5th-6th Sept 2018 Dublin, Ireland

The eternal significance of microRNAs (7)

Sales of human pheromone-enhanced fragrance products have been virtually eliminated by the pseudoscientific nonsense touted by neo-Darwinian theorists and Big Bang cosmologists. I may revisit their ridiculous claims at ScentofEros.com and Pheromones.com, but prefer to continue moving forward via my other domains: RNA-mediated.com and Autophagy.pro.

Summary: 2018 Update: Sympatric speciation has been linked to species diversity as an example of an ecologically validated proof-of-concept in all living genera.

Theorists, other psedoscientists and nearly all so-called science journalists have failed to use common sense in their ridiculous representations.
See for example: Beating the Odds for Lucky Mutations: If DNA repair makes useful mutations more likely, it could accelerate cells’ adaptations to harsh environments (8/16/17) by Jordana Cepelewicz
See: 4/18/18 Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems by James V. Kohl
My model of ecological adaptations was placed into the context of this article in Quanta Magazine by Jordana Cepelewicz — less than one year after she published her article on “lucky mutations” in Aeon.
5/10/18 A Thermodynamic Answer to Why Birds Migrate

…research makes a forceful argument that energy supply and demand is a driving ecological principle shaping the global structure of biodiversity.

See for comparison: 10/12/16 Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

Evolutionary theorists and Big Bang cosmologists are forced to plagiarize the intellectual property of others like me and pretend that they are saying something new about the origin of all energy-dependent biophysically constrained biodiversity.
Jordana Cepelewicz is among the most serious offenders. I wonder why she thinks she can get away with directly contradicting the claims she made less than one year ago.
I have neglected some of the domains I established during the past 7 years because it became clear that pseudoscientists were not going to let people know that all aspects of sympatric speciation have been detailed in the context of food energy-dependent pheromone-controlled reproduction, which is required to biophysically constrain viral latency.
That fact was placed into the context of the cell biology game “Cytosis,” which was delivered to backers in October 2017.

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

See also: A transmissible RNA pathway in honey bees (2018)
The authors link my model of food energy-dependent pheromone-controlled biophysically constrained sympatric speciation from atoms to ecosystems in all living genera via my 2013 published review and my unpublished invited review of nutritional epigenetics.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013)

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.

For a historical perspective, see: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014 preprint)

Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

The facts about sympatric speciation for comparison to the neo-Darwinian pseudoscientific nonsense about mutation-driven evolution have been placed in to the context of 3 more recently published works.
A 360 degrees view of circular RNAs: From biogenesis to functions (2018)
Circular RNAs: Unexpected outputs of many protein-coding genes (2017)
The Output of Protein-Coding Genes Shifts to Circular RNAs When the Pre-mRNA Processing Machinery Is Limiting (2017)
It is no longer possible to successfully put the facts about sympatric speciation back into the context of ridiculous theories about the emergence of energy and evolution of all life on Earth. Anyone who returns to the links or to the published works I have posted here, will realize that pseudoscientists and most so-called science journalists know virtually nothing about food energy-dependent RNA-mediated cell type differentiation in any species.

5th-6th Sept 2018 Dublin, Ireland

Light-controlled cell biology (revisited)

See Sci-Bay Scholar for citations and downloads of more than 3300 published works that link viruses to microRNAs
Summary: …either the organized genomes of all cell types use the energy source, or viruses use the biophysically constrained energy of the cell types. No extant species can be used as an example of how the virus-driven theft of quantized energy can be linked from natural selection to the evolution of a new species.
See also, with my emphasis:

Light Offers New Way to Control Cell Biology (3/16/17)

…the power of light-sensitive proteins is that they can be used to study the inner workings of any living cell.

Archaea:

Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no known species of archaea does both.

George Church At 15:10

…the cyanobacteria turn out that they fix light ah as well or better than land plants…

From the transcript:

The cyanobacteria fix [carbon via] light as well or better than land plants. Under ideal circumstances, they can be maybe seven to ten times more productive per photon.

The difference between the fixation of light and the fixation of carbon is that (see above)  no known species of archaea does both. That fact supports the claim that the ability to fix light is an ecological adaptation that links the quantized energy of sunlight to all biophysically constrained biodiversity in the context of energy-dependent viral latency.

Archaea that do not use sunlight as their energy source probably become L-forms in the context of the virus-driven degradation of their messenger RNA, which has been linked from mutations to all pathology in the context of one-carbon metabolism. Quantized energy is the obvious link from the fixation of light to the fixation of carbon in all carbon-based life forms on Earth.

Simply put, either the organized genomes of all cell types use the energy source that fixes carbon, or the viruses use the biophysically constrained energy of the cell types. For comparison, no extant species can be used as an example of how the virus-driven theft of quantized energy can be used in the context of natural selection and evolution.

See also:L-form bacteria

The cell wall is important for cell division, which, in most bacteria, occurs by binary fission. This process usually requires a cell wall and components of the bacterial cytoskeleton such as FtsZ. The ability of L-form bacteria to grow and divide in the absence of both of these structures is highly unusual, and may represent a form of cell division that was important in early forms of life.[1]
 
If the claim that L-forms are an early form of life was placed into the perspective of claims by Carl Woese about the different domains of life, theorists would need to explain how the cell wall “evolved” before all life on Earth evolved from archaea to bacteria and every other species.
 

For comparison, I claim that quantized energy as information carried by light is the link from the creation of the cell wall to all epigenetically-effected biophysically constrained food energy-dependent pheromone-controlled biodiversity. However, Carl Zimmer seems to want someone to redefine “heredity” to make the definition fit back into the context of evolution outside the context of Dobzhansky (1973) Nothing in Biology Makes Any Sense Except in the Light of Evolution

(quotes)

I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation.

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.

See also: Clinically Actionable Genotypes Among 10,000 Patients With Preemptive Pharmacogenomic Testing

…different SNPs may be present and confer risk for inefficacy or toxicity among AAs, as well as Asians, Hispanics, or other populations.

The light energy-dependent differences in the SNPs confer the diversity of morphological and behavioral phenotypes in all living genera. The SNPs also are linked to healthy longevity or pathology via the fixation of RNA-mediated amino acid substitutions. That fact must be placed into the context of pheromone-controlled reproduction and transgenerational epigenetic inheritance. That is why Carl Zimmer wants people to think that we need a new definition of heredity.
See the book description for: She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity

We need a new definition of what heredity is…

See for comparison: 6 Bacteria with Awesome Superpowers (Excerpt)

Chemolithoautotrophic, which means they get their energy from inorganic compounds in their environment

SARCASM ALERT: If neo-Darwinian evolutionary theorists make claims about chemolithoautotrophic heredity, will you still believe them?

See also: March for Science: How Democracy Kills Expertise (3/20/17)

“People don’t care how much you know until they know how much you care.”

Until the public is convinced that scientists and journalists care about truth and society, then I fear all of our labors will be in vain.

Serious scientists care about the truth and about society. Many so-called science journalists want the efforts of people who care to be viewed in the context of their pseudoscientific nonsense about heredity via evolution.
See: Changes in the vascular system may trigger Alzheimer’s disease (3/21/17)

The plasma protein, called Factor XII, is part of a cascade of enzymes that induces blood coagulation and inflammation.

If Alzheimer’s disease evolved, you do not need to know about the energy-dependent cascade of enzymes that starts with the creation of ATP synthase. What if you had become a so-called science journalist who did not know that proteins do not create themselves? For example, that’s how energy-dependent changes in the microRNA/messenger RNA balance can be linked to all healthy longevity. You wouldn’t know that.
Virus-driven energy theft causes Alzheimer’s and all other pathology. All serious scientists know that. All pseudoscientists, atheists, and theorists do not want you to know it. For example, viruses cause antibiotic resistance.

This antibiotic will ruin you (3/18/17)

It gets worse. There is no cure. No treatment. No relief. No specialist even.

2011 Researchers to study positive genetic contributions of viruses (3/18/11)

  1. The two-year, $550,000 grant has been awarded to K. Eric Wommack…
  2. These discoveries come from the study of marine ecosystems but allow researchers to learn more about the predominant biological features of viruses overall, which can affect how human conditions – such as cancer – are diagnosed and treated. “Within some of the samples we’ve collected, we found genes critical to protein folding,” says Polson. “In many cases, protein has to be directed to fold in the proper way. Protein misfolding is a component in the cause of some diseases, so this knowledge can be very important in our understanding of viral infection processes.”

Reported as: Social selection: genetic contribution of viruses to life on earth

… science fiction author Greg Bear successfully predicted the involvement of specific viruses in speciation (read Darwin’s Radio and Darwin’s Children). This new report attests to the likelihood that the mechanisms may someday be found. Bear’s concept of viral induction of species evolution — with further consideration given after reading this article — also sheds light on differences between what most people call “natural” selection and what some people are beginning to call “social” selection. There may be no evidence of transitionary species in the fossil record because viruses elicited comparatively sudden and dramatic changes in the genotype and phenotype of extant organisms as other organisms became extinct. One of the mechanisms involved in speciation, as indicated by Bear, is likely to be pheromones that signal similarities and differences in species that occupy similar social niches. I’m now suggesting that transfer of genetic material between species — not just single genes, but large segments of genetic code – could rather suddenly result in what might at first appear to be a newly evolved organism. If ever a newly evolved organism is found, it might be a good idea to look around its neighborhood for genetic clues that provide evidence of parenthood, or of Creation.

Virus-mediated archaeal hecatomb in the deep seafloor (2015)

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

See for updates: Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory (2017)

While information from aquatic systems and medical microbiology suggests the potential for viral influences on nutrient cycles, food web interactions, gene transfer, and other key processes in soils, very few empirical data are available. To understand the soil virome, much work remains.

Re-examination of the relationship between marine virus and microbial cell abundances (2017)

…viral effect sizes derived from ‘representative’ abundances require substantial refinement to be extrapolated to regional or global scales.

If you let them, researchers like these will spend millions of dollars and never learn that viral latency is biophysically constrained in the context of the sun’s anti-entropic energy and the physiology of food energy-dependent pheromone-controlled feedback loops.
See for comparison: What is life? (1944)

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.)

What is life when it is not protected from virus driven entropy (2016)

See also: MicroRNA and autophagy

5th-6th Sept 2018 Dublin, Ireland

The MicroRNAome Strikes Back: A Sokalian hoax (10)

Linda Buck, Ben Feringa, Michael Gazzaniga, Christof Koch, Nick Lane and Svante Paabo are among the presenters who will almost undoubtedly discuss some or all of my claims.
Prepare to ask questions or intelligently discuss accurate representations of top-down causation by watching this:

The energy-dependent creation of the microRNAome protects the organized genomes of all living genera from the virus-driven degradation of messenger RNA that links mutations to all pathology.
See: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

MicroRNA present in mature sperm appears to not only be left over from spermatogenic processes, but may actually serve important regulatory roles in fertilization and early developmental processes. Further, our results indicate the possibility that environmental changes may impact the expression of specific miRNA.

See also: Dynamic control of chirality and self-assembly of double-stranded helicates with light
See for comparison: A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria (2014)

We conclude that the enzymes involved took these alternatives by chance in independent populations that had already evolved distinct ion pumps. Our model offers a quantitatively robust explanation for why membrane bioenergetics are universal, yet ion pumps and phospholipid membranes arose later and independently in separate populations. Our findings elucidate the paradox that archaea and bacteria share DNA transcription, ribosomal translation, and ATP synthase, yet differ in equally fundamental traits that depend on the membrane, including DNA replication.

The microRNA-mediated creation of enzymes is quantized energy-dependent and biophysically constrained by phosphorylation in the context of food energy and the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes in species from bacteria to primates. Membrane divergence in archaea occurs via the virus-driven degradation of messenger RNA, which links the loss of quantized energy from mutations to all pathology. The degradation of the cell membrane links archaea to L-forms, the last remnant of the life of a cell. See: The Inner Life of the Cell (video)
See also: Virus-mediated archaeal hecatomb in the deep seafloor (2016)

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

So far as I know, none of the people who are presenting at “The Future of Biology” meeting have linked Schroedinger’s claims from the past to what is known about the conserved molecular mechanisms of energy-dependent biophysically constrained RNA-mediated cell type differentiation in species from microbes to humans. Even if they are not evolutionary theorists, most have not linked the energy-dependent fixation of RNA-mediated amino acid substitutions to increasing organismal complexity and some have even reversed what is known about top-down causation. For example, Nick Lane, like Gunter P. Wagner have used mathematical models of correlations.
See: Pervasive correlated evolution in gene expression shapes cell and tissue type transcriptomes
They start with this admission”

A major challenge for interpreting this data is that cell type transcriptomes may not evolve independently…

They seem to think they can use statistics and interpretations to address the challenge of facts about increasing organismal complexity.

Our study provides a statistical method to measure and account for correlated gene expression evolution when interpreting comparative transcriptome data.

See for comparison: From Fertilization to Adult Sexual Behavior and Nutrient-dependent/pheromone-controlled adaptive evolution: a model
The fact that what organisms eat has been linked from the food energy-dependent creation of enzymes, receptors, and hormones to the affect of hormones on behavior in all invertebrates and vertebrates was placed into the context of the cell biology game, Cytosis.

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

During the month of January (2018), 2831 people learned from my twitter profile about the domains RNA-mediated.com and Autophagy.pro and some of them learned from more than 100,000 impressions how energy must be linked to RNA-mediated biophysically constrained viral latency by autophagy.
Jan 2018 Summary
Tweets
1,199
Tweet impressions
102,000
Profile visits
2,831
Mentions
71
New followers
29
 

Why do I have only 29 new followers? Are theorists really that scared? If so, how will they help to prevent the next viral apocalypse, if it has not already started before September, 2018?

See also:

If my claims about biophysically constrained energy-dependent RNA-mediated cell type differentiation are not discussed by Linda Buck, Ben Feringa, Michael Gazzaniga, Christof Koch, Nick Lane, and Svante Paabo others will have another example of what happens after a paradigm shift.

 In the past nothing happened because serious scientists failed to acknowledge this fact: Feedback loops link odor and pheromone signaling with reproduction. The article was co-authored by LInda Buck. There is no mention of mutations or evolution and Linda Buck is scheduled to present what can best be described as a refutation of neo-Darwinian evolution.

For God and Country

Diet-driven RNA interference and cancer prevention (4)

Excerpt: What I perceive as apathy can be attributed to the lack of empathy for anyone who suffers from the preventable or controlled virus-driven pathology that, sooner or later, kills us all.
In the case of our Vietnam veterans, naturally occurring prevention or effective treatment of glioblastoma might be achieved by dietary intervention with a curcumin supplement.
“micrornas”[MeSH Terms] OR “micrornas”[All Fields] OR “microrna”[All Fields] Items: 1 to 20 of 68871
See:  The tipping point (revisited): 68,000 publications
69,000 published works on microRNAs will be the next “tipping point.” Predictably, it will be reached during the same 28 day period in which my tweets (@jvkohl have received more than 70,000 impressions.
On 1/18/18: Tweet impressions 71.2K 602.0%
The 602.0% increase has not been accompanied by a significant increase in followers or a significant increase in engagements.
What I perceive as apathy can be attributed to the lack of empathy for anyone who suffers from the preventable or controlled virus-driven pathology that, sooner or later, kills us all.
In the case of our Vietnam veterans, naturally occurring prevention or effective treatment of glioblastoma might be achieved by dietary intervention with a curcumin supplement.
See: A curcumin-loaded polymeric micelle as a carrier of a microRNA-21 antisense-oligonucleotide for enhanced anti-tumor effects in a glioblastoma animal model

DP-Cur is an efficient carrier of miR21ASO and the combined delivery of miR21ASO and curcumin may be useful in the development of combination therapy for glioblastoma.

See also: Pharmacological blockade of ASCT2-dependent glutamine transport leads to antitumor efficacy in preclinical models

This is the first study, to our knowledge, to demonstrate the utility of a pharmacological inhibitor of glutamine transport in oncology, representing a new class of targeted therapy and laying a framework for paradigm-shifting therapies targeting cancer cell metabolism.

Reported as: Researchers find a way to ‘starve’ cancer

Glutamine is an essential amino acid for many cell functions including biosynthesis, cell signaling and protection against oxidative damage. Because cancer cells divide more rapidly than do normal cells, they need more glutamine.

A protein called ACST2 is the primary transporter of glutamine into cancer cells. Elevated ASCT2 levels have been linked to poor survival in many human cancers, including those of the lung, breast and colon. Genetic studies that silence the ACST2 gene in cancer cells have produced dramatic anti-tumor effects.

See also: MicroRNA[s] and glutamine Items: 1 to 20 of 65
The facts about food energy-dependent microRNA-mediated RNA-directed DNA methylation and fixation of RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all living genera were removed from this report. Use off the cryo-EM technology links energy-dependent changes in electrons to healthy longevity in all ecosystems. It is apparent that some researchers do not want more people to learn about that fact.
See: Structural basis of RNA polymerase III transcription initiation

The unwound DNA directly contacts both sides of the Pol III cleft. Topologically, the Pol III PIC resembles the Pol II PIC, whereas the Pol I PIC is more divergent. The structures presented unravel the molecular mechanisms underlying the first steps of Pol III transcription and also the general conserved mechanisms of gene transcription initiation.

The information that links the virus-driven theft of quantized energy from the negative supercoiling (unwinding) of supercoiled DNA was removed in this attempt to support the neo-Darwinian pseudoscientific nonsense about the three domains of life. The bastardization of the use of cryo-EM technology occurred in the following context(s).
1) There is no mention of the quantized anti-entropic virucidal energy as information that is required to create ATP and RNA.
2) The energy-dependent creation of ATP and the creation of RNA is not linked to healthy longevity in all living genera via the physiology of pheromone-controlled reproduction.
3) The fixation of RNA-mediated amino acid substitutions that stabilize the differentiated cell types of all living genera are viewed in the context of negative supercoiling that occurs in an ATP-independent manner.
4) A spontaneously formed transcription bubble links the energy-dependent stability of supercoiled DNA to cell type differentiation in species from bacteria to humans.
5) The claim that promoters can be opened without ATP hydrolysis is used to suggest that no energy-dependent supercoiling is required to link the three kingdoms of life — assuming that there are three kingdoms of life.
6) The fact that the virus-driven degradation of messenger RNA in humans causes them to become non-human primates and the fact that it also cause bacteria to archaea and L-forms is ignored.
See: Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

By deliberately removing virus-archaea interactions from the representations reported as: Scientists zoom in to watch DNA code being read, pseudoscientists have reverted to promotion of their ridiculous gene-centric theories.
See for comparison: “Cytosis

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

See also: Attacked from All Sides: RNA Decay in Antiviral Defense

…RNA decay machinery plays important roles in antiviral defense. This can involve either direct effects on vRNA stability or indirect regulation of the intracellular milieu. Furthermore, an emerging theme suggests that many RNA binding proteins can be repurposed from their endogenous roles in the nucleus to antiviral roles in the cytoplasm. Future studies are necessary to further elucidate how these RNA binding proteins recognize foreign RNAs and how they interface with the RNA decay machinery to restrict vRNA replication.

Accurate representations of how natural selection for food energy-dependent codon optimality links the physiology of pheromone-controlled reproduction to the transgenerational epigenetic inheritance of healthy longevity will continue to be attacked from all sides.
Biologically uninformed theorists and philosophers can do nothing else but attack after proclaiming the nonsense of mutation-driven evolution during the past decades. They have failed to link their nonsense to the prevention of all pathology or to effective treatments via optimization of autophagy: the innate antiphage defense mechanism of all living genera.

Alternative splicing of pre-mRNA

Energy-dependent coulombic, autophagic, polycombic healthy longevity

Mitophagy is the selective degradation of mitochondria by autophagy.
See also this excerpt:

Disorders in energy creation by mitochondria can cause cellular degeneration…

Mitochondria do not create energy.  They link the creation of the sun’s anti-entropic virucidal energy to RNA-mediated cell type differentiation via biophysically constrained DNA repair. Energy-dependent autophagy links mitophagy to supercoiled DNA via the innate immune system and RNA-mediated repair of damaged DNA.
Repair is nutrient-energy dependent. Separating mitophagy from autophagy is one way to prevent people from realizing how energy-dependent viral latency and healthy longevity is typically achieved outside the context of ridiculous neo-Darwinian theories. Mitophagy and autophagy are two terms used to describe the same energy-dependent molecular mechanisms. In this case, we see the claim that energy creation by mitochondria obfuscates the fact that energy cannot be created or destroyed in the context of what is known about how quantum physics must be linked from quantized energy to biologically-based cause and effect.
Selective removal of deletion-bearing mitochondrial DNA in heteroplasmic Drosophila
Re:  mtDNA deletion (mtDNAΔ) in adult Drosophila muscle.
Excerpt:

Stimulation of autophagy, activation of the PINK1/parkin pathway or decreased levels of mitofusin result in a selective decrease in mtDNAΔ.

Conclusion:

A key question is whether occasional manipulations of cell physiology that promote mtDNA quality control, in otherwise healthy individuals, can bring about a more general ‘housecleaning’ that keeps the frequency of mutant DNA below the threshold for causing cellular dysfunction in diverse tissues without incurring other organismal costs.

My comment: The innate immune system links selective removal of dysfunctional mitochondria to nutrient energy-dependent healthy longevity via the physiology of reproduction in all living genera. Everything known to all serious scientists about energy-dependent thermodynamic cycles of protein biosynthesis and degradation should not lead to the “key question” above. It is too obvious that virus-driven energy theft stimulates autophagy, which typically allows natural selection for nutrient energy-dependent codon optimality to repair damaged DNA.
For example, energy-dependent changes in base pairs link single nucleotide polymorphisms (SNPs) to fixation of RNA-mediated amino acid substitutions in supercoiled DNA via successful reproduction. Fixation of the amino acids substitutions in different cell types of different species is the hallmark of successful reproduction. For contrast, de Vries (1902) defined the term “mutation” in the context of what he claimed were sudden “jump-like” changes in energy. His definition became the basis for the invention of neo-Darwinian pseudoscientific nonsense, which has prevailed among the biologically uninformed.
For comparison, serious scientists have learned that virus-driven energy theft prevents fixation of the amino acid substitutions in host populations. Energy theft facilitates fixation of amino acid substitutions in viruses. For example, fixation via energy-dependent viral replication contributes to the stability of the viral genome via a single amino acid substitution in the influenza virus.
See: The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
The increasing instability of the human host’s organized genome can be viewed in the context of accumulated mutations caused by virus-driven energy theft. That instability eventually leads to all virus-driven pathology. The innate immune system is compromised by virus-driven energy theft, and that biological fact also is a historical fact.
See: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants
Excerpt:

Of the putatively deleterious protein-coding SNVs, 86.4% arose in the last 5,000 to 10,000 years, and they are enriched for mutations of large effect (Supplementary Fig. 14) as selection has not had sufficient time to purge them from the population.

My comment: No experimental evidence of biologically-based cause and effect suggests that mutations are purged by selection. Natural selection for energy-dependent codon optimality clearly shows that virus-driven energy theft is biophysically constrained. The biophysical constraints link viral latency to healthy longevity in species from microbes to humans. Bacteria are more ecologically adapted than archaea, for example.
See: Virus-mediated archaeal hecatomb in the deep seafloor
Concluding sentence:

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

My comment: Virus-human interactions clearly play the central role in the history of all life-sustaining cycles of protein biosynthesis and degradation. The transgenerational epigenetic inheritance of Zika virus-damaged DNA is the only proof of that fact that any serious scientist needs.
See for example: Small non-coding RNAs associated with viral infectious diseases of veterinary importance: potential clinical applications (April 4, 2016)
Excerpt:

The emerging correlation between miRNA expression and disease pathogenesis and outcomes suggests the potential use of miRNAs as biomarkers.

See also: MicroRNAs in the Host Response to Viral Infections of Veterinary Importance (October 17, 2016)
Excerpt:

Viruses, particularly DNA viruses [Marek’s disease virus (MDV), bovine herpesvirus] and even retroviruses (e.g., bovine leukemia virus), can also encode their own miRNAs, but due to space limitations, this topic is not emphasized in this review, and we refer the reader to excellent existing reviews [e.g., Ref. (8, 9)].

See also this invited (unpublished) review of nutritional epigenetics. Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems  (It was returned without review.)

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: Turning back the aging clock

Most people start off life with some level of heteroplasmy, and the levels of mutant mtDNA increase throughout life. When a critical threshold level of mutant mtDNA is passed, cells become nonfunctional or die.

The accumulation of mutant mtDNA over a lifetime is thought to contribute to aging and degenerative diseases of aging such as Alzheimer’s, Parkinson’s, and sarcopenia—age-related muscle loss and frailty. Inherited defects in mtDNA are also linked to a number of conditions found in children, including autism.

My comment: Virus-driven energy theft is clearly linked from changes in the nutrient energy-dependent microRNA/messenger RNA balance to all pathology. The most recent example of this was reported a few days ago in the context of autism: Shared epigenetic changes underlie different types of autism.
See also: Energy-dependent purifying selection / autophagy (2)
See also: Controlled amino acid treatment of all pathology