The tipping point (revisited): 95K (3)

On 11/19/19 there were 94059 indexed published works on microRNAs.

See the update: microRNA

In 20 days ~ 1000 more indexed publications have been added.

These three examples of scientific truths are among the additions:

1) Translational landscape of protein-coding and non-protein-coding RNAs upon light exposure in Arabidopsis 12/3/19

Light is one of the most essential environmental clues for plant growth and morphogenesis. Exposure to blue monochromatic light from darkness is a turning point for plant biological activity and as a result dramatic changes in gene expression occur. To understand the translational impacts of blue light, we have performed ribosome profiling analysis and called translated ORFs de novo within not only mRNAs but also non-coding RNAs. Translation efficiency of 3,823 protein-coding ORFs, such as nuclear chloroplast-related genes, was up-regulated by blue light exposure. Moreover, the translational activation of the microRNA biogenesis-related genes, DCL1 and HYL1, was induced by blue light.

2) A Brassica miRNA Regulates Plant Growth and Immunity through Distinct Modes of Action 11/30/19

…under natural conditions, miR1885 was kept in low levels to maintain normal development and basal immunity but peaked during the floral transition to promote flowering. Interestingly, upon Turnip mosaic virus (TuMV) infection, miR1885-dependent trans-acting silencing of BraCP24 was enhanced to speed up floral transition, whereas miR1885-mediated R gene turnover was overwhelmed by TuMV-induced BraTNL1 expression, reflecting an integrative regulation of the arms race between plants and pathogens. Collectively, our results demonstrate that a single Brassica miRNA dynamically regulates both innate immunity and plant growth and responds to viral infection, therefore demonstrating an integrative strategy for Brassica in modulating the interplay between growth, immunity and pathogen infection.

3) Explaining Gene Expression Using Twenty-One MicroRNAs 12/2/19

Our analysis of poorly explained genes shows that they are enriched for olfactory receptor processes, sensory perception, and nervous system processing, which are necessary to receive and interpret signals from outside the organism. Therefore, it is reasonable for those genes to be always active and not get downregulated by miRs. In contrast, highly explained genes are characterized by genes translating to proteins necessary for transport, plasma membrane, or metabolic processes that are heavily regulated processes inside the cell. Other genetic regulatory elements such as transcription factors and methylation might help explain some of the remaining variation in gene expression.

See for comparison: The Key to Good Luck Is an Open Mind 3/26/18.

Regurgitated today because “chance favors only the prepared mind.” — Louis Pasteur 12/7/1854

Pasteur was a Creationist. Both he and Darwin (1859) presciently linked light-activated microRNA biogenesis to the “conditions of life” that protect all organized genomes from the virus-driven degradation of mRNA. See 3/30/16

See also: Thousands of Mutations Accumulate in the Human Brain Over a Lifetime 12/7/17

Mutation accumulation could therefore be “a reasonable model for how age-related cognitive decline might come about,” he says.

Walsh’s team also noted that the types of SNVs varied with age, with those apparently caused by oxidative damage being more prevalent in the elderly. That fits “with previous literature that suggests that one cause of aging in the brain might have to do with oxidative damage,” he says.

Fred Gage of the Salk Institute in La Jolla, Michael McConnell of the University of Virginia School of Medicine, Yale School of Medicine’s Flora Vaccarino, and Christopher Walsh of Harvard Medical School and Boston Children’s Hospital came close to telling everyone that the accumulation of mutations is caused by the virus-driven degradation of mRNA, which has been linked to all pathology.

For comparison, food energy-dependent oxidative phosphorylation links God’s Creation of sunlight and water to the Creation of all oxygen-dependent life on Earth via the physiology of reproduction.  But 2 years later, pseudoscientists/cancer researchers refuse to admit it.

This approach revealed noncanonical target sites unique to each miRNA, miRNA-specific differences in canonical target-site affinities, and a 100-fold impact of dinucleotides flanking each site. These data enabled construction of a biochemical model of miRNA-mediated repression, which was extended to all miRNA sequences using a convolutional neural network. This model substantially improved prediction of cellular repression, thereby providing a biochemical basis for quantitatively integrating miRNAs into gene-regulatory networks.

Theories about the coevolution of species were portrayed in the context of a biochemical basis for quantitatively integrating miRNAs into gene-regulatory networks via a convolutional neural network. The convolutional approach is consistent with what has been known to all serious scientists, since 1964. The coevolutionary approach is not,

See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

McGeary et al, (2019) deliberately obfuscated the facts that link the ATP-dependent synthesis of RNA from RNA interference to biophysically constrained viral latency and healthy longevity via a convolutional neural network.

For comparison, the facts about how RNA synthesis is linked to convolutional neural networks were also placed into the context of light-activated microRNA biogenesis in XenomiRs and miRNA homeostasis in health and disease (9/1/12) via evidence that diet and dietary miRNAs directly and indirectly influence circulating miRNA profiles.

1) …diet-derived exogenous miRNAs (or “xenomiRs”) affect total miRNA profiles as part of a circulating miRNA homeostasis that is altered in many diseases.

2) … the largest pachyderm in the disease biomarker room, though, is diet, which may exert 3-fold modulation on circulating miRNA profiles:

Biologically uninformed theorists should prepare for their heart attack by reading Arctigenin alleviates myocardial infarction injury through inhibition of the NFAT5-related inflammatory phenotype of cardiac macrophages/monocytes in mice (12/2/19) before reading A Brassica miRNA Regulates Plant Growth and Immunity through Distinct Modes of Action 11/30/19

“…a single Brassica miRNA dynamically regulates both innate immunity and plant growth and responds to viral infection…”

Read that again: One microRNA is all that’s required to link biophysically constrained viral latency from innate immunity to plant growth.

Why hasn’t everyone learned that light-activated microRNA (miRNA) biogenesis links biophysically constrained viral latency from innate immunity to healthy longevity in more than 95K indexed published works?

Why are only two of these four stages of acceptance accepted by theorists?

See: “The four stages of acceptance”– JBS Haldane (1963)

1. This is worthless nonsense

2. This is an interesting, but perverse, point of view

3. This is true, but quite unimportant

4. I always said so

When you are ready to admit that all four stages of acceptance have prevailed,

see also: MicroRNAs buffer genetic variation at specific temperatures during embryonic development

…phenotypes may arise at specific temperatures while remaining silent at others, even within typical temperature ranges. Our work uncovers that miRNAs mask genetic variation at specific temperatures to increase embryonic robustness, highlighting another layer of complexity in miRNA expression.

But wait, there’s more.

See: Plant MicroRNAs in Cross-Kingdom Regulation of Gene Expression 7/10/18

We also discuss possible miRNA horizontal transfer mechanisms from one species to another and analyze the relationship between miRNA-mediated cross-kingdom regulation and coevolution during a long-term specific host⁻pathogen interaction.

See also:  Competing endogenous RNA crosstalk at system level 11/1/19

miRNAs mediate a weak but resilient and context-independent network of cross-regulatory interactions that interconnect the transcriptome, stabilize expression levels and support system-level responses.

What do virus-driven mutations do to the coordinated coherence of system-level responses? See

Using coherence to enhance function in chemical and biophysical systems 3/30/17 co-authored by President Trump’s scientific advisor, K. Birgitta Whaley

…we survey …recent discoveries…that suggest… coherence can be used in complex chemical systems…as a design element in realizing function.

All realized functions are energy-dependent and biophysically constrained by the physiology of reproduction. Light-activated microRNA biogenesis appears to be a design element for realizing function.

If so, it is long past time for the ridicule of all theorists, see 

Would you rather avoid the ridicule, or continue to prevent scientific progress via your failure to link what pseudoscientists call coevolution to energy-dependent biophysically constrained viral latency and convolutional neural networks?

Author: James Kohl

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