The MicroRNAome Strikes Back: A Sokalian hoax (4)

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

In this Sokalian hoax series, all food energy-dependent pheromone-controlled biodiversity has clearly been linked from the speed of light on contact with water to biophysically constrained viral latency in all genera via the physiology of reproduction and autophagy, the innate phage defense mechanism.
Will water link RNA modifications to stem cell self-renewal, or will light-activated endogenous substrates and biophysically constrained RNA-mediated amino acid substitutions be tossed into the brickyard for the win?

I reiterate the most obvious facts by mentioning again:

 Virus-mediated archaeal hecatomb in the deep seafloor

Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

See also: The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition

Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding, and no net change in affinities. This phenomenon—termed enthalpy/entropy (H/S) compensation—hinders efforts in biomolecular design, and its incidence—often a surprise to experimentalists—makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting—and, perhaps, avoiding or exploiting—this phenomenon in biophysical systems.

The John Templeton Foundation typically seems to be involved in funding research reported that obfuscates facts that link science to Biblical Genesis. The claims about understanding energy-dependent biomolecular recognition in biophysical systems, which must biophysically constrain viral latency, invite more criticism of the Templeton-funded biologically uninformed theorists.

Does the “Extended Synthesis” Replace or Not Replace Neo-Darwinism? — What Has Templeton Funded?

Many terms in science have a different meaning from the public usage, because they depend on particular definitions of the phenomena to which they apply.

See for comparison: Do Human Pheromones Exist? January 23, 2018

The people interviewed are not Nobel Laureates. For comparison, LInda Buck, co-author of Feedback loops link odor and pheromone signaling with reproduction is a 2004 Nobel Laureate.
I suspect that all serious scientists have since learned that pheromones biophysically constrain food energy-dependent viral latency in species from insects to mammals via the conserved molecular mechanisms of microRNA-mediated cause and effect. Serious scientists tend to be more likely than theorists or other pseudoscientists to recognize patterns.
For instance: Insect pheromone in elephants

SIR – (Z)-7-dodecen-l-yl acetate is used by the females of more than 126 species of insects, especially Lepidoptera, as part of their pheromone blends to attract insect males1. Female Asian elephants, Elephas maximus, also use a pheromone to signal to males their readiness to mate2.

That claim links what insects eat to the pheromone-controlled physiology of reproduction of s via the food energy-dependent creation of microRNAs in species from microbes to mammals.

See: Juvenile hormone and sesquiterpenoids in arthropods: Biosynthesis, Signaling, and role of MicroRNA (with my emphasis)

Dynamic and complex mechanisms have evolved to regulate sesquiterpenoid production. Noncoding RNAs such as the microRNAs are primary regulators. This article provides an overview of microRNAs that are known to regulate sesquiterpenoid production in arthropods.

insects, arachnids, and crustaceans are arthropods. No experimental evidence of biologically-based cause and effect suggest that complex mechanisms evolved in any species. For contrast, the link from microRNAs to juvenile hormone crosses species via the molecular mechanisms that link the food energy-dependent creation of microRNAs from what is known about gonadotropin releasing hormone (GnRH) pulsatility to luteinizing horrmone secretion via the food energy-dependent GnRH-directed physiology of pheromone-controlled feedback loops in all mammals.

That fact has been placed into the context of ecological variation and biophysically constrained ecological adaptations.

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes 

…lack of genome information hinders the understanding of the adaptation

See for comparison: Differential expression of microRNAs in luteinising hormone-treated mouse TM3 Leydig cells

Results showed that miRNAs might be involved in the regulation of LH to Leydig cells.

One way to understand the adaptations revealed in the context of mussel genomes involves ignoring all claims about how complex mechanisms “evolved to regulate” anything. The overwhelming systems complexity of biophysically constraints demand that all ecological adaptations be examined from the intelligent perspective of serious scientists.

The well-detailed understanding of how the light energy-dependent creation of microRNAs is linked to all nutrient-dependent pheromone-controlled ecological adaptations. But the facts were again placed back into the context of complex mechanisms that automagically evolved in  Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs

…pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4.

The established biodiversity is obviously pH-dependent and oxidative phosphorylation was linked to the stability of organized genomes in 1964: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”. Other serious scientists moved forward in the context of the energy-dependent hydrophobicity of supercoiled DNA.
See: Structural diversity of supercoiled DNA

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

Outside the context of the epigenetic effect of anti-entropic virucidal energy from sunlight on supercoiled DNA, or perhaps in the context of minimal exposure to ultraviolet light, the metagenomic diversity of bacteria in caves with sulfur water springs led  Bautista et. al., (2018) to conclude:

…20,901 reads of bacterial 16S rRNA gene sequences spanning V1–V3 hypervariable regions corresponded to seven phyla: Proteobacteria, Firmicutes, Chloroflexi, Chlorobi, Bacteroidetes, Actinobacteria and Acidobacteria. Proteobacteria phylum dominance could be due to the increased presence of organic matter, not only of bat guano but also that caused by man and animals, directly or through infiltrations. For the UJAT5 sample, we generated 6,691 reads, which, due to the
physicochemical characteristics (Table 1) and relative frequency obtained (Figure 4), could confirm the presence of acidophilic Proteobacteria in VL caves. All the bacterial communities identified are characteristic of caves, while Acidobacteria, Proteobacteria, and Actinobacteria are typical of volcanic surface terrain.

Simply put, they seem to assume that the increased presence of organic matter is the food energy that supports the pheromone-controlled physiology of reproduction in the different species. But they do not link the creation of sunlight to differences in the food the organisms eat.
By skipping the link from the creation of sunlight — as did Nonomura (2018) in his Sokalian hoax, evolutionists have tried to convince others who are biologically uninformed that the eyes of blind cave fish exemplify evolution in the process of the fish becoming blind.
See: Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish
See (pun intended) Blind Cavefish Can Produce Sighted Offspring  (2008)

It’s a miracle! Blind cavefish, despite having adapted to their lightless environment for more than a million years, can produce sighted offspring in just a single generation, a new study reveals.

This means that even though the fish are blind, they basically have functional visual systems that have been deactivated by a few key mutations, said Jeffery, who was unaffiliated with the study.

See also: The fish evolved from surface-dwelling ancestors during the past million years. (2003)
Everything biologically uninformed theorists report must be linked toi evolution and back by mutations. They refuse to differentiate between mutations and food energy-dependent ecological adaptations because they cannot accept the fact that all biophysically constrained biodiversity is food energy-dependent and constrained by energy-dependent viral latency.
For comparison, what serious scientists see happening in the blind cave fish is the regression of food energy-dependent visual acuity in organisms that can find food without  the energy-dependent creation of G protein-coupled photoreceptors. Only the energy-dependent creation of chemoreceptors is required to link pH-taxis to survival of the microbes and the blind cave fish via what is known about oxidative phosphorylation in other species that display receptor-mediated behaviors.
What science journalists see happen is causing them to back away from their pseudoscintific claims from the past. See for example:

Hydration as a design element in biomaterials  Philip Ball January 24, 2018

John Hewitt January 24, 2018 N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications 
Will water link RNA modifications to stem cell self-renewal, or will light-activated endogenous substrates and biophysically constrained RNA-mediated amino acid substitutions be tossed into the brickyard for the win?

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