Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

The eternal significance of microRNAs (2)

Summary: What is known for sure, however, is that biological processes called “nature” are not simplistic. Neither is the entity called “the environment.” The two separate worlds overlap and intertwine so only a single interactive one exists. Yes, it may be simpler to look at each singly, but one does so at intellectual peril.
The Immune Landscape of Cancer (2018)

Multiple control modalities of the intracellular and extracellular networks (transcription, microRNAs, copy number, and epigenetic processes) were involved in tumor-immune cell interactions, both across and within immune subtypes.

More than 725 collaborators linked the anti-entropic virucidal energy of sunlight  from  the energy-dependent creation of microRNAs and biophysically constrained viral latency to cell type differentiation via autophagy.
See for comparison: From Fertilization to Adult Sexual Behavior (1996)

What is known for sure, however, is that biological processes called “nature” are not simplistic. Neither is the entity called “the environment.” The two separate worlds overlap and intertwine so only a single interactive one exists. Yes, it may be simpler to look at each singly, but one does so at intellectual peril.

Richard P. Feynman placed the intellectual peril into the context of food energy and human idiocy.
See:

See also: The Translation Machinery Is Immune from miRNA Perturbations: A Cell-Based Probabilistic Approach

Mature microRNAs (miRNAs) are non-coding RNA that regulate most human genes through base-pairing with their targets.

Base-pairing is energy-dependent and biophysically constrained. See: Structural diversity of supercoiled DNA and the parody: All About that Base (Meghan Trainor Parody) 12/10/14
Others now appear to be following on the heels of the late Eshel Ben-Jacob’s works, which showed that the “stochastic nature of miRNA action” is light energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction in species from microbes to humans.
See: MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination
MicroRNA-based regulation is obviously the key to biophysically constrained viral latency in the context of everything known about the eternal significance of microRNAs.
See also: microRNA 
The quantized energy-dependent differential expression of microRNAs has been linked to healthy longevity or from virus-driven energy theft to all pathology in more than 71,000 indexed published works.
Serious scientists now know that John McCain’s glioblastoma can probably be effectively treated with the microRNA-mediated immunotherapy that led to the remission of Jimmy Carter’s brain cancer.
See: John McCain’s brain cancer prognosis is ‘not very good,’ medical expert says
The reporters touch on the likely link from melanoma to brain cancer via microRNAs, and then dismiss it.
See for comparison: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene
Would you like to target the regulation of your cell death genes?
See: The Remarkable Cancer Treatment That Helped Jimmy Carter Combat Brain Tumor

…his doctors have said he no longer needs cancer treatment thanks in part to a groundbreaking new kind of medication that trains the immune system to fight cancer tumors.

Anyone who is interested in learning how to prevent all diseases of the body and the brain (e.g., suicide prevention) may want to select the following link. Broad Anti-tumor Activity of a Small Molecule that Selectively Targets the Warburg Effect and Lipogenesis.
The Warburg Effect links virus-driven energy theft to all pathology in the context of sympatric speciation, which is food energy-dependent and controlled by feedback loops that link the food energy to the pheromone-controlled physiology of reproduction.
Unfortunately, the Warburg effect is commonly used to explain mutation-driven evolution outside the context of the food energy that is required for sympatric speciation. Biologically uninformed theorists continue to display what Feynman referred to as human idiocy — as if no one on Earth can stop them.
But see: Cytosis. You could learn that the cure for all pathology is food energy-dependent and microRNA-mediated in the context of biophysically constrained viral latency.
See also: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution
Anyone who makes claims about “viral evolution”  should be forced to explain why they have not learned how fixation of RNA-mediated amino acid substitutions have been linked to healthy longevity.

Editor’s summary: Five antigenic sites in the virus surface hemagglutinin protein, which together comprise 131 amino acid positions, are thought to determine the full scope of antigenic drift of influenza A virus. Koel et al. (p. 976) show that major antigenic change can be caused by single amino acid substitutions.

See also: Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity

Brain gene expression profiling studies of suicide and depression using oligonucleotide microarrays have often failed to distinguish these two phenotypes. Moreover, next generation sequencing approaches are more accurate in quantifying gene expression and can detect alternative splicing.

Who doesn’t want others to know that our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation included a section on “molecular epigenetics” and alternative splicing? See: From Fertilization to Adult Sexual Behavior

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Is meat protein unhealthy? (2)

See also: Microbiome-Grade DNA Extraction Kits

…the thermal and chemical methods effectively lyse the gram-negative organisms and boost their population in the final profile, amplifying the bias.

This suggests that all links from food energy-dependent de novo creation of the pheromone-controlled biophysically constrained bull sperm microRNAome have been misinterpreted in the context of virus-driven fescue toxicosis.

The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

…the miRNA profile of mature ejaculated sperm may in fact have downstream consequences upon embryonic development. The potential for sperm miRNA affecting zygote development has recently been reported in the literature [18] and has interesting implications for the use of sperm miRNA profiles as indicators of potential male fertility.

Fescue toxicosis links the virus-driven creation of enzymes to the degradation of messenger RNA in bull sperm and to the transgenerational epigenetic inheritance of mutations, which all serious scientists have linked from damage to supercoiled DNA to all pathology in humans and other species.

Eating the meat from other animals that have not ecologically adapted to the virus-driven theft of quantized energy has been linked from the viruses in their genomes to human pathology via the degradation of messenger RNA in bacteria that become archaea and L-forms.

See also: Dobzhansky (1973)

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.

See also: The Breadth of Viruses in Human Semen

The presence of viruses in semen is probably more widespread than currently appreciated, and the absence of virus in genital secretions should not be assumed for traditionally non–sexually transmitted viruses. The investigation of virus detection and persistence in semen across a range of viruses is useful for clinical and public health reasons, in particular for viruses that lead to high mortality or morbidity rates or to epidemics.

No serious scientist has ever reported a link from the Virus-mediated archaeal hecatomb in the deep seafloor to the evolution of anything except pathology. All serious scientists have, for comparison, linked ecological variation to food energy-dependent  polycombic ecological adaptations via biophysically constrained viral latency in species from microbes to humans.

From Fertilization to Adult Sexual Behavior (1996)

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation…

See also: Cytosis: A Cell Biology Board Game for ages 10+

 A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

5th-6th Sept 2018 Dublin, Ireland

Is meat protein unhealthy? (1)

Patterns of plant and animal protein intake are strongly associated with cardiovascular mortality
Reported as: Meat protein is unhealthy, but protein from nuts and seeds is heart smart

In the context of everything known about how the creation of anti-entropic virucidal light must be linked to all biodiversity on Earth, watch this ridiculous misrepresentation of the honeybee model organism. Food energy-dependent microRNA-mediated pheromone-controlled biophysically constrained viral latency is portrayed as if visual input was most important.

Bee swarms work like giant brains

See instead:

RNA-mediated nutritional psychiatry

RNA-mediated nutritional psychiatry (2)

Psychophysical Laws of Biology: RNA-mediated nutritional psychiatry (3)

Learn how to prevent more school shootings via what is known about how the “Psychophysical Laws” of Biology are linked to food energy-dependent biophysically constrained behaviors via microRNA-mediated cell type differentiation and the fixation of RNA-mediated amino acid substitutions like COMT Val158Met during the transition from adolescence to adulthood.

Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults (Epub Oct 16 2014)

"Evolution of Man. - Undoubtedly there once lived upon the earth races of men who were much lower in their mental organization than the present inhabitants.

Autophagy is the antiphage defense strategy (2)

2/15/17 Energy as information and constrained endogenous RNA interference (video)
The 6.46 minute-long technical presentation (above) from the Precision Medicine Virtual Conference is difficult to understand.Thus, 10 months later, Nik Willmore asked:

12/24/17 What are your insights into CRISPR and mTOR, for a young audience? I’m not mocking you…yet, Humpty Dumpty. What is the basis of your unifying principle? Vibration? Bohmian morphogenetic fields? Modified Darwin? God? –Nik Willmore 

12/25/17 Replying to

God created the anti-entropic virucidal energy of sunlight and all energy-dependent biodiversity via the physiology of pheromone-controlled reproduction. I co-authored a book about that for a young audience in 1995/2002, and a 6-part series for today.

1/1/18 Replying to

Do you understand any aspect of how to model biophysically constrained biologically-based energy-dependent top-town causation and bottom-up effects on cell type differentiation via the physiology of reproduction and autophagy? The “walking fish” walks straight from quantum physics to quantum souls (2)

1/9/18 Viral suppressors of RNAi employ a rapid screening mode to discriminate viral RNA from cellular small RNA

My paraphrased summary:

RNA interference (RNAi) is our indispensable antiphage defense mechanism. Viruses escape the defense system by the theft of quantized energy, which encodes RNAi suppressors that prevent elimination of viral RNAs. The suppressors ensure energy-dependent virus accumulation.

1/12/18 Human cytomegalovirus-encoded miR-UL112 contributes to HCMV-mediated vascular diseases by inducing vascular endothelial cell dysfunction

The significantly altered pathways mainly include the mitogen-activated protein kinase signaling pathway, cell adhesion molecules, chemokine signaling pathway, cytokine-cytokine receptor interaction, circadian rhythm-mammal, mineral absorption, protein processing in the endoplasmic reticulum, proximal tubule bicarbonate reclamation, vasopressin-regulated water reabsorption, and arachidonic acid metabolism. In conclusion, hcmv-miR-UL112 could serve as a potential biomarker, and the miRNA-mediated regulation of signaling pathways might play significant roles in the physiological effects of hcmv-associated diseases.

1/12/18 H5N1 influenza virus-specific miRNA-like small RNA increases cytokine production and mouse mortality via targeting poly(rC)-binding protein 2

We conclude that miR-HA-3p is the first identified influenza virus-encoded microRNA-like functional RNA fragment and a novel virulence factor contributing to H5N1-induced ‘cytokine storm’ and mortality.

Virus-encoded microRNA-like functional RNA fragments are not novel virulence factors. They link the virus-driven degradation of messenger RNA to all pathology in all living genera via the theft of quanitzed energy, which typically links the fixation of RNA-mediated amino acid substitutions to healthy longevity.
See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs
All serious scientists know what goes wrong in the context of host microRNA-mediated regulation of viruses. They also know how it goes wrong. See Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

The serious scientists do not claim that viruses evolve. Scientists who make claims about evolution  typically do not know how to link the creation of sunlight from ecological variation to food energy-dependent pheromone-controlled ecological adaptation via the physiology of biophysically constrained reproduction and biophysically constrained viral latency. Indeed, most pseudoscientists do not know the difference between a mutation and an RNA-mediated amino acid substitution.
See for comparison: Mechanisms of Recombination conference Start: Sunday, May 20, 9.00am Finish: Tuesday, May 22, 6.45pm

Description

Genetic recombination provides an important mechanism for the repair of chromosome breaks caused by DNA damage or replication fork demise. Defects in the recombination process have been linked to cancer predisposition, in particular breast cancers caused by mutations in BRCA1, BRCA2 and PALB2, and also acute leukemias associated with the rare genetic disease Fanconi anemia. Understanding precisely how recombination occurs is of interest to workers in the fields of meiosis, DNA repair, replication, chromosome architecture and interactions, and chromatin biology.

Download provisional conference program
Excerpts:

Douglas Bishop (University of Chicago, US)
A primary function of the ATPase activity of E. coli RecA is to prevent accumulation of a toxic form of the protein bound to undamaged chromosomal sites

Maria Jasin (Memorial Sloan Kettering Cancer Center, US)
Protecting the genome by homologous recombination

The energy-dependent microRNA-mediated creation of enyzmes protects all organized genomes from the virus-driven degradation of messenger RNA that links the theft of quantized energy from mutations to all pathology.  Pseudoscientists who do not start with the creation of energy, have bastardized Darwin’s claims. His claims were based on placing “conditions of life” before natural selection. Conditions of life are energy-dependent and biophysically constrained by the mechanisms of pheromone-controlled recombination, which have been linked to autophagy by all serious scientists since 1925.
See also my RNA-mediated Facebook page and/or my RNA-mediated Facebook group and other tweets @jvkohl
The number of my tweet impressions since December 21, 2017 has climbed to more than 68,000 as the number of published works that mention “microRNA” has climbed to nearly 69,000. See for comparison: The tipping point (revisited): 68,000 publications, which was published to my other blog site on December 21, 2017.
See also: What Darwinists Fail to Consider (discussion attempt)
See also, this discussion attempt about the “spark of life.”
See also: Noncoding RNA Helps Cells Recover from DNA Damage

“The most logical, simple explanation is that the [noncoding RNA] counteracts the protein encoding form…”

My comment to the Scientist:

There is clear evidence that femtosecond blasts of UV light repair DNA in the context of energy-dependent changes in the microRNA/messenger RNA balance and autophagy, which protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA.

The failure to integrate the Nobel Prize winning works of Ben Feringa (Chemisty 2016) and Yoshinori Ohsumi (Physiology or Medicine 2016) prevents theorists from linking what organisms eat to their pheromone-controlled physiology of reproduction in the context of Schrodinger’s claims in “What is Life?”(1944) and this claim by Roger Penrose in the reprint edition:

“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” (Roger Penrose 8 August 1991)

See also: From Fertilization to Adult Sexual Behavior  In our section on molecular epigenetics, we wrote:

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…

The food energy that is linked from alternative splicing techniques of pre-mRNA to the chemistry of protein folding and the pheromone-controlled physiology of reproduction in all living genera seems to be largely ignored by those who are not Nobel Laureates.

See also: Search Results for “autophagy”

Alternative splicing of pre-mRNA

Pseudoscientists hate what science explains! (3)

See also: Pseudoscientists hate what science explains (2)
Summary: In addition to germline silencing via information transfer to the physical landscape of supercoiled DNA, multicopy transgene arrays are linked from changes in the microRNA/messenger RNA balance to variation in their somatic expression level. That fact helps to establish the difference between healthy longevity and pathology across generations.
Problems with DNA replication can cause epigenetic changes that may be inherited for several generations
My summary: The polycomb repressive complex 2, additional chromatin- and small RNA–related pathways carry quantized energy as information from the epigenetic landscape. The information causes changes in microRNAs that modify histones, which links the energy to the transgenerational epigenetic inheritance of morphological and behavioral phentypes in the nematode model organism.
In addition to germline silencing via information transfer to the physical landscape of supercoiled DNA, multicopy transgene arrays are linked from changes in the microRNA/messenger RNA balance to variation in their somatic expression level. That fact helps to establish the difference between healthy longevity and pathology across generations.
The difference is food energy-dependent, RNA-mediated, and biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera.
See for comparison: From Fertilization to Adult Sexual Behavior (1996)

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes…. Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans… That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

We propose that CNEs [conserved non-coding elements] represent the ‘hard-wired’ sequence traces of these core animal group-specific GRNs [gene regulatory networks]. The alternative core GRNs of different animal lineages are reflected in their having alternative CNEs. However, because of their co-evolution from a common metazoan ancestor, the core GRNs of different animal groups often utilize the same regulatory genes. As a result, distinct yet parallel sets of CNEs have become irreversibly associated with the same genes that coordinate core developmental networks in diverse animal groups. Indeed, this evolution of regulatory elements may underlie the astounding diversification of animal body plans that was seen during the Cambrian period approximately 550 million years ago.

No experimental evidence suggests that regulatory elements evolved.
Predicting phenotypic variation in yeast from individual genome sequences
No experimental evidence predicts a link from gain of function mutations to evolution
Differential DNA mismatch repair underlies mutation rate variation across the human genome
All experimental evidence links natural selection for energy-dependent codon optimality to mutation rate variation across species and to individual differences in the human genome via the pheromone-controlled physiology of reproduction.

3D structures of individual mammalian genomes studied by single-cell Hi-C

Reported as: Scientists have determined the 3D structures of intact mammalian genomes from individual cells, showing how the DNA from all the chromosomes intricately folds to fit together inside the cell nuclei. The research is published in Nature this week. http://go.nature.com/2n6psaw

My comments:

See also: 3D RNA and Functional Interactions from Evolutionary Couplings “…the ongoing explosion of available sequence data means that the outlook for elucidating functional interactions in mRNAs, lncRNAs, and viral genomes, as well as their protein-binding partners, is promising.” http://dx.doi.org/10.1016/j.cell.2016.03.030

Virus-driven energy theft causes the degradation of messenger RNA in all organized genomes. That fact threatens anyone who has ever reported results in the context of mutations, natural selection and evolution because natural selection occurs only for energy-dependent codon optimality.

It would be even more amazing if they told the truth about energy-dependent amino acid substitutions that stabilize supercoiled DNA, which links chromosomal rearrangement to all biodiversity via the physiology of reproduction in species from microbes to humans. See: http://science.sciencemag.org/content/355/6328/910

See other comments to this Nature Facebook page
Addendum: Say goodbye to mutation-driven evolution. Everything known to serious scientists about biophysically constrained endogenous RNA interference and the pheromone-controlled physiology of reproduction has been linked from the de novo creation of nucleic acids to energy-dependent amino acid substitutions that differentiate all cell types in all living genera via fixation in organized genomes.
See: Transgenerational transmission of environmental information in C. elegans
They link diet- and stress-induced changes in heterochromatin from repressed repetitive elements that escape epigenetic reprogramming to phenotypic variation in mammals. It is obvious that heterochromatin provides the link from the molecular mechanisms of biophysically constrained protein folding chemistry to the epigenetic transmission of information between generations. But they speculate that the transgenerational epigenetic inheritance of environmentally triggered changes in expression from repressed chromatin may be linked to ecological adaptations.
See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

 …the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

Ben Lehner and his co-authors have consistently tried to sneak up from behind and link explanations of energy-dependent top-down causation from mutations to evolution.
Others are also ignoring the experimental evidence that links energy-dependent changes in microRNAs to healthy longevity or from virus-driven energy theft to all stress-linked pathology.
See: Stress-induced changes in miRNA biogenesis and functioning
See for comparison: I am not a story

Reported as: Life is not a neat narrative, it’s a patchwork of competing, even contradictory, forces. Sensations are too spurious and memory too fickle for the formation of reliable storylines. Reject the impulse to narrativise. Summer Reads from the Aeon archive: http://ow.ly/bLd430ekoJn

Re: Sensations are too spurious and memory too fickle for the formation of reliable storylines.

My comment: Too late for more of this nonsense. See: Olfaction Warps Visual Time Perception

 

The sense of smell in bacteria has been linked from the physiology of pheromone-controlled reproduction to our visual perception of mass and energy in the context of the space-time continuum via food energy.

See for comparison: Quantum common sense

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking

My comment: No, it’s Santa Claus who sees you when your sleeping; He knows when you’re awake. And he knows if you’ve been bad or good, so be good for goodness sake.

Alternative splicing of pre-mRNA

UV light and non-coding RNA

UV Irradiation Induces a Non-coding RNA that Functionally Opposes the Protein Encoded by the Same Gene

…these events underlie a switch to expression of short mRNA isoforms and preferential use of alternative last exons in a number of genes, including ASCC3. Intriguingly, the switch between ASCC3 isoforms occurs on more than one level, in that the long mRNA isoform encodes a protein, functioning in the context of the ASCC complex and required for maintaining transcriptional suppression in the late stages of the DNA damage response, whereas the short isoform functions as a nuclear non-coding RNA that is required for transcription to recover. Intriguingly, the short and long isoforms constitute an autonomous regulatory module and functionally interrelate, so that the effect of deleting one can be at least partially compensated for by deleting the other (Figure 7H).

There is no such thing as an autonomous regulatory module. All RNA-mediated protein folding chemistry is energy dependent and functional interrelations link differences in the energy of photons from natural selection for energy-dependent codon optimality to all biodiversity on Earth via the physiology of reproduction.
Reported as: Noncoding RNA Helps Cells Recover from DNA Damage

“If the protein is made from the long pre-mRNA, then global transcription is repressed. But if the short RNA is made, it helps recover transcription hours after damage.”
Uncovering mechanisms
How the short isoform aids repair remains unknown.

My comment to The Scientist: There is clear evidence that femtosecond blasts of UV light repair DNA in the context of energy-dependent changes in the microRNA/messenger RNA balance and autophagy, which protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA.
The failure to integrate the Nobel Prize winning works of Ben Feringa (Chemisty 2016) and Yoshinori Ohsumi (Physiology or Medicine 2016) prevents theorists from linking what organisms eat to their pheromone-controlled physiology of reproduction in the context of Schrodinger’s claims in “What is Life?”(1944) and this claim by Roger Penrose in the reprint edition:

“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” (Roger Penrose 8 August 1991)

See also: From Fertilization to Adult Sexual Behavior  In our section on molecular epigenetics, we wrote:

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…

The food energy that is linked from alternative splicing techniques of pre-mRNA to the chemistry of protein folding and the pheromone-controlled physiology of reproduction in all living genera seems to be largely ignored by those who are not Nobel Laureates.

terrarium-eco-system

Draining the academic swamp of parasites

National Academies Revise Conflict of Interest Policy

The proposed changes follow revelations in recent years that committee members preparing reports for the Academies did not disclose industry relationships.

By Ashley P. Taylor | May 3, 2017
Excerpt: They are also thinking about including not only current activities and relationships, as they do now, but past ones when determining whether or not a committee member has a COI.
See for comparison: Ian Hodder: Çatalhöyük, Religion & Templeton’s 25%
My comment: Past funding from the Templeton Foundation virtually guarantees results and recommendations that are tailored to fit into the context of neo-Dawinian pseudoscientific nonsense. But Ian Hodder concludes:

The Templeton Foundation has never put any pressure on me to define religion in any particular way or to come up with any particular results about religion. It’s been entirely pressureless as far as I’m concerned.

My comment: No pressure? 2004 Templeton Prize winner George FR Ellis published a book, which I reviewed here How Can Physics Underlie the Mind? Top-Down Causation in the Human Context.

Others linked the sun’s anti-entropic virucidal energy from energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

After George Ellis failed to link anything he knew about my peer-reviewed published works from energy-dependent top-down causation to healthy longevity or from virus-driven energy theft to all pathology, Susan Mazur helped attest to the importance of energy-dependent RNA-mediated cell type differentiation in a book which I reviewed here: Royal Society: The Public Evolution Summit.
Now see this: Surprising link between blood sugar and brain cancer found
Excerpt: “This may suggest that the tumor itself affects blood glucose levels or that elevated blood sugar or diabetes may paradoxically be associated with a protective factor that reduces brain tumor risk,” Schwartzbaum said.
My comment: Serious scientists do not make suggestions outside the context of what is known about biophysically constrained biologically-based cause and effect. The protective factor is energy-dependent RNA-mediated DNA repair. The conserved molecular mechanisms of repair link an endogenous substrate in all cell types to healthy longevity in all living genera until virus-driven energy theft links the degradation of messenger RNA to all pathology via mutations.
The mutations arise at the level of hydrogen-atom transfer in DNA base pairs in solution, which typically links energy as information to all biodiversity via the physiology of reproduction. If you see anyone who has ever been funded by the Templeton Foundation report findings in the contest of energy-dependent healthy longevity or virus-driven energy theft linked to all pathology via the degradation of messenger RNA, you will have evidence that support for the findings comes from an unbiased source.

See these three articles that come from researchers in China. Individually and collectively the researchers make it clear that nutrient energy-dependent microRNAs are the link from apoptosis and autophagy to healthy longevity and that the virus-driven degradation of messenger RNA is the link to all pathology.

MicroRNA-17-5p mediates hypoxia-induced autophagy and inhibits apoptosis by targeting signal transducer and activator of transcription 3 in vascular smooth muscle cells.

Associations between prediagnostic blood glucose levels, diabetes, and glioma

Identification of miRNA-7 by genome-wide analysis as a critical sensitizer for TRAIL-induced apoptosis in glioblastoma cells

See for comparison: A New Generation Overthrows Gender

I think we’re seeing a new gender revolution,” says clinical psychologist Diane Ehrensaft. “It’s erased boxes and created gender infinity instead.

This is what all serious scientists expect to see come from pseudoscientists who know nothing about how ecologically derived biophysically constrained RNA-mediated energy-dependent sex differences in cell types are controlled by feedback loops that link food odors and pheromones to the physiology of reproduction in all living genera.

Feedback loops link odor and pheromone signaling with reproduction

See also: Commensal bacteria and essential amino acids control food choice behavior and reproduction

Reported as: Gut bacteria tell the brain what animals should eat

…the notion that microbes might also be able to control behavior seems a big conceptual leap. Yet that’s what the new study shows.

See the big conceptual leap from 2013: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Warning: This ecological model was reported to be a refutation of neo-Darwinian pseudoscientific nonsense in: Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

The editor dismissed the criticisms, and only recently was my model linked to another ecological model.

See: Variable habitat conditions drive species covariation in the human microbiota

Reported as: Resource availability drives person-to-person variations in microbes living in the body

Ecological model reveals relationships between resource availability and microbe species abundance

Simply put, ecological models must link what organisms eat from the physiology of reproduction to biophysically constrained energy-dependent RNA-mediated biodiversity via what is known to all serious scientists about supercoiled DNA and chromosomal inheritance.

IMG_2329-e1413855233208-958x718

Wikipedia refutes theistic evolution

RNA-Directed DNA Methylation

Besides RNA molecules, a plethora of proteins are involved in the establishment of RdDM, like Argonautes, DNA methyltransferases, chromatin remodelling complexes and the plant-specific Polymerase IV and Polymerase V. All these act in concert to add a methyl-group at the 5′ position of cytosines. In contrast to animals, cytosines at all sequence context (CG, CHG, CHH) may get de novo methylated in plants.

There is no such thing as de novo methylation. Methylation is energy-dependent. Virus-driven energy theft prevents methylation and links mutations to all pathology via everything known to young earth creationists, which some of them have been reporting since the late 1990’s. That fact explains why theorists were forced to change RNA-Directed DNA Methylation to RNA interference in a face-saving attempt. Many pseudoscientists have claimed the creationists cannot be scientists and their attacks on young earth creationists have been among the most vicious of all attacks. But now, the young earth creationists have this:

RNA interference (RNAi) RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules. Historically, it was known by other names, including co-suppression, post-transcriptional gene silencing (PTGS), and quelling. Only after these apparently unrelated processes were fully understood did it become clear that they all described the RNAi phenomenon.

The so-called unrelated processes linked to RNAi phenomenon were place into the context of what was known about molecular epigenetics in our section on molecular epigenetics from this 1996 Hormones and Behavior review.
From Fertilization to Adult Sexual Behavior

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

The alternative splicings are energy-dependent.
See also: Contribution of epigenetic mechanisms to variation in cancer risk among tissues

Because de novo modification appears to take place almost exclusively on CpG islands that are already silenced by polycomb in the normal tissue (8), we suggest that this modification works by preventing these genes from becoming activated, thereby inhibiting normal tissue differentiation, causing clonal selection for cells that may predispose to cancer (31). Indeed, many of these methylation targets have been shown to be “driver” genes in a number of different cell types (Fig. S6).

Virus-driven energy theft prevents what they claim are the de novo modifications and the energy theft links contraint-breaking mutations from viral latency to all pathology. Only biologically uninformed pseudoscientists have continued to portray energy-dependent changes in methylation as if the changes occurred in the context of de novo modification.
See for comparison. These creationists start with energy and link it to experience-dependent cell type differentiation via what is known about sensing and signalling in all living genera.
Multipurpose plant sensors startle scientists

Evolutionary scientists did not predict such elaborate sensory integration in a single protein system.

Sensing and signalling in all living genera is links the physiology of reproduction in soil bacteria to the phyisology of pheromone-controlled reproduction in all livng genera. See for example:
The genome of Chenopodium quinoa

The TSARL1 transcript was alternatively spliced in the sweet progeny of Kurmi and 0654. A SNP in the last position of exon 3 (G2078C) co-segregates with the presence of saponins in the Kurmi × 0654 progeny. The G2078C SNP alters the canonical intron/exon splice boundary (Fig. 4e), probably leading to the alternative splicing at an upstream cryptic splice site in the sweet lines (Fig. 4e). This alternative splicing of TSARL1 results in a premature stop codon…

See also: Start codons in DNA may be more numerous than previously thought

Start codons are important to understand because they mark the beginning of a recipe for translating RNA into specific strings of amino acids (i.e., proteins).

See also: Codon optimality controls differential mRNA translation during amino acid starvation (2016)
They help to make the fact clear that all organisms must eat.
See also:Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (2016)
They make it clear that the bias between codons or amino acids, and mRNA expression is the link from natural selection for energy as information that links the selection of food to efficient, accurate translation, and folding of  expressed genes.  Simply put, the energy-dependent amino acid optimality code  differentiates between theories of evolution and facts about how ecological variation must be linked to ecological adaptation via the physiology of pheromone-controlled energy-dependent reproduction and supercoiled DNA in all living genera.
Obviously, pseudoscientists who cannot link energy-dependent changes in codon optimality have indirectly been responsible for all virus-driven pathology because they failed to link the viral hecatomb from archaea to the transgenerational epigenetic inheritance of Zika virus-damaged DNA or to all other pathology, including cancer and degenerative diseases.
Thank God, Bill Gates and President Trump are among the billionaires who have decided to help others who have been combating evolutionary theorists to fight disease for several decades.
See also: Combating Evolution to Fight Disease

fruit-dove

ATP-dependent creation of RNA

An Argonaute phosphorylation cycle promotes microRNA-mediated silencing
They suggest that deep evolution somehow conserved energy-dependent phosphorylation sites. The sites somehow link changes in the microRNA/messenger RNA balance from RNA-mediated cell type differentiation to morphological and behavioral diversity via amino acid substitutions in supercoiled DNA. But they do not mention chirality, autophagy, or supercoiled DNA in the context of molecular mechanisms that optimize microRNA activity in diverse species.
Reported on January 25, 2017 as: Partnering MicroRNAs & Targets in a Molecular Dance
The authors of the article and the science journalist fail to link an energy source to the molecular dance and they fail to link virus-driven energy theft to the end of the biophysically constrained dance.
My summary: Their failure to link changes in the speed of light on contact with water from chirality to energy-dependent RNA-mediated autophagy and biophysically constrained cell type differentiation exemplifies the failure of Precision Medicine to link nutrient energy-dependent endogenous RNA interference (RNAi) to healthy longevity and all biodiversity via metabolic networks and genetic networks to the physiology of reproduction.
Instead, the fact that RNAi targets exogenous genes in models of viral infection has been touted in the context of a “A Billion Dollar Baby in Therapy.” See: Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy
See for comparison: Fire A (1999) RNA-triggered gene silencing.
Facts about ATP and the energy-dependent creation of RNA, which is required for gene silencing, seems to be missing from every aspect of energy-dependent gene activation and biophysically constrained RNA-mediated protein folding chemistry. See: DEPENDENCE OF RNA SYNTHESIS IN ISOLATED THYMUS NUCLEI ON GLYCOLYSIS, OXIDATIVE CARBOHYDRATE CATABOLISM AND A TYPE OF “OXIDATIVE PHOSPHORYLATION” (1964)
Fifty-two years later we have this representation of what is known

That representation can be compared to what is known about endogenous RNA interference and cell type differentiation in the context of virus-driven energy theft and all pathology.

See also: Bistability, Stochasticity, and Oscillations in the Mitogen-Activated Protein Kinase Cascade

Our stochastic modeling reveals that small changes in protein abundances can have large effects on MAPK activation. Additionally, data on protein turnover suggests that protein degradation plays an important role in regulating the pheromone pathway. Pheromone-stimulated degradation has been documented previously for the receptor (Ste2) (8), a regulator of G-protein signaling (Sst2) (9), components of the effector kinase cascade (Ste11, Ste7) 9., 10. and 11., and the transcription factor (Ste12) (12).

Bistability, Stochasticity, and Oscillations have been linked from femtosecond blasts of virucidal UV light to RNA-mediated DNA repair and cell type differentiation that links feedback loops from odors and pheromones to the physiology of reproduction in all living genera. That’s why all serious scientists are Combating Evolution to Fight Disease. That fact makes it difficult for me to accept any more claims about deep evolution.
See also: microRNA “amino acid”
For example: Essential amino acid ratios and mTOR affect lipogenic gene networks and miRNA expression in bovine mammary epithelial cells.
For example: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition.
Given the ease of finding supporting evidence that links nutrient-energy-dependent endogenous RNA interference to all cell type differentiation via natural selection for energy-dependent codon optimality and the physiology of reproduction, I wonder why Mendell’s group still touts “deep evolution” in the context of energy-dependent phosphorylation.

Alternative splicing of pre-mRNA

Energy-dependent chirality

See also: Achiral glycine
Summary: Virus-driven energy theft alters the interactions between physics and chemistry that maintain biophysically constrained biodiversity. That’s how viruses are linked from mutations to all pathology. Nutrient energy-dependent changes in the context of the pheromone-controlled physiology of reproduction biophysically constrain biodiversity via the fixation of amino acid substitutions in supercoiled DNA, which protects organized genomes from virus-driven pathology.
Chirality (chemistry)

Two enantiomers of a generic amino acid that is chiral
The chirality of amino acids is energy-dependent and biophysically constrained by the physiology of reproduction in all living genera. For example, the substitution of achiral glycine in position 6 of the decapeptide gonadotropin releasing hormone (GnRH) stabilizes the organized genomes of all vertebrates by helping to protect them from virus-driven energy theft.

(S)-Alanine (left) and (R)-alanine (right) in zwitterionic form at neutral pH

See also:The acid-base behavior of amino acids

There is an internal transfer of a hydrogen ion from the -COOH group to the -NH2 group to leave an ion with both a negative charge and a positive charge.

Energy as information is placed into the context of the sun’s anti-entropic virucidal link from hydrogen-atom transfer in DNA base pairs in solutions. For example, as water in the ocean can be linked to all biodiversity via the physiology of reproduction and fixation of RNA-mediated amino acid substitutions in the supercoiled DNA of all living genera.

Any nutrient energy-dependent change in pH can be linked from hydrogen-atom transfer in DNA base pairs in solution to healthy longevity. All virus-driven energy theft can be linked from changes in pH and hydrogen-atom transfer in DNA base pairs in solution to pathology.
The difference between healthy longevity and pathology is viral latency. Unless the virus-driven energy theft is biophysically constrained by the anti-entropic virucidal force of the sun’s energy, life on Earth is not possible.
See also: A single ion impacts a million water molecules
That fact helps to explain what is intuitively obvious to all serious scientists. They understand how the energy-dependent difference between bacteria and archaea links the degeneration of messenger RNA from bacteria to the degenerate mophological and behavioral phenotypes of archaea.
See: Virus-mediated archaeal hecatomb in the deep seafloor
For comparison, see: From Fertilization to Adult Sexual Behavior

… epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

All differentiation in all cell types of all living genera exemplifies nutrient energy-dependent pheromone-controlled RNA-mediated polycombic ecological adaptation. That fact can be compared to the fact that virus-driven energy theft exemplifies the hecatombic evolution of all pathology. Both facts can be placed into the context of everything known about energy-dependent alternative splicings and amino acid substitutions in supercoiled DNA.
For comparison, see this representation of how “minimal mutational distance” might still be used by biologically uninformed theorists who do not know the difference between a mutation and an amino acid substitution:
Construction of Phylogenetic Trees

Determining the Mutation Distance The mutation distance between two cytochromes is defined here as the minimal number of nucleotides that would need to be altered in order for the gene for one cytochrome to code for the other. This distance is determined by a computer making a pair-wise comparison of homologous amino acids (8).

The choice is perfectly clear. You can accept the claims of theorists who use computers to make “…a pair-wise comparison of homologous amino acids,” or accept the claims of serious scientists who have linked energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which typically protects all living genera from virus-driven energy theft and all pathology.
See also: Multipurpose Plant Sensors Startle Scientists
See also: J. B. S. Haldane [“When I am dead,” in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.
This discussion attempt failed to convince anyone that Haldane, who was one of the theorists who helped to invent neo-Darwinism, was like all the others who knew nothing about biophysically constrained energy-dependent cell type differentiation.

Peter Berean who invented the term “bio-functional information” concluded:

What is your chain of logic (in your own words) that leads to your belief that energy = information?

—————————–
DEFINITION

—————————–
in·for·ma·tion
1. facts provided or learned about something or someone.
“a vital piece of information”
synonyms: details, particulars, facts, figures, statistics, data; More
2.
what is conveyed or represented by a particular arrangement or sequence of things.
“genetically transmitted information”

—————————–
en·er·gy

1.
the strength and vitality required for sustained physical or mental activity.
“changes in the levels of vitamins can affect energy and well-being”
synonyms: vitality, vigor, life, liveliness, animation, vivacity, spirit, spiritedness, verve, enthusiasm, zest, vibrancy, spark, sparkle, effervescence, ebullience, exuberance, buoyancy, sprightliness; More
2.
power derived from the utilization of physical or chemical resources, especially to provide light and heat or to work machines.
—————————–

Conclusion: Energy and Information are two completely different things. They are NOT the same thing.

Claims that energy is not information, which are based on definitions, continue to frustrate the effort of intelligent scientists who are combating evolution to fight disease.
The casualties on the side of the serious scientists can be attributed to theorists and journalists who write articles with conclusions like this.
See: The queen does not rule

Division of labour is a human innovation, drawing on our ability to learn and improve by practice, and to trade goods and services. The growing recognition that natural processes work differently from our symphonies and armies will allow us to see the natural world more clearly. Ant colonies are not factories or fortresses; instead they use simple interactions to adjust to changing conditions. Ant societies, organised by distributed algorithms rather than division of labour, have thrived for more than 130 million years.

Division of labor is nutrient energy-dependent and pheromone-controlled via the physiology of reproduction in all living genera. For example XIST links differences in energy-dependent RNA-directed DNA methylation to chromosomal rearrangements and sex differences in species from yeasts to humans via the pheromone-controlled physiology of reproduction.
See: Chemical tags on RNA silence female X chromosome

“We found that methyl modification is a normal feature of most RNAs in the cell,” he said. “This includes messenger RNAs that encode proteins, as well as noncoding RNAs such as XIST.”

Others have shown that energy-dependent changes in the microRNA/messenger RNA balance link methylation to every aspect of healthy longevity and that they link virus-driven energy theft to all pathology via the conserved molecular mechanisms of cell type differentiation in all living genera.
See: microRNA
For one of 56,700 other examples see: MicroRNA-29 impairs the early phase of reprogramming process by targeting active DNA demethylation enzymes and Wnt signaling
See also: The real problem

…fundamental aspects of our experiences of conscious selfhood might depend on control-oriented predictive perception of our messy physiology, of our animal blood and guts. We are conscious selves because we too are beast machines – self-sustaining flesh-bags that care about their own persistence.

We are not self-sustaining. The real problem is the ignorance of theorists who have failed to tether their ridiculous theories to facts about Darwin’s “conditions of life” that have been detailed by serious scientists.
For example, see: Feedback loops link odor and pheromone signaling with reproduction
See also: Involvement of Host Non-Coding RNAs in the Pathogenesis of the Influenza Virus
See for comparison: My comment to the Science site and to the Atlantic site:

The idea of biophysical constraints seems antithetical to the idea of nature somehow selecting mutations that cause amino acid substitutions. However, I am not a biophysicist or evolutionary theorist.

The problem may be my focus on nutrient-dependent receptor-mediated amino acid substitutions in species from bacteria to humans (non-viral organisms). Since I am not a virologist or physicist, I’m not sure that the laws of physics apply to viruses and their replication.

If they do, natural selection for random mutations is not likely to result in amino acid substitutions because the thermodynamics of changes in organism-level thermoregulation preclude such randomness. Stability of protein biosynthesis and degradation that probably depends on protein folding must somehow be controlled. Besides, I don’t know how random mutations in viruses could be naturally selected for inclusion in the human virome (or in the virome of any organism capable of thermoregulating its thermodynamic intercellular signaling).

If the Second Law of Thermodynamics does not apply to viruses, which means the chemical bonds that enable the amino acid substitutions can form at random and somehow be naturally selected, the details of biophysical constraints in this article seems out of place, since I do not think in terms of constrained random mutations and natural selection in mutation-driven evolution.

Hopefully, someone with a background in biophysics will address my confusion in case others are confused. In addition, I wonder if the consequences of understanding the evolutionary mechanisms that govern viruses extend to consequences important to understanding the evolution of species from bacteria to humans via constrained random mutations and natural selection?

My comment was removed from the Science site and this appeared:

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

My comment is still available from the Atlantic site
See also: Virus-driven mutation or amino acid substitution
See also: Energy-dependent chirality (2)