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

Ecological adaptations vs the randomness of evolution (3)

Summary: Fifty years later, only theorists and other pseudoscientists have failed to recognize the facts that link experimental evidence of differences in the energy of photons to the proton motive force, which links the potential of hydrogen (pH) to biophysically constrained viral latency and all biodiversity on Earth. In that context, Carl Zimmer serves as an important example of human idiocy each time he makes claims about evolution.
Serious scientists will meet during Schrödinger at 75 – The Future of Biology – September 2018 to discuss the overwhelming amount of human idiocy exemplified in the works of theorists who failed to learn that life is “All about that base.”
Without the quantized energy-dependent creation of the base pairs, viral latency could not be biophysically constrained and entropy would be used to explain the evolution of biodiversity manifested in sympatric speciation.
See for comparison: The costs of living at the edge: Seasonal stress in wild savanna-dwelling chimpanzees

Adaptations associated with shifting from a predominately forested habitat to a more open environment are considered a crucial step in hominin evolution.

The adaptations are food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans. For example, higher levels of dehydroepiandrosterone in humans are an adaptation.
See:  Dehydroepiandrosterone – is the fountain of youth drying out?

…humans are unique in having adrenals that secrete large amounts of the prohormone, dehydroepiandrosterone (DHEA) and its sulfate, DHEA-S, into the bloodstream of males and females. Even non-human primates produce only ~10% of the DHEA found in humans

Carl Zimmer places everything known about how ecological variation must be linked to energy-dependent ecological adaptations into the context of human evolution.
See: Hints of Human Evolution in Chimpanzees That Endure a Savanna’s Heat

Millions of years ago, our apelike ancestors gradually moved from woodlands to savannas and began walking upright at some point. The Fongoli chimpanzees demonstrate just how difficult that transition would have been — and how that challenge may have driven some major changes in our evolution, from evolving sweat glands to losing fur and walking upright.

Before she graduated from her medical technologist course (circa 2014), I mentioned to Misty ______ the importance of  β-lactamase testing to understanding how the energy-dependent creation of microRNAs would soon be linked to all biophysically constrained biodiversity on Earth via antibiotic susceptibility testing in the hospital medical laboratory.
Shared strategies for β-lactam catabolism in the soil microbiome

A hydrolase from the put operon was found to degrade in vitro benzylpenicilloic acid, the β-lactamase penicillin product.

This clearly exemplifies how the virus-driven degradation of messenger RNA in β-lactamase positive organisms is linked to antibiotic resistance via what all serious scientists know about the molecular mechanisms of energy-dependent cell type differentiation.
The findings were reported in the ridiculous context of claims about How Bacteria Eat Penicillin

…some of the bacteria could, in fact, eat the drugs… As it turned out, they were everywhere. He also found examples of the phenomenon in the scientific literature going back to the 1960s.

In 1964, McEwen et al, linked the creation of the sun’s anti-entropic virucidal energy from Schrödinger’s claims in What is Life? (1944) to the creation of ATP and the creation of RNA. Now, others like McEwen know that RNA interference biophysically constrains viral latency.
In 1968, Frohlich speculated that the highly ordered storage of quantized energy in species from microbes to humans linked hydrogen-atom transfer to the functional structure of cell membranes via the hydrogen bonds of molecules, or other dipolar constituents, which he linked to the shared energy supply that biophysically constrains life.
Fifty years later, only theorists and other pseudoscientists have failed to recognize the facts that link experimental evidence of differences in the energy of photons to the proton motive force, which links the potential of hydrogen (pH) to biophysically constrained viral latency and all biodiversity on Earth. In that context, Carl Zimmer serves as an important example of human idiocy each time he makes claims about evolution.
See also: UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs

By integrating proteomic and genomic analyses, we link these changes to UTX regulation of ATP-dependent chromatin remodeling, coordination of the COMPASS complex and enhanced pioneering activity of ETS factors during evolution to AML.

They linked the anti-entropic virucidal energy of sunlight from the creation of ATP to chromatin remodeling during the evolution of pathology, which all serious scientists know is biophysically constrained by the physiology of food energy-dependent pheromone-controlled reproduction.
See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] (1994)

A study of the influence of pheromone stressor(s) on proliferating germ and somatic cells was performed on laboratory lines of house mouse in the context of the physiological hypothesis of mutation process, proposed by M.E. Lobashev in 1947. Data from experiments are presented, and results obtained during last 10-15 years are discussed. The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

The interorganism systems of genetic regulation have since been placed into the context of sympatric speciation by all serious scientists.
See: Direct estimation of mutations in great apes reveals significant recent human slowdown in the yearly mutation rate
See also: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

5th-6th Sept 2018 Dublin, Ireland

Less evolvable RNA-mediated ecological adaptations

No experimental evidence of biophysically constrained RNA-mediated cell type differentiation supports the claim about “…the evolutionary plasticity of the regulatory regions involved in transcriptional regulation…” The overwhelming systems complexity of energy-dependent RNA-mediated cause and effect can no longer be placed into the context of the pseudoscientific nonsense touted by theorists. Watch Andrea Wagner’s group try to escape from the claims made by losers.
But first see: Kalevi Kull: Censorship & Royal Society Evo Event

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull

RNA-mediated gene regulation is less evolvable than transcriptional regulation

…nucleic acid binding sites of RNA-mediated gene regulation are less evolvable than those of transcriptional regulation. This observation is consistent with the high levels of mRNA target conservation for RBPs (10, 82, 83) and the evolutionary plasticity of the regulatory regions involved in transcriptional regulation (84⇓–86) as well as their role in the evolution of myriad adaptations and innovations (11, 87, 88).

It is obvious to anyone who has followed the works of Andreas Wagner that his group has reached an impasse.
See: Evolution of Viral Proteins Originated De Novo by Overprinting (2012)

We found that young de novo genes have a different codon usage from the rest of the genome.

There is no such thing as a de novo gene.
See: From de novo to “de nono”: most novel protein coding genes identified with phylostratigraphy represent old genes or recent duplicates

I collectively refer to the putative de novo genes that failed to pass the validation criteria as the ‘de nono’ genes.

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

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Natural selection for energy-dependent codon optimality links what organisms eat to their pheromone-controlled physiology of reproduction in species from microbes to humans. Ecological variation is linked to ecological adaptations only in the context of biophysically constrained viral latency. That fact is now perfectly clear in the context of more than 71,000 indexed published works that link the energy-dependent creation of ATP synthase to the creation of ATP and the creation of RNA in the context of McEwen et al., (1964) and Frohlich (1968).
People like Andreas Wagner are stuck with their ridiculous claims about evolution, when all serious scientists know that only the hecatombic evolution of virus-driven pathology is possible. Healthy longevity requires food energy-dependent biophysically constrained polycombic ecological adaptations. The metabolism of food to species-specific pheromones links RNA-mediated autophagy to all biodiversity. The virus-driven degradation of messenger RNA is linked to all pathology.
Andreas Wagner reversed every aspect of what is known in: Arrival of the Fittest: Solving Evolution’s Greatest Puzzle (2014)

…he has found that adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take.

See for comparison: Kohl’s Laws of Biology in Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

Life is nutrient-dependent. That is a Biological Law. The ecological origin of all biological laws is apparent 1) in the context of systems biology (P. Kohl, et al., 2010); 2) in the context of the metabolism of nutrients by microbes (K. D. Kohl, 2012); and 3) in the context of how the metabolism of nutrients results in species-specific pheromones that control the physiology of reproduction (J. Kohl, Ostrovsky, Frechter, & Jefferis, 2013). Taken together, the systems biology of nutrient metabolism to species-specific pheromones, which control the physiology of reproduction, can be expressed in a summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent. See for review (J. V. Kohl, 2012; M. Lynch, 2007). The physiology of reproduction is pheromone-controlled. See for review (J. V. Kohl, 2013). In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior (J. V. Kohl, et al., 2001), which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences (J.V. Kohl, 2007).

Andreas Wagner, and others like him, will probably continue to misrepresent what is known about how the creation of sunlight must be linked to food energy-dependent pheromone-controlled reproduction by natural selection for codon optimality. But the facts about how energy must be linked to increasing organismal complexity are not going to change.
See: Schrödinger at 75 – The Future of Biology – September 2018
and/or 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!

 
 
 

Lethal virus kills 5 billion people?

A Mathematical Model Links Quantum Physics to Quantum Souls (3)

Thursday, January 4, 2018 at 7 pm Eastern Time:
Your Tweets earned 3,525 impressions over the last 24 hours
Please calculate the number of potential victims who might be saved by the information in my tweets. I will sleep better if you know that you may not be among those who survive.
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See: A Mathematical Model Links Quantum Physics to Quantum Souls (2)
See: Viruses exacerbate disease caused by Leishmania parasite

How do parasite viruses worsen parasitic diseases?

It’s important to remember that people are not infected with both a parasite and a virus. Rather, people are infected with a parasite that has a virus hidden inside it. What we think happens is that immune cells kill some invading parasites, releasing the virus. The body then generates an immune response to fight off the virus. But when you’re infected with a parasite, this is the wrong kind of immune response. It doesn’t kill the parasite; it seems to help the parasite make the disease worse.

What makes the disease better? SARCASM ALERT: Could it be the anti-entropic virucidal energy of sunlight that is consistently linked from the food the organisms eat to their biophysically constrained physiology of pheromone-controlled viral latency via the transgenerational epigenetic inheritance of all phenotypes in all living genera?
Alternatively, see: A virus-bacteria coevolutionary ‘arms race’ solves diversity by ‘killing the winner’

Theoretical models of population dynamics have not presented a fully satisfactory explanation for what has come to be known as the diversity paradox.

And so they developed another theoretical model

Goldenfeld and Xue developed a stochastic model that accounts for multiple factors observed in ecosystems, including competition among species and simultaneous predation on the competing species. Using bacteria and their host-specific viruses as an example, the researchers showed that as the bacteria evolve defenses against the virus, the virus population also evolves to combat the bacteria. This “arms race” leads to a diverse population of both and to boom-bust cycles when a particular species dominates the ecosystem then collapses—the so-called “Kill the Winner” phenomenon. This coevolutionary arms race is sufficient to yield a possible solution to the diversity paradox.

Simply put, they advise you to just say no to autophagy, and to ignore the information at Autophagy.pro 
For comparison: This was reported in 2005: A universal trend of amino acid gain and loss in protein evolution

We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.

The likelihood that the universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms was ignored again in this report Study of 385-million-year-old shark suggests humans and sharks shared common ancestor 440 million years ago.

Scientists explore mysteries behind diversity of DNA composition among species

The study was published in the journal Nature Ecology and Evolution.

To err is universal

Driving evolution are DNA mutations, errors in the genome that are introduced and passed along to the next generation, so that over time, providing the fuel for the invention of new adaptations or traits.

See for comparison: The Secret to Long Life? It May Lurk in the DNA of the Oldest Among Us and The secret to safe DNA repair

…if you don’t have this enzyme, then this error-free repair is stopped. You can’t do it. If you can’t do the error-free repair, among other things that happen is that you expect these cells to be cancer prone.

Career summary
I often wonder how I found myself in a career as a medical laboratory scientist at a time when some people still believe in mutation-driven evolution. See for comparison: The Darwin Code

Perhaps the most intriguing method of gene swapping in bacteria is the bacteriophage, or bacterial virus. Bacteriophages–phages for short–can either kill large numbers of host bacteria, reproducing rapidly, or lie dormant in the bacterial chromosome until the time is right for expression and release. Lytic phages almost invariably kill their hosts. But these latter types–known as lysogenic phages–can actually transport useful genes between hosts, and not just randomly, but in a targeted fashion. In fact, bacterial pathogens frequently rely on lysogenic phages to spread toxin genes throughout a population. Cholera populations become pathogenic in this fashion. In outbreaks of E. coli that cause illness in humans, lysogenic phages have transported genes from shigella–a related bacterial type–conferring the ability to produce shiga toxin, a potent poison.

See also: The evolution of RNAi as a defence against viruses and transposable elements

RNA interference (RNAi) is an important defence against viruses and transposable elements (TEs). RNAi not only protects against viruses by degrading viral RNA, but hosts and viruses can also use RNAi to manipulate each other’s gene expression, and hosts can encode microRNAs that target viral sequences.

Claims about the evolution of food energy-dependent endogenous RNA interference have been made by biologically uninformed theorists.”Endogenous” is used to indicate that fact that RNA interference is an energy-dependent biophysically constrained example of creation.
See for details: Energy as information and constrained endogenous RNA interference
See for an example: AlmG, responsible for polymyxin resistance in pandemic Vibrio cholerae, is a glycyltransferase distantly related to lipid A late acyltransferases December 22, 2017
Reported as:  An unusual form of antibiotic resistance in pandemic cholera

AlmG is structured differently from other lipid A-modifying enzymes, with a different active site responsible for carrying out the modification. In addition, AlmG can add either one or two glycines to the same A molecule, which has also not been observed in other bacteria.

The enzymatic addition of achiral glycine in position 6 of the GnRH decapeptide helps to protect the organized genomes of all vertebrates from the virus-driven degradation of messenger RNA that links mutations to all pathology.
For comparison, antibiotic resistance is driven by ecological adaptations in viruses. The viruses steal the quantized energy that host cells need to use for error free DNA repair of the cell membrane which contains quantized energy as information that is required for species-specific survival. If the availability of food is restricted, the virus-driven degradation of messenger RNA is linked to all species-specific and cell type-specific pathology.
See also: Waiting for the big one: A new flu pandemic is a matter of time (Subscription required)

At least two flu strains are only a few mutations away from developing deadly human-to-human transmission. So how do we minimise the impact?

You minimize the impact by learning how quantized energy-dependent RNA-mediated biophysically constrained cell type differentiation occurs. Then, you stop claiming that different strains of the flu virus evolve.
The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

The Spanish flu of 1918 remains the worst flu pandemic on record, but there have been several milder ones since (see chart, below). A pandemic is a global epidemic and, in theory, flu does that every year in the northern and southern winters. But with flu, the term is reserved for when an influenza A virus emerges that isn’t just a slightly mutated version of last winter’s flu, but a complete novelty, with surface proteins most people have no immunity to.

Novel viruses are constantly evolving in the birds, pigs and other animals that also carry influenza A, and they can shuffle their genes with human strains, or just adapt to mammals directly. Virologists consider flu pandemics inevitable. The World Bank says a bad one “

How much worse could it be? Spanish flu of 1918 killed 50 million people in a world with a much smaller population size and less ability to quickly travel from one part of the world to another.
12 Monkeys

The movie uses its future world as a home base and launching pad for the central story, which is set in 1990 and 1996, and is about a time traveler trying to save the world from a deadly plague.

…  lives with a handful of other human survivors in an underground shelter put together out of scrap parts and a lot of wire mesh. The surface of the planet has been reclaimed by animals, after the death of 5 billion people during a plague in 1996.

Thursday, January 4, 2018 at 7 pm Eastern Time:
Your Tweets earned 3,525 impressions over the last 24 hours
Please calculate the number of potential victims who might be saved by the information in my tweets. I will sleep better if you know that you may not be among those who survive.

GPX4-Cys bypasses the requirement of selenoproteins for cell viability

Quantized energy-dependent viral trophism

…mutations cause activation of your death gene.
Conclusion: You may be able to stop the ongoing activation of your death gene by a change in diet.
See: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene
See also: A Concise Review of MicroRNA Exploring the Insights of MicroRNA Regulations in Bacterial, Viral and Metabolic Diseases
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Daniel L.Hurdiss (@DanielHurdiss) announced publication of this refutation of neo-Darwinian pseudoscientific nonsense in his twitter feed before the start of the new year with no indication that it refutes all theories of emergence and evolution.
Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus

…receptors are important determinants of viral tropism…

The quantized energy-dependent creation of the receptors biophysical constrains viral latency via feedback loops that link the de novo creation of enzymes from microRNA-mediated metabolism to the species-specific pheromones that biophysically constrain autophagy.
That fact has become clearer since the 1994 publication of  Pheromonal Regulation of Genetic Processes: Research on the House Mouse (Mus musculus L.)
The exquisite clarity led to this:

Previously, , Ariane Briegel @BriegelAriane blocked me from following her tweets (one of which led me to the tweet by Daniel Hurdiss).
In 2014, (with others) she published Structure of bacterial cytoplasmic chemoreceptor arrays and implications for chemotactic signaling [Two of the authors are not based in the United States and Ariane Briegel now has her own lab in Leiden — in the Dutch province of South Holland.]

Most motile bacteria sense and respond to their environment through a transmembrane chemoreceptor array whose structure and function have been well-studied, but many species also contain an additional cluster of chemoreceptors in their cytoplasm.

Phototaxis must first be linked to energy-dependent pH-taxis and chemotaxis, which is why I commented on her publication of The dark side of the new popularity of cryo-electron microscopy.  It appeared to be yet another attempt to keep people in the dark about what is already known to serious scientists about light-activated endogenous substrates and cell type differentiation.
[Researchers based outside the United States are probably less likely to support the Trump administration’s efforts to drain the academic swamp.] See for comparison: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
My invited review of nutritional epigenetics was returned without review and Briegel has since decided it is a good idea for reviewers to be fair. I will add that blocking specific people from seeing your tweets is not an effective strategy. Simply put, it is not fair. If it was, the President of the United States of America would probably have used a tweet blocking strategy by now.
Instead, he was falsely accused of censorship when the director of the CDC suggested that certain key words, such as “transgender” should not be used in funding attempts. What about Briegel’s censorship?
I suspect that President Trump will keep tweeting away in his attempts to drain the academic swamp. In any case, that’s what I will keep doing. Watch what happens to those who hide their claims each time a serious scientist asks them to explain why they failed to link their results from quantum physics to quantum souls — in the context of words that might otherwise be used in future funding attempts. For example, words like food and energy could be used in funding attempts that would clearly show that food energy biophysically constrains viral latency.
See for example: Selenium Utilization by GPX4 Is Required to Prevent Hydroperoxide-Induced Ferroptosis

… a variety of dietary compounds such as… selenium… [target] a sequence of cellular and molecular pathways.

In the context of dietary microRNAs and exosomes, a change in the diet is an attractive option for the prevention/treatment of pathology.
That fact was placed into the context of Cytosis, a successful non-government funded 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!

The cell biology game links the creation of the sun’s anti-entropic virucidal energy from quantum physics to quantum souls via the creation of ATP, and the light-induced creation of messenger RNA.
The first time that experimental evidence of that fact was published may have been in 1964. See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”
See also: Effects of Carnitine on Fatty-Acid Oxidation by Muscle (1959), which was published in “Science Magazine.” McEwen and his co-author, Irving B. Fritz claimed:

…it is relevant to ask by what means serum fatty acids are transported from blood vessels through the interstitial space to the active sites for fatty-acid oxidation in muscle cells.

See also: Pheromones: a new term for a class of biologically active substances (1959) Was published in “Nature.”
It made it equally relevant to ask how fatty-acid oxidation in muscle cells was biophysically constrained in the context of the food energy-dependent pheromone-controlled physiology of reproduction.
It should be obvious that the dumbing down of “Science” has not effectively eliminated the intelligent approach that the Trump administration must take to Make America Great Again, by draining the academic swamp. However, for an example of what he is fighting against, see:
pH-Taxis of Biohybrid Microsystems (published in one of the Nature Publishing Group’s journals)

The motion analysis of microrobots also sheds light on the propulsion dynamics of the flagellated bacteria as bioactuators. It is expected that similar driving mechanisms are shared among pH-taxis, chemotaxis, and thermotaxis. By identifying the mechanism that drives the tactic behavior of bacteria-propelled microsystems, this study opens up an avenue towards improving the control of biohybrid microsystems.

The identified mechanism was place into the context of the weekend resurrection of the bacterial flagellum (in Science Magazine, 2015). The mechanism is food energy-dependent and controlled by the physiology of reproduction in species from microbes to humans via food energy-dependent fixation of RNA-mediated amino acid substitutions, which were reported to be mutations.The mutations cause activation of your death gene.
Conclusion: You may be able to stop the ongoing activation of your death gene by a change in diet.
See: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene
See also: A Concise Review of MicroRNA Exploring the Insights of MicroRNA Regulations in Bacterial, Viral and Metabolic Diseases
See also: Autophagy.pro

For God and Country

Losers: Rediscovering an epigenetic key (2)

Genome-wide meta-analysis associates HLA-DQA1/DRB1 and LPA and lifestyle factors with human longevity

Validation of associations reported elsewhere by all serious scientists

Validation of associations reported elsewhere by lookup in LifeGen. A search of recent literature suggested the gene regions shown here were most likely to harbour associations with lifespan, beyond the four loci identified in Table 2, which are further explored in the Discussion. The most powerful LifeGen analysis (i.e., European ancestry, father and mother combined) was used for validation. The odds ratio (OR) for extreme long-livedness is presented for the reported life-shortening allele (i.e., the OR for long-livedness < 1) in the original study, but not necessarily in LifeGen. The LifeGen OR of being long-lived was estimated empirically on the assumption that the relationship between the LifeGen observed hazard ratio (HR) and the OR is stable across allelic effects, with APOE results from LifeGen and CHARGE-EU 90+ 6 being used to estimate the ratio of ln HR to ln OR (−4.7). These estimates will only fully align with the published ORs if the shape of the effect on lifespan is similar to APOE, as is true under the proportional hazards assumption, nonetheless the pattern is suggestive. Further details are shown in Supplementary Data 3


“Validation of associations reported elsewhere,” includes the detailed associations from 1996 in the molecular epigenetics section of: From fertilization to adult sexual behavior  and in my 2013 refutation of neo-Darwinian theories:
Nutrient-dependent/pheromone-controlled adaptive evolution: a model 
(Val370Ala is also known as rs3827760, also known as 1540T/C, 370A. It is a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2.)
Excerpt:

Two additional recent reports link substitution of the amino acid alanine for the amino acid valine (Grossman et al., 2013) to nutrient-dependent pheromone-controlled adaptive evolution. The alanine substitution for valine does not appear to be under any selection pressure in mice. The cause-and-effect relationship was established in mice by comparing the effects of the alanine, which is under selection pressure in humans, via its substitution for valine in mice (Kamberov et al., 2013).

These two reports (Grossman et al., 2013; Kamberov et al., 2013) tell a new short story of adaptive evolution. The story begins with what was probably a nutrient-dependent variant allele that arose in central China approximately 30,000 years ago. The effect of the allele is adaptive and it is manifested in the context of an effect on sweat, skin, hair, and teeth. In other mammals, like the mouse, the effect on sweat, skin, hair, and teeth is due to an epigenetic effect of nutrients on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones control the nutrient-dependent hormone-dependent organization and activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates as previously indicated. That means the adaptive evolution of the human population, which is detailed in these two reports, is also likely to be nutrient-dependent and pheromone-controlled, since there is no other model for that.

Identifying Recent Adaptations in Large-Scale Genomic Data

TLR5L616F and EDARV370A demonstrate the power of our framework to move from genomic scans to the characterization of a novel adaptive mutation and elucidation of distinct mechanisms of evolution.

term=TLR5L616F: No items found.
term=EDARV370A
The adaptive variant EDARV370A is associated with straight hair in East Asians.
Characteristics of dental morphology in the Xinjiang Uyghurs and correlation with the EDARV370A variant.
EDARV370A associated facial characteristics in Uyghur population revealing further pleiotropic effects.
Carcinogenesis of nasopharyngeal carcinoma: an alternate hypothetical mechanism.

It is perhaps possible that EBV resides within the salivary glands, instead of the epithelium, during latency. This claim is indirectly supported by observations that the East Asian phenotype shares the characteristics of an increased susceptibility to NPC and immature salivary gland morphogenesis, the latter of which is influenced by the association of salivary gland morphogenesis with an evolutionary variant of the human ectodysplasin receptor gene (EDAR), EDARV370A. Whether the immature salivary gland represents a more favorable nidus for EBV is uncertain, but in patients with infectious mononucleosis, EBV has been isolated in this anatomical organ. The presence of EBV-induced lymphoepitheliomas in the salivary glands and lungs further addresses the possibility of submucosal spread of the virus. Adding to the fact that the fossa of Rosen Müller contains a transformative zone active only in the first decade of life, one might be tempted to speculate the possibility of an alternative carcinogenic cascade for NPC that is perhaps not dissimilar to the model of human papillomavirus [HPV] and cervical cancer.

SurePath Specimens Versus ThinPrep Specimen Types on the COBAS 4800 Platform: High-Risk HPV Status and Cytology Correlation in an Ethnically Diverse Bronx Population

In our population there appears to be a higher-than-previously-reported percentage of HPV-positive results in the cytologic-testing category of “negative [results] with reactive changes.”21-23 This finding may reflect the genetic diversity of our study population, whose demographics were similar to those of the surrounding population of the Bronx county. African American and Latino patients represented 30% and 26% of patients, respectively, whereas whites made up only 17% of the study group. The remainder of the study participants belonged to other ethnic groups, including “mixed ethnicity” and those who did not identify their ethnicity. Alternately, the reactive changes may truly represent early morphologic evidence of HPV infection.

The human ectodysplasin receptor gene (EDAR) variant Val370Ala — also known as rs3827760, also known as 1540T/C, 370A — could be the link from an energy-dependent change in a base pair to the creation of a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2. If so, the pheromone-controlled physiology of reproduction appears to link everything known about ecological variation and ecological adaptation to food energy-dependent RNA-mediated cell type differentiation and the chromosomal inheritance of all morphological and behavioral biodiversity.
See also: miRNA as viral transcription tuners in HPV-mediated cervical carcinogenesis, “…with a special focus on miRs that may regulate expression of the host and viral factors particularly responsible for viral transcription leading to carcinogenic progression of the lesion. Further, the review attempts to assess the therapeutic potential of miR-based strategies in therapeutic targeting of HPV infection during cervical carcinogenesis.”
and Study Indicates 11 Million Men And 3.2 Million Women In US Have Oral HPV Infections

The New York Times (10/16, Bakalar, Subscription Publication) “Well” blog reports that research published in the Annals of Internal Medicine indicated “11 million men and 3.2 million women in the” US have “oral HPV infections.” Among these individuals, “7 million men and 1.4 million women” have “strains that can cause cancers of the throat, tongue and other areas of the head and neck.”

TIME (10/16, Sifferlin) reports that the investigators “note that the number of men with HPV-related cancer of the oropharynx – the tongue, tonsils and back of the throat – has rapidly increased and has already surpassed the incidence of cervical cancer among women.”

Reuters (10/16, Rapaport) reports that the research suggested “men were at the highest risk of developing oral HPV when they had oral sex with other men or also had genital HPV infections.”

CNN (10/16, Scutti) reports the study also found “HPV infections overall and high-risk HPV oral infections in particular were ‘significantly associated’ with cigarette and marijuana use.” While “an HPV vaccine is available for both men and women and can protect against infection…many men are over the eligibility age of 26, and younger men have low vaccination rates.”

Cytology correlations appear to confirm everything known to serious scientists about biophysically constrained viral latency that varies among different human populations. The variations now appear to link more than two decades of published works to the prevention of all pathology via food energy and species-specific pheromones.
See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] (1994)
See also: Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain (2014)

Humans also have various pheromone-induced physiological effects, especially those associated with reproduction [46, 47]. This suggests that the human olfactory system is still an effective pathway for influencing environmental factors on the human nervous system. Various psychoemotional states of the human nervous system can, in turn, disrupt the integrity of the chromosomal apparatus of target cells, for instance lymphocytes [41, 42]. Therefore, studies on the oppositely directional modulation of the mutagenic consequences of stress in rodents with the use of specific, volatile, and zoosocial important chemosignals are a promising approach both to modeling posttraumatic stress disorders in humans [36] and to searching for mehods of their treatment.

[46] is Kohl, J.V., Atzmueller, M., Fink, B., and Grammer, K., Human pheromones: integrating neuroendocrinology and ethology, Neuroendocrinol. Lett., 2001, vol. 22, pp. 309–321.
See also: Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems (2015)
For comparison, see (with my emphasis): Epigenetic mechanisms modulate differences in Drosophila foraging behavior

Little is known about how genetic variation and epigenetic marks interact to shape differences in behavior. The foraging (for) gene regulates behavioral differences between the rover and sitter Drosophila melanogaster strains, but the molecular mechanisms through which it does so have remained elusive. We show that the epigenetic regulator G9a interacts with for to regulate strain-specific adult foraging behavior through allele-specific histone methylation of a for promoter (pr4). Rovers have higher pr4 H3K9me dimethylation, lower pr4 RNA expression, and higher foraging scores than sitters.

The authors have linked everything known about nutrient stress and social stress from what organism eat to the species-specific pheromones that control the physiology of reproduction and the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes in all living genera. But, they place what is known to serious scientists back into the ridiculous context of a gene-centric theory that attempts to support past claims that genes regulate the energy-dependent production of amino acid substitutions, which they refer to in the context of protein isoforms. They do not link the direct effects from energy to the de novo creation of genes and the behavioral differences that arise only after the genes are epigenetically-effected.
See also for comparison: Induction and characterization of anti-tumor endothelium immunity elicited by ValloVax therapeutic cancer vaccine
Video
See for comparison: microrna angiogenesis
Whether or not you are told that angiogenesis and tumorogeneis are energy-dependent, the use of cancer vaccines and other vaccines for virus-driven pathology should allow you to link food energy from the pheromone-controlled physiology of reproduction to chromosomal inheritance of healthy longevity, or to link the virus-driven degradation of messenger RNA from mutations to all pathology.
If you cannot yet link food energy from the pheromone-controlled physiology of reproduction to healthy longevity in all human populations, see: Korean Red Ginseng extract induces angiogenesis through activation of glucocorticoid receptor

Conclusion

KGE was found capable of inducing angiogenesis both in vivo and in vitro models through activating GR. This study provides a valuable insight into the angiogenic mechanisms depicted by KGE in relation to specific miRNAs.

See also: Olfactory experience primes the heat shock transcription factor HSF-1 to enhance the expression of molecular chaperones in C. elegans
Reported as: Worms learn to smell danger
See for comparison: Olfaction Warps Visual Time Perception 
This group linked the sense of smell in bacteria to the physiology of pheromone-controlled reproduction in all living genera and to our visual perception of energy and mass in the context of the space-time continuum. Anything published since then that does not integrate what is known to all serious scientists about biophysically constrained RNA-mediated protein folding chemistry may appear to be nothing except a desperate plea for more funding.

For a brief review of the current understanding of how virus-driven energy theft causes the degradation of messenger RNA that all serious scientists have linked from mutations to all pathology, see:

Energy as information and constrained endogenous RNA interference

Then register for this Webinar, in case I missed something important.

The essential role of miRNA and mRNA on cancer progression and biomarker discovery using TaqMan® advanced miRNA chemistry

Nov 15, 2017 | 09:00am PST, 12:00pm EST

Learning Objectives:

Study of miRNAs in Oncology Gene Expression

Understanding the interplay between miRNA and mRNA impacts cancer development and progression

Use of Data Analysis tools for Gene Expression studies involving miRNA and mRN

Understanding molecular mechanisms that may potentially have an underlying role in various diseases

Also see: Genetic Association between Amyotrophic Lateral Sclerosis and Cancer

Moving forward, we will see that all genetic associations are energy-dependent and RNA-mediated and that virus-driven energy theft links the degradation of messenger RNA to all pathology.

 

Alternative splicing of pre-mRNA

Evolution outside the context of "the light of evolution" (2)

See first: Evolution outside the context of “the light of evolution”

How many proponents of Intelligent Design never learned that Darwinian evolution was based on his “conditions of life?”

ch 4 IV. Natural Selection; or the Survival of the Fittest  “IF under changing conditions of life…”

ch 5 http://www.bartleby.com/11/5002.html “…the greater variability of species having wider ranges than of those with restricted ranges, lead to the conclusion that variability is generally related to the conditions of life…”

“…we cannot tell how much to attribute to the accumulative action of natural selection, and how much to the definite action of the conditions of life.”

ch 6 http://www.bartleby.com/11/6001.html “By my theory these allied species are descended from a common parent; and during the process of modification, each has become adapted to the conditions of life…

How many biologically uninformed science idiots do not know that conditions of life are nutrient energy-dependent and controlled by the physiology of reproduction?

Intelligent Design – Science & Philosophy Discussion attempt: 

https://lh3.googleusercontent.com/M3lHqwXQtKTjApLzM1L43lyjhKKtNHviQEu8EJvcvH2PwjUxJIfzFY4JsND9Nb2b2Uv1crMERBWlRBGu4FTOG837c1H1ULTAE8BPdG1NaPYK9tNYMMcJVdu-xFjUCz7I8FWHRVj1
 

Food energy-dependent RNA-directed DNA methylation alters the shifting of membrane helices. The alterations prevent the virus-driven degradation of messenger RNA and all pathology via fixation of amino acid substitutions in organized genomes. The physiology of reproduction and pheromone-controlled chromosomal inheritance link the fixation of amino acid substitutions in all cell types of all living genera to all biodiversity.

Andréia Silva James Kohl you won the Nobel prize for refuting evolution, correct?

Yoshinori Ohsumi won last year for doing that: A protein conjugation system essential for autophagy

This [energy-dependent] conjugation can be reconstituted in vitro and depends on ATP.

Ben Feringa also won last year: Dynamic control of chirality and self-assembly of double-stranded helicates with light

Did you not get the memo? They linked the speed of light on contact with water from energy-dependent changes in chirality to all biodiversity via ATP, which is required for the creation of RNA.
 
The link from self-assembly to autophagy includes a light-activated endogenous substrate that links the innate immune system of all species to protection from the virus-driven degradation of messenger RNA, which links mutations to all pathology.
 

All serious scientists are waiting for all pseudoscientists to realize the level of ignorance they have displayed for at least the past 50 years and take responsibility for the unnecessary suffering and premature deaths their ridiculous theories have caused.

Thank God, some serious scientists have taken the lead.

See:  Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation

Pathway analyses found a significant enrichment for “xenobiotic metabolism signaling” and “PXR/RXR activation” pathways. Our H3K27ac ChIP-seq identified 9,514 peaks that are PenStrep responsive. These peaks were enriched near genes that function in cell differentiation, tRNA modification, nuclease activity and protein dephosphorylation. Our results suggest that PenStrep treatment can significantly alter gene expression and regulation in a common liver cell type such as HepG2, advocating that antibiotic treatment should be taken into account when carrying out genetic, genomic or other biological assays in cultured cells.

Reported as: Common use of antibiotics in cells grown for research could distort tests

“…we treat cells with antibiotics all the time in cell culture and nobody’s looked at how this might affect and ,” said Ahituv.

Admitting that you and your colleagues once were biologically uninformed science idiots is the first step towards recovery. The antibiotic treatment caused the constraint-breaking mutations that all serious scientists have linked to all pathology. Food energy and the pheromone-controlled physiology of reproduction link biophysically constrained viral latency to healthy longevity.

The worst part of all this is that it clearly indicates Carl Woese was wrong. There is one domain of life and the virus-driven degradation of messenger RNA links the theft of quantized energy from the creation of bacteria to the creation of archaea.
 
Virus-driven energy theft also links the creation of humans to the creation of non-human primates via the same molecular mechanisms that link the food energy-dependent pheromone-controlled physiology of reproduction in bacteria to healthy longevity in species from microbes to humans.
 
My antagonists will continue to hate me for revealing that fact, but it was first revealed in Biblical Genesis. If I link the virus-driven theft of quantized energy to the creation of L-forms, I may be martyred.
 
But wait, I already did that and so did Paul in 1 Corinthians 15:36. I’m not quoting scripture, even though it parallels facts from what some people might call the book of “nature” even though there is only one book about that. 

Cytosis

God vs host-derived creation of virus-driven pathology (2)

When you next see someone claim that “…there is very little knowledge about the gut microbiome” you may associate that claim with the ignorance touted by neo-Darwinian theorists and compare it to what anyone 10 years-old or older will learn when they play the cell biology game “Cystosis.” A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
Moving forward: Food energy is required to build enzymes, hormones and receptors and fend off attacking viruses. The metabolism of food to species-specific pheromones that control the physiology of reproduction in species from microbes to humans is represented in this presentation from 2009 by Eshel Ben-Jacob.
 

At 39:10, he declares that the link from food energy to pheromones and behavior is “epigenetic.”‘
See also: Energy as information and constrained endogenous RNA interference (video)

Published on 15 Feb 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.
The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.
This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes.
For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

See for comparison: Preprocessing of emotional visual information in the human piriform cortex

To conclude, our findings support the specific role of the piriform cortex beyond a mere sensory relay up to a higher-order associative brain area. We are the first to demonstrate that the human piriform cortex processes emotional visual information before odor perception. Moreover, we found a common activation pattern in regions of the olfactory network such as piriform cortex, orbitofrontal cortex, amygdala and hippocampus for the subsequent integration of the emotional visual information while processing the actual odor. Matching behavioral results reveal that the emotion of a facial expression influences the valence rating of an odor. Thus, the behavioral observation as well as brain activation data jointly point towards a preprocessed integration of emotional visual information that modulates olfactory processing.

Their ridiculous conclusion, which is based on brain imaging linked to behavior, makes it appear that humans are primarily visual creatures.For comparison, see: Olfaction Warps Visual Time Perception

Our perception of the world builds upon dynamic inputs from multiple senses with different temporal resolutions, and is threaded with the passing of subjective time. How time is extracted from multisensory inputs is scantly known. Utilizing psychophysical testing and electroencephalography, we show in healthy human adults that odors modulate object visibility around critical flicker-fusion frequency (CFF)-the limit at which chromatic flickers become perceived as a stable color-and effectively alter CFF in a congruency-based manner, despite that they afford no clear environmental temporal information. The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.
They linked what is known about natural information processing in bacteria: Learning from Bacteria about Natural Information Processing to what is known about how Feedback loops link odor and pheromone signaling with reproduction in all living genera.
The feedback loops typically prevent virus-driven energy theft from causing the mutations that have been linked to all pathology by all serious scientists.For comparison, see: Finding what fuels the ‘runaway train’ of autoimmune disease

It has been a long-standing observation in the clinic that autoimmune diseases evolve over time, attacking an ever-expanding array of organs and tissues – a phenomenon known as ‘epitope spreading…

The observation fails to link the virus-driven degradation of messenger RNA to all pathology via energy-dependent changes in the microRNA/messenger RNA balance. See for comparison: microRNA  Items: 1 to 20 of 63935

 
“It’s truly natural selection on a microcosm,” says van der Poel. “Once activated, there are ten different possible colors to represent different B cell clones. Over a week or two, the color diversity begins to shift—eventually one color dominates, representing a single clone winning out.”
 
It’s energy-dependent RNA-mediated autophagy. Activation is energy-dependent and RNA-mediated. Natural selection for energy-dependent codon optimality must be linked from ecological variation to ecological adaptation via the physiology of reproduction in all living genera. These researchers are making unsubstantiated claims about the “evolution” of pathology at a time when all serious scientists know that all pathology is caused by virus-driven energy theft.
Cytosis

The Origin of Information (3)

Summary: I presented two poster sessions during the Labroots virtual conference “Neuroscience,” March 16-17, 2016
One linked sunlight to energy as the origin of information. The other linked energy as information to biophysically constrained viral latency via the pheromone-controlled physiology of reproduction in all living genera.
Additional experimental evidence of top-down causation has since confirmed that the creation of sunlight can be linked from energy as information to all biodiversity via its anti-entropic virucidal effects. The direct quantitative measurement of top-down causation supports the claims made by all serious scientists, and also refutes all the claims made by evolutionary theorists and “Big Bang” cosmologists.
See:  The Origin of Information (1) 7/28/16 From hydrogen atom transfer in DNA base pairs to ecosystems

The Origin of Information (2) 7/28/16 RNA mediated molecular epigenetics and virus driven entropy (working title: The Origin of Information)
 
A good model predicts. See also: Direct quantitative measurement of the C═O⋅⋅⋅H–C bond by atomic force microscopy

The direct measurement of the interaction with a hydrogen atom paves the way for the identification of three-dimensional molecules such as DNAs…

Reported on 7/31/17 as: Scientists Decode DNA; See and Touch the Force That Gives Us Life
My summary: Hydrogen (H) t is the most abundant energy source in the Universe. It is also an indispensable source of the energy that is required for life. The energy links nucleic acids (DNA, RNA) and proteins to the creation of life via hydrogen bonds between molecules.
Energy as information is crucial for encoding the secrets of life. Those who cannot understand the concept of energy as information cannot understand anything about the energyd-dependent creation of life or the energy-dependent physiology of pheromone-controlled reproduction, which links energy as information to all biodiversity.
For instance, the biodiversity of all morphological and behavioral phenotypes is food energy-dependent. Richard Feynman put that fact into the perspective of something that many people are intuitively able to understand.

Feynman also presciently placed the measurement of energy into its current context. He somehow knew that technological advances would someday allow serious scientists to measure the energy in a hydrogen atom and link what organisms eat to all biodiversity.
See also: Hydrogen bonds directly detected for the first time

The measured forces and distances between the oxygen atoms at the tip of the atomic force microscope and the propellane’s hydrogen atoms… show that the interaction clearly involves hydrogen bonds. The measurements mean that the much weaker van der Waals forces and the stronger ionic bonds can be excluded.

The fact that experimental evidence established the primacy of the hydrogen bond in the interactions that link energy-dependent changes from chirality to autophagy and from angstroms to ecosystems in all living genera can be placed into the context of the food energy-dependent physiology of reproduction for comparison to: Mutation-Driven Evolution, which was published on the same day in 2013 as Nutrient-dependent/pheromone-controlled adaptive evolution: a model
The good news is that neo-Darwinian theories have been replaced with Darwin’s energy-dependent “conditions of life.” That is bad news for all theorists.
For example, yesterday, Jay R. Feierman again threatened to ban me from participation on the Human Ethology Yahoo Group. Our history of friction began in 1995 but it was amplified in 2013, when I wrote:

Evolution by natural selection cannot be the outcome if something is not first selected. Selection is always for nutrients. It is as simple as that.

Feierman responded:
7/25/13
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.
7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
As first author of the award-winning review Human pheromones: integrating neuroendocrinology and ethology, I may be the only former member of the International Society for Human Ethology (1) who still participates on the yahoo group they own (2). See also their FB page (3).

  1. The International Society for Human Ethology (ISHE) promotes ethological perspectives in the scientific study of humans worldwide. We aim to achieve this goal through:
    • Encouraging empirical research in the field of human behavior, using the full range of methods developed in biology and the human behavioral sciences, and operating within the conceptual framework provided by evolutionary theory.
    • Promoting the exchange of ethological knowledge and opinions with the other empirical sciences of human behavior.
  2. The International Society for Human Ethology (ISHE), http://www.ishe.org/, a not-for-profit scientific organization, is the owner of this listserv, whose purpose is to facilitate communication among persons interested in human ethology and to attract new persons to the field. The language is English. The current moderator is Jay R. Feierman.
  3. The International Society for Human Ethology (ISHE) aims at promoting ethological perspectives in the scientific study of humans worldwide. ISHE encourages empirical research in all fields of human behavior.

If I am the only person who has detailed the facts about the Origin of Information, and Jay R. Feierman bans me from participation in the ISHE’s group, he will help to eliminate discussion of empirical research such as  Feedback loops link odor and pheromone signaling with reproduction.
There are a few other people like Jay R. Feierman, who have helped prevent the dissemination of accurate information about the Origin of Information and all biodiversity in the context of our visual perception of energy and mass, which has been placed into the context of everything known about the space-time continuum. See: Olfaction Warps Visual Time Perception.
But, to my knowledge, no one besides Jay R. Feierman has claimed that “Variation is not nutrient availability and the something that is doing the selecting is not the individual organism.” According to Feynman, Jay R. Feierman exemplifies “human idiocy.”
But, see also this comment from James Gray (August 1, 2017):

Jay,

I just want you to note my support for your warning to Jim Kohl.  Too bad that his attempts at comments are so incomprehensible.

After Feierman blocked another one of my posts to the group, I wrote:

It can only get worse from here, Jay. Even if you will not admit to the fact that you were dead wrong, others will learn that you caused the death of their loved ones via your ignorance and arrogance.
You are an example of what Feynman’s referred to as human idiocy.
 

Feierman responded (to the group)

This is warning #1. Say something equally offensive again to me in a personal email or on the group and you will be permanently banned from the Yahoo Human Ethology Group.
Sadly, no one ever responds to your posting because they are incomprehensible. I post them out of human compassion for you. But that does not give you license for being rude and flaming.
I’m copying this to the human-ethology group as well, so other members will know why you are gone from the group, if your flaming re-occurs.

Jay

Jay R. Feierman, Moderator Yahoo Human-Ethology Group

See for comparison: http://www.odedrechavilab.com/About.aspx

Our principle aim in the lab is to attack scientific dogmas. Mainly, we aim to use powerful genetic tools to discover novel biological principles by which RNA affects formation and inheritance of complex traits. While linking rare Mendelian traits to specific sequence variations has been accelerated, the genetic basis of many common diseases is not understood despite the undertaking of many genome wide association studies. It appears that our current genetic models fall short of faithfully explaining the inheritance of most complex traits.

Replaced by: Laboratory for radical science
See also: Principles of Transgenerational Small RNA Inheritance in Caenorhabditis elegans

…how these modifications regulate RNAi or small RNA inheritance was until recently unclear. Integrating the very latest literature, we suggest that changes to histone marks may instigate transgenerational gene regulation indirectly, by affecting the biogenesis of heritable small RNAs. Inheritance of small RNAs could spread adaptive ancestral responses.

The changes to histone marks are energy-dependent and they link hydrogen-atom transfer in DNA base pairs to the food energy-dependent fixation of RNA-mediated amino acid substitutions in supercoiled DNA, which prevents virus-driven energy theft from causing the degradation of messenger RNA that links mutations to all pathology.

On August 1, 2017 Jay R. Feierman wrote: 88186 “A genetic correlate of attachment and personality”

This is not a genetic correlate. The COMT VaL158Met amino acid substitution exemplifies the facts detailed in the context of: Hydrogen bonds directly detected for the first time The facts about hydrogen-atom transfer in DNA base pairs in solution have since been linked to all energy-dependent pheromone-controlled biodiversity in: Principles of Transgenerational Small RNA Inheritance in Caenorhabditis elegans

…how these modifications regulate RNAi or small RNA inheritance was until recently unclear. Integrating the very latest literature, we suggest that changes to histone marks may instigate transgenerational gene regulation indirectly, by affecting the biogenesis of heritable small RNAs. Inheritance of small RNAs could spread adaptive ancestral responses.
 

The changes to histone marks are energy-dependent and they link hydrogen-atom transfer in DNA base pairs to the food energy-dependent fixation of RNA-mediated amino acid substitutions in supercoiled DNA. The substitutions prevent virus-driven energy theft from causing the degradation of messenger RNA that links mutations to all pathology.

See for comparison: How to teach evolution when students hold creationist views

Teaching evolution is pointless.

See: Cytosis

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

Anyone ten years old or older will learn that natural selection for energy-dependent codon optimality is the key to healthy longevity and that the virus-driven degradation of messenger RNA links mutations to all pathology.

Amino acid modification FA_Epigenetics_Table1

Thinking about energy is not radical re-thinking

The brain: a radical rethink is needed to understand it

…Optogenetics, a technique that uses genetic modification of neurons so that their electrical activity can be controlled with light pulses – can help us to explore their specific contribution to brain function.

Optogenetics links the speed of light on contact with water to what is known about all energy-dependent cell type differentiation in all individuals of all living genera. Serious scientists, for example, have linked angstroms to ecosystems in all living genera because they know that brain function is experience-dependent and RNA-mediated.

Even in organisms that have no brain, cell type differentiation occurs in the context of biophysically constrained RNA-mediated protein folding chemistry. All chemistry is energy-dependent quantum chemistry and chemistry links quantum physics from the de novo creation of G protein-coupled receptors to the biological basis for all biodiversity on Earth.
For example, food odors link natural selection for energy-dependent codon optimality to the metabolism of food to pheromones. Biophysically constrained RNA-mediated feedback loops link the metabolism of food from the physiology of reproduction to supercoiled DNA, which protects all organized genomes from virus-driven entropy.
Simply put, quantum physics, quantum chemistry, and energy-dependent quantum biology prevent virus-driven entropy, which links everything known to serious scientists about niche construction to consciousness.
The Penrose Institute was established to link that fact to human consciousness in the context of everything known about cell type differentiation to everyone since the time that Lewis Thomas began making claims olfaction and smell.
A Fear of Pheromones (1971)
On Smell (1980)

The act of smelling is remarkably like the act of thinking itself.

See also:

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

In 1991, Roger Penrose, summarized what was known about all the mysteries in his forward to the reprint of Schrodinger’s “What is Life?”

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?

For comparison, see this comment by “Sonny” Williams to the International Society for Human Ethology’s yahoo group:

The empirical evidence is overwhelming that the brain is composed of highly specialized regions, whose neuronal members are unique in their cytoarchitecture (down to the molecular level).  Moreover, empirical evidence reveals that genes have directed these neural variations during corticogenesis; that is, most specialized neurons are differentiated early during development and directed to their place in the brain by intrinsic cues, and not activity-dependent cues.  This fact does not preclude later “rewiring,” or changes that are activity-dependent (plasticity), but this range of plasticity is constrained by the genetically derived regions.

Thus, the metaphor that the brain is “modular” is as accurate as any other metaphor.  HOWEVER, “modular” and functionally specialized regions has always included the fact that functional outcomes require a widely distributed network of specialized regions.  That is, modules do not exist in isolation, as islands of specialized function, but rather there existence as a specialized region is predicated upon their iterative communication with many other equally specialized regions.

I cannot recall any comment by Clarence “Sonny” Williams that might ever have made sense to a serious scientist. He is, in my opinion, a biologically uninformed science idiot. I once wondered who could have taught anyone to believe what biologically uninformed people believe in, or why they think what they were taught makes sense to serious scientists.
Then, I tried to discuss what I know about the energy-dependent links from angstroms to ecosystems in all living genera with the senior author of Complex Spike Patterns in Olfactory Bulb Neuronal Networks by Alister U Nicol, Anne Segonds-Pinchon, and Magnus S. Magnussen. It was also published as a book chapter in Discovering Hidden Temporal Patterns in Behavior and Interaction: T-Pattern Detection and Analysis with THEME™
Background:

T-pattern analysis is a procedure developed for detecting non-randomly recurring hierarchical and multiordinal real-time sequential patterns (T-patterns).

CONCLUSIONS:

We conclude that such sequences are an important physiological property of the neural system studied, and suggest that they may form a basis for encoding sensory information.

My summary: They link everything known to serious scientists about energy as information to non-randomly recurring patterns of biophysically constrained RNA-mediated protein folding chemistry and “…characterize these patterns in light of their putative role in processing sensory information.”
They ignore the fact that sunlight is the anti-entropic virucidal source of the energy that prevents genomic entropy via the pheromone-controlled physiology of reproduction in all living genera.
Apparently, like other biologically uninformed theorists, they did not realize what Dobzhansky (1973) did when he linked the light of evolution to all biophysically constrained biodiversity via the nutrient energy-dependent pheromone-controlled physiology of reproduction.
Dobzhansky was one of the first self-declared Creationists to level the playing field with his joke about evolution as if it occurred over billions of years.

I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation. Creation is not an event that happened in 4004 B.C.; it is a process that began some 10 billion years ago and is still under way.

Anyone who followed Dobzhansky’s works probably got the joke. He knew there was experimental evidence of God’s Creation. For example, he linked sensory input from what organisms eat and their physiology of reproduction to amino acid substitutions that differentiate all cell types in all living genera. He also knew that theorists had not found experimental evidence of biologically-based cause and effect that supported their claims about millions to billions of years of evolution.
All serious scientists were made aware of Dobzhansky’s rabbinical form of debate in 1964. He began by referring to theorists as bird-watchers and butterfly collectors.  A rather well known form of rabbinical begins with: “Thou fool….”
Dobzhansky was far less damning when he started his address with this:

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.

Dobzhansky probably was referring to himself in the third person when he made the claim about the unidentified Professor of Zoology. Still, to avoid ridicule by biologically uninformed theorists, he tempered the claim.

Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.

Clearly, Dobzhansky knew that his claims about amino acid substitutions would be accepted by serious scientists and rejected by pseudoscientists, who have continued to reject the claims of all serious scientists. That’s what pseudoscientists have always done.
See for instance:

3/09/17 Jay Feierman: One can’t have Darwinian evolution by natural selection without either “random” mutations or directional selection. They are both necessary, proximate, contributing causes for genes and the proteins they code for changing in frequency over time in a population and by which the population becomes adaptively configured to the current environment.

3/17/17 Jay R. Feierman [NEW]: We are adaptively configured to the current environment because we are the most successful mammal on earth by any measure. There are 7 billion of us and we inhabit every continent on earth. We accomplished this by Darwinian natural selection adaptively influencing the structural design features we call genes and the proteins they make as well as the extra-genetic structural design features developed through our creativity and ingenuity where we pass the instructions on how to make them across generations by social learning. An iPhone is an example today and an obsidian arrow head was an example in the past.

My comment:  After attempts to discuss energy-dependent biophysically constrained RNA-mediated cause and effect with Magnus S. Magnusson, I was not surprised to find support for some of Feierman’s claims about human adaptations in:

Complex spike patterns in olfactory bulb neuronal networks

Indeed, adaptations occur. But, in the same article, they failed to support Feierman’s claims that the adaptations randomly occur.

Abstract excerpt:

BACKGROUND:

T-pattern analysis is a procedure developed for detecting non-randomly recurring hierarchical and multiordinal real-time sequential patterns (T-patterns).

Conclusion: We conclude that such sequences are an important physiological property of the neural system studied, and suggest that they may form a basis for encoding sensory information.

My conclusion: People like Jay R. Feierman should try to support their assertions about adaptations with experimental evidence of biologically-based cause and effect like the evidence that was cited in the article linked above.

Any claims about how a population becomes adaptively configured to the current environment are not true outside the context of what is known about energy as information and biophysically constrained RNA-mediated protein folding chemistry. If those ridiculous claims were true, the experimental evidence of top-down causation that theorists think support the claims could be used to convince serious scientists that something besides natural selection for energy-dependent codon optimality and the physiology of pheromone-controlled reproduction could replace facts to support theories about mutation-driven evolution.

See also 3/18/17: [MODERATOR NOTE: I’m posting this submission even though it misquotes Feierman, who did not ever say or imply that “adaptations randomly occur.” jrf]
See alson 3/18/17: [MODERATOR NOTE: Adaptations and mutations are not synonyms. An adaptation is a mutation acted upon by natural selection to configure a population to the current environment. It would be an oxymoron to say that “adaptations randomly occur.” By definition, adaptations are mutations that have been acted upon by natural selection by which their frequency is increased in a population over time in a specific environment. jrf]