The tipping point (revisited): 80,000 publications

By: James V. Kohl | Published on: November 22, 2018

(click to enlarge)

Excerpt: They linked the diet of larval moths from light-activated microRNA biogenesis in mulberry leaves to every aspect of food energy-dependent biophysically constrained viral latency via the physiology of pheromone-controlled reproduction and species-specific degradation of the silk gland.
For review:

10,000 reasons to believe in biophysical constraints (11/1/18)
The tipping point (revisited): 78,000 publications (1) (10/2/18)
79,000 reasons to believe in biophysical constraints (11/3/18)

See also: MicroRNA Items: 1 to 20 of 79970 11/22/18 (Thanksgiving Day, USA)
Summary: Non-mendelian Inheritance in Mammals Is Highly Constrained because MicroRNAs buffer genetic variation
The nonsense placed into the context of bioinformatics and ridiculous theories is now irrelevant to discussions of top-down energy-dependent causation and RNA-mediated cell type differentiation via the physiology of reproduction.
See also: miRBase: from microRNA sequences to function

Over 500 000 sentences from 18 542 papers contain microRNA names. We score these sentences for functional information and link them with 12 519 microRNA entries.

If you haven’t linked light-activated microRNA biogenesis in plants from the physiology of pheromone-controlled reproduction in bacteria to biophysically constrained RNA interference and sympatric speciation, you probably have less than one month to reconsider your support for ridiculous theories.
This is why: microRNA response in potato virus Y infected tobacco shows strain-specificity depending on host and symptom severity

The observed strain-specific alteration of miRNAs and their targets are host dependent and corresponds to the symptom severity and the viral HC-Pro RNA levels.

Translation: Light-activated microRNA biogenesis biophysically constrains strain specificity in host organisms. Cause and effect are manifested in symptom severity in all living genera.
See: Phyto-miRNA: A molecule with beneficial abilities for plant biotechnology
Light-activated microRNA biogenesis/phyto-miRNA in plants links strain-specific alteration of miRNAs and their targets link from changes in base pairs to single nucleotide polymorphisms and single amino acid polymorphisms. The physiology of reproduction links fixation of the single amino acid polymorphisms to healthy longevity. The virus-driven degradation of messenger RNA links mutations to all pathology in all living genera.
Simply put, healthy longevity is biophysically constrained in species from microbes to insects and humans via the metabolism of food to species-specific pheromones. Light-activated microRNA biogenesis is the link to plant growth. If you would like to restate your case for mutation-driven evolution, prepare to be ridiculed for missing all the links from food energy to the pheromone-controlled physiology of reproduction in species from microbes to humans.

See for example: Three vital RNA functions and interactions in the process of silk gland apoptosis in silkworm Bombyx mori 11/11/18

…miRNAs play an important role in the molecular regulation of the silk gland apoptosis compared with that of lncRNAs…”

The vital functions of RNA link light-activated microRNA biogenesis in mulberry leaves from the diet of larval moths to every aspect of food energy-dependent biophysically constrained viral latency via the physiology of pheromone-controlled reproduction and species-specific virus-driven RNA-mediated degradation of the silk gland.
That fact links the 1959 definition of pheromones to biophysically constrained viral latency in species from microbes to humans.
See: Pheromones: a new term for a class of biologically active substances (Nature 183:4653 p 55-56)

….substances which are secreted to the outside by an individual and received by a second individual of the same species, in which they release a specific reaction, for example, a definite behavior, or a developmental process.”

Also, the creation of sunlight was linked from epigenetic effects on hormones to affects on behavior during developmental processes. The strain-specific effects of stress on species from microbes to humans was predicted in Effects of Carnitine on Fatty-Acid Oxidation by Muscle (1959) and in McEwen et al., (1964): Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

The food energy-dependent synthesis and biophysically constrained degradation of RNA have since been linked to a single amino acid substitution in mice and humans. A sexually dimorphic pre-stressed translational signature in CA3 pyramidal neurons of BDNF Val66Met mice and to other variants, such as EDAR V370A and COMT Val158Met. All the links are food energy-dependent and the energy comes from the sun via light-activated microRNA biogenesis in the context of plant growth.
The levels of energy-as-information-dependent biophysically constrained development in all living genera have led to somewhat concealed claims about human pheromones, which obviously effect the hormones of infants that affect the behavior of infants, albeit at a level of effects linked to unconscious affects.
The odour of human milk: Its chemical variability and detection by newborns
They linked light-activated microRNA biogenesis from the pheromone-controlled physiology of reproduction in insects to humans via the 2005 publication of: Feedback Loops Link Odor and Pheromone Signaling with Reproduction
Despite the obvious effects of light-activated microRNA biogenesis in plants on the physiology of reproduction in species from microbes to insects, others have:

“…questioned whether RNAi [RNA interference] has any function during insect-bacteria interactions.”

But see: MicroRNAs as therapeutic agents
The fact that microRNAs are used as therapeutic agents links naturally occurring RNA interference from insect-bacteria interactions and all other interactions that lead to food energy-dependent pheromone-controlled sympatric speciation in all living genera.
Without the virucidal effect of sunlight on light-activated microRNA biogenesis, theorists are stuck with ridiculous theories that fail to link the creation of sunlight to the source of anti-entropic that serious scientists and most intelligent people have linked to all biodiversity. Even when people do not know all the details of how to link the creation of subatomic particles to healthy longevity, only pseudoscientists start with beneficial mutations and link them to the evolution of new species.
See for comparison: Upregulation of Helicoverpa armigera core RNAi genes by bacterial infections and its effect on the insect-bacteria interaction

The antiviral role of the RNAi pathway in insects is well documented; however, the relevance of this pathway in other aspects of insect immunity is largely unknown. In this study, we questioned whether RNAi has any function during insect-bacteria interactions.

…dicer1 and dicer2 affected larval survival and the replication rates of the pathogenic bacteria suggesting their roles in the interactions.

I reiterate. The constrained replication rates of pathogens are food energy-dependent and pheromone-controlled in species from microbes to mammals. Claims that dicer1 and dicer2 affect larval survival should consider the fact that effects of food energy and pheromones on hormones that affect behavior are biophysically constrained. The failure to differentiate effect and affect is a common problem among theorists who fail to realize that Non-mendelian Inheritance in Mammals Is Highly Constrained 11/15/18

In this issue, Kazachenka, Bertozzi, and colleagues identify elements in the mouse genome with epigenetic variability between littermates, a phenomenon linked to transmission of phenotypes over generations. This addresses two questions that remained unanswered despite intense speculation: how prevalent are these alleles, and what is their effect, within and across generations?

See: Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance (open access)

Highlights

•Repertoire of variably methylated repeat elements defined in inbred mice
•VM-IAPs are flanked by CTCF binding sites, and very few act as promoters
•Methylation variability is re-established from one generation to the next
•Memory of parental methylation state is an exception rather than the rule
The fact that food energy-dependent pheromone-controlled methylation variability is re-established from one generation to the next led to this claim by Ewan Birney, who is the European Molecular Biology Laboratory’s director of the European Bioinformatics Institute (EMBL-EBI)

Ewan Birney tweeted:

I don’t think multi-generational trans-generational epigenetics is an important part of mammalian (including human) biology, and this paper provides the most thorough examination of the most credible source of this.

AND

Note – this doesn’t mean that epigenetic modification (better called: DNA and histone modification) aren’t critical in development and environmental memory inside a particular individual – just that >2 generational transgenerational epigenetics is super rare.

The Director of the European Bioinformatics Institute claims that epigenetic modifications are better called DNA and histone modification. He pits the fact that bioinformatics is no longer required to link top-down energy-dependent causation to biophysically constrained viral latency and all biodiversity against the fact that “Methylation variability is re-established from one generation to the next.” Indeed, Targeted RNA Expression Profiling has established the facts about methylation variability across kingdoms, species, and individuals. The fact eliminate the pseudoscientific nonsense touted by gene-centric theorists with their ridiculous mathematical models.
SARCASM ALERT: Let’s call epigenetic modification “DNA and histone modification” because pseudoscientists failed to recognize the facts about light-activated microRNA biogenesis and biophysically constrained viral latency.

All serious scientists recognize the facts about transgenerational epigenetic inheritance. Food energy links light-activated microRNA biogenesis and biophysically constrained viral latency to all biodiversity in the context of the physiology of reproduction. In species from microbes to humans, the metabolism of food to species specific pheromones links biophysically constrain viral latency to sympatric speciation.

Epigenetic modification is not called DNA and histone modification because an energy source is required for the epigenetically-effected modifications. Most serious scientists understand how that fact is linked to Biblical Genesis via claims in “Past 5,000 years prolific for changes to human genome“

…the majority of variants, including potentially harmful ones, were picked up during the past 5,000–10,000 years.

For comparison, see: For the 40th anniversary of @NYTScience, Carl Zimmer wrote this essay on what we’re learning about how we became human—on a planet crowded with lots of mysterious relatives of humans. How Did We Get to Be Human?

…we are still living with them. Both Neanderthals and Denisovans interbred…. Still mosaics, after all this time.

It is disingenuous to continue to put light-activated microRNA biogenesis and epigenetically-effected sympatric speciation back into the context of the fossil record, which is what Carl Zimmer did.
See for comparison: Living with the Neanderthals

Science is driven by politics, and politics by fear. Greg Bear’s latest novel, Darwin’s Children, grapples with the biases of our society, and the machinations of science, politics and science policy, in the face of its most formidable challenge… the next step in human evolution.

Bear told a story about ecological adaptations and subsequently tried to assure us that the virus-driven degradation of messenger RNA would link the hecatombic evolution of pathology to our extinction in “Quantico.” For comic relief, see: Jon Stewart interviews Greg Bear (6/1/2007)
@NYTScience is as desperate as European Bioinformatics Institute to misrepresent the hecatombic evolution of virus-driven pathology because Carl Zimmer’s pseudoscientific nonsense has repeatedly been revealed in articles like this: Testing the retroelement invasion hypothesis for the emergence of the ancestral eukaryotic cell

… nonhomologous end-joining (NHEJ), a mechanism of DNA repair found in all extant eukaryotes [known to all serious scientists as alternative splicing]… significantly enhances the efficiency of retrotransposition and the effects of retroelements on the host. We hypothesize that the interplay of NHEJ and retroelements may have played a previously unappreciated role in the evolution of advanced life.

The effects of the retroelements on the host are biophysically constrained in the context of light-activated microRNA biogenesis and the fixation of RNA-mediated amino acid substitutions that stabilize the cell types of all cells in all individuals of all living genera. The bottom line is that all bacteria, insects, and mammals use what they eat to biophysically constrain endogenous retroviruses (ERVs) in the context of the pheromone-controlled physiology of reproduction.
See also: Happy 40th to Science Times (@NYTScience):

In 2003, on the 25th anniversary of the section, reporters offered up their thoughts on the most pressing questions in science. Fifteen years later, the questions have changed. But we’re still curious.

On Smell

I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece, all the mysteries” (p. 732). — Lewis Thomas as cited in The Scent of Eros: Mysteries of Odor in Human Sexuality

See also: Olfaction Warps Visual Time Perception
A follow-up by Thomas Lin from Quanta promotes the book: Alice and Bob Meet the Wall of Fire: The Biggest Ideas in Science
Lin asks:

With experiments at the LHC unable to move particle physics past the Standard Model, where does science go from here?

Science has left all the contributors to the book behind. Included are Philip Ball, K. C. Cole, Robbert Dijkgraaf, Dan Falk, Courtney Humphries, Ferris Jabr, Katia Moskvitch, George Musser, Michael Nielsen, Jennifer Ouellette, John Pavlus, Emily Singer, Andreas von Bubnoff, Frank Wilczek, Natalie Wolchover, and Carl Zimmer
The failure to move particle physics beyond the Standard Model was addressed in: Kalevi Kull: Censorship & Royal Society Evo Event

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

Biologically uninformed science journalists and other theorists are among the worst of the losers. They may continue to report their pseudoscientific nonsense outside the context of the creation of subatomic particles (see Subatomic) and biophysically constrained microRNA-mediated viral latency (see Cytosis).
You can recognize the losers among those who failed to report the obvious link from the creation of the sun’s anti-entropic virucidal energy to the creation of enzymes, the innate immune system, the olfactory system and the ability to regenerate cell types in the brain.
See for comparison: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
See also: Bioprocessing strategies to enhance the challenging isolation of neuro-regenerative cells from olfactory mucosa
See for comparison: Genome-wide association studies of brain imaging phenotypes in UK Biobank
Remember what the late Jaak Panksepp said in Affective Neuroscience with Jaak Panksepp (BSP 65)

My feeling is that the social brain has many levels. If you don’t understand the foundational level, then you can do brain imaging until you’re blue in the face, but you still will not understand the process at a deep causal level.

Lee and colleagues found the same short variants when they analysed genomic DNA from the neurons, suggesting that APP-variant mRNAs might be transcribed from matching genomic DNA sequences — named genomic complementary DNAs (gencDNAs) by the authors — that had become permanently embedded in the genomes of neurons.

Pseudoscientists use bioinformatics and invent terms such as nonhomologous end-joining and genomic complementary DNAs (gencDNAs) to obfuscate the fact that they have contributed more than most to the unnecessary suffering and premature death, which serious scientists know is caused by the virus-driven degradation of messenger RNA that links mutations to neurodegenerative diseases and cancer.
See: microRNA diagnostic panel for Alzheimer’s disease and epigenetic trade-off between neurodegeneration and cancer

…the directions of the miRNA changes are usually opposite in cancer and AD, indicative of an epigenetic trade-off between the two diseases.

The epigenetic trade-off is caused by the virus-driven degradation of messenger RNA. Energy-dependent healthy longevity is linked to pathology by the conserved molecular mechanisms of microRNA-mediated cell type differentiation in species from plants to humans. When light-activated microRNA biogenesis fails, or when stress-induced viral replication perturbs autophagy, it makes no difference if you die from cancer or a neurodegenerative disease.