An evolutionary theory killer

A single base change refutes theistic evolution (2)

Announcing publication of a model that links the creation of quantized energy from changes in subatomic particles to biophysically constrained viral latency and sympatric speciation in all living genera.

Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems

This angstroms to ecosystems model of ecological adaptation links nutrient energy-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA/messenger RNA balance and chromosomal rearrangements via the physiology of reproduction in species from microbes to humans.

The invited review of nutritional epigenetics was returned without review and the preprint was posted 4 years ago as:

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

The only significant change to the manuscript was a change in the title. Atoms to ecosystems became Angstroms to Ecosystems when quantized energy-dependent changes in angstroms were linked to ecological adaptation by what is known to all serious scientists in this 2014 parody.
All About that Base (Meghan Trainor Parody) 12/10/14
Repeat after them (and me): “… every angstrom is dynamic from the 5 prime to the three…”
See also the 2015 publication: Structural diversity of supercoiled DNA

DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases.

See also: RNA-Guided Human Genome Engineering

George Church and others may have been the first to place the naturally occurring biophysically constrained energy-dependent processes of ecological adaptations into the context of a patent. (It is extremely unusual for anyone to attempt to patent a naturally occurring process.) That explains why there is no patent litigation, which still plagues those who claimed to discover the CRISPR-Cas 9 innate immune system of bacteria, which biophysically constrains viral latency and prevents the degradation of messenger RNA that links the energy-dependent creation of bacteria to the virus-driven creation of archaea and L-forms. All biophysically constrained virus-driven pathology has since been placed back into the context of embryogenesis and the dynamics of energy-dependent gene expression at the level of single-cell resolution as if bacteria somehow evolved into humans.

See:

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis
Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution
Chronicling embryos, cell by cell, gene by gene
Reported as: How one cell gives rise to an entire body
See for comparison our section on molecular epigenetics in: From Fertilization to Adult Sexual Behavior (1996)
Watch pseudoscientists continue to make ridiculous claims that fail to link the creation of biophysically constrained thermonuclear energy to autophagy and all biodiversity in the context of the cell biology game Cytosis and most of the forthcoming presentations during Schrödinger at 75 – The Future of Biology – September 2018.
Remember to note that at the end of the parody All About that Base, the research group politely refers to Neil deGrasse Tyson as a big ass (er, a bass). Try not to use the acronym ROTFLMAO in attempts to discuss what is known to all serious scientists with theorists.

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

Cytosis

From base editing to RNA editing (2)

Summary: The link from the creation of the sun’s anti-entropic virucidal energy and the physiology of pheromone-controlled reproduction to fixation of RNA-mediated amino acid substitutions in the organized genomes of all living genera is all that is required to claim adaptation for comparison to Koonin’s moronic assertion that the amino acid composition of proteins varies because the composition evolved.
Digital reconstruction of the Ceprano calvarium (Italy), and implications for its interpretation

A “fresh” (i.e., not yet “fossil”) bone can be plastically deformed before it breaks because it is still rich in collagen and because the calcium crystals that constitute large part of the bony matrix are not yet substituted by other minerals, as happens during the process of mineralization34. Such a diagenetic process may occur in environments that are rich in water, like a riverbed or a perilacustrine paleosol; the latter was probably the case in the Ceprano area5.

The virus-driven degradation of messenger RNA links the diagenetic process in living tissue links to the fossil record via changes that appear to have occurred during the past 5-10,000 years.
See for instance: MicroRNA-32 promotes calcification in vascular smooth muscle cells: Implications as a novel marker for coronary artery calcification
The increased level of calcification in smooth muscle cells, which is associated with increased rates of coronary artery calcification is a clear indicator that the proliferation of viruses in organized genomes causes the negative supercoiling of DNA, which serious scientists have linked to all pathology.
See also: A Post Mortem Case Study: Diffuse Pulmonary Ossification and Sudden Death
Case studies have no explanatory power outside the context of models that link electrons to ecosystems in all living genera. In this case study, it is clear that the pulmonary ossification and sudden death can be placed into the context of my model of nutritional epigenetics.
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. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. 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.

Attempts to support theories about random mutations and evolution have failed miserably and have largely been replaced with facts about energy-dependent RNA-mediated cell type differentiation.
See: RNA Editing Possible with CRISPR-Cas13

The tool itself could be further developed, adds computational biologist Eugene Koonin of the National Center for Biotechnology Information who also was not involved in the study. “This paper is not the end of the road,” he says. It’s possible that Cas13b could be fused to a variety of editing enzymes that would allow a range of different sequence changes. The possibilities are numerous, Koonin says, and “the best is still to come.”

This paper is the end of the road for pseudoscientists and biologically uninformed theorists, like Eugene Koonin, who made this ridiculous claim in 2005:
Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. –Jordan et al., (2005) A universal trend of amino acid gain and loss in protein evolution
See for comparison: The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis… (2015) — Eugene Koonin
See also Koonin’s attack on all models of ecological adaptation: Splendor and misery of adaptation, or the importance of neutral null for understanding evolution (2016)

…population genetic theory, combined with the data of comparative genomics, clearly indicates that such a “pan-adaptationist” approach is a fallacy. The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection. To claim adaptation, the neutral null has to be falsified.

The link from the creation of the sun’s anti-entropic virucidal energy and the physiology of pheromone-controlled reproduction to fixation of RNA-mediated amino acid substitutions in the organized genomes of all living genera is all that is required to claim adaptation for comparison to Koonin’s moronic assertion that the amino acid composition of proteins varies because the composition evolved.
Each time a new claim attests to the facts about energy-dependent RNA-mediated biophysically constrained cause and effect, remember how long those facts have been placed on hold by people like Eugene Koonin and Jay R. Fiereman, who is the moderator of the International Society for Human Ethology’s Yahoo Group.
See this attempt to discuss mysterious DNA changes with Jay R. Feierman who on 7/25/13 wrote:

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.

All DNA modifications are energy-dependent and RNA-mediated. Publications in Science and Nature attest to the foolishness of those who have tried to link base editing and RNA editing to human cell type differentiation without starting with the fact that RNA-mediated amino acid substitutions are food energy-dependent.
Clearly there are no mysterious stress-linked DNA modifications. Nutrient stress and/or social stress cause the proliferation of viruses. Typically the proliferation of viruses is biophysically constrained by food energy and the pheromone-controlled physiology of reproduction in species from microbes to humans.
See “Cytosis” for the game-ending details that placed the nonsense about neutral null falsification back into the historical perspective of the “Dark Ages.”
See also: Tempo and mode of genome evolution in a 50,000-generation experiment (with my emphasis)

Evidence for beneficial mutations

We sought to understand what proportion of the genomic changes in the non-mutator populations was adaptive, and how that proportion changed over time. One line of evidence derives from the expectation that synonymous substitutions—point mutations in protein-coding genes that do not affect the amino-acid sequence—are neutral and should therefore accumulate at a rate equal to the underlying mutation rate20,35. This expectation is not strictly true owing to selection on codon usage, RNA folding, and other effects, but it is generally thought that such selection is extremely weak, affects only a small fraction of sites at risk for synonymous mutations, or both 36,37.

RNA-mediated protein folding chemistry is biophysically constrained. It is nutrient energy-dependent and biodiversity is controlled by the energy-dependent physiology of reproduction. In 2015, Lenski’s group admitted to their lie about the beneficial mutations, with the claim “This expectation is not strictly true owing to selection on codon usage…”
No beneficial mutations have been found by serious scientists. But Lenski’s group clearly indicated they would continue to lie about all aspects of energy-dependent biodiversity. They hoped to make it appear that all energy-dependent biodiversity emerged and then automagically evolved. If they could do that, they knew that their idiot minions were not likely to examine selection for energy-dependent codon usage. But then,
See for comparison: The dynamics of molecular evolution over 60,000 generations
After 10,000 more generations, Lenski’s group reported that standard models of mutation-driven evolution has not been supported by their experimental evidence. Instead, they placed their results into the context of natural selection for energy-dependent codon usage and long-term adaptation, which obviously occurred outside the context of mutation–selection balance and neutral mutation accumulation.
They clearly indicated that the complexity of ecological variation and energy-dependent ecological adaptation must be considered before reporting anything in the context of natural genetic variation. Simply put, they refuted all the pseudoscientific nonsense their past claims caused to be touted by other biologically uninformed theorists. They reported that ecological adaptation occurs outside the context of the mutations and evolution.
But see: Molecular evolution: No escape from the tangled bank

Ecological interactions emerge spontaneously in an experimental study of bacterial populations cultured for 60,000 generations, and sustain rapid evolution by natural selection.

The claim that there is no escape from the tangled bank is true. Joshua B. Plotkin took Lenki’s group’s refutation of mutation-driven evolution and placed it back into the context of the spontaneous emergence of energy-dependent ecological interactions. And then, he again touted the nonsense about evolution by natural selection.
See also: Rapid and Inexpensive Evaluation of Nonstandard Amino Acid Incorporation in Escherichia coli (2017)

…we developed a toolkit for characterizing any Escherichia coli OTS that reassigns the amber stop codon (TAG). It assesses OTS performance by comparing how the fluorescence of strains carrying plasmids encoding a fused RFP-GFP reading frame, either with or without an intervening TAG codon, depends on the presence of the nsAA. We used this kit to (1) examine nsAA incorporation by seven different OTSs, (2) optimize nsAA concentration in growth media, (3) define the polyspecificity of an OTS, and (4) characterize evolved variants of amberless E. coli with improved growth rates.

Even with the tools available, which have refuted all ridiculous theories of mutation-driven evolution, the claims that variants “evolved” continues to plague all serious scientists. It seems that placing the claims that variants evolved into the context of natural selection for energy-dependent codon optimality and the physiology of pheromone-controlled reproduction in all living genera serves no purpose. However, even if biologically uninformed science idiots are not willing to admit that top-down causation requires first consideration for the energy source, there is hope for the future. Most people intuitively understand that the food energy from what organisms eat must be linked to the metabolism of food and the metabolism of food to species-specific pheromones is the only known link from the physiology of reproduction to all biophysically constrained biodiversity in the context of viral latency.
Epigenetic effects must be linked to affects on behavior and the difference between an effect on hormones and an affect of hormones on behavior must be considered in the context of how food odors and pheromones are linked to the physiology of human reproduction by serious scientists.
For example, see: Feedback loops link odor and pheromone signaling with reproduction
 
 

Lethal virus kills 5 billion people?

Predicting who wins the 2017 Nobel Prizes

The Nobel Prize in Physiology or Medicine 2017 will be announced on Monday 2 October, 11:30 a.m. at the earliest.
The Nobel Prize in Physics 2017 will be announced on Tuesday 3 October, 11:45 a.m. at the earliest.
The Nobel Prize in Chemistry 2017 will be announced on Wednesday 4 October, 11:45 a.m. at the earliest.
The Nobel Prize in Literature 2017 According to tradition, the Swedish Academy will set the date for its announcement later.
The Nobel Peace Prize 2017  will be announced on Friday 6 October, 11:00 a.m.

My Predictions

Wen Zhou wins the 2017 Nobel Prize in Physiology or Medicine

See: Why the First Drawings of Neurons Were Defaced  by R. Douglas Fields

Even in this age of electron microscopy and nuclear magnetic resonance imaging, his drawings retain their power to inspire and inform. While I was at the institute, Toledano opened one of the black boxes of glass microscope slides and held up a histological section of human brain cut and stained by Cajal at the turn of the 20th century. “This one I used in my new paper on senile dementia,” he said with a smile.

See for comparison: Link to Little-known nerve may be secret to lust 

“You take those facts and form a hypothesis, and that’s exactly where we are,” he said.

Fields has supporters, among them James Kohl, co-author of “The Scent of Eros,” a book on pheromones.

“He’s right on,” Kohl said. “We have known there is some physical link, but [nerve zero] really helps to define it. Maybe a lot of neuroscientists don’t know about it, but people who study the olfactory system and pheromones see that and say that’s really important.”

Here’s exactly where we are 10 years later: Olfaction Warps Visual Time Perception
My summary: The sense of smell in bacteria has been linked from their energy-dependent pheromone-controlled physiology of reproduction to our visual perception of energy and mass in the context of the time-space continuum. Their findings and the findings of all serious scientists suggest that neural energy represents a warped perception of time in the context of multisensory input at subsecond scales.
The reality of the weekend resurrection of the bacterial flagellum in P. fluorescens attests to the fact that all neo-Darwinian theories will be eliminated when Wen Zhou wins the 2017 Nobel Prize in Physiology or Medicine.

Gianmarc Grazioli  wins the 2017 Nobel Prize in Physics

m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs
Reported as: DNA’s dynamic nature makes it well-suited to serve as the blueprint of life
By linking energy-dependent changes from physics and chirallity to the RNA-mediated stability of base pairs,Gianmarc Grazioli crossed the disciplines that Wen Zhou crossed to win her Nobel Prize in Physiology or Medicine.
See also: Chemists know (parody)
See also: RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly

Mutations that destabilize native P5abc decrease the assembly rate up to 100-fold.

Lynn Zechiedrich wins the 2017 Nobel Prize in Chemistry

See: Structural diversity of supercoiled DNA
Zechiedrich has linked the energy-dependent transfer of hydrogen atoms in DNA base pairs in solution from quantum physics to chemistry and the functional structure of DNA via RNA-directed DNA methylation and fixation of amino acid substitutions that differentiate all cell types in all living genera in the context of their pheromone-controlled physiology of reproduction.
See also: All about that base (parody)

Bruce McEwen wins the 2017 Nobel Peace Prize

Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

Bruce McEwen has since helped others to link nutrient-stress and social stress from the virus-driven degradation of messenger RNA to amino acid substitutions in the context of the physiology of pheromone-controlled reproduction. For example, the substitution of one amino acid in the cell types of mammals protects them from the virus-driven energy theft that links amino acid substitutions in viruses to all pathology. McEwen’s works are the only known works of a serious scientist who has continued to refute the pseudoscientific nonsense touted by neo-Darwinian theorists since before 1964.
He will receive the “Peace Prize” for helping to establish and reestablish the fact that all organisms must forage and find food or they do not become part of a species. And, no organism has ever mutated into an organism that became a member of another species. That fact will lead to world peace if all those who are ecologically adapted to life in their energy-dependent ecosystems eat the most nutritious foods they can find and avoid eating too much. Eating too much causes the virus-driven degradation of messenger RNA that links excess energy to the proliferation of viruses that typically is constrained by food and pheromones.
See for comparison: Dr. David Sinclair, Discoverer of Anti-aging NAD Fad, Speaks About Human Trials of NMN

DNA damage, if not repaired, is a significant cause of the diseases of aging such as declining energy levels, cancer, chronic inflammation and a host of other diseases. Unfortunately, our body’s natural DNA repair mechanisms decline with age. Boosting our DNA repair mechanisms could help us ward off the chronic illnesses of old age, such as flagging energy levels, chronic inflammation, and cancer. If NAD boosting with NMN supplementation repairs human DNA, it could be one of the greatest anti-aging and disease-preventing inventions of all time.

A conserved NAD+ binding pocket that regulates protein-protein interactions during aging  NADH stands for “nicotinamide adenine dinucleotide (NAD) + hydrogen (H). The virus-driven theft of quantized energy has been linked from the degradation of messenger RNA to all pathology by serious scientists who do not make claims that the facts about energy-dependent healthy longevity have not been linked from viruses to all pathology. Serious scientists link hydrogen-atom transfer in DNA base pairs in solution to all biodiversity via the pheromone-controlled physiology of reproduction, which biophysically constrains viral latency.

Greg Bear wins the 2017 Nobel Prize in Literature

He predicted everything known about biophysically constrained viral latency in a series of novels that started with “Blood Music” (1985) and continued with “Darwin’s Radio” (1999), “Darwin’s Children” (2003) and Quantico (2006). The fact that he followed in the footsteps of the 1930 Nobel Prize winner in Literature, will be mentioned in the context of claims by Sinclair Lewis about viruses in bacteria that have since been linked to all pathology via the theft of quantized energy.
See also: Relating protein functional diversity to cell type number identifies genes that determine dynamic aspects of chromatin organisation as potential contributors to organismal complexity
See for comparison: 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).

 

Cytosis

God vs host-derived creation of virus-driven pathology

Summary: The virus-driven theft of quantized energy forces cells to compete for nutrient energy-dependent RNA-mediated reprogramming in the context of the structure of photons, one-carbon metabolism, autophagy, and the physiology of reproduction, which links energy-dependent changes in chirality from base pairs to RNA-mediated amino acid substitutions.

Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton (with my emphasis)

Viruses often carry genes acquired from their host. In the present work, we show that a virus of a marine alga carries a gene encoding a transporter protein that mediates nutrient uptake. We confirm that the viral transporter protein is expressed during infection and show that the protein functions to take up sources of nitrogen. This is important because acquisition of nutrients often determines the ecological success of phytoplankton populations. This work demonstrates how a virus can amend host–viral dynamics by modulating acquisition of nutrients from the environment.

Reported as: Virus reprograms ocean plankton

The virus has stolen a gene from the phytoplankton, which has the surprising effect of making the infected plankton better at absorbing certain nutrients for a period – before the virus kills them.

Much of the planet’s carbon is stored in the sea by a process of algae dying and sinking to the ocean floor, and this research shows a new feature of that process.

“Availability of vitamins and nutrients determine how these phytoplankton function,” said Professor Thomas Richards, of the University of Exeter.

“We have shown that this virus reprogrammes how the phytoplankton obtain nutrients, which affects how they grow and is likely to affect how they absorb carbon dioxide.

“Cells that have the virus are more competitive in the short-term.

The virus-driven theft of quantized energy forces cells to compete for nutrient energy-dependent RNA-mediated reprogramming in the context of the structure of photons, quantum entanglement, one-carbon metabolism, autophagy, and the physiology of reproduction, which links energy-dependent changes in chirality from base pairs to RNA-mediated amino acid substitutions. The amino acid substitutions stabilize the organized genomes of all living genera. Virus-driven energy theft links amino acid substitutions to the stability of viruses at the expense of the stability of organized genomes in all living genera.
The significance of Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton can be viewed in the context of prescient predictions made by young earth creationists and other serious scientists. Unfortunately, most of them failed to link energy-dependent RNA-mediated cell type differentiation to all biophysically constrained biodiversity via viral latency.

Pseudoscientists did not mention the likelihood that viruses cause the mutations, which all serious scientists have linked to all pathology. That may be the most recognizable difference between a pseudoscientist and a serious scientist.
See for information reported by serious scientists: Who rules the waves? – Viruses might just be bit players in the drama of the seas. Then again, they could be major actors (1996)

Most consider viruses to be a legion of cripples, sterilised by ultraviolet radiation and rendered impotent by hosts that are largely immune to their threat. But a few researchers take the opposite view. And if they turn out to be right, viruses could radically alter the balance of life in the oceans, ripping away huge parts of the food web that supports whales, sea birds and the fisheries on which many people rely.

See also: 1999 Did God Make Pathogenic Viruses? (1999)
See also: Where do viruses come from? (2004)

“…when virus-infected bacterial cells burst, their energy-rich cell contents spill into the water for other bacteria to scavenge. ‘Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,’ says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.”

See also: Viral Genome Junk Is Bunk (2015)

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

See for comparison from 2017:
Overthrowing the Hegemony of the Culture of Margulis?
Asgard archaea illuminate the origin of eukaryotic cellular complexity
Mitochondria are not captive bacteria

Carl Woese failed to place his ideas about the three domains of life into the context of how biophysically constrained viral latency links the anti-entropic virucidal energy of sunlight from the physiology of pheromone controlled reproduction to all biodiversity. Woese was wrong about everything. There is one domain of life. In all living genera, the pheromone-controlled physiology of reproduction is energy-dependent and RNA-directed DNA methylation links amino acid substitutions in supercoiled DNA to all biodiversity.

See for comparison this example of human idiocy, On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

Only neo-Darwinian theorists insist on playing word games to link what they refer to as “enigmatic spacer repertoires” to biodiversity outside the context of energy-dependent changes in the microRNA/messenger RNA balance that link electrons to ecosystems via hydrogen-atom transfer in DNA base pairs in solution.

“Human idiocy” was the term used by Feynman before Roger Penrose reminded us that all organisms must eat. See: “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?” (1991)

For comparison see: Fink et al., (2017) Cross-Cultural Investigation of Male Gait Perception in Relation to Physical Strength and Speed Fink also is a co-author of the award-winning review: Human pheromones: integrating neuroendocrinology and ethology (2001)
See for comparison: A BRIEF ESSAY ON HOW COMPARATIVE PSYCHOLOGY BECAME AN ENDANGERED SPECIES (link opens pdf)

Rather than continue to link food energy from the pheromone-controlled physiology of reproduction to all biodiversity in all living genera, Fink joined the pseudoscientists. He appears to be following the lead of people like Jay R. Feierman. As moderator of the International Society for Human Ethology’s Yahoo Group, Feierman has inadvertently eliminated all works of human ethologists from any further consideration, and he admits it.

See: 8/21/17 [HUMAN ETHOLOGY MODERATOR NOTE: I could write a similar essay on why human ethology is an endangered species but the causes would be different.  I’m old enough to have seen many academic disciplines disappear and new ones take their place. It is rather easy to put this process into a cultural evolution model. Academic disciplines are like species, most of the ones who have ever lived are now extinct. New species are born and old species die…. jrf]

On July 25, 2013, Feierman [jrf] wrote: 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.
Four years later, the concept of “new species are born and old species die” is divorced from the claims Jay R. Feierman made.
See for comparison: Linking mental health and the gut microbiome

The main idea of our review is that there is strong communication between the gastrointestinal tract and the brain, and that changes to the microbiome-gut-brain axis could be associated with the etiology of different neuropsychiatric disorders such as depression…

Food energy-dependent changes in the microbiome-gut-brain axis link nutrient stress and social stress from the de novo creation of microRNAs in plants to changes in the microRNA/messenger RNA balance of animals via links from food odors to pheromone-controlled ecological adaptations in species from microbes to humans.
See: Feedback loops link odor and pheromone signaling with reproduction
See for comparison: “I Am I and My Bacterial Circumstances”: Linking Gut Microbiome, Neurodevelopment, and Depression

A better perception of the significance of the MGB axis in the etiology of depression will help us to obtain a better understanding about the pathophysiology of this syndrome. Also, it opens the possibility to offer better treatment strategies to our patients. This will be possible only if we accomplish to decipher the genetic, anatomical, functional, and behavioral characteristics of the human microbiota. The most important limitation in the area of the MGB axis’ research lies in the fact that there is very little knowledge about the gut microbiome.

The claim that there is very little knowledge about the gut microbiome can be compared to what is known about the link from the virus-driven degradation of messenger RNA in soil bacteria to all pathology in all living genera. Everything known to serious scientists was detailed in the context of this report: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression The changes in the microRNAome included the link to the transgenerational epigenetic inheritance of all pathology in all living genera. The links from the transgenerational epigenetic inheritance of cancer and the transgenerational epigenetic inheritance of behavioral disorders were place into the context of links from quantum physics to quantum souls.
See: Quantum Souls and Welcome to the official YouTube Channel of Quantum Souls.
Video interview about the death of Robin Williams
Superbugs, Bacteriophages and Phage Therapy: An Interview with James Kohl
Food Energy-Dependent Cell Type Differentiation Refutes Theory of Evolution
How to Treat Cancer as a Disorder of Energy Transfer
Charles Darwin Taught Conditions of Life, Not Mutations
Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 1
Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 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!

Biology to a Physicist

Measuring energy vs human idiocy (social science)

Summary:
The “… universal applicability for determination of various targets such as metal ions, miRNAs, DNAs and proteins…” is the key to understanding the differences in the energy-dependent assembly of cell types with fixed amino acid substitutions that link natural selection for energy-dependent changes in base pairs from atoms to ecosystems in all living genera.

Richard Feynman complains about all the different units that are used to measure the single concept of Energy in this snippet  from one of his lectures in the series “The character of Physical Law.”

For an example of how the anti-entropic virucidal energy of sunlight can be measured and linked to the creation of microRNAs, see: Universal Ratiometric Photoelectrochemical Bioassay with Target-Nucleotide Transduction-Amplification and Electron-Transfer Tunneling Distance Regulation Strategies for Ultrasensitive Determination of microRNA in Cells

…using microRNA-141 (miRNA-141) as target model, the constructed biosensor demonstrated favorable accuracy and excellent sensitivity down to femtomolar level. Impressively, the proposed assay overcame the heavily dependence of target on photoactive materials in current ratiometric PEC assay, and demonstrated admirably universal applicability for determination of various targets such as metal ions, miRNAs, DNAs and proteins by merely two different photoactive materials

The “… universal applicability for determination of various targets such as metal ions, miRNAs, DNAs and proteins…” is the key to understanding the differences in the food energy-dependent assembly of cell types with fixed amino acid substitutions that link changes in base pairs from atoms to ecosystems in all living genera.
There is a model for that: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
See for comparison: A step-by-step microRNA guide to cancer development and metastasis

We propose that the balance between oncogenic versus tumor suppressive miRNAs acting within transcription factor-miRNA regulatory networks, influences both the multistage process of neoplastic transformation, whereby normal cells become cancerous, and their stress responses.

See for comparison: Feynman on social science
See also: Quantum common sense

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

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

Energy-dependent physical and biophysical constraints (9)

Summary: Energy determines genome compaction because activity in the nucleus is energy-dependent. Chromatin chains link energy-dependent changes in base pairs from single nucleotide polymorphisms to fixation of RNA-mediated amino acid substitutions in organized genomes via the physiology of pheromone-controlled reproduction. It’s all about the base.

Energy-dependent physical and biophysical constraints (8)

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells
Excerpt 1)

The chromatin structure of DNA determines genome compaction and activity in the nucleus.

My comment: Energy determines genome compaction because activity in the nucleus is energy-dependent.
Excerpt 2)

Chromatin chains have many different particle arrangements and bend at various lengths to achieve structural compaction and high packing densities.

My comment: Chromatin chains link energy-dependent changes in base pairs from single nucleotide polymorphisms to fixation of RNA-mediated amino acid substitutions in organized genomes via the physiology of pheromone-controlled reproduction.
Reported as: Scientists solve longstanding biological mystery of DNA organization

Besides potentially upending the textbook model of DNA organization, the team’s results suggest that controlling access to chromatin could be a useful approach to preventing, diagnosing and treating diseases such as cancer.

“We show that chromatin does not need to form discrete higher-order structures to fit in the nucleus,” adds O’Shea. “It’s the packing density that could change and limit the accessibility of chromatin, providing a local and global structural basis through which different combinations of DNA sequences, nucleosome variations and modifications could be integrated in the nucleus to exquisitely fine-tune the functional activity and accessibility of our genomes.”

The packing density of supercoiled DNA is energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera. Sunlight is the source of all biophysically constrained energy on Earth.The anti-entropic virucidal effect of sunlight biophysically constrains the degradation of messenger RNA.
Virus-driven energy theft causes negative supercoiling of supercoiled DNA. Without food energy-dependent RNA-mediated DNA repair (autophagy), viruses cause the degradation of messenger RNA that links mutations to all pathology. The sun’s anti-entropic virucidal energy links changes in chirality to autophagy and the de novo creation of enzymes, hormones and receptors that are needed to protect all organized genomes from viruses.
The textbook model of DNA organization was represented in Mutation-driven evolution for comparison to “Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which was published on the same day more than 4 years ago.
Masatoshi Nei used an ambiguous definition of mutation and linked any energy-dependent nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc, (any change in the structure of supercoiled DNA) from natural selection to an evolutionary process initiated by mutation.
In my review, I used examples of food energy-dependent changes in base pairs to link the honeybee model of nutrient-dependent pheromone-controlled biodiversity to a history of published works that began with The Scent of Eros: Mysteries of Odor in Human Sexuality (reviewed by Mark Sergeant)
The index from The Scent of Eros: Mysteries of Odor in Human Sexuality may help others to establish all the known links from the energy-dependent de novo creation of microRNAs to the creation of G protein-coupled receptors and gonadotropin releasing hormone (GnRH) secretion, which was linked to all biodiversity. See, for example, these entries from page 217:

See also: Cytosis: A Cell Biology Board Game

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

See also: Energy-dependent physical and biophysical constraints (10) in prep

Amino acid modification FA_Epigenetics_Table1

Francis S. Collins refutes theistic evolution

Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. — Andrew Jones, BA

Editor’s note

The 2013 review article by James Vaughn Kohl published in Socioaffective Neuroscience & Psychology and criticized in the above Letter to the Editor was subjected to standard peer review and the revised version was accepted by me after it had been accepted by both reviewers.

See for comparison: The Language of God: A Scientist Presents Evidence for Belief, by Francis S. Collins. The current director of the NIH also is a co-author of Genetic regulatory signatures underlying islet gene expression and type 2 diabetes

…T2D risk alleles that overlap with RFX footprints uniformly disrupt the RFX motifs at high-information content positions. Together, these results suggest that common regulatory variations have shaped islet TF footprints and the transcriptome and that a confluent RFX regulatory grammar plays a significant role in the genetic component of T2D predisposition.

No experimental evidence of biologically-based cause and effect suggest that any common regulatory variations has ever evolved. Let me make that fact perfectly clear in the words of the co-authors:

“Individuals who are heterozygous for a frameshift mutation in RFX6 have increased 2-h glucose levels (33). Importantly, rare autosomal recessive mutations that alter DNA-contacting amino acids in the DNA binding domain of RFX6 result in Mitchell–Riley syndrome, which is characterized by neonatal diabetes (29).

The frameshift mutation and rare autosomal recessive mutations occur outside the context of energy-dependent endogenous RNA interference (RNAi). For comparison RNA-directed DNA methylation (aka endogenous RNAi) typically links DNA-contacting amino acids to healthy longevity via the transgenerational epigenetic inheritance of morphological and behavioral phentoypes in species from microbes to humans. It is difficult to describe all the links, but it is clear that RNAi links RNA-directed DNA methylation from energy-dependent changes in chirallity to base pairs, single nucleotide polymorphisms (SNPs) and autophagy via the innate immune system.
Without any mention of how virus-driven energy theft links mutations from SNPs to pathology, Francis S. Collins and his co-authors link the rare autosomal recessive mutations to altered DNA-contacting amino acids. Apparently, they do not want to mention anything about the fact that natural selection for energy-dependent codon optimality is the link from RNA-mediated protein folding chemistry to all biophysically constrained healthy longevity. Instead, they seem willing to ignore the facts about energy-dependent fixation of RNA-mediated amino acid substitutions in cell types.
Indeed, they seem to put everything known to serious scientists into the context of the theistic evolution of pathology. Serious scientists know that nutrient energy-dependent pheromone-controlled cell type differentiation is the link from atoms to ecosystems in models of ecological adaptation.
Clearly, anyone who does not want to expose the pseudoscientific nonsense touted by neo-Darwinian theorists and theistic evolutionists should not mention “amino acid” and “mutation” in the same context. Using only the definitions of both terms in the same sentence (above) alerts all serious scientists to the fact that nutrient energy-dependent amino acid substitutions are not the same as mutations, which are caused by virus-driven energy theft.
Reported as: Diabetes in your DNA? Scientists zero in on the genetic signature of risk

…for now, it’s the first demonstration that many Type 2 diabetes-linked DNA changes have to do with the same DNA-reading molecule. Called Regulatory Factor X, or RFX, it’s a master regulator for a number of genes.

The regulation of genes is energy dependent.

“RFX is probably unable to read the misspelled words, and this disruption of regulatory grammar plays a significant role in the genetic risk of Type 2 diabetes.”

The concept of “misspelled words” is appropriate for use only in the context of pseudoscientific nonsense that fails to address facts about natural selection for energy-dependent codon optimality. Codon optimality links the speed of light on contact with water to biophysically constrained RNA-medidated cell type differentiation in all living genera.

They characterized differences not just in DNA sequences, but also in the way DNA was packaged and modified by epigenetic factors, and the levels of gene expression products that indicated how often the genes had been read and transcribed.

Epigenetically-effected reading and transcription is energy dependent and biophysically constrained via the speed of light and hydrogen-atom transfer in DNA base pairs in solution such as seawater and blood. Serious scientists noticed that pattern and linked virus-driven energy theft from pathology in bacteria to archaea and from the transgenerational epigenetic inheritance of Zika-virus damaged DNA in human infants. The craniofacial morphology and brain development of infected human infants clearly links energy-dependent fixation of amino acids to the morphological and behavioral phenotypes of all living genera.
See: Nothing in Biology Makes Any Sense Except in the Light of Evolution

E. Margoliash, W. M. Fitch, and others have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.

Facts about nutrient energy-dependent codon optimality also are known to be refutations of neo-Darwinian pseudoscientific nonsense because codon optimality links Darwin’s “conditions of life” to the physiology of reproduction in all living genera.
See: Codon optimality controls differential mRNA translation during amino acid starvation and Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See for comparison: Epigenetic Editing of Ascl1 Gene in Neural Stem Cells by Optogenetics

Each DNA change might alter this binding in a different way, leading to a slightly different effect on Type 2 diabetes risk or blood sugar regulation. But the common factor for many of these changes was its effect on the area where RFX is predicted to bind, in the cells of pancreatic islets.

So, says Parker, this shows how the genome – the actual sequence of DNA—can influence the epigenome, or the factors that influence gene expression.

The sequence of DNA cannot influence the epigenome before the energy-dependent sequence has been created via natural selection for codon optimality. That is why epigenetically-effected nutrient-dependent pheromone-controlled energy-dependent changes in supercoiled DNA were linked from the weekend resurrection of the bacterial flagellum in Pseudomonas fluorescens to all biodiversity in all living genera via the conserved molecular mechanisms that link light energy-induced changes in microRNAs to all biodiversity.
See also: Optokinetically encoded nanoprobe-based multiplexing strategy for microRNA profiling
Programmable artificial phototactic microswimmer

For active drug delivery, the nanomotor should be able to orient towards specific chemical signals, such as those demonstrated in chemotaxis21–25 and pH taxis26.

See also: pH-Taxis of Biohybrid Microsystems

…assuming that it is possible to tune the preferred pH of bioactuators by genetic engineering, these biohybrid microsystems could potentially be applied to sense the pH gradient induced by cancerous cells in stagnant fluids inside human body and realize targeted drug delivery.

If naturally occurring chemotaxis could not readily be linked from pH-taxis and phototaxis to natural selection for codon optimaility and supercoiled DNA, light energy as information could not be linked to communication between the microscopic and the macroscopic world.
Light Could Propel Nanorobots on a “Fantastic Voyage” Through the Human Body

“Light is a more effective option to communicate between the microscopic world and the macroscopic world,” said Tang.

The fact that the energy-dependent virucidal effects of sunlight have been linked to the weekend resurrection of the bacterial flagellum in an organism that fluoresces on exposure to UV light was placed into the context of claims about two amino acid substitutions that were reported as if they were mutations.
Summary: Francis S. Collins, current NIH director, is a theistic evolutionist. He should not use his position to tout the pseudoscientific nonsense of evolution. He is supposed to link experimental evidence of biologically-based facts to healthy longevity or to pathology.
See also: United states health care reform: Progress to date and next steps

All of the individuals who assisted with the preparation of the manuscript are employed by the Executive Office of the President.

Former President Barrack Obama should not have used his position or his employees to mislead the voters in the United States of America. He correctly stated that “…partisanship and special interest opposition remain…,” which ensured that “…experience with the Affordable Care Act…” would demonstrate “…that positive change is achievable on some of the nation’s most complex challenges.” That claim was placed into the context of misrepresentations made by ~50% of people who are biologically uninformed theorists and/or those who are atheists. Clearly there is overlap among those groups of people. Hopefully, others will see why. They’ve been taught to believe in theistic evolution or nothing.
Experimental evidence of biologically-based cause and effect refutes theistic evolution by linking virus-driven energy theft to all pathology in all living genera. In the context of  Genetic regulatory signatures underlying islet gene expression and type 2 diabetes, Francis S. Collins revealed either his ignorance or his treachery.
The article links the nutrient energy-dependent pheromone-controlled physiology of reproduction to the weekend resurrection of the bacterial flagellum in P. fluorescens via RNA synthesis, not mutations.
Virus-driven energy theft influences energy-dependent RNA-mediated gene expression, and the energy theft is clearly linked to mutations. See for example: 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.

See also: microRNA “Regulatory Factor X” 
 

fruit-dove

Tasting light links energy from creation to adaptation

Biology to a Physicist
The C. elegans Taste Receptor Homolog LITE-1 Is a Photoreceptor

“In Brief: A taste receptor homolog absorbs UV light and mediates avoidance behavior in C. elegans in response to light exposure.”

Excerpt: Light sensation is critical for all phyla of life, ranging from bacteria to humans (Wang and Montell, 2007; Yau and Hardie, 2009). Organisms have evolved various types of photoreceptor proteins…

Photoreceptors are G protein-coupled receptors (GPCRs). No experimental evidence of biologically-based cause and effect links the evolution of any type of photoreceptor to any other type of G protein-coupled receptor (GPCR). Nothing except energy-dependent hydrogen-atom transfer in DNA base pairs in solutions like sea water and blood links the de novo creation of olfactory receptor genes, which are GPCRs, to all biodiversity via the physiology of reproduction and supercoiled DNA in all living genera.
The facts about supercoiled DNA link energy-dependent RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of all living genera via the claim that “…a taste receptor homolog absorbs UV light and mediates avoidance behavior in C. elegans in response to light exposure.”
That claim can be readily linked to the energy-dependent experience-dependent nutrient-dependent RNA-mediated de novo creation of all GPCRs and experience-dependent behavior that links chemotaxis from the de novo creation of olfactory receptor genes to phototaxis via the nutrient energy-dependent de novo creation of photoreceptors and/or all other receptors.
Reported as: Tasting light: New type of photoreceptor is 50 times more efficient than the human eye

1) …within the protein, having the amino acid tryptophan in two places was critical to its function.

2) Breaking it apart, or “denaturing” it, completely stops its ability to absorb light, rather than just diminishing it — showing that it really is a different model, Xu said.

The two nutrient energy-dependent RNA-mediated amino acid substitutions link UV light from DNA repair to all biophysically constrained pheromone-controlled biodiversity via the innate immune system and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. The claim that the are using a different model to do that should be placed into the context of the only model that links angstroms to ecosystems in all living genera to all nutrient energy-dependent RNA-mediated amino acid substitutions and pheromone-controlled biodiversity.
Also reported as: Powerful New Photoreceptor Found in Roundworms

Because the “genetic code” of these photoreceptor proteins are so much different than that of other photoreceptors found in the animal kingdom, there is a ton of untapped potential in this discovery.

There is only one genetic code. It links the epigenetic landscape to the physical landscape of supercoiled DNA via energy-dependent changes in base pairs, which link natural selection for codon optimality to the physiology of reproduction by protecting the organized genomes of all living genera from virus-driven energy theft.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Conclusion:

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

See also: Meaning = Information + Evolution

Notions like meaning, signal, intentionality, are difficult to relate to a physical word. I study a purely physical definition of “meaningful information”, from which these notions can be derived. It is inspired by a model recently illustrated by Kolchinsky and Wolpert, and improves on Dretske classic work on the relation between knowledge and information. I discuss what makes a physical process into a “signal”.

Energy as information becomes a signal via its effect on hydrogen-atom transfer in DNA base pairs in solution. The information links the anti-entropic virucidal energy of sunlight to all biophysically constrained cell type differentiation in all living genera via the innate immune system, which links the physiology of reproduction to supercoiled DNA.
For more experimental evidence of this established link to biologically-based cause and effect, which was not presented in the context of my model from 2013, see:
Dynamic control of chirality and self-assembly of double-stranded helicates with light
Physicochemical mechanism of light-driven DNA repair by (6-4) photolyases

Clearly, if one photon provides just enough energy to perform repair, two photons are even better. However,
these are speculations…

UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair
Control of pH responsive peptide self-association during endocytosis is required for effective gene transfer
Analysis of Viral and Cellular MicroRNAs in EBV-Infected Cells
A Framework for integrating multiple biological networks to predict microRNA-disease associations
Without a framework that links energy-dependent changes from angstroms to ecosystems in all living genera via their physiology of reproduction and fixation of RNA-mediated amino acid substitutions in supercoiled DNA, which protects organisms from virus-driven energy theft and genomic entropy, all that’s left is the pseudoscientific nonsense of neo-Darwinian theories.
For comparison, with a framework that links the sun’s anti-entropic virucidal energy to cell type differentiation in all genera, it is likely that the cure for all pathology is within sight. For example all pathology appears to be is epigenetically controlled at the level of quantized energy.
See also: Melanocytic Nevi and the Genetic and Epigenetic Control of Oncogene-Induced Senescence
Melanocytic nevi represent benign clonal proliferations of the melanocytes in the skin that usually remain stable in size and behavior or disappear during life. Infrequently, melanocytic nevi undergo malignant transformation to melanoma. Understanding molecular and cellular mechanisms underlying oncogene-induced senescence should help identify pathways underlying melanoma development, leading to the development of new strategies for melanoma prevention and early detection.
See also: microRNA
More than 55,000 published works link energy-dependent changes in the microRNA/messenger RNA balance to the framework that links amino acid substitutions to cell type differentiation and healthy longevity compared to virus-driven energy theft, which has been linked to all pathology by amino acid substitutions that stabilize viruses.
Here is some background on the concept of sunlight as energy that links information to all biodiversity via natural selection for energy-dependent RNA-mediated codon optimaility.
Light Absorption, Reflection, and Transmission

If a light wave of a given frequency strikes a material with electrons having the same vibrational frequencies, then those electrons will absorb the energy of the light wave and transform it into vibrational motion. During its vibration, the electrons interact with neighboring atoms in such a manner as to convert its vibrational energy into thermal energy. Subsequently, the light wave with that given frequency is absorbed by the object, never again to be released in the form of light. So the selective absorption of light by a particular material occurs because the selected frequency of the light wave matches the frequency at which electrons in the atoms of that material vibrate. Since different atoms and molecules have different natural frequencies of vibration, they will selectively absorb different frequencies of visible light.

The absorption of ultraviolet light links the anti-entropic virucidal energy of the sun to all biophysically constrained biodiversity.

What is life when it is not protected from virus driven entropy

The anti-entropic force of virucidal ultraviolet light (UV) links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

See also: Royal Society: The Public Evolution Summit  Page 12
Witzany is organizing a conference symposium for July 2018 “Evolution-genetic innovations without error replication”
The title may change to “You are what you eat.” He has already linked energy and information-dependent changes from physics to chemistry and all the biodiversity of life.
See also: Life is physics and chemistry and communication

Manfred Eigen extended Erwin Schroedinger’s concept of “life is physics and chemistry” through the introduction of information theory and cybernetic systems theory into “life is physics and chemistry and information.” Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language. However, the basics of scientific knowledge changed dramatically within the second half of the 20th century. Unfortunately, Eigen ignored the results of the philosophy of science discourse on essential features of natural languages and codes: a natural language or code emerges from populations of living agents that communicate. This contribution will look at some of the highlights of this historical development and the results relevant for biological theories about life.

Biological facts about life link energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of reproduction and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. Why hasn’t everyone already accepted the facts that Schrodinger helped to detail in What is Life?

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)

See also from the forward to the reprint edition:

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

Eliminating energy-dependent creation and Darwin’s “conditions of life” was probably not de Vries intention when he defined the term mutation in 1902. But, neo-Darwinian theorists took his claims about sudden energy jumps and assumed the jumps could explain what would happen if accumulated random mutations had somehow caused one species to evolve into another.
In that view of evolution, millions of years are required to link the sudden energy jumps to all morphological and behavioral diversity. Serious scientists have since learned that all energy-dependent changes in organized genomes link what organisms eat to their physiology of reproduction. That is how biodiversity is biophysically constrained by the availability of food and how food odors and pheromones are linked to the physiology of reproduction by feedback loops.
See: Feedback loops link odor and pheromone signaling with reproduction
Neo-Darwinian theorists eliminated energy and the nutrient energy-dependent feedback loops that link odors and pheromones to biophysically constrained biologically based cause and effect.
See for comparison: Scientists Seek to Update Evolution and Genetic and mechanistic diversity of piRNA 3′-end formation.
The news article by Carl Zimmer and the journal article ignore all accumulated experimental evidence of biologically-based energy-dependent top-down causation. The authors of the journal article invent the term “egoistic genes” as if no one had refuted the pseudoscientific nonsense of Richard Dawkins’ “The Selfish Gene.”
Pseudoscientists seem to think that serious scientists must prove their pseudoscientific nonsense is nonsense. Serious scientists do not try to do that because they are not taught to believe in theories. Serious scientists are taught to find experimental evidence of biologically-based cause and effect that supports their claims.

See for an example of the energy-dependent de novo creation of G protein-coupled receptors: Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo

See for comparison: Mutation-Driven Evolution

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements” (p. 199).

See also: 30 Reasons to Never Put Another M&M in Your Mouth Ever Again
See also: The Sea Slug That Eats The Sun
See also: Sci-hub  Our mission is to remove any barrier which impeding the widest possible distribution of knowledge in human society!
See also: Purkinje effect: Physiology:
The effect occurs because the color-sensitive cones in the retina are most sensitive to green light, whereas the rods, which are more light-sensitive (and thus more important in low light) but which do not distinguish colors, respond best to green-blue light.[4] This is why humans become virtually color-blind under low levels of illumination, for instance moonlight.
The effect links the sun’s anti-enrtopic virucidal biological energy to all biophysically constrained cell type differentiation via the physiology of reproduction in all living genera.
Light and Color – Detailed Help

Jack is wearing a red shirt. The shirt is illuminated with white light. Jill views Jack’s shirt while looking through a magenta filter. To Jill, Jack’s shirt will appear ____.

If you look at a red shirt through a red filter, you will most likely claim that the shirt is white. If you eliminate the sun’s biological energy from your claims about evolution, you will eliminate everything known to serious scientists about the energy-dependent creation of all biodiversity.
The fact that light and color are clearly linked to the morphological and behavioral phenotypes of the fruit dove, pictured above, is hard to dismiss, no matter how biologically uninformed others are.

Alternative splicing of pre-mRNA

Energy-dependent coulombic, autophagic, polycombic healthy longevity

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

Disorders in energy creation by mitochondria can cause cellular degeneration…

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

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

Conclusion:

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

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

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

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

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

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

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

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

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

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

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

See for comparison: Turning back the aging clock

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

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

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