Plenty of Room at the Bottom

Environmental selection is natural selection (2)

I believe that if you put enough biologically uniformed theorists in the same room, they will invent more theories to support the pseudoscientific nonsense they have touted in the past. See for example:

Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk

Acknowledgments

The synthesis presented here is a product of the American Association for the Advancement of Science’s 2017 annual meeting, as the ideas came together in the session entitled “Beringia and the Dispersal of Modern Humans to the Americas.”
 

Every aspect of every level of biophysically constrained food energy-dependent biologically-based cause and effect is placed back into the context of a ridiculous theory of human migration and evolution. The theory accurately attests to the link from one food energy-dependent base pair change to biodiversity in human populations via fixation of one amino acid substitution. But then, something goes horribly wrong.

The theory requires the fixation of the amino acid substitution to automagically occur in the context of the sun’s anti-entropic virucidal energy. The theory fails to mention the fact that the physiology of pheromone-controlled reproduction and the microRNA-mediated creation of all cell types in all living genera is required.

See for comparison: Anything published since the time I learned about the importance of microRNAs during the 2012 Society for Neuroscience annual meeting in New Orleans, LA.

From 2000/10/15 to 2012/10/15 microRNA Items: 1 to 20 of 19910

From 2012/10/15 to 2018/04/26 microRNA Items: 1 to 20 of 53458

The number of biologically informed serious scientists who have linked the energy-dependent creation of microRNAs to biophysically constrained viral latency and all biodiversity via the pheromone-controlled physiology of reproduction in bacteria continues to rapidly increase.

This begs the question: When will biologically uninformed science idiots stop attending meetings that facilitate their attempts to invent more ridiculous theories?

Caption: Contemporary analyses of cell metabolism have called out three metabolites: ATP, NADH, and acetyl-CoA, as sentinel molecules whose accumulation represent much of the purpose of the catabolic arms of metabolism and then drive many anabolic pathways. Such analyses largely leave out how and why ATP, NADH, and acetyl-CoA (Figure 1) at the molecular level play such central roles. Yet, without those insights into why cells accumulate them and how the enabling properties of these key metabolites power much of cell metabolism, the underlying molecular logic remains mysterious. Four other metabolites, S-adenosylmethionine, carbamoyl phosphate, UDP-glucose, and Δ2-isopentenyl-PP play similar roles in using group transfer chemistry to drive otherwise unfavorable biosynthetic equilibria. This review provides the underlying chemical logic to remind how these seven key molecules function as mobile packets of cellular currencies for phosphoryl transfers (ATP), acyl transfers (acetyl-CoA, carbamoyl-P), methyl transfers (SAM), prenyl transfers (IPP), glucosyl transfers (UDP-glucose), and electron and ADP-ribosyl transfers (NAD(P)H/NAD(P)+) to drive metabolic transformations in and across most primary pathways. The eighth key metabolite is molecular oxygen (O2), thermodynamically activated for reduction by one electron path, leaving it kinetically stable to the vast majority of organic cellular metabolites

Odor activation of ATP (2)

Metabolic Regulation of Cytoplasmic DNA Synthesis (1974)

The curve that results when the rate of DNA synthesis is plotted as a function of ATP concentration is sigmoidal, suggesting that more than one site on the enzyme interacts with ATP and that these sites are acting cooperatively.

Odor activation of ATP is the obvious link to RNA-mediated feedback loops that control the food energy-dependent pheromone-controlled physiology of reproduction via the rate of DNA repair in species from microbes to humans.
See: “ATP activation
See for comparison: Feedback loops link odor and pheromone signaling with reproduction (2005)
See also: “ATP activation” microRNA
See also: Mapping malaria by combining parasite genomic and epidemiologic data

Here, we discuss the spatial epidemiology of malaria in the context of transmission-reduction interventions, and the challenges and promising directions for the development of integrated mapping, modeling, and genomic approaches that leverage disparate data sets to measure both connectivity and transmission.

The sun’s anti-entropic virucidal energy has been linked to protective food energy-dependent hemoglobin variants via 1700+ examples. The variants link interethnic similarities and differences to all extant human populations.
HbVar: A Database of Human Hemoglobin Variants and Thalassemias
SNPs or indels [insertions/deletions] link amino acid substitutions to hemoglobin variants. Molecular defects [mutations] in regulatory or coding regions of the human genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.
What can be said about so-called scientists and so-called science journalists who do not know the difference between how a food energy-dependent amino acid substitution is linked to ecological adaptations and how a mutation is linked to diseases?
Who was the first to say it?

Who will be the next to disagree:
7/25/13
Jay R. Feierman:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

Darwin repeatedly asserted that “conditions of life” must be placed before natural selection. Without the sun’s anti-entropic energy, no species on Earth can adapt to ecological variation.

Lethal virus kills 5 billion people?

The "walking fish" walks straight from quantum physics to quantum souls (5)

Evolutionary determinants of genome-wide nucleotide composition January 1, 2018
1) They place their thoughts about mutation rates into the context of compatibility with mutational spectra.
2)They claim the mutation rate can be linked to mutational spectra that may be free to wander across evolutionary time.
3) They ignore facts that link the energy-dependent maintenance of a suppressed constant genome-wide deleterious rate that obviously occurs in the context of the Virus-mediated archaeal hecatomb in the deep seafloor
4) They eliminate the need for food energy and the pheromone-controlled physiology of reproduction, which protect all organized genomes from the virus-driven degradation of messenger RNA.
5) They link the mutations caused by the degradation of messenger RNA to increasing organismal complexity via mutational spectra.
Summary, these researchers appear to be biologically uninformed science idiots.
See also Luo lab at CUHK publications Microbial Evolution and Ecology
The fact that microbes do not evolve and the fact that ecological variation is biophysically constrained by the food energy-dependent pheromone-controlled physiology of reproduction does not appear to have occurred to any coauthors of any articles from this group with one notable exception.
Singlecell genomics-based analysis of virus-host interactions in marine surface bacterioplankton

Viruses are the most abundant biological entities on Earth, surpassing the number of their potential host cells by at least one order of magnitude (). In the ocean, viral infections kill ~10–20% of planktonic biomass each day (; ). These infections are believed to have a major impact on microbial community composition, evolution and global geochemical cycles ().

See also: Marine phage genomics: the tip of the iceberg
At some point, all serious scientists expect others to acknowledge the fact that the role bacteriophages play in pathology extends from marine phage genomics to the energy-dependent antiphage defense mechanism referred to as autophagy. Autophagy links food energy from the biophysically constrained pheromone-controlled physiology of reproduction to healthy longevity in all living genera.  The facts about autophagy refute all the pseudoscientific nonsense touted by theorists.
See for instance: Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods

By resolving carbon and nitrogen enrichment in viral particles, we demonstrate the power of nanoSIMS tracer experiments in obtaining quantitative estimates for the total number of viruses produced directly from a particular production pathway (by isotopically labeling host substrates). Additionally, we show through laboratory experiments and a pilot field study that BONCAT can be used to directly quantify viral production (via epifluorescence microscopy) with minor sample manipulation and no dependency on conversion factors. This technique can also be used to detect newly synthesized viral proteins. Together these tools will help fill critical gaps in our understanding of the biogeochemical impact of viruses in the ocean.

The resolve of the carbon and nitrogen enrichment in P. fluorescens was linked to autophagy via the nutrient-dependent pheromone-controlled weekend resurrection of the bacterial flagellum. See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The claim about the “evolutionary resurrection” exemplifies the amount of pseudoscientific nonsense that theorists have placed into the context of energy-dependent pheromone-controlled fixation of RNA-mediated amino acid substitutions that differentiate the cell types of all individuals of all living genera.
A single nucleotide polymorphism (SNP) in ntrB in strain AR2S caused an amino acid substitution [Thr97→Pro97 (T97P)] within the PAS domain of the enzyme sensor NtrB.  Another SNP in the fast-spreading strain AR2F in the σ54-dependent EBP gene ntrC alters an amino acid (R442C) within the DNA binding domain. The alteration in the two amino acids were reported as if they were mutations in the context of evolution, which occurred over-the-weekend.
See for comparison Diet and cancer prevention: Dietary compounds, dietary MicroRNAs, and dietary exosomes October 4, 2017

,,,a variety of dietary compounds such as curcumin, green tea, folat, selenium, and soy isoflavones show a wide range anti-cancer properties. It has been showed that these compounds via targeting a sequence of cellular and molecular pathways could be used as suitable options for cancer chemoprevention and cancer therapy. Recently, dietary microRNAs and exosomes have been emerged as attractive players in cancer prevention and cancer therapy. These molecules could change behavior of cancer cells via targeting various cellular and molecular pathways involved in cancer pathogenesis. Hence, the utilization of dietary compounds which are associated with powerful molecules such as microRNAs and exosomes and put them in dietary patterns could contribute to prevention or treatment of various cancers.

Natural agents mediated autophagic signal networks in cancer

When growth factors are withdrawn, the autophagosome forms to induce autophagy [14].

A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution
Classical physics cannot explain how Darwin’s “conditions of life” are linked to the biophysically constrained energy that is released during cell type signalling, which appears to be absolutely and precisely quantized in the context of tunnelling. However, nothing known to serious scientists about tunneling has been linked from experimental evidence of top-down causation to the energy-dependent tunneling. The spurious use of the term “evolution” should be placed into that context.
Docosahexaenoic acid–mediated, targeted and sustained brain delivery of curcumin microemulsion

Conclusion: The superiority of CUR DHA ME in enabling targeted brain delivery of CUR by both intravenous and intranasal administration presents this new formulation as a promising and versatile formulation for application in brain cancer.
MicroRNA: A Novel Target of Curcumin in Cancer Therapy

…curcumin has a variety of pharmacological effects such as antioxidant, anti-cancer, anti-inflammatory, and anti-microbial activities. Anti-cancer effects of curcumin are due to targeting of a wide range of cellular and molecular pathways involved in cancer pathogenesis including NF-kB, MAPK, PTEN, P53, and microRNAs (miRNA) network. Multiple lines of evidence have indicated that curcumin exerts its therapeutic effects via regulating miRNA expression (e.g. miR-1, miR-7, miR-9, miR-34a, miR-181, miR-21 and miR-19) which could lead to the regulation of underlying cellular and molecular pathways involved in cancer pathogenesis.

At some point, the facts must be recognized by even the most biologically uninformed researchers in the world. See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

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.

A Mathematical Model Links Quantum Physics to Quantum Souls (1)

Historical facts: All energy-dependent cell type differentiation is biophysically constrained by the de novo creation of microRNAs and enzymes that metabolize food and drugs. All food energy-dependent metabolism occurs in the context of microRNA-mediated cause and effect and the physiology of pheromone-controlled reproduction. The food energy-dependent pheromone controlled physiology of reproduction in bacteria links what organisms eat to the transgenerational epigenetic inheritance of their morphological and behavioral phenotypes. The virus-driven degradation of messenger RNA has been linked to all pathology in the context of the National Microbiome Initiative, the Precision Medicine Initiative, Alpha Genomix profiling of pathways linked to the creation of CYP enzymes and test results that differentiate the most likely response to some medications based on fixation of  RNA-mediated amino acid substitutions in the organized genomes of different people and different populations of modern humans.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)
The ingestion of sago palm-like leaves linked increased endogenous vitamin C from the stability of the mouse genome to the stability of the organized genome in a modern human population via one base pair change and the fixation of one RNA-mediated amino acid substitution.
See also: Towards a systemic paradigm in carcinogenesis: linking epigenetics and genetics (2015)

The SMT’s [Somatic mutation theory’s] fundamental assumption is that there is no cancer without genetic or chromosomal harm.

See for comparison: Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention
Watch as 2 of 3 co-authors of the article about can prevention tell the world that cancer is caused by “bad luck.”

Now see one of the 3 co-authors admit to his overwhelming ignorance in: Why Is This Bacterium Hiding in Human Tumors?

“The whole idea of bacteria in tumors is fascinating and unexpected,” said Dr. Bert Vogelstein, a colon cancer researcher at Johns Hopkins.

  1. The fundamental assumption that there is no cancer without genetic or chromosomal harm links the virus-driven degradation of messenger RNA in bacteria to the food energy-dependent pheromone-controlled physiology of reproduction in bacteria and healthy longevity via error-free DNA repair.
  2. The fundamental assumption that there is no cancer without genetic or chromosomal harm links virus-driven pathology to cell type-specific and species-specific pathology in all cell types of all individuals of all living genera via the failure of microRNA-mediated error-free DNA repair.

There is now a mathematical model of top-down causation that links the sun’s anti-entropic virucidal energy on contact with water to the physiology of pheromone-controlled reproduction and all biodiversity via RNA-mediated error-free DNA repair. The mathematical model refutes the pseudoscientific nonsense touted by neo-Darwinian theorists because it starts with the creation of the sun, which biophysically constrains viral latency. The importance of linking this mathematical model to all models of biologically-based cause and effect cannot be overstated.
See: Quantum Vacuum Dynamics, Coherence, Superluminal Photons and Hypercomputation in Brain Microtubules

After the Schrodinger’s intuition, expressed in his book “What is life?” [12], the first systematic approach to a quantum interpretation of biological process dated back to the model proposed by Frohlich [13] several years ago. He suggested the occurrence, in biological matter, of macroscopic quantum phenomena able to explain the energy transport without loss in the living organisms and signal transfer based on collective coherent oscillations associated to a branch of longitudinal
electric modes in the frequency range [ ] also known as Frohlich frequency. So in living systems, according to Frohlich’s model, energy could be stored in a thin two – dimensional layer placed beneath the cell membrane, that in this way would act as a biological superconducting medium, under dipolar propagating waves without thermal loss [13].

The ridiculous assumptions about thermal loss and evolution were placed into the context of other ridiculous assumptions that failed to start from the creation of the sun and link the anti-entropic virucidal energy of the sun from food energy to all biodiversity via the physiology of pheromone-controlled reproduction.
For comparison see: Reversing the thermodynamic arrow of time using quantum correlations

We observe a spontaneous heat flow from the cold to the hot system. This process is enabled by a trade off between correlations and entropy that we quantify with information-theoretical quantities.

Reported as: Experiment shows that arrow of time is a relative concept, not an absolute one

The second law of thermodynamics says that entropy, or disorder, tends to increase over time, which is why everything in the world around us appears to unfold forward in time. But it also explains why hot tea grows cold rather than hot. In this new effort, the researchers found an exception to this rule that works in a way that doesn’t violate the rules of physics as they have been defined.
The idea of entangled particles has been in the news a lot lately as researchers around the world attempt to use it for various purposes—but there is another lesser-known property of particles that is similar in nature, but slightly different. It is when particles become correlated, which means they become linked in ways that do not happen in the larger world. Like entanglement, correlated particles share information, though it is not as strong of a bond. In this new experiment, the researchers used this property to change the direction of the arrow of time.

Succinctly stated as:

This observation did not violate the second law of thermodynamics, the group explains, because the second law assumes there are no correlations between particles.

The ridiculous assumption that there are no correlations between subatomic particles led to assumptions that energy emerged and that all life evolved in the context of mutations and natural selection, which led to the “bad luck” theory of cancer.
Frohlich’s model was dismissed and so was the the fact that “…energy could be stored in a thin two – dimensional layer placed beneath the cell membrane, that in this way would act as a biological superconducting medium, under dipolar propagating waves without thermal loss [13].
[13.] Long-range coherence and energy storage in biological systems (1968)

Biological systems are expected to have a branch of longitudinal electric modes in a frequency region between 1011 and 1012 sec−1. They are based on the dipolar properties of cell membranes; of certain bonds recurring in giant molecules (such as H bonds) and possibly on pockets of non-localized electrons. In Section 2 it is shown quit generally that if energy is supplied above a certain mean rate to such a branch, then a steady state will be reached in which a single mode of this branch is very strongly excited. The supplied energy is thus not completely thermalized but stored in a highly ordered fashion. This order expresses itself in long-range phase correlations; the phenomenon has considerable similarity with the low-temperature condensation of a Bose gas. General consequences and proposals of experiments are discussed in section 3.

Four years earlier, McEwen et al., (1964) linked the creation of the sun’s anti-entropic virucidal energy to the creation of ATP and the creation of RNA.
See: 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.

That same year, Dobzhansky (1964) first asserted this claim:

The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.

In 1973, Dobzhansky again mocked all the pseudoscientists whose mathematical model failed to link the creation of the sun’s anti-entropic energy from the physiology of pheromone-controlled reproduction to RNA-mediated fixation of amino acid substitutions that differentiate all cell types in all living genera.
See: Nothing in Biology Makes Any Sense Except in the Light of Evolution
He assumed that all serious scientists would recognize that the light of evolution linked Schrodinger’s claims about sunlight to all biodiversity via the food energy-dependent pheromone-controlled fixation of RNA-mediated amino acid substitutions.
He claimed

“…one can calculate the minimum numbers of single mutations needed to change the cytochrome C of one organism into that of another.”

He linked that calculation to this fact:

…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.

The levels of complexity that must be addressed by the calculations have since been addressed and reported in: Quantum Vacuum Dynamics, Coherence, Superluminal Photons and Hypercomputation in Brain Microtubules
Nothing has changed about the facts that all serious scientists have linked from biophysically constrained viral latency to all biodiversity via the physiology of pheromone-controlled reproduction.
For example, 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.

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

Alternative splicing of pre-mRNA

MicroRNAs and the Cassandra syndrome (revisited)

Conclusion: Serious scientists can explain every aspect of energy-dependent biophysically constrained viral latency in the context of details about these pathways and everything that links changes from electrons to ecosystems in all living genera. Why are the serious scientists still challenged by “…the tendency of academia to reject any academic-like work from outside academia?” What aspect of the academic contribution that could lead to the cure for all pathology do biologically uninformed academics want to continue to reject and attack?
See: Creating genes and species

The “Cassandra syndrome” theme prevails throughout the history of all serious scientists. They are cursed with being able to predict the future because they are always disbelieved.

See for instance: Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice
The authors claim that differential effects of m6A may depend on interactions between microRNAs and cis-acting elements that are present on the RNA molecule.
Simply put, the interactions are energy-dependent and RNA-mediated. Pseudoscientists do not know where the energy came from that creates new cells and they do not know what kills the new cells.
But see: When You Learn, Your Brain Swells with New Cells — Then It Kills Them

In a new opinion paper, published online Nov. 14 in the journal Trends in Cognitive Sciences, researchers proposed that this swelling and shrinking of the brain is a Darwinian process.

The claim that this is a Darwinian process comes from: Expansion and Renormalization of Human Brain Structure During Skill Acquisition

MRIs use complex physics to peer through the walls of the skull into the brain.

Jaak Panksepp’s group won the 2002 award that my group won in 2001 for publication of Human pheromones: integrating neuroendocrinology and ethology. See for comparison:

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. — Dr. Jaak Panksepp, Author of Affective Neuroscience: The Foundations of Human and Animal Emotions

The foundational level is food energy-dependent. See RNA-mediated.com or the FB group RNA mediated.
See the missing foundational level extended from a Darwinian process of swelling and shrinking of the brain to claims about human evolution.
From the Human Ethology Yahoo Group moderated by Jay Feierman.
Human evolution was uneven and punctuated, suggests new research

…this process was not a straightforward, smooth one – instead, it seems to have been punctuated, with different evolutionary patterns in different geographical regions.

More than 1300 hemoglobin variants attest to the obvious fact that evolutionary theorists cannot recognize any pattern that links food energy from what humans eat to the biophysically constrained pheromone-controlled physiology of reproduction. They ignore every aspect of food energy-dependent RNA-mediated amino acid substitutions, which protect all organized genomes from the virus-driven degradation of messenger RNA. The degradation of messenger RNA links mutations to all pathology.
See for examples of food energy-dependent pathology prevention: HbVar: A Database of Human Hemoglobin Variants and Thalassemias
To place food energy-dependent prevention of pathology into the perspective of difference in primates, see:

For example, 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 (p. 127).”

See also: Humans And Chimps Differ At Level Of Gene Splicing
The fact that gene splicing is linked to a single amino acid that differentiates the cell types of 2 primate species from the gorilla, led me to ask: What do other people do when they learn that everything they were taught to believe about evolution is a lie?
I placed the question to the Neuroscience FB group into this context: The Academic Ape: Instinctive aggression and boundary enforcing behaviour in academia

The Cassandra Effect describes the tendency of academia to reject any academic-like work from outside academia and that the more “academic” the contribution, the more strongly it is rejected and attacked.

This is the accurate representation of food energy-dependent pheromone-controlled learning and memory that has consistently been attacked or ignored since the time we published our 1996 Hormones and Behavior review. In our section on molecular epigenetics, we wrote:

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….

Alternative splicing techniques of pre-mRNA have since been linked to every aspect of cell type differentiation in all individuals of all species. The pre-mRNAs are called microRNAs and detailed examples of how food energy-dependent changes in the microRNA/messenger RNA balance can be linked to what has been known about RNA-mediated cell type differentiation to serious scientists. For example, serious scientists know that all changes in the microRNA/messenger RNA balance are energy-dependent. No changes are random. All changes are biophysically constrained. The changes constrain viral latency. That fact has been established in more than 67,000 indexed published works.

See: microRNA Items: 1 to 20 of 67307

What do theorists do when they are repeatedly presented with overwhelming experimental evidence that links food energy-dependent microRNAs to refutation of all their ridiculous theories and all the pseudoscientific nonsense of neo-Darwinian evolution?

 

Jay R. Feierman:

“Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.”

See for comparison: Food derived microRNAs
and

 
See also: Exploitation of microRNAs by Japanese Encephalitis Virus in human microglial cells

The microRNA gene targets, gene ontology, annotations and pathways were identified through various bioinformatics tools. Additionally, the pathways were mostly found common to “ubiquitin mediated proteolysis”, “cytokine signaling”, “maintenance of barrier function/cell junctions”, JAK/STAT pathway” “Toll-like receptor signaling”, “Wnt-signaling”, “adhesion molecules”, “apoptosis”, “endocytosis”, “vesicle mediated transport” etc.

Serious scientists can explain every aspect of energy-dependent biophysically constrained viral latency in the context of details about these pathways and everything that links changes from electrons to ecosystems in all living genera. Why are the serious scientists still challenged by “…the tendency of academia to reject any academic-like work from outside academia?” What aspect of the academic contribution that could lead to the cure for all pathology do biologically uninformed academics want to continue to reject and attack?

For God and Country

Energy-dependent structure and function: Until death (5)

Summary: If a player starts with evolution instead of the creation of energy that links ATP to the creation of RNA, the player is a loser.
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
Secular: Ancient Viruses Are Buried in Your DNA (2017) by Carl Zimmer

…early embryos may have come to depend on the tricks viruses use to manipulate them. “We’re exploiting a property that has evolved for the virus’s benefit,” Dr. Katzourakis said.

Science fiction novelist: The Darwin Code by Greg Bear

In 1996, I proposed to my publishers a novel about the coming changes in biology and evolutionary theory. The novel would describe an evolutionary event happening in real-time–the formation of a new sub-species of human being. What I needed, I thought, was some analog to what happens in bacteria. And so I would have to invent ancient viruses lying dormant in our genome, suddenly reactivated to ferry genes and genetic instructions between humans.

To my surprise, I quickly discovered I did not have to invent anything. Human endogenous retroviruses are real, and many of them have been in our DNA for tens of millions of years. Even more interesting, some have a close relationship to the virus that causes AIDS, HIV.

Serious Young Earth Creationist: Did God Make Pathogenic Viruses? (1999)

…viruses are not living, and in order to reproduce and to make ATP, they require all of the complex cellular machinery present in bacterial cells.

Serious scientist: Where do viruses come from? (2004)

“Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,” says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.’ — Holmes, B., Who Rules the Waves? New Scientist 152(2054):8–9, supp, 1996

Serious Young Earth Creationist/Scientist: Viral Genome Junk Is Bunk

So, where do viruses come from that essentially share the same sequences as those found in their host genomes? Perhaps the evolutionists have placed the cart before the horse on this issue, as proposed by several creationist scientists.4,6 In fact, in an ironic twist, the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6

Secular/Young Earth Creationist: Celebrate Your Inner Virus (2017)

It is important that we understand the design present in viruses because God made them. All creatures of our God demonstrate his handiwork, and viruses are no different.

Infographic: Evolving Virulence

…under natural conditions, a newly emergent, highly lethal pathogen that kills very rapidly is expected to evolve lower virulence. At the same time, however, the host species is evolving resistance to the infection…

Natural selection for energy-dependent codon optimality biophysically constrains viral latency in the context of the physiology of pheromone-controlled reproduction. See: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition and Olfaction Warps Visual Time Perception
My comment to The Scientist:

Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution (2013)

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

One nutrient energy-dependent change in a base pair is linked to fixation of the amino acid substitution in the virus and one nutrient energy-dependent change in a base pair is linked from the physiology of pheromone-controlled physiology of reproduction to fixation of amino acid substitutions in the organized genomes of hosts. Fixation is a function of the innate immune system, which  biophysically constrains viral latency.

Simply put, it’s “All about that base” See also: Structural diversity of supercoiled DNA

Nutrient stress and social stress act on the same molecular mechanisms that link the virus-driven degradation of messenger RNA to mutations and all pathology. That fact can now be examined in the context of everything know about how the cryo-EM technology links energy-dependent changes in electrons to ecosystems via the physiology of reproduction. Alternatively, everything known to serious scientists about ecological variation and energy-dependent ecological adaptations can be place back into the context of ridiculous theories about evolution.

See for example, these claims about a model for how the brain controls foraging.
Brain modelling: Does the brain control foraging?

The brain might instead act as a mediator between controlling factors in the environment and behavioural output. Perhaps, like evolution, it functions as a tinkerer, equipped with a range of signalling or other mechanisms that allow adaptation (see F. Jacob Science 196, 1161–1166; 1977).

Claims that the brain evolved have been replaced by claims that the brain is an energy-dependent ecological adaptation. Claims about its ability to function as a tinkerer have been replaced with facts that link electrons to ecosystems via the 2017 Nobel Prize-winning technology called cryo-EM. Developers of the technology won the Prize in Chemistry.
Cryo-EM can now be viewed in this context of biophyiscally constrained protein folding chemistry and claims from 2005.
See: Feedback loops link odor and pheromone signaling with reproduction
The claims about feedback loops can be placed into the context of what anyone who is 10 years-old can learn about cell biology and virus-driven energy theft by playing the game “Cytosis.”
If a player starts with evolution instead of the creation of energy that links ATP to the creation of RNA, the player is a loser.

A rendering of how changes in an electron's motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln

Energy-dependent physical and biophysical constraints (10)

Summary: The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…— Eugene Koonin
My comment: Viruses are not life forms. They steal the quantized energy that links sunlight to viral latency in the context of everything known to all serious scientists about the fact that Feedback loops link odor and pheromone signaling with reproduction
See for comparison: Olfaction Warps Visual Time Perception Energy as information links the sense of smell in bacteria to our visual perception of energy and mass in the context of the space-time continuum and food odors that link the physiology of reproduction in bacteria to the pheromone-controlled physiology of reproduction and biophysically constrained viral latency in all living genera.
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Energy-dependent physical and biophysical constraints (9)

2010 A single amino acid substitution confers enhanced methylation activity of mammalian Dnmt3b on chromatin DNA

…the I662N substitution in mammalian Dnmt3b conferred enhanced chromatin DNA methylation activity and contributed to functional adaptation in the epigenetic system.

Energy-dependent amino acid substitutions link what organisms eat to their pheromone-controlled physiology of reproduction and chromosomal rearrangements that have been linked to all biodiversity via the sense of smell in bacteria and quorum sensing.
2013 Nutrient-dependent/pheromone-controlled adaptive evolution: a model

CONCLUSION:

An environmental drive evolved from that of nutrient ingestion in unicellular organisms to that of pheromone-controlled socialization in insects. In mammals, food odors and pheromones cause changes in hormones such as LH, which has developmental affects on pheromone-controlled sexual behavior in nutrient-dependent reproductively fit individuals across species of vertebrates.

2013 The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
2017 Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention

There are at least four sources of R mutations in normal cells: quantum effects on base pairing (30), mistakes made by polymerases (31), hydrolytic deamination of bases (32), and damage by endogenously produced reactive oxygen species or other metabolites (33).

2015 Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes

…their covalently bonded 13C/15N nuclei were assigned using heteronuclear single/multiple quantum coherence correlation experiments (HSQC or HMQC).

2017 Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer

…/the observed extremely fast decoherence should be viewed as general, bringing to question any significant quantum coherent transport contributions to photosynthesis.

2017 Recent progress on the effects of microRNAs and natural products on tumor epithelial-mesenchymal transition
My summary: Two researches in NATURE denied the role that microRNAs play epithelial-mesenchymal transition in tumors and their denial of everything known about food energy-dependent biophysically constrained pheromone-contolled biodiversity is discussed in this review. See for comparison the section on Regulation of miRNA on EMT in tumors
The role of miRNA/ZEB in head and neck squamous cell carcinoma, in breast cancer, in lung cancer, in pancreatic cancer and in bladder cancer was anticipated in reports by serious scientists such as the late Eshel Ben-Jacob. See: MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination, which was reported as:

They found that there is a molecular “on” and “off” switch that cancer cells use to determine their fate. Evidently, there is an on or off state for metastasis (migration), but also a third possibility, according to this recently-discovered molecular data.

The researchers discovered that there was an intermediate function, which is termed a “ternary,” or three-way switch. This function relates to the fact that ZEB has the ability to turn itself on due to a positive feedback system. This allows a cell to keep intermediate levels of all four proteins required for the switch. Ben-Jacob notes that the hybrid, or partially on-off state, also supports cancer metastasis by enabling collective cell migration and by imparting stem-cell properties that help migrating cancer cells evade the immune system and anticancer therapies.

See also: Stability of the hybrid epithelial/mesenchymal phenotype

Our results suggest that partial EMT, i.e. a hybrid E/M phenotype, need not be ‘metastable’, and strengthen the emerging notion that partial EMT, but not necessarily a complete EMT, is associated with aggressive tumor progression.

The food energy-dependent stability of the hybrid epithelial/mesenchymal phenotype has been linked from photosynthesis to the creation of energy-dependent microRNAs in plants and in animals via what has been known to all serious scientists about the physiology of pheromone-controlled reproduction in bacteria.
See:
2003 Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment
2006 Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information
2009 Learning from Bacteria about Natural Information Processing with my emphasis

Focusing on the energy, matter, and thermodynamic imbalances provided by the environment, Schrodinger proposed that life required the consumption of negative entropy, that is, the use of thermodynamic imbalances in the environment. From the perspective of thermodynamics, each bacterium can be viewed as a complex system that is composed of an “engine” that uses imbalances in the environment to do work, and a “machine” that uses this energy (to act against the natural course of entropy increase) for the synthesis of organic substances.13 A third information-processing system is also needed for the coordination and synchronization of the functioning of the engine and the machine. Namely, a living cell is analogous to a complex man-made cybernetic system, or a “chimera,” composed of information processing systems and of at least two thermodynamic elements. In addition, using the outer membrane, cells sense the environment.

We proposed that, besides “negative entropy,” organisms sense the environment to extract latent embedded information.13 By latent information we refer to data embedded in the environment that, once processed cognitively, initiates change in the organism’s function or behavior. Information induces changes; hence it can be used to generate an internal condensed description (model or usable information) of the environment, which guides the organism’s functioning.

Conclusion: Olfaction Warps Visual Time Perception Energy as information links the sense of smell in bacteria to our visual perception of energy and mass in the context of the space-time continuum and food odors that link the physiology of reproduction in bacteria to the pheromone-controlled physiology of reproduction in all living genera.
See for comparison (Koonin is a co-author): On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires
…another cause of the lack of detectable protospacers is likely to be the existence of a virtually untapped pool of mobile genetic elements that, at any given time, are not represented in a given environment (10). This paucity of spacer matches is conceivably explained by the vastness and diversity of viromes…
Biologically uninformed evolutionary theorists have failed to link the anti-entropic virucidal energy of the sun to all biodiversity and failed to link the virus-driven degradation of messenger RNA to all pathology via changes in the microRNA/messenger RNA balance. The release of the game “Cytosis” in September (2017) will make all theorists appear to be among the biologically uninformed science idiots who invented ridiculous theories in attempts to explain away Darwin’s “conditions of life.”
See: Cytosis: A Cell Biology Board Game 
A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
See also the comments on: Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention
For example:  2017 Jul 28 06:45 a.m. (research profile) challenges the “bad luck” theory of cancer.

Cancer etiology: assumptions lead to erroneous conclusion

The authors claim that cancer is caused and driven by mutations, and that two-thirds of the mutations required for cancer are caused by unavoidable errors arising during DNA replication. The first claim is based on the somatic mutation theory. The second claim is based on a highly positive correlation between the lifetime number of stem cell divisions in a tissue and the risk of cancer in that tissue, and on their method for estimating the proportion of mutations that result from heredity (H mutations), environmental factors (E mutations) and unavoidable errors arising during DNA replication (R mutations). These claims raise several questions:

1. Sequencing studies have found zero mutations in the genes of a variable proportion of different cancer types (see, e.g., https://dx.doi.org/10.1093/jnci/dju405 and references therein). If cancer is caused by mutations in driver genes, could the authors explain what causes these cancers with zero mutations? Could the authors use their method for estimating the proportion of cancer risk that is preventable and unpreventable in people with tumors lacking driver gene mutations?

2. Environmental factors are known to affect stem cell division rates. According to IARC, drinking very hot beverages probably causes esophageal cancer (Group 2A). If you drink something hot enough to severely damage the cells lining the esophagus, the stem cells located in deeper layers have to divide to produce new cells to replace the damaged cells. These stem cell divisions, triggered by an environmental factor, will lead to mutations arising during DNA replication. However, these mutations are avoidable if you do not drink very hot beverages. Should these mutations be counted as environmental mutations (H mutations) or as unavoidable mutations arising during DNA replication (R mutations)?

3. The authors’ work is based on the somatic mutation theory. This theory is primarily supported by the idea that cancer incidence increases exponentially with age. Since our cells are known to accumulate mutations throughout life, the accumulation of driver gene mutations in our cells would perfectly explain why the risk of cancer increases until death. However, it is now well established that cancer incidence does not increase exponentially with age for some cancers (acute lymphoblastic leukemia, testicular cancer, cervical cancer, Hodgkin lymphoma, thyroid cancer, bone cancer, etc). It is also well known that cancer incidence decreases late in life for many cancer types (lung cancer, breast cancer, prostate cancer, etc). For example, according to SEER cancer statistics review, 1975-2014, men in their 80s have approximately half the risk of developing prostate cancer than men in their 70s. The somatic mutation theory, which is the basis for this article, does not explain why the lifetime accumulation of driver gene mutations in the cells of many tissues is not translated into an increase in cancer incidence throughout life. Are the authors’ conclusions applicable to all cancers or only to those few cancers in which incidence increases exponentially with age until death?

4. The authors estimate that 23% of the mutations required for the development of pancreatic cancer are associated with environmental and hereditary factors; the rest (77%) are mutations arising during DNA replication. However, Notta et al. recently found that 65.4% of pancreatic tumors develop catastrophic mitotic events that lead to mutations associated with massive genomic rearrangements (https://doi.org/10.1038/nature19823). In other words, Notta et al. demonstrate that cell division not only leads to mutations arising during DNA replication, but also to mutations arising during mitosis. For this cancer type, the authors could introduce a fourth source of mutations, and estimate the proportion of mutations arising during mitosis (M mutations) and re-estimate those arising during DNA replication (R mutations). Alternatively, they could reanalyze their raw data without assuming that the parameters “stem cell divisions” and ”DNA replication mutations” are interchangeable. Cell division, process by which a cell copies and separates its cellular components to finally split into two cells, can lead to mutations occurring during DNA replication, but also to other cancer-promoting errors, such as chromosome aberrations arising during mitosis, errors in the distribution of cell-fate determinants between the daughter cells, and failures to restore physical interactions with other tissue components. Would the authors’ conclusions stand without assuming that the parameters “stem cell divisions” and ”DNA replication mutations” are interchangeable?

5. The authors report a striking correlation between the number of stem cell divisions in a tissue and the risk of cancer in that tissue. They do not report any correlation between the number of mutations in a tissue and the risk of cancer in that tissue; in fact, these parameters are not correlated (see. e.g., https://doi.org/10.1038/nature19768). In addition, the authors discuss that most of the mutations required for cancer are a consequence, not a cause, of the division of stem cells. So, why do the authors use their correlation to say that cancer is caused by the accumulation of mutations in driver genes instead of saying that cancer is caused by the accumulation of cell divisions in stem cells?

For references and additional information see: Comment on ‘Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention’ DOI: 10.13140/RG.2.2.28889.21602 https://www.researchgate.net/publication/318744904; also https://www.preprints.org/manuscript/201707.0074/v1/download

See also: Miguel Lopez-Lazaro
My comment: Like him, others from a new generation of researchers, will no longer tolerate the pseudoscienitfic nonsense touted by evolutionary theorists and “Big Bang” cosmologists who know nothing about natural selection for energy-dependent codon optimality, which links the physiology of reproduction to biophysically constrained viral latency.

Big Bang

Richard P. Feynman refuted theistic evolution

Summary: Among other delightful examples of his expertise in physics, Feynman presciently linked natural selection for energy-dependent codon optimality from food energy-dependent pheromone-controlled biophysically constrained chromosomal rearrangements to healthy longevity. He also linked the radiation-induced theft of quantized energy to mutations in phages via amino acids that increase the virulence of the viruses. Updated information is presented in the context of refutations by many others who might otherwise claim to believe in theistic evolution.
The miR-23a~27a~24-2 microRNA cluster buffers transcription and signaling pathways during hematopoiesis
This is an uncorrected proof.
They link food energy-dependent changes in the microRNA/messenger RNA balance from amino acid substitutions to cell type differentiation via the physiology of pheromone-controlled reproduction in species from microbes to humans in the context of this claim from Dobzhansky (1973) Nothing in Biology Makes Any Sense Except in the Light of Evolution.

…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 (p. 127).

Cell type differentiation during hematopoiesis links the amino acid substitution that differentiates the alpha chains of hemoglobin to the differentiation of all other cell types in all other individuals of all vertebrate species via the conserved molecular mechanisms of energy-dependent pheromone-controlled cell type differentiation in all invertebrates.

See for comparison: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

This is my invited review of nutritional epigenetics that was returned without review by the guest editors of a special edition of the journal “Nutrients.”

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

See for comparison: Surely You’re Joking, Mr. Feynman! (Adventures of a Curious Character)

Chapter 10: A Map of the Cat?

My summary: Among other delightful examples of his expertise in physics, Feynman presciently linked natural selection for energy-dependent codon optimality from food energy-dependent pheromone-controlled biophysically constrained chromosomal rearrangements to healthy longevity. He also linked the radiation-induced theft of quantized energy to mutations in phages via amino acids that increase the virulence of the viruses.

The delayed dissemination of accurate information about biophysically constrained biologically-based cause and effect has already contributed to the unnecessary suffering and premature deaths of thousands to millions of people since the time that Richard Feynman reported on mutations in bacteriophages. He realized that the mutations link the theft of quantized energy from living organisms to the amino acid substitutions in viruses that cause the degradation of messenger RNA, which links mutations to all pathology. If not for his love of physics and the pseudoscientific nonsense of neo-Darwinian theorists, all serious scientists would have linked quantum physics to quantum souls.

See for example: Olfaction Warps Visual Time Perception

Our perception of the world builds upon dynamic inputs from multiple senses with different temporal resolutions, and is threaded with the passing of subjective time. How time is extracted from multisensory inputs is scantly known. Utilizing psychophysical testing and electroencephalography, we show in healthy human adults that odors modulate object visibility around critical flicker-fusion frequency (CFF)-the limit at which chromatic flickers become perceived as a stable color-and effectively alter CFF in a congruency-based manner, despite that they afford no clear environmental temporal information. The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.

See also: The Sense of Smell Impacts Metabolic Health and Obesity

A PubMed search for microRNA and the disease you wish to prevent or effectively treat will help you to eliminate the foolishness of theorists who have failed to link the de novo creation of microRNAs to all biodiversity via the physiology of reproduction and biophysically constrained viral latency.

For example: microRNA alzheimers

To place your searches into the proper context, see: Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition

Biologically uniformed theorists invented the term “enhancer” for ambiguous use in the context of energy-dependent changes in the microRNA/messenger RNA balance. They obfuscate facts about food energy and feedback loops that link pheromones to the biophysically constrained viral latency the enables ecological adaptations via use of “enhancer function.”

See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

Natural selection for energy-dependent codon optimality links food energy-dependent changes in the microRNA/messenger RNA balance to protection from the virus-driven degradation of messenger RNA, which links mutations to all pathology unless terms such as enhancers and enhancer function are used to obfuscate facts about The phylogenetic utility and functional constraint of microRNA flanking sequences

Both miRNAs and their flanking sequences provide phylogenetic signals suitable for the inference of phylogeny with high levels of accuracy, when sufficient numbers of this type are concatenated. As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

There is no such thing as de novo assemblies of genomes. Food energy must be linked to the pheromone-controlled physiology of reproduction to link ecological variation to ecological adaptation via feedback loops.

See: Feedback loops link odor and pheromone signaling with reproduction

See for comparison:7/25/13

Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

7/26/13

Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.

See also: Researchers find new mechanism for genome regulation

Interestingly, this type of liquid-liquid phase separation is very sensitive to changes in temperature, protein concentration, and pH levels.

The sensitivity is food energy-dependent and RNA-mediated. Pseudosciedntists should stop their foolishness long enough to realize there is nothing new about the mechanisms of genome regulation. The mechanisms controlled by pheromones link the physiology of reproduction and chromosomal inheritance to healthy longevity unless they link virus-driven energy theft to all pathology via changes in the microRNA/messenger RNA balance.

See also: CSmiRTar: Condition-Specific microRNA targets database

…(Condition-Specific miRNA Targets). CSmiRTar collects computationally predicted targets of 2588 human miRNAs and 1945 mouse miRNAs from four most widely used miRNA target prediction databases (miRDB, TargetScan, microRNA.org and DIANA-microT) and implements functional filters which allows users to search (i) a miRNA’s targets expressed in a specific tissue or/and related to a specific disease…

See for comparison: Creationism support is at a new low. The reason should give us hope.

Stuart Kauffman refutes theistic evolution

Cytosis

Epigenetic effects of stress by Bruce McEwen (2)

Summary:

…rapid mRNA turnover starts with the energy-dependent de novo creation of microRNAs and ends with the virus-driven degradation of messenger RNA, which links mutations to all pathology.
 
This was reported in the following context: “RNA molecules live short lives” July 12, 2017

See also: Epigenetic effects of stress by Bruce McEwen (1)

Summary:

In the early 1990’s, Bruce McEwen inspired my life’s works, which link the epigenetic effects of nutrient-stress and/or social stress to the fact that RNA biosynthesis is ATP-dependent. That fact helped all serious scientists link the virus-driven energy theft of quantized energy to the degradation of messenger RNA, which links mutations to all pathology.

Pseudoscientists refuse to accept that fact.

New research uncovers the secrets of photosynthesis that could help develop computer technology

Energy and charge transfer is what drives photosynthesis and any solar-to-chemical or electrical-to-chemical energy conversion.

That fact links the anti-entropic virucidal energy of sunlight from the de novo creation of microRNAs to all biodiversity. Bruce McEwen published on the role that microRNAs play in: Characterization of the vulnerability to repeated stress in Fischer 344 rats: possible involvement of microRNA-mediated down-regulation of the glucocorticoid receptor (2008)

We also identified that microRNA (miR)-18a inhibited translation of GR mRNA in cultured neuronal cells and that increased expression of miR-18a in the PVN was observed in F344 rats compared with SD rats. These strain differences in GR protein levels were not found in the hippocampus and prefrontal cortex, and the expression of miR-18a was much lower in these brain regions than in the PVN. Our results suggest that F344 rats could be a useful animal model for studying vulnerability to repeated stress, and that miR-18a-mediated down-regulation of GR translation may be an important factor to be considered in susceptibility to stress-related disorders.

See also: Early Life Stress Enhances Behavioral Vulnerability to Stress through the Activation of REST4-Mediated Gene Transcription in the Medial Prefrontal Cortex of Rodents (2010)

Figure 3.

Expression analyses of mRNAs of RE-1-containing genes and brain-enriched pre-microRNAs in the mPFC of the maternally separated rats. A, B, The expression of mRNAs (A) and pre-microRNAs (B) of a variety of RE-1-containing genes in the mPFC of AFR, HMS15, and HMS180 rats at P14 were quantified by Q-PCR (n = 6 for all groups). C, D, The expression of mature microRNAs in the mPFC of AFR, HMS15, and HMS180 rats at P14 were quantified by Northern blotting analysis (n = 5–6 for each group). E, The mRNA and pre-microRNA expression of RE-1-containing genes in the mPFC of adult AFR, HMS15, and HMS180 rats were quantified by Q-PCR (n = 6 for all groups). *p < 0.05.

Bruce McEwen subsequently linked what is known about energy-dependent changes in single nucleotide polymorphisms to effects of hormones on behavior in mice and humans via a food energy-dependent biophysically constrained amino acid substitution.

See: Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity (2015)

Excitatory amino acids play a key role in both adaptive and deleterious effects of stressors on the brain, and dysregulated glutamate homeostasis has been associated with psychiatric and neurological disorders. Here, we elucidate mechanisms of epigenetic plasticity…  In WT mice after CRS and in unstressed mice with a BDNF loss-of-function allele (BDNF Val66Met), we show that the epigenetic activator of histone acetylation, P300, plays a pivotal role in the dynamic up- and down-regulation of mGlu2 in hippocampus via histone-3-lysine-27-acetylation (H3K27Ac) when acute stressors are applied. These hippocampal responses reveal a window of epigenetic plasticity that may be useful for treatment of disorders in which glutamatergic transmission is dysregulated.

See also: Multiplexed gene control reveals rapid mRNA turnover (open access)

The rapid mRNA turnover starts with the energy-dependent de novo creation of microRNAs and ends with the virus-driven degradation of messenger RNA, which links mutations to all pathology.
 
This was reported in the following context: “RNA molecules live short lives” July 12, 2017
“Sometimes it is hard to believe that scientists could have unknowingly worked with methods that produce inconsistent results for almost 30 years”, says Becskei.
 
Becskei adds insult to the injury, unnecessary suffering, and the premature death caused by misrepresentations of biologically-based cause and effect. An accurate representation was reported in 1964 as: 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 fact that some researchers still do not know that the synthesis of RNA is energy-dependent makes it impossible for them to link virus-driven energy theft from the degradation of messenger RNA to mutations and all pathology in all living genera.

It will soon become “child’s play” for anyone over 10 years old. See: Cytosis: A Cell Biology Board Game

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

Amino acid modification FA_Epigenetics_Table1

Biologically uninformed biologists fight back and lose

Novel layers of RNA polymerase III control affecting tRNA gene transcription in eukaryotes 22 Feb 2017

A subset of tRNA genes shows low responsiveness to both environmental and cellular signals. Notably, this group contains at least one tRNA for each amino acid. Together these findings suggest the existence of a basal subset of housekeeping tRNA genes [36]. This concept is consistent with the mode of Maf1-mediated repression of actively transcribed tRNA genes in human cells subjected to serum starvation [104].

See also the citation to (with my emphasis): Kimura M, Ishihama A. 1995 Functional map of the alpha subunit of Escherichia coli RNA polymerase: amino acid substitution within the amino-terminal assembly domain. J. Mol. Biol. 254, 342–349.
The fact that an enzymatic reaction linked energy to the amino acid substitution seems to have been virtually ignored by theorists

See for example comparison: Richard Lenski – Evolution in a Flask

Published on 24 Feb 2017

Dr. Stan Maloy talks with Richard Lenski Ph.D., Hannah Professor of Microbial Ecology, Michigan State University, about his research into the evolution of bacteria and the new frontier of digital evolution.Episode 61 of MicrobeWorld Video, filmed at the American Association for the Advancement of Science Meeting in Vancouver, Canada on February 17th, 2012.

Lenski’s Long Term Evolution Experiment with E. coli has seen over 50,000 new generations since its inception in 1998. This has led to insights such as how viruses can evolve from types that don’t infect humans to ones that do.

Lenski’s work with E. coli has also led him into the digital world. Using computers, Lenski can achieve precise, rapid results by manipulating digital organisms. Software that evolves much like bacteria in the real world.

Lenski is optimistic about the future of evolution research. Applying the generalities that have resulted from his studies to any number of other microbial species. He also sees large potential in applying what he’s learned to the study of antibiotic resistance and bioengery.

The fact that Richard Lenski failed to acknowledge what was known about the nutrient energy-dependent RNA-mediated amino acid substitution that stabilized the organized genome of E. coli, his model organism, attests to how much pseudoscientific nonsense about mutations, natural selection, and evolution he has been touting for more than 2 decades.
For comparison, see: Measurements of translation initiation from all 64 codons in E. coli
Reported as: Start codons in DNA may be more numerous than previously thought
See also: Biodiversity is autocatalytic

…it was recently shown using the RAF algorithm that the metabolic network of Escherichia coli forms a large autocatalytic set of close to 1800 reactions (Sousa et al., 2015). As far as we know, this is the first formal proof that living organisms
(or at least essential parts thereof) are indeed autocatalytic sets.

Reported as: Autocatalytic biodiversity hypothesis aims to supplant Darwin’s ‘war of the species (February 9, 2017)

A species emerges from this environment and is an expression of those interactions. In other words, species are expressed and maintained by a complex interacting ecological network.

Contrary to Darwin’s beliefs, biodiversity, according to Dr. Cazzolla Gatti, does not derive “from the war of nature, from famine and death,” but from the power of life to enable other life; not from war, but from coexistence; not from competition but from the avoidance of it, e.g. from cooperation and facilitation, i.e., by autocatalysis.

The power of life to enable other life is nutrient energy-dependent and controlled by the physiology of reproduction. That fact explains why virus-driven energy theft is being linked to all pathology in the science news that is reported each day. The obfuscation is clear in the fact that there is no such thing as a genomic pathway outside the context of epigenetic effects that link metabolic networks to genetic networks in all living genera. When you see a report that does not link energy-dependent epigenetic effects to supercoiled DNA or to virus-driven pathology, you should learn to recognize the tactics that are used to frame experimental evidence of biologically-based cause and effect in the context of evolutionary theories about evolutionary pathways and/or genomic pathways.
Faulty genomic pathway linked to schizophrenia developing in utero, study finds

“This research shows that there is a common dysregulated gene program that may be impacting more than 1,000 genes and that the great majority of those genes are targeted by the dysregulated nuclear FGFR1,” Stachowiak said.

When even one of the many schizophrenia-linked genes undergoes mutation, by affecting the INFS it throws off the development of the brain as a whole, similar to the way that an entire orchestra can be affected by a musician playing just one wrong note, he said.

See the obfuscatory attempt in:

See also: Epigenome: The symphony in your cells
The “symphony” is energy-dependent and RNA-mediated via endogenous RNA interference in the context of the physiology of reproduction.