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.

High-throughput sequencing and analysis of microbial community cDNA (#metatranscriptomics) are providing valuable insight into in situ microbial activity and metabolism in the oceans.

The eternal significance of microRNAs (4)

Conclusion: Conserved energy biophysically constrains viral latency.
Metatranscriptomics

High-throughput sequencing and analysis of microbial community cDNA are providing valuable insight into in situ microbial activity and metabolism in the oceans.

When faced with the eternal significance of quantized energy-dependent natural selection for codon optimality, theorists must attack the basics of what is known to serious scientists about biophysically constrained life on Earth.
See for example: Virus-mediated archaeal hecatomb in the deep seafloor
By starting with “raw assemblies” instead of the energy from sunlight that must be linked to the “Assemblies Trinity,” pseudoscientists link “data” to codon optimality. They fail to link the creation of virucidal light from differential gene expression before they link the data to results that are meaningless outside the context of an energy source.
All results can be predicted only in the context of the energy-dependent biophysical constraints that prevent the virus-driven degradation of messenger RNA from destroying the supercoiled DNA that is required to maintain viral latency and healthy longevity.
Nutrition, microRNAs, and Human Health (2017)

MicroRNAs (miRs) hybridize with complementary sequences in mRNA and silence genes by destabilizing mRNA or preventing translation of mRNA.

The authors recapitulate the claims from my 2014 invited review of nutritional epigenetics but fail to address the most important aspect of biophysically constrained viral latency, which requires the energy-dependent creation of microRNAs that prevent the translation of mRNA. The destabilizing effects of viruses are eliminated when enough food energy is available to support RNA-directed DNA methylation and fixation of amino acid substitutions in organized genomes.
See:  Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

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: Prediction of 5-Fluorouracil Toxicity Associated With Dihydropyrimidine Dehydrogenase Gene (DPYD) Polymorphism Using the Secondary Structure Prediction Programs
The predicted toxicity must be linked from the energy-dependent creation of dehydrogenase gene polymorphisms. The failure to do that has led to class action litigation.
See also:  DPYD dihydropyrimidine dehydrogenase [ Homo sapiens (human) ]

The protein encoded by this gene is a pyrimidine catabolic enzyme and the initial and rate-limiting factor in the pathway of uracil and thymidine catabolism. Mutations in this gene result in dihydropyrimidine dehydrogenase deficiency, an error in pyrimidine metabolism associated with thymine-uraciluria and an increased risk of toxicity in cancer patients receiving 5-fluorouracil chemotherapy. Two transcript variants encoding different isoforms have been found for this gene.

Finding isoforms is of little use if researchers do not know how the isoforms are created.
medical Definition of isoform.:

any of two or more functionally similar proteins that have a similar but not identical amino acid sequence and are either encoded by different genes or by RNA transcripts from the same gene which have had different exons removed.

Most researchers know nothing about energy-dependent biophysical constraints on the creation of amino acid substitutions in the isoforms.
See for example: NSF’s Big Ideas: Understanding the Rules of Life and The Quantum Leap
The rules of life that include fixation of amino acid substitutions in organized genomes could have been linked from the quantum leap to biophysically constrained viral latency and healthy longevity in all living genera. Instead the presenters failed to answer any of my questions.

1) Has anyone place the rules of Life and the Quantum Leap into the context of food energy-dependent biophysically constrained viral latency and sympatric speciation?
2) Do you think that this parody accurately represents what was known in 2014 about the importance of energy-dependent base pair changes to biophysically constrained protein folding chemistry? All About that Base (Meghan Trainor Parody) 12/10/14
3) Do you agree that questions about genome adaptations compared to the evolution of organized genome are ambiguous in the context of what is known about natural selection for quantized energy-dependent codon optimality?
4) Has the difference in the energy of two photons been linked from altered proton gradients to the protential of hydrogen (pH) and RNA-mediated DNA repair via the creation of microRNAs and enzymes?
NSF funding is largely used to support theories about the emergence of energy and evolution of all biodiversity.
This work would be funded by NSF: The evolutionary history of vertebrate RNA viruses
They claim that the evolutionary history of vertebrates matches the history of the RNA viruses, which they claim is because the viruses evolved. Viruses must steal the quantized energy of sunlight from cell types or they cannot replicate. Does that sound like vertebrate viruses are capable of evolution?
That nonsense was reported as: New study transforms understanding of virus origins and evolution
See also: Estimating evolutionary rates in giant viruses using ancient genomes

…this suggests that these viruses could have diverged at least hundreds of thousands of years ago, and hence have evolved over longer time-scales than previously suggested. We propose that the evolutionary rate and time-scale of pithovirus evolution should be reconsidered in the light of these observations and that future estimates of the rate of giant virus evolution should be carefully examined in the context of their biological plausibility.

All their suggestions have become more ridiculous as more facts about the creation of microRNAs have been placed into the context of biophysically constrained viral latency.
See: MicroRNAs in neural development: from master regulators to fine-tuners

The proper formation and function of neuronal networks is required for cognition and behavior. Indeed, pathophysiological states that disrupt neuronal networks can lead to neurodevelopmental disorders such as autism, schizophrenia or intellectual disability. It is well-established that transcriptional programs play major roles in neural circuit development. However, in recent years, post-transcriptional control of gene expression has emerged as an additional, and probably equally important, regulatory layer. In particular, it has been shown that microRNAs (miRNAs), an abundant class of small regulatory RNAs, can regulate neuronal circuit development, maturation and function by controlling, for example, local mRNA translation. It is also becoming clear that miRNAs are frequently dysregulated in neurodevelopmental disorders, suggesting a role for miRNAs in the etiology and/or maintenance of neurological disease states. Here, we provide an overview of the most prominent regulatory miRNAs that control neural development, highlighting how they act as ‘master regulators’ or ‘fine-tuners’ of gene expression, depending on context, to influence processes such as cell fate determination, cell migration, neuronal polarization and synapse formation.

See also: Learning-dependent chromatin remodeling highlights noncoding regulatory regions linked to autism
They identified a single nucleotide polymorphism known as rs6010065. It is associated with differences in microRNAs linked to autism spectrum disorder.
See also: A Common Allele in FGF21 Associated with Sugar Intake Is Associated with Body Shape, Lower Total Body-Fat Percentage, and Higher Blood Pressure
A single nucleotide polymorphism known as rs838133 was linked from food energy-dependent changes in microRNAs to biophysically constrained viral latency and healthy longevity in the mouse-primate-human model of pheromone-controlled reproduction.
I reiterate: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

In the context of quantized energy as information-driven changes in the microRNA/messenger RNA balance, a single nucleotide polymorphism known as rs3827760, 1540T/C, 370A, V370A, and/or Val370Ala was linked to conserved morphological and behavioral phenotypes in mice and humans.

See: Epigenetics and Autism Spectrum Disorder: Is There a Correlation?

At a time when all serious scientists have linked energy-dependent changes in electrons to ecosystems, questions about correlations are irrelevant.

See: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

Functional connectivity is energy dependent and biophysically constrained by by the energy-dependent physiology of reproduction.

It is time for all biologically uniformed science idiots to admit that the source of all energy-dependent changes in every organism on Earth is sunlight.

See: Resolving sub-cellular miRNA trafficking and turnover at single-molecule resolution

Regulation of microRNA (miRNA) localization and stability is critical for their extensive cytoplasmic RNA silencing activity and emerging nuclear functions. Here, we have developed single-molecule fluorescence-based tools to assess the subcellular trafficking, integrity, and activity of miRNAs.

The regulation of microRNA (miRNA) localization and stability is quantized energy-dependent and pheromone controlled in the context of everything known to serious scientists about biophysically constrained protein folding chemistry and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.
Why symmetry gets really interesting when it is broken

Energy is conserved…because the laws of physics are the same now as they were a millennium ago…

Long-range coherence and energy storage in biological systems (1968)

The supplied energy is thus not completely thermalized but stored in a highly ordered fashion.

Conserved energy biophysically constrains viral latency.

5th-6th Sept 2018 Dublin, Ireland

Nick Lane refutes theistic evolution (1)

Neo-Darwinian theorists and others who are biologically uninformed will learn this in September (2018).
Synopsis: The difference in two photons has been linked to the Proton motive force. It drives the activity of the enzyme, ATP synthase, which makes ATP. All energy-dependent biophysically constrained viral latency has since been linked from the creation of ATP synthase and the creaton of ATP to changes in the microRNA/messenger RNA balance and healthy longevity. For comparison, the virus-driven degradation of messenger RNA has been linked to all pathology.
There is no such thing as an intrinsic biogeochemical cycle of energy-dependent protein biosynthesis. Light activated endogenous substrates are required for energy-dependent protein biosynthesis. Energy-dependent biophysical constraints on protein biosynthesis link the intrinsic biogeochemical cycle to biophysical constraints on the virus-driven degradation of messenger RNA.
After the presentations during Schrödinger at 75 – The Future of Biology – September 2018, some theorists may need to be placed on a suicide watch due to the availability of “Cytosis” and the ability of students aged 10+ to learn more about cell biology than theorists have learned during the past 75 years.
See for example: Hard Two-Photon Contribution to Elastic Lepton-Proton Scattering Determined by the OLYMPUS Experiment (2017)
Reported as: OLYMPUS experiment sheds light on structure of protons

…unlike the theoretical predictions, analysis of the OLYMPUS measurements suggests that, most of the time, only one of the photons has high energy, while the other must carry very little energy indeed…

The link from differences in the energy of photons to the amount of ATP that must be be biophysically constrained has been largely ignored since the time that McEwen et al., (1964) linked the creation of ATP to the creation of RNA via oxidative phosphorylation.
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 difference in two photons have been linked to the Proton motive force. It drives the activity of the enzyme, ATP synthase, which makes ATP. All energy-dependent biophysically constrained viral latency has since been linked from the creation of ATP synthase and the creaton of ATP to changes in the microRNA/messenger RNA balance and healthy longevity. For comparison, the virus-driven degradation of messenger RNA has been linked to all pathology.
See for instance this 6-7 minute-long video: Energy as information and constrained endogenous RNA interference (February 15, 2017)

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy.

See for comparison: The energy expansions of evolution (April 28, 2017) with my emphasis.

Sunlight is a consequence of the planet’s position in the Solar System, whereas geochemical energy is an intrinsic property of the Earth. Geochemical energy arises when water reacts with basalts and other rocks…

Although sources of geochemical energy can be at or near Earth’s surface, they need not be: many are deep within the planet, out of reach of sunlight.

That fact became clear in the context of bacteria that eat electrons and the physiology of their reproduction, which was linked to the creation of uranium isotopes.
See: Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

Many low-temperature ores display similar isotopic fractionation59,60 as found here suggesting an under-recognized importance of biological processes in roll-front ore formation.

The origin of microbial life and the creation of uranium ores via the energy-dependent pheromone-controlled physiology of reproduction in bacteria appears to have gone missing in the context of pseudoscientific nonsense touted by theorists who are already scheduled to present during: Schrödinger at 75 – The Future of Biology – September 2018
 
See also: Proton gradients at the origin of life (May 16, 2017) by Nick Lane
People like Nick Lane still claim that biochemistry emerged from geochemistry. They link the origins of biochemistry to the emergence of genetically encoded catalysts, such as ribozymes, ATP synthase and other enzymes. Then they proceed to tell others about naturally occurring evolutionary processes. The evolutionary processes supposedly link the automagical creation of ATP sythase in some geochemical settings to the biochemistry of our last universal common ancestor (LUCA).
See: Evolution of ATP Synthase (Video) Jackson Wheat claims that ATP and ATP synthase might link the Last Universal Common Ancestor to the evolution of all biodiversity on Earth.
See for comparison the claim from A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

The magic and logic of evolution now start with the evolution of an enzyme (ATP synthase) linked from ATP to the creation of RNA and RNA-mediated amino acid substitutions that differentiate all cell types in all living genera only in the context of the physiology of energy-dependent biophysically constrained reproduction.
See for comparison: 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.

Unfortunately, Nick Lane and others appear to initially missed the connection from the virus-driven theft of quantized energy to the creation of archaea from bacteria. He reported the bioenergetic basis for divergence as if DNA replication somehow arose in LUCA outside the context of everything known to serious scientists about the biophysically constrained top-down energy-dependent creation of membranes.
See: A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria (2014)

Because the bacterial replicon is attached to the plasma membrane during cell division [58]–[60], this complex presumably arose after (or coevolved with) the bacterial membrane, which must have driven a deep phylogenetic disparity, even if DNA replication had arisen in LUCA.

Anyone who still touts claims of emergence or pretends to think that the complexity of the plasma membrane in bacterial replicons automagically arose or coevolved in the context of phylogenetic disparities, may want to attend Schrödinger at 75 and laugh at the nonsense touted by Nick Lane and other neo-Darwinian theorists who are scheduled to present.
See: Schrödinger at 75 – The Future of Biology – September 2018
Nick Lane is an evolutionary biochemist
Beth Shapiro is an evolutionary biologist
Svante Pääbo is a Swedish biologist specialising in evolutionary genetics.
In 2012, I attended a conference presentation on microRNAs and the speaker confirmed the fact that every aspect of cell type differentiation occurs downstream from changes in microRNAs. He claimed that is what had been learned during the past 10 years. I confirmed that others who attended his presentation also knew the facts about biophysically constrained RNA-mediated cell type differentiation before publishing a refutation of neo-Darwinian nonsense in 2013.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
After the presentations during Schrödinger at 75, all neo-Darwinian theorists and most big bang cosmologists who have no valid model for comparison may need to be placed on a “suicide watch” for losers.
Kalevi Kull: Censorship & Royal Society Evo Event (2016)

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.

Published works by people like Nick Lane, Beth Shapiro, and Svante Pääbo have not been at the cutting edge since 1964.
See: Biology, molecular and organismic

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.

Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule.

See also: Patterns of shared signatures of recent positive selection across human populations

…we present a catalogue of selective sweeps in humans, and identify those that overlap and share a sweeping haplotype. We connect these sweep overlaps with potential biological mechanisms at several loci, including potential new sites of adaptive introgression, the glycophorin locus associated with malarial resistance and the alcohol dehydrogenase cluster associated with alcohol dependency.

The failed pattern recognition of biologically uninformed theorists has led serious scientists to proclaim that the pseudoscientists have no way out. Every aspect of life on Earth is energy-dependent, RNA-mediated and biophysically constrained in the context of viral latency.
See: No way out: when RNA elements promote nuclear retention

Virus-mediated archaeal hecatomb in the deep seafloor

Carl Zimmer refutes theistic evolution (2)

Carl Zimmer refutes theistic evolution (1)
Carl Zimmer recognizes the need for a new definition of what heredity is. But he refuses to tell others what he knows about the role that viruses play in the transgenerational epigenetic inheritance of all pathology.
Examples of inherited pathology typically include his misrepresentations among others who fail to link ecological variation to ecological adaptation in the context of energy-dependent biophysically constrained viral latency.
See: Ancient Viruses Are Buried in Your DNA  by Carl Zimmer
His conclusion:

In other words, 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.

No experimental evidence of biologically-based cause and effect suggests anything except virus-driven pathology has evolved.
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.

We estimated that viral infections were responsible for the abatement of 1.0 to 2.2% day−1 (on average 1.6% day−1) of the bacterial abundance and 2.3 to 4.3% day−1 (on average 3.2% day−1) of the archaeal abundance in deep-sea sediments (Fig. 6).

The amount of virus-driven degradation of messenger RNA in archaea is clearly biophysically constrained via the energy-dependent physiology of the pheromone-controlled reproduction in bacteria. Neo-Darwinian theorists and so-called science journalists misrepresent the facts about how the virus-driven theft of quantized energy as information is biophysically constrained.
They trick people into believing that viruses and organisms evolve by failing to to mention that viral replication is not possible outside the context of energy theft from the host. Zimmer, for example, has consistently led others to believe in anything except how viral latency is biophysically constrained by what organisms eat and how metabolism is linked to reproduction.
Others like Zimmer are directly to blame for the level of ignorance reported in the context of this project.
The Global Virome Project

Our ability to mitigate disease emergence is undermined by our poor understanding of the diversity and ecology of viral threats, and of the drivers of their emergence.

The diversity and ecology of viral threats has always been linked to stress-induced changes in endogenous substrates. Light activation of endogenous substrates has been linked from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency and healthy longevity in species from bacteria to humans.
Nutrient-stress and social stress have been linked from the degradation of messenger RNA in bacteria to the creation of archaea and L-forms, in which the membrane required for biophysically constrained viral latency is missing.
Zimmer and many other biologically uninformed journalists ignore this threat: Beware ‘Disease X’: the mystery killer keeping scientists awake at night 
The threat would not exist if de Vries 1902 definition of mutation had not been accepted by people with not enough common sense to know that food energy must be linked to heredity via biophysical constrained viral latency.
See: Polymaths and paradigm shifts: from Asimov to Bear (in prep)

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.

How to biophysically constrain the flu virus (1)

Excerpt: John E Walker (Factor-dependent archaeal transcription termination) will probably explain the molecular mechanism of how ATP is made, which may be important to know for those who have learned how important ATP is by playing “Cytosis.” The creation of ATP can be linked to the creation of RNA and the prevention of messenger RNA degradation in the context of the Virus-mediated archaeal hecatomb in the deep seafloor.
What the flu does to your body, and why it makes you feel awful

…when you have an influenza infection, you can rest assured that it is because your body is fighting hard. It’s combating the spread of the virus in your lungs and killing infected cells.

Why suffer needlessly or die prematurely. 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! (2 to 5 Players, Ages 10 & up, Plays in 50 to 75 mins)

Download the “Science Behind the Game” to learn how food energy-dependent alternative splicings of pre-mRNA protect all cell types, or see Alternative splicing and the evolution of phenotypic novelty.
Link the alternative splicings to species-specific behaviors via the physiology of reproduction in From Fertilization to Adult Sexual Behavior and anything else I have published or presented during the past two decades.
All behavior is energy-dependent. The energy comes from sunlight. Quantized energy as information from sunlight is linked to healthy longevity via its anti-entropic virucidal effect.
For example: Special UV light safely kills airborne flu virus, finds study

Scientists have known for decades that broad-spectrum UVC light, which has a wavelength of between 200 to 400 nanometers, or nm), is highly effective at killing bacteria and viruses by destroying the molecular bonds that hold their DNA together.

For comparison to vaccinations:
Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases

A key advantage of the UVC based approach, which is in clear contrast to vaccination approaches, is that UVC light is likely to be effective against all airborne microbes. For example, while there will almost certainly be variations in UVC inactivation efficiency as different influenza strains appear, they are unlikely to be large7,10. Likewise, as multi-drug-resistant variants of bacteria emerge, their UVC inactivation efficiencies are also unlikely to change greatly9.

In the context of vaccinations:
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.

Clearly, vaccinations may not protect you and prevention via use of UV light is desirable.
When you learn how UV light protects you at the level of particle physics, you will understand the horrors of neo-Darwinian theory and big bang cosmology .
See Subatomic
The link from quantum physics to quantum chemistry was reported last month. Modern diversification of the amino acid repertoire driven by oxygen.
Schrödinger at 75, The Future of Biology is scheduled for September 2018
John E Walker (Factor-dependent archaeal transcription termination) will probably explain the molecular mechanism of how ATP is made, which may be important to know for those who have learned how important ATP is by playing “Cytosis.” The creation of ATP can be linked to the creation of RNA and the prevention of messenger RNA degradation in the context of the Virus-mediated archaeal hecatomb in the deep seafloor.
People who have played “Cytosis” can predict what will happen at the Schrödinger at 75 conference. They will jump ahead of most academics if they play “Subatomic” and link particle physics to all biophysically constrained biodiversity.
The fun factor is important to most people. They don’t care about supercoiled DNA or the virus-driven degradation of messenger RNA. But other scientists are having fun watching the creator of the genious games teach facts to theorists. We are especially pleased about his help in teaching the facts about energy-dependent cell biology to anyone who wants to have fun, prevent or survive the flu, or to become a serious scientist.
Alternatively, play the Mutation-driven evolution game (available only as an outdated 2013 textbook).
But remember:  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
Simply put, you could be dead by the time pseudoscientists start to tell the truth. For example, this is the truth:

There had been years of biophysical experiments and biochemical experiments, and it was always assumed that there was just one dynein molecule,” Lander adds.

Lander just admitted that their assumptions may have made many serious scientists wrong about every aspect of energy-dependent life on Earth.
See also: Real Heroes Have the Guts to Admit They’re Wrong

…one reason we can’t admit we have the facts wrong is that it’s too painful to our self-conception as smart, right-thinking people—or to our political tribal identity.

In the past year alone, mathematicians have pulled papers when they’ve learned their proofs don’t hold and economists have retracted work after finding they’d misclassified their data. The Harvard stem-cell biologist Douglas Melton had a hit 2013 paper that got cited hundreds of times—but when colleagues couldn’t replicate the finding, he yanked it.

They discount the fact that any claims that have been placed into the context of neo-Darwinian theories have been invalidated first by Schrödinger in “What is Life? (1944) and since then by all serious scientists who have linked  the sun’s anti-entropic virucidal energy from the physiology of reproduction to biophysically constrained viral latency and all biodiversity.
See also: Windowed Granger causal inference strategy improves discovery of gene regulatory networks

Significance

Discovery of gene regulatory networks (GRNs) is crucial for gaining insights into biological processes involved in development or disease. Although time-resolved, high-throughput data are increasingly available, many algorithms do not account for temporal delays underlying regulatory systems—such as protein synthesis and posttranslational modifications—leading to inaccurate network inference. To overcome this challenge, we introduce Sliding Window Inference for Network Generation (SWING), which uniquely accounts for temporal information. We validate SWING in both in silico and in vitro experimental systems, highlighting improved performance in identifying time-delayed edges and illuminating network structure. SWING performance is robust to user-defined parameters, enabling identification of regulatory mechanisms from time-series gene expression data.

Reported as: New machine learning algorithm uncovers time-delayed interactions in cells

SWING puts together a more complete picture of the cause-and-effect interactions happening among genes by incorporating time delays and sliding windows. Rather than only looking at the individual perturbations and responses, SWING uses time-resolved, high-throughput data to integrate the time it takes for those responses to occur.

Researchers will continue to scramble in attempts to put their findings into the context of what has already been presented in: Olfaction Warps Visual Time Perception
and in:

 

 

Alternative splicing of pre-mRNA

Energy-dependent chirality

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

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

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

See also:The acid-base behavior of amino acids

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

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

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

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

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

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

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

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

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

—————————–
DEFINITION

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

—————————–
en·er·gy

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Alternative splicing of pre-mRNA

80 years of causal analysis (1936 – 2016)

Roles of Mutation and Selection in Speciation: From Hugo de Vries [1902 definition of mutation] to the Modern Genomic Era
Excerpt:

…mutation is crucial in speciation because reproductive barriers cannot be generated without mutations.

My comment: Chromosomal rearrangements link autophagy from energy-dependent changes in RNA-mediated amino acid substitutions and supercoiled DNA to all biodiversity via speciation.

Some Principles of Causal Analysis in Genetics (1936)

Extract:

…high frequency radiation and particles of high velocity are very important components of the environment, causing heritable changes by a process called mutation. Even if we could conduct our experiments behind 30 metres of lead the fact that mutation has a temperature coefficient is enough to show that it depends in part on energy fluctuations which are uncontrollable.

My comment: In 1902, De Vries defined the uncontrollable energy fluctuations in the context of his definition of “mutation.” Others have since linked Darwin’s “conditions of life” from  energy fluctuations to natural selection for energy-dependent codon optimality and healthy longevity via biophysically constrained polycombic ecological adaptation.
See for example: miR-125a-5p regulates differential activation of macrophages and inflammation

My comment: Nutrient energy-dependent changes in the microRNA/messenger RNA balance link autophagy to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

See for ~54,000 examples: microrna and autophagy

See for comparison: A new function for oncoproteins of DNA tumor viruses

Excerpt: 

…the same five amino acid sequence that binds cGAS also binds cellular proteins (such as Rb), disrupting their function and leading to uncontrolled cell growth!

Re: Could both functions have been simultaneously selected for?
My comment: No. Both functions could not have been simultaneously selected for!
Nothing known to serious scientists about top-down causation suggests that the RNA-mediated amino acid sequences in proteins can be simultaneously selected to link natural selection for energy-dependent codon optimality to healthy longevity and to simultaneously link virus-driven energy theft to all pathology. In the context of everything known to serious scientists about all living genera, cell type differentiation is energy-dependent and it must be biophysically constrained.
For a review of the biophysical constraints that link all invertebrates to all vertebrates, see: From Fertilization to Adult Sexual Behavior

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

My comment: In 1996, we reviewed the established facts about energy-dependent biophysically constrained polycombic ecological adaptation based on what was known about the small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb.  The facts about energy-dependent polycombic ecological adaptation have not changed. Only the pseudoscientific nonsense of neo-Darwinian theories has been forced to include the changes portrayed in the context of virus-driven hecatombic evolution.
See for comparison:  Virus-mediated archaeal hecatomb in the deep seafloor

We estimated that viral infections were responsible for the abatement of 1.0 to 2.2% day−1 (on average 1.6% day−1) of the bacterial abundance and 2.3 to 4.3% day−1 (on average 3.2% day−1) of the archaeal abundance in deep-sea sediments (Fig. 6).

My comment: The claim that viruses kill ~1.6% of bacteria each day and ~3.2 % of archaea in deep-sea sediments is buried in technical jargon. It was previously resurrected in the report of the weekend resurrection of the bacterial flagellum.
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The nutrient energy-dependent pheromone-controlled weekend resurrection of the bacterial flagellum eliminates the confusing rhetoric that theorists use to explain how differences in cell death from archaea to bacteria might be attributed to evolution. The differences are obviously linked from ecological variation to nutrient-dependent pheromone-controlled ecological adaptation in all living genera. For comparison to hecatombic evolution, healthy longevity exemplifies polycombic ecological adaptation.
The cause of death in all cell types is linked to virus-driven energy theft and nutrient energy-dependent healthy longevity is linked from cell type differentiation to all biodiversity. Simply put, virus-driven energy theft is linked from hecatombic evolution to all pathology.
The claim that mutation-driven hecatombic pathology and polycombic ecological adaptation could be simultaneously selected is a claim that only a biologically uninformed theorist would make, or accept.
See for comparison: Neurons adjust their proteins during homeostatic scaling
Excerpt:

Changes in the synthesis of cellular proteins lie at the heart of all adaptations that cells undergo.

My comment: That fact was reported in the context of this publication. Nascent Proteome Remodeling following Homeostatic Scaling at Hippocampal Synapses
Excerpt:

In addition, although it has not been explicitly addressed here, it is obvious that the regulated degradation of proteins must also play a role in sculpting the proteome during homeostatic scaling. Indeed, we observed many proteins in the ubiquitin proteasome pathway that were regulated by scaling (Figure 3C; Table S3).

My comment: Nascent proteome remodeling links nutrient energy-dependent autophagy from natural selection for codon optimality to changes in protein biosynthesis and degradation. The changers link RNA-mediated amino acid substitutions to the differentiation of all cell types in all living genera in the context of the physiology of reproduction.  Pseudoscientists, atheists, and most science journalists do not seem to understand that fact.
For comparison, serious scientists do not need more proof that autophagy did not simply emerge to link energy as information to all biodiversity via the conserved molecular mechanisms of cell type differentiation that link angstroms to ecosystems in species from microbes to humans. Serious scientists do not need more proof that all neo-Darwinian pseudoscientific nonsense is nothing more than one theory added to another after de Vries defined “mutation” in 1902.
Do you know any serious scientists who has used any definition in the context of reporting their results of testing in the medical laboratory? For example, have you ever used a definition to link the results of a blood gas analysis from hydrogen-atom transfer in DNA base pairs in solution to the patient’s outcome?

See also (video): Feynman explains the difference between science and the pseudoscientific nonsense of neo-Darwinian theory with added feedback on the claims of expert theoretical physicists who have failed to link energy-dependent changes from angstroms to ecosystems in all living genera.
http://dai.ly/x24hxji
My comment: Experimental evidence of biologically based cause and effect links physics and chemistry to the conserved molecular mechanisms of cell type differentiation that we detailed in our 1996 Hormones and Behavior review.
See for comparison: Different rates of mRNA degradation can be explained by the existence of different regulatory mechanisms.


My comment: Researchers like him should stop ignoring the facts. Energy-dependent autophagy mediates the mRNA turnover rate and links nutrient energy-dependent RNA-mediated amino acid substitutions to healthy longevity via the physiology of reproduction and transgenerational epigenetic inheritance of morphological and behavioral phenotypes. Virus-driven energy theft links mRNA degradation to all pathology.
See also: This virus may have stolen deadly DNA from black widow spiders (10/12, Feltman) reports researchers have discovered that the WO virus, which infects bacteria, contains “snippets” of DNA from several animals including black widow spiders, according to a study published in Nature Communications. The virus infects the Wolbachia bacteria, which primarily affects arthropods including insects and spiders. Researchers found that the WO virus “contains part of the gene for latrotoxin, the chemical that gives the black widow spider venom its punch.”

The Virus With Spider DNA (10/12, Yong) reports the researchers suspect that the virus obtained the genetic material directly from the spiders infected by Wolbachia, or the bacteria may have obtained it from the spiders before passing it on to the virus.

        Additional coverage is provided by: How the Heck Did Black Widow Spider DNA Get Inside a Virus? (10/11, Choi) and Virus stole poison genes from black widow spider (10/12, Rincon).
My comment: Virus-driven energy theft occurs in only one direction. It links cell type death from archaea to Zika virus damage in human infants via transgenerational epigenetic inheritance of pathology. The idea that a virus that infects bacteria could have come from the DNA of animals is one that misrepresents everything currently known to serious scientists about autophagy.
Ideas like that are the source of pathology that alters the behavior of family members who believe that any idea is as good as a model of biologically-based cause and effect.

Biologically uniformed family members have unfriended me on Facebook because they do not want anyone to become informed.

Jeanette C Seeman Wow, I’m sorry to hear that. The subject seems complex and a little grace could go a long way. They could have unfollowed you instead of unfriending you. Hope they will see you in person. Wishing you the best.
James Kohl
James Kohl Thanks for putting their actions into perspective, Jeanette C Seeman.
I’ve learned that expertise on any given topic may cause embarrassment in non-experts who think experts are insulting their intelligence or criticizing their beliefs. This is true at all levels. 2004 Templeton Prize winner, George FR Ellis, who is or was an active Quaker, unfriended me when I commented on the book he published in June. He left out the information on my model, even after he claimed I was correct.
He has had an ongoing disagreement with Roger Penrose about the fact that the source of all information links the creation of the sun to energy-dependent healthy longevity. Ellis and Penrose have co-authored with Stephen Hawking. I linked energy as information to the Resurrection of Christ via everything currently known to all serious scientists about biologically-based cause and effect. George FR Ellis refuses to address that fact in any context.
This is what he is avoiding. In 1991, Roger Penrose wrote: “How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?”
Last month, this assault on the beliefs of all who tout nonsense about the emergence of everything from nothing and neo-Darwinian theories about millions of years of evolution should have cinched the election of Donald Trump for President. http://dx.doi.org/10.1038/nnano.2016.164
Trump, for example, is supported by young earth creationists such as Mike Pence and Dr. Ben Carson. Now, we have examples of ignorance from a well-respected cosmologist/astrophysicist (Ellis), for comparison to a mathematical physicist, mathematician and philosopher of science (Penrose), and Mike Pence and Dr. Ben Carson.
If Hillary wins, we will have another example of what the term “reprobate mind” actually means. It means people would rather believe anything they are told as long as it cannot be placed into the context of physics, chemistry, biology and Biblical Genesis via what is known about molecular epigenetics, which is that “…we eat food in order to gain energy?” The energy biophysically constrains the viral apocalypse that the liberals predictably will cause.
This is science, not religion: https://www.ncbi.nlm.nih.gov/pubmed/24693353 Why do you think it was published in Socioaffective Neuroscience & Psychology? What has any pseudoscientist/atheist written for comparison?

Socioaffect Neurosci Psychol. 2013 Jun 14;3:20553. doi: 10.3402/snp.v3i0.20553. eCollection 2013. Review
ncbi.nlm.nih.gov|By Kohl JV
James Kohl
James Kohl See also: http://dx.doi.org/10.1038/nnano.2016.164

nature.com

See also my attempt to discuss the fact that: NONE of the papers establish that SOMETHING can come into existence from NOTHING.

//Do you reject any of those claims?”//

I simply do not see the evidence for the claim that Viruses cause ALL pathology.
– Bacteria can cause pathology.
– Toxins can cause pathology.
– Heavy metals can cause pathology.
– Fungi can cause pathology.
– Parasites can cause pathology.
I do not see the warrant to state that NONE of the above can cause pathology and so ONLY viruses can cause pathology.

What is known about energy-dependent autophagy is the evidence for the claim that viruses cause all pathology. The 2016 Nobel Laureate in Physiology or Medicine won the prize for experimental evidence that autophagy was the link to chromosomal rearrangements and all biodiversity, which was addressed by the 1933 Prize winner, and 2004 Prize Winners. You are claiming to not see the evidence that I put into this context:
 
“Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.
 
These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.
 
That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.”
 
Read more at: http://phys.org/news/2014-01-americans-dont-evolution.html#jCp
See also:

Conclusion: Everything known to serious scientists about physics, chemistry, molecular epigenetics, chemical ecology, and adaptation is included in Biblical Genesis. Only biologically uninformed atheists and Demoncrats continue to challenge the only accurate representation of biologically-based cause and effect that starts with ‘you are what you eat’ and claims that ‘if you eat this you will surely die.’

Tweets

Future of environmental research in the age of epigenomics and exposomics
Excerpt:

Epigenetic mechanisms, particularly DNA methylation and miRNA expression, attract increasing attention as potential links between the genetic and environmental determinants of health and disease. Unlike genetics, epigenetic mechanisms could be reversible and an understanding of their role may lead to better protection of susceptible populations and improved public health.

See also my attempt to discuss: How new traits “emerge” in evolution
Peter Berean wrote:

I am an ex-atheist, a Philosophical Theist and a Mere-Christian.

James Kohl

I have asked that you offer experimental evidence of biologically-based cause and effect. You provide nothing but rhetoric and fail to address any of the evidence I have provided. I have asked you which part of the Holy Bible you believe in, and your only answer seems to be that you are a Christian.

Peter Berean James Kohl,
You asked be for scientific evidence for OEC (a old universe and/or an old-earth) and so I did so (see my comments above).
———————————————————————-
In Addition:
1) I subscribe to the view that Some Pathology can be caused by Bacteria. You do not appear to subscribe to that view?
2) I subscribe to the view that Some Pathology can be caused by some Biological Toxins that are Not Viruses. You do not appear to subscribe to that view?
3) I subscribe to the view that Some Pathology can be caused by some Inorganic Toxins such as some heavy metals. You do not appear to subscribe to that view?
4) I subscribe to the view that SOME Pathology can be caused by Viruses. You do not appear to subscribe to that view because of the word SOME?
5) All of the evidence you have provided shows that Viruses cause SOME pathology. However, NONE of the evidence you provided shows that Viruses cause ALL pathology.
6) I am arguing that the evidence is consistent with the view that there are MULTIPLE Causes for Pathology.
7) You appear to be arguing that there is ONLY ONE cause for Pathology (viruses).
Please correct me if I am wrong in understanding your positions regarding the numbered questions/points I bring up above.
Cordially.
James Kohl
James Kohl I asked for experimental evidence of biologically-based cause and effect and you twisted that request into one for scientific evidence. You may think you are devilishly clever, but no serious scientist would agree.
I do not care what you subscribe to and will not answer any more questions about my views. They have been detailed in a series of published works during the past 20 years and no one has refuted the model we presented in the molecular epigenetics section of this review. From Fertilization to Adult Sexual Behavior