realize that non-cell-autonomous pathways link sunlight to the activation of endogenous substrates (e.g., enzymes) that are created in the context of what happens when the speed of light hits water.
See: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
Reported as: … the conditions that produce nucleic acid precursors also create the starting materials needed to make natural amino acids and lipids. That suggests a single set of [light activated] reactions could have given rise to most of life’s building blocks simultaneously.
I noticed that this pinned post now appears first @rnomics:

Reconstructed ancient ocean reveals secrets about the origin of life (2014)

This was a report on Non‐enzymatic glycolysis and pentose phosphate pathway‐like reactions in a plausible Archean ocean
Fabrice Leclerc @rnomics seems to be ignoring the retractions of Jack Szostak’s works. See: Retraction Watch
Researchers who study the origins of life on Earth have hypothesized that RNA evolved before DNA or proteins. Szostak’s works seemed to suggest that RNA replicated itself without enzymes. Supposedly, a certain type of peptide — which may have existed in our early history — made it possible for RNA to copy itself. But where did the peptide come from?
Who cares? In subsequent experiments, no one reproduced the 2016 findings. Indeed, the peptide did not appear to provide an environment that fostered RNA replication. With two retraction of his groups works, claims about the microRNAome should have been placed into the context the energy-dependent creation microRNAs and enzymes.
The problem that serious scientists expect to be addressed is the one that links the nutrient-energy dependent source of the materials for developing germ cells to the development of differentiated cell typed in the context of metabolism and signaling. Again, we see how Nonomura helps to eliminate the magic of evolution without admitting to the hoax. Light energy is required, and he did not mention that fact.
For comparison, science journalist Philip Ball took the the magic several steps further. He placed the availability of the quantized energy as information, which is required for the creation of nutrients, into this context:

To turn quantum to classical, we don’t need a conscious mind to measure or look; we just need an environment full of stuff. With or without us, the Universe is always looking.

Nonomura claims that little is known about the mechanism that promotes the energy-dependent intercellular movement of small RNAs in plant reproductive organs. But, he also claims that the mechanism in humans is part of an energy-dependent exosome-mediated system, which was recently reported in the context of small RNA transfer in organ cross-talk. Philip C. Ball’s claims are based on the automagical creation of an environment full of stuff.
The link from the availability of nutrient-energy in pollen (i.e., Ball’s environment full of stuff) to energy-dependent foraging behavior and the pheromone-controlled physiology of reproduction in the honeybee model organism is missing. Nonomura’s conclusion is another example of Sokal-like wit. The cell membrane must automagically create itself before direct evidence for energy-dependent microRNA-mediated cell type differentiation can be linked to healthy longevity in all living genera via the physiology of reproduction in grasses like fescue.
The energy source for the transfer of materials or information between SCs [somatic cells] and the vegetative cell (VC) nucleus in not mentioned in Nonomura’s attack on the intelligence of theorists and science journalists who have failed to link the virus-driven theft of quantized energy from mutations to the transgenerational epigenetic inheritance of all pathology.
For comparison: My top tweet from this month was posted on January 5, 2018. So far it has accumulated 1484 impressions. In case you missed it:
A cartoon representation of “Long-range coherence and energy storage in biological systems” (1968) might help others establish facts about how the construction of the cell membrane protects against virus-driven genomic entropy.
A comic about the problems with the -omics, illustrated by Matteo Farinella
The problem with -omics, and especially with the ridiculous representation from 2014 as a pinned post @rnomics, has repeatedly been detailed in articles from social scientists and other theorists who fail to link what is known to serious scientists about the microRNAome to their theories. Pseudoscientists and biologically uninformed science journalists continue to create bricks that clutter the metaphorical physical landscape (an environment full of stuff) and human idiocy prevents the epigenetic landscape from being linked to all cell type differentiation via the nutrient energy-dependent pheromone-controlled links from atoms to ecosystems in all living genera.
The MicroRNAome Strikes Back: A Sokalian hoax (3)
See also: The Postmodernism Generator web page (generates a random postmodernist article each time loaded)
See also: Social science is pseudoscience
 

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