Alternative splicing of pre-mRNA

Energy-dependent oscillating gene networks organize life

Nascent, innate, intrinsic, and biofunctional are among the “weasel words” used by theorists who ignore the fact that all life-sustaining energy comes from the sun via hydrogen-atom transfer in DNA base pairs in solution. See how Jon Lieff continues to misrepresent that fact, by placing everything known about RNA-mediated cell type differentiation back into the context of evolution.

Like all pseudoscientists, he starts with energy but fails to mention where the energy came from or where it goes when virus-driven energy theft is linked from mutations and genomic entropy to all pathology via base pair changes and RNA-mediated amino acid substitutions in viruses that stabilize genes in the viruses at the expense of genomic stability in all living genera.

Individual Cell Clocks and Immunity

Energy from the sun is transformed into energy and material for the cell to use in sync to these rhythms. The rhythms also are related to how the cell develops in particular organs and responses to damage and distress. It is not yet clear how these individual unique 24 hour clocks in each cell translates to the rhythms of the entire animal. In evolution, the development of these clocks appears to be vital to provide the needed resources for DNA repair at the proper time of day.

My comment to Jon Lieff’s blog site: Thank you for helping to deliver Schrodinger’s, Turing’s, and Witzany’s message about the anti-entropic virucidal effects of sunlight on alternative RNA splicings, which serious scientists know link autophagy to all biodiversity via RNA-mediated amino acid substitutions.
Please stop placing top-down causation into the context of evolution since no experimental evidence suggests that energy-dependent effects occur outside the context of the de novo creation of G protein-coupled receptors and the physiology of reproduction in species from microbes to humans.
Also, Suzan Mazur acknowledged me and my domain, RNA-mediated.com as sources of information on biologically-based cause and effect for comparison to pseudoscientific nonsense about evolution in: Royal Society: The Public Evolution Summit

It would be great if you would also acknowledge my works as your source of information or acknowledge others whose life’s works are presented in your blog posts.

Thank you for your acknowledgement more than 3 years ago in:

Alternative RNA Splicing in Evolution

My comment:

In our 1996 Hormones and Behavior review, we wrote:”Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans.”

From Fertilization to Adult Sexual Behavior

The alternative splicings are nutrient-dependent and appear to be enabled by the experience-dependent de novo creation of olfactory receptor genes, which enable additional receptor-mediated nutrient uptake and the metabolism of nutrients to species-specific blends of pheromones that control reproduction in species from microbes to man.

Your focus on the importance of pre-mRNA and alternative splicing is exemplary, especially in the context of neuronal plasticity.

C. elegans is the model organism of neurogenic niche construction that links nutrient-dependent ecological and pheromone-controlled social niche construction to socio-cognitive niche construction in vertebrates and invertebrates. See for review:

Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors

What you are helping to detail is self-assembly with evidence of olfactory/pheromonal self-organization that is currently missing from evolutionary theory, which attributes speciation to mutation-initiated natural selection even though there is no experimental evidence for that (as I mentioned elsewhere).

On 10/27/13 Jon Lieff wrote:

I very much appreciate your comments on pheromone communication and its rapid and critical link to the olfactory brain. I look forward to any current references and future work to help understand the immune brain connection as well as communication in general.

Thanks

Jon Lieff

See for comparison: What is life when it is not protected from virus driven entropy

See the citation to: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

The full text is free. Compare the claims to Jon Lieff’s claim:

In evolution, the development of these clocks appears to be vital to provide the needed resources for DNA repair at the proper time of day.

See also Peter Berean’s claims about bio-functional information and his claims that energy is not information in the context of his denigrations of my life’s works.

See also: Guardians of the Blood Brain Barrier by Jon Lieff

Just curious where most of your information comes from? I’m a graduate student and would love the primary sources for reference!

See also: Scientists say your “mind” isn’t confined to your brain, or even your body

In math, complex systems are self-organizing, and Siegel believes this idea is the foundation to mental health. Again borrowing from the mathematics, optimal self-organization is: flexible, adaptive, coherent, energized, and stable. This means that without optimal self-organization, you arrive at either chaos or rigidity—a notion that, Siegel says, fits the range of symptoms of mental health disorders.

In biology, the idea that mathematical models are relevant to the required links from ecological variation to energy-dependent ecological adaptation is considered in the context of a joke, or parodies.
See for comparison: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
My comment: Val158Met is an amino acid substitution. Its function is known to be affected by a functional single nucleotide polymorphism (SNP) in COMT (G-to-A base-pair substitution) leading to a methionine (Met) valine (Val) substitution at codons 108/158 (COMT Val158Met). Carriers of the Met allele have been found to display a fourfold decrease in enzymatic activity compared to Val allele carriers going along with an increase of prefrontal DA activity (Lachman et al. 1996; Lotta et al. 1995).

Alternative splicing of pre-mRNA

Re-inventing mutation-driven evolution (2)

… we suspected that splicing efficiency, as defined by the fraction of pre-mRNA converted into mature mRNA, must have contributed to temperature-dependent Cirbp mRNA accumulation

Splicing efficiency is energy-dependent in the context of temperature-dependent oscillations that link the sun’s anti-entropic virucidal energy to all biodiversity via Turing’s claims and my model.

In 1951, the brilliant British scientist Alan Turing published a paper proposing a theory in chemistry called morphogenesis, which explains how cells are grouped together within an organism.

According to Turing, oscillating chemical reactions predictable by mathematical formula are partially responsible for organizing cells to form organs, bone, and tissue.

Could Turing’s claim be linked to Peter Berean‘s claims about differences between “bio-functional information” and energy as information?

See also: Cellular Clocks and Metabolism

..each tissue and organ appears to have unique 24 hour cycles related to the specific functions of the organ and the unique metabolic functions. Also, cycles of available material and cellular activity appears to ubiquitous.

The cellular clock mechanisms are nutrient energy-dependent and linked RNA-mediated amino acid substitutions in supercoiled DNA to the differentiation of all tissues in all organs in all living genera via biophysically constrained protein-folding chemistry in the context of the physiology of reproduction.

See also: Monoplacophoran mitochondrial genomes: convergent gene arrangements and little phylogenetic signal

Although we could not shed light on deep evolutionary traits of Mollusca we found unique patterns of gene arrangements that are common to monoplacophoran and chitonine polyplacophoran species but not to acanthochitonine Polyplacophora.

There are no deep evolutionary traits because all traits are energy-dependent. All traits must link RNA-mediated autophagy from the innate immune system to supercoiled DNA in the context of the physiology of reproduction. That fact links everything known to serious scientists about nutritional epigenetics from autophagy to the biophysically constrained protein folding chemistry of all genera.

For example, nutrient energy-dependent supercoiled DNA protects all organized genomes from virus-driven energy theft and genomic entropy. Phylogenetic trees may be established by patterns of viral latency.

Viral latency recapitulates the past effects of virus-driven energy theft on gene activation via what is known about energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution that link angstroms to ecosystems in all living genera. Nutrient energy-dependent gene activation links the mitochondria to effects that viruses had on hydrogen-atom transfer before the anti-entropic virucidal effects of ultraviolet light linked ecological variation to ecological adaptation of organized genomes in species from bacteria to archaea.

Placing bacteria and archaea into different domains of life was a mistake made by Carl Woese who did not link the nutrient energy-dependent physiology of reproduction from autophagy to supercoiled DNA because he failed to consider the role of virus-driven energy theft in all pathology. That pathology is exhibited in the number of viruses in archaea compared to the number of viruses in ecologically adapted bacteria  and in ecologically adapted humans.

See also: Stanford manufactures gene-engineered cells to cure the incurable

1) To fix this, Stanford researchers use a virus to deliver a correct version of the gene onto batches of skin cells, then coax them to form sheets of healthy skin.

2) Cells are nurtured in a broth of sugars, carbohydrates, fats, growth factors and hormones, warmed at body temperature: 98.6 degrees Fahrenheit.

The virus links the natural information processing of all cell types from the innate immune system to autophagy and the nurturing helps to ensure that the pluripotent state leads to energy-dependent biophysically constrained protein folding chemistry that typically links the pheromone-controlled physiology of reproduction to all biodiversity via RNA-mediated amino acid substitutions and supercoiled DNA, which protects all organized genome from virus-driven entropy.
See also: Perspectives on the history of evo-devo and the contemporary research landscape in the genomics era

In addition, over the past 15 years, a myriad of non-coding, but functional RNAs have been discovered, including microRNAs and long non-coding RNAs that can regulate transcription [42] but more commonly translation [43] of protein coding genes. Mutations affecting non-coding genes can thus lead to changes in the repertoire of proteins that determines cell behaviour in developmental programmes, resulting in phenotypic evolution. Long non-coding RNAs have been associated with development and evolution but they are less well studied than shorter microRNAs and small RNAs [44].

During the past 15 years nutrient energy-dependent changes in the microRNA/messenger RNA balance have been linked from RNA-mediated protein folding chemistry to all biophysically constrained biodiversity via autophagy and supercoiled DNA in the context of the physiology of reproduction. There are now more than 56,000 published works that link energy as information from changes in hydrogen-atom transfer in DNA base pairs in solution to all extant biodiversity via the physiology of reproduction.
See: microRNA (56,324 citations)
See also: Long noncoding RNAs in the p53 network

p53 regulates the expression of a repertoire of lncRNAs, and some of these lncRNAs are critical regulators of cell cycle arrest, DNA damage repair, chromosomal stability and apoptosis, altogether contributing to tumor-suppressor function of p53. LncRNAs are dysregulated in a variety of cancers and therefore can be utilized as biomarkers for disease progression and as therapeutic targets.98

Energy-dependent changes in the microRNA/messenger RNA balance are linked from every aspect of biophysically constrained protein folding chemistry to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans. The sun’s anti-entropic virucidal energy has been linked to DNA damage repair, chromosomal rearrangements and chromosomal stability. Rather than continue to ignore the facts about energy-dependent healthy longevity for comparison to virus-driven energy theft and all pathology, some people may still be interested in seeing this:
What is life when it is not protected from virus driven entropy

The anti-entropic force of virucidal ultraviolet light 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.

 

Alternative splicing of pre-mRNA

Energy-dependent de novo creation and neurogenesis (2)

See also: Energy-dependent de novo creation and neurogenesis
12/7/16 Atlas of the RNA universe takes shape
Excerpt:

MicroRNA are very mysterious. They are really relics of the RNA world—pieces of RNA that are highly reactive, very small and which pair and bind other RNA and facilitate catalytic reactions,” Mangone says. “We don’t know much about them—where they come from or how they regulate gene expression, but they are very misregulated in many diseases.

See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model Published 14 Jun 2013
Excerpt:

…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.

My comment: Only if you lived among wolves or among theorists for the past 10 years would you not know that more than 55,000 indexed publications link energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity. For comparison, all serious scientists also know that virus-driven energy theft links viral microRNAs from mutations to all pathology.
You need only search for “RNA mediated” to find information on how cellular and viral microRNAs are linked from energy-dependent changes to RNA-mediated amino acid substitutions and biophysically constrained protein folding chemistry. For example, this is all it takes to recognize the amount of pseudoscience that is packaged in claims that we don’t know much about microRNAs.
See also: Published to Figshare 10 April 2014

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.

See also: MicroRNAs: the future of genomic science?
Excerpt:

The ubiquity of miRNA occurrence is reflected in the current literature, which reports a wide range of potential biomarker applications for this highly conserved molecule.

My comment: MicroRNAs are biomarkers that clearly link energy-dependent biophysically constrained changes in base pairs from RNA-mediated amino acid substitutions to cell type differentiation in all living genera. The energy-dependent links from the innate immune system to the physiology of reproduction also link all metabolic networks to all genetic networks in species from microbes to humans.
See for comparison: A single splice site mutation in human-specific ARHGAP11B causes basal progenitor amplification

…we hypothesize that the novel, human-specific C-terminal sequence of modern ARHGAP11B has a key role in the mechanism by which this protein promotes BP amplification. In this regard, the present data show that this sequence is due to a single C→G base substitution, which creates a novel splice donor site that results in the replacement of the ancestral C-terminal sequence of the ARHGAP11B GAP domain. The present data also demonstrate that this single C→G base substitution underlies the ARHGAP11B-mediated BP amplification implicated in neocortex expansion.

Reported as: Small Mutation Contributed to Evolution of Bigger Human Brains
Excerpt:

A single base change in a human gene likely played an important role in evolutionary expansion of the human brain, researchers say.

My comment: They claim that a single cytosine to guanine substitution created a novel splice site. They failed to mention that base pair (BP) amplification is nutrient energy-dependent. They also failed to mention that the de novo creation of a novel splice donor site must be linked from the energy-dependent fixation of an RNA-mediated amino acid substitution to the physical landscape of supercoiled DNA via the physiology of reproduction.

Svante Paabo is one of the co-authors who reported this:

Hence, it is not the ARHGAP11 partial gene duplication event ~5 million years ago, as such, that impacted human neocortex evolution. Presumably, ARHGAP11A and ancestral ARHGAP11B coexisted as functionally similar proteins for some time after the gene duplication event. The ability of ARHGAP11B to amplify BPs likely arose more recently from a change that is tiny on a genomic scale but substantial in its functional and evolutionary consequences.

My comment: No experimental evidence of biologically-based cause and effect suggests that any partial gene duplication event ~5 million years ago could have linked a mutation and the altered de novo creation of genes that Svante Paabo (and co-authors) placed into the context  of biophysically constrained biodiversity in:

Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees

My comment: Natural selection for energy-dependent codon optimality is the only way to link the de novo creation of genes from autophagy to RNA-mediated amino acid substitutions and nutrient-dependent polycombic ecological adaptation.
See: From Fertilization to Adult Sexual Behavior

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

See also: PTBP1 and PTBP2 Serve Both Specific and Redundant Functions in Neuronal Pre-mRNA Splicing
Excerpt:

…the two paralogs displayed similar RNA binding across the transcriptome, indicating that their differential targeting does not derive from their RNA interactions, but from possible different cofactor interactions.

My comment: The cofactors are nutrient energy-dependent microRNAs, which are linked to healthy longevity and all biodiversity and viral microRNAs, which are linked from mutations to all pathology.
See also: Viral and cellular messenger RNA targets of viral microRNAs

…viral miRNAs may be particularly important for regulating the transition from latent to lytic replication and for attenuating potentially inhibitory host antiviral immune responses.

See also: Nothing in Biology Makes Any Sense Except in the Light of Evolution
Excerpt:

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).”

See also: Light- and Carbon-Signaling Pathways. Modeling Circuits of Interactions

…carbon either attenuated or potentiated light repression of ASN1 in light-grown plants. These studies indicate the interaction of carbon with blue, red, and far-red-light signaling and set the stage for further investigation into modeling this complex web of interacting pathways using systems biology approaches.

My comment: When did theorists decide to take the light as information and energy out of systems biology and ecological adaptations? Who decided to replace the anti-entropic virucidal energy of light with mutations and evolution?

Alternative splicing of pre-mRNA

Politicized science: The demise of RNA-mediated.com?

A post-Presidential election change indicates that politicized science in the USA may be the cause of the steady decline in the number of pages read on this domain. The decline is paired with an increased bounce rate each time I post anything that pits the science of creation against the pseudoscientific nonsense of neo-Darwinian theories.
If this domain were used in the context of a social science experiment, the statistics would show that ridiculous theories have left the USA relatively defenseless against the threat of gene-editing technology. That technology has has been advanced in countries where students are not taught to believe in mutation-driven evolution.
See: Combating evolution: Battlefield medicine vs politicized science (December 4, 2016)
Each example of energy-dependent de novo creation is met with an increase number of bounces and decreased number of pages read. See:

RNA-mediated.com metrics

Founded February 2015: 43937 page views since inception until November 15, 2016
Last 90 days till Jun 7, 2016 4977 page views 14.62% bounce rate 3.1 pages per session
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See for comparison: Complex Cellular Conversations about Food Allergies

Previous posts have emphasized that complex cellular conversations determine physiology. This is certainly the case with food allergies. The fact that we don’t have many more allergies with so many new chemicals in food, demonstrates how T cells are trained to avoid food allergies.

The mechanisms are now found to be varied and very complex. This constant communication between gut cells, microbes, T cells, dendritic cells, macrophages, and many other cells are what produce tolerance to food and lack of food allergies.

Jon Lieff is on the verge of refuting neo-Darwinian theories with accurate representations of how the innate immune system links energy-dependent autophagy from natural selection for codon optimaility to ecological adaptations via the physiology of nutrient-dependent pheromone-controlled reproduction in species from microbes to humans.
Watch as he continues to put everything known about energy-dependent changes in angstroms to ecosystems into his representations of the complexity, which others have thoroughly detailed during the past decade.
See for comparison:

What is Life? (first published in 1944) from 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

Sometime soon, Jon Lieff may link nutrient-energy to the de novo creation of G protein-coupled receptors (GPCRs_ and try to put chemotaxis and phototaxis back into the context of alternative splicings of pre-mRNA and ridiculous theories about evolution.
If so, he will make it perfectly clear that all others failed to include any creationist perspectives or information on virus-driven energy theft and the loss of GPCRs.
The loss of GPCRs links virus-driven energy theft to all pathology except that which is biophysically constrained by the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to humans.
See: A Framework for integrating multiple biological networks to predict microRNA-disease associations
Has anyone ever successfully taught a theorist the difference between an algorithm and experimental evidence of energy-dependent biologically-based cause and effect? For example, the experimental evidence shows that Carl Woese was wrong.
The experimental evidence of virus-driven energy theft links Virus-mediated archaeal hecatomb in the deep seafloor to the Analysis of Viral and Cellular MicroRNAs in EBV-Infected Cells via everything known to creationists about the anti-entropic energy of virucidal ultraviolet light.
See: Viral Genome Junk Is Bunk

…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 also:  Who rules the waves? – Viruses might just be bit players in the drama of the seas. Then again, they could be major actors
 

Alternative splicing of pre-mRNA

Energy-dependent purifying selection / autophagy (4)

Energy-dependent purifying selection / autophagy (3)

My question: What is an abiotic environment?

See:

abiotic factors found in aquatic systems may be things like water depth, pH, sunlight, turbidity (amount of water cloudiness), salinity (salt concentration), available nutrients (nitrogen, phosphorous, etc.), and dissolved oxygen (amount of oxygen dissolved in the water). Abiotic variables found in terrestrial ecosystems can include things like rain, wind, temperature, altitude, soil, pollution, nutrients, pH, types of soil, and sunlight.

My question: When did Schrodinger’s negative entropy of sunlight become an abiotic factor/variable?

See: What is Life? (1944)

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

Erwin Schrödinger (1887–1961) is best known as a co-recipient of the 1933 Nobel Prize in Physics, which is the same year that Thomas Hunt Morgan won the Nobel Prize in Physiology or Medicine for discoveries elucidating the role that the chromosome plays in heredity. Simply put, between two 1933 Nobel Laureates from different disciplines, we learned why the concept of the environment must include everything from energy-dependent changes in angstroms to ecosystems in all living genera.

See for instance:

The concept of the environment used for our discussion is very broad; it incorporates considerations of both the molar and the molecular levels.(1996)

See also, the alternative:  One crank dies, another rises to take his place

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.

That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

The unprovoked attack on my accurate representation of biologically-based cause and effect can only be compared to the attacks of PZ Myers on the accurate representations of others. For comparison, Roger Penrose may become best known for leading the way with his support of Schrodinger’s claims in this concise statement:

“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)

I hope that PZ Myers will become well known for ignoring all the claims that have ever been made by serious scientists and for touting only the claims made by other pseudoscientists and their idiot minions.

See: Energy-dependent purifying selection / autophagy (5)

Alternative splicing of pre-mRNA

Epigenetics and autophagy vs mutations and evolution (2)

Plants send light to roots to ‘see’ underground
My comment: Sending light requires an energy-dependent link from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects all organanized genomes from virus-driven energy theft and genomic entropy.
See Schrodinger (1944)
Excerpt:

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)

Ongoing confirmations of facts have escaped the attention of most theorists.

My comment:  The physics of life is the same as the physics that underlies inorganic chemistry. There is no such thing as chemoautotrophic or chemoheterotrophic metabolism. Metabolism is energy-dependent. Chemosynthesis and symbiogenesis are energy-dependent and controlled by the physiology of reproduction, not by the magic of evolution.
How can anyone not understand the link from information transfer in the context of physics or not link quantized energy from chemistry to RNA-mediated cell type differentiation in species from microbes to humans via the physiology of reproduction.
If the anti-entropic virucidal effects of UV light did not cause RNA-mediated DNA repair in soil bacteria, plants could not grow. Instead, sunlight is the link from the nutrient-dependent pheromone-controlled physiology of reproduction in soil bacteria to all biodiversity via the conserved molecular mechanisms of epigenetics that we first detailed in our 1996 review.
See: From Fertilization to Adult Sexual Behavior
Excerpt:

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

Alternative splicing of pre-mRNA

From Precis to Proof in 6000 years (2)

See: From Precis to Proof in 6000 years
Why now? See from 2014 Israeli Middle Schools School to Include Theory of Evolution
Excerpt:

“…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.”

See also: President Obama on Atheism
We have since seen the rise of claims about natural information processing link energy-dependent changes to healthy longevity in species from microbes to humans via the physiology of reproduction. We have also seen facts presented that link virus-driven energy theft to all pathology. After everyone else in the world has learned about the failure of neo-Darwinian pseudoscientific nonsense, who thinks a Democrat can save us from the viral apocalyse that has been predicted for at least two decades?

See for comparison: Regulation of RNA-binding proteins affinity to export receptors enables the nuclear basket proteins to distinguish and retain aberrant mRNAs
Introduction:

Following transcription, messenger ribonucleic acids (mRNAs) are transported to the cytoplasm to transfer genetic information and direct synthesis of functional proteins1. Multiple co-transcriptionally occurring processes applied on precursor mRNA (pre-mRNA) are followed by the engagement of several key proteins and complexes, including RNA-binding proteins (RBPs), along the length of pre-mRNA2,3, eventually forming an export-competent ribonucleoprotein (mRNP) prepared for efficient export through the nuclear pore complex (NPC). Splicing, 5′ capping, 3′ cleavage and polyadenylation are the four well-known processing steps prior to nuclear export, while failure in any of these steps yields aberrant mRNAs1,3. These processes are quality controlled by various evolutionary conserved and highly efficient mechanisms in eukaryotic cells3,4.

My comment: The processes are quality controlled by the availability of energy. They do not control themselves without it and nothing is conserved outside the context of the energy-dependent pheromone-controlled physiology of reproduction in species from microbes to humans.
Reported as: New Details on how Cells Keep RNA Errors in Check

…many interactions between proteins allow the cell to ensure the quality of mRNA. RNA-binding proteins bind to every strand of mRNA and aid in the recruit of export receptors. Nuclear basket proteins use the interaction between export receptors and RNA-binding proteins to locate and retain aberrant mRNA.

My comment: Conserved molecular mechanisms link nutrient energy-dependent autophagy from the innate immune system of bacteria to the pheromone-controlled physiology of cell type differentiation in all living genera. The innate immune system is the link from energy-dependent changes in pre-mRNAs to supercoiled DNA prevents virus-driven energy theft from causing all pathology in species from archaea to humans.
See: From Fertilization to Adult Sexual Behavior
Excerpt:

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

See: Virus-mediated archaeal hecatomb in the deep seafloor
Excerpt:

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

See also: Dynamics of Human and Viral RNA Methylation during Zika Virus Infection

…we investigated the role of m6A during ZIKV infection of human cells. We found that the depletion or overexpression of the central RNA methylation enzymes impacts viral replication, demonstrating that the host RNA methyltransferase machinery acts as a negative post-transcriptional
regulator of ZIKV virus.

See for comparison: Uncovered: the mysterious killer triffids that dominate life in our oceans
Excerpt:

Based on our findings, we have proposed a new model for life in our oceans, arguing that the traditional split between the “plant-like” phytoplankton (microalgae) and the “animal-like” microzooplankton used to describe the oceanic food-web is no longer tenable. This model could overturn a century’s worth of our understanding of marine biology.

My comment: The fact that only one domain of life exists has forced theorists to invent a new player in their game of who can invent the next best theory.

See for comparison: Nobel prize-winning autophagy research laid groundwork for potential Parkinson’s treatment

Excerpt:

During starvation, cells break down proteins and nonessential components and reuse them for energy. Cells also use autophagy to destroy invading viruses and bacteria, sending them off for recycling. And cells use autophagy to get rid of damaged structures. The process is thought to go awry in cancer, infectious diseases, immunological diseases and neurodegenerative disorders. Disruptions in autophagy are also thought to play a role in aging.

See this discussion attempt: “WHY don’t we have a plethora of random life forms alive today… nor in the fossil record”?

My comment: The more people learn about the birds and the bees, the more biological regularities attest to the fact that birds did not automagically evolve from dinosaurs during the past 6000 years, or ever.

Chemical composition of preen wax reflects major histocompatibility complex similarity in songbirds

Conclusion:

The salience of MHC genotype to fitness in songbirds [45] suggests that selection should favour the ability to signal and assess MHC profiles. The relationship between MHC and chemical distances for mixed-sex dyads suggests that provided song sparrows can detect chemical cues, this information should be useful in the context of mate choice, regardless of whether a self-referent or a known-kin criterion is used. By contrast, chemical cues do not appear to reflect MHC diversity. Our findings implicate preen secretions as potential semiochemicals in songbirds, a group in which chemical communication has only recently been explored. Further testing is warranted to determine if songbirds can perceive MHC-related variation in chemical profiles. Still, our findings suggest that chemosignalling may be more taxonomically widespread than previously thought, and could help to maintain adaptive genetic diversity in natural populations.

My comment: In my model, nutrient energy-dependent chemosignalling links the pheromone-controlled physiology of reproduction from species of microbes to humans via the conserved molecular mechanisms known to all serious scientists.

See also: Thomas Hunt Morgan (September 25, 1866 – December 4, 1945)[1] was an American evolutionary biologist, geneticist, embryologist, and science author who won the Nobel Prize in Physiology or Medicine in 1933 for discoveries elucidating the role that the chromosome plays in heredity.[2]

See also:  Genes located in a chromosomal inversion are correlated with territorial song in white-throated sparrows
Excerpt:

The white-throated sparrow is a useful model system in which to study the consequences of an inversion on gene expression. By suppressing recombination between alleles, chromosomal rearrangements can foster the evolution of co-adapted alleles, or ‘supergenes’ (Dobzhansky, 1970). Inversions that encompass multiple genes involving a suite of phenotypic traits might therefore maintain both behavioral and color polymorphism within a species (reviewed in McKinnon & Pierotti, 2010). Alternatively, a single gene with pleiotropic effects might be responsible for both behavioral and color polymorphism. Likely candidates are transcription factors and hormones. Transcription factors have the capacity to coordinate the expression of multiple genes that share a cis-regulatory region. Hormones can activate transcription factors and act through nongenomic signaling pathways. We cannot determine from our current study whether co-adapted alleles or a small number of pleiotropic genes can explain the behavioral polymorphism. It will be interesting to determine in future studies the extent to which manipulating expression of a single gene can influence behavior in this species.

My comment: A single base pair change and single RNA-mediated amino acid substitution link energy-dependent changes in morphological and behavioral phenotypes  across all species.
See for example: Genome divergence and diversification within a geographic mosaic of coevolution
Excerpt:

Our results further characterize a striking example of coevolution driving speciation within perhaps as little as 6000 years.

Reported as:   Biologists Use Genomics to Identify Evolving New Bird Species in Southern Idaho
Excerpt:

The finch feeds voraciously and exclusively on the pine seeds, which caused the tree to evolve seed defenses that make it harder for the birds to harvest the seeds. The birds counter-evolved against those defenses as evolution favored deeper-beaked crossbills, resulting in a coevolutionary arms race that has driven evolutionary divergence of this unique bird population.

My comment: The idea that bird species and trees co-evolved during the past 6000 years is one that can be placed into the context of nutrient-dependent pheromone-controlled weekend resurrection of the bacterial flagellum because all individuals in all species must eat to reproduce and pheromones control the physiology of nutrient-energy reproduction.
Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Reported as: Evolutionary Rewiring
See my comments. For example:

The ‘backup system’ appears to protect against the damage caused by viruses and viral microRNAs that perturb the biophysically constrained chemistry of nutrient-dependent protein folding and reproduction in species from microbes to humans.

See: Viruses and cell type differentiation

Alternative splicing of pre-mRNA

Polycombic ecological adaptation as a science, not a theory (2)

Evolutionary Constraints in the β-Globin Cluster: The Signature of Purifying Selection at the δ-Globin (HBD) Locus and Its Role in Developmental Gene Regulation

Conclusion:

… the results here presented indicate that purifying selection is driving not only HBD evolution but also its neighbor pseudogene, HBBP1. In the light of recent advances in the characterization of the β-globin cluster, we propose that the complex patterns of diversity observed in this genomic region arose from distinct functional constraints related with the intricate process of chromatin and protein interactions coordinating the differential expression of genes at the β-globin cluster during development.

My comment: No experimental evidence of biologically-based cause and effect suggests that any locus of genes or any pseudogene has ever evolved. Purifying selection cannot drive evolution. Only energy-dependent variations can can be linked to polycombic ecological adaptation, and only virus-driven energy theft has been linked to the creation of pseudogenes in the context of biophysical constraints on viral latency.

See for comparison: microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection

Excerpt:

miRNA function is generally limited to cytokine levels in response to RNA viruses

Reported as: Mount Sinai Researchers Use Cellular miRNA-Elimination Tool to Study Viral Infection Dynamics

Excerpt:

…while the loss of miRNAs had a negligible impact on the cell’s immediate reaction to a virus or the short-term biology of the cell, sustained depletion had dramatic results on gene expression that was coupled to a burst of cytokines. The researchers concluded in the paper that miRNA function is limited to modulating the biology of the cell over long periods of time.

My comment: In my model, energy-dependent changes in the microRNA/messenger RNA balance link nutrient energy-dependent changes to all healthy longevity and virus-driven energy theft is linked to all pathology. Over long periods of time, autophagy is the link to polycombic ecological adaptation or virus-driven hecatombic evolution of pathology via energy-dependent biophysically constrained RNA-mediated protein folding chemistry. For example, fixation of amino acid substitutions differentiates all cell types in all individuals of all living genera in the context of the physiology of reproduction. For comparison, virus-driven hecatombic pathology is linked from mutations to all pathology.

Simply put, in my model of polycombic ecological adaptation, differential gene expression is nutrient-dependent and controlled by the physiology of reproduction.

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’.

My comment: Claims about RNA-mediated polycombic ecological adaptation were first placed into the context epigenetic imprinting in our 1996 review.

See: From Fertilization to Adult Sexual Behavior

Excerpt:

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

My comment: Polycombic ecological adaptation appears to link energy-dependent epigenetic effects on hormones (i.e., proteins) to chromatin structure in telomeric regions, which links the effect on transcription and silencing of various genes to hormone-organized and hormone-activated affects on behavior. The hormone-organized and hormone-activated behaviors link the epigenetic landscape of yeasts to the physical landscape of supercoiled DNA in species from bacteria to invertebrates and all vertebrates via the de novo creation of G protein-coupled receptors, which link chemotaxis and phototaxis to all biodiversity.

For comparison, see: Mutation-Driven Evolution

Excerpt:

Mutation… includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc.

My comment: The definition above links mutations to any change in any genome.

See for comparison: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

Excerpt:

Single nucleotide substitutions or indels [insertions/deletions] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects [mutations] in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.

My comment: The facts about nutrient energy-dependent amino acid substitutions link hemoglobin variants from ecological adaptation to healthy longevity and the facts also link molecular defects from mutations to the pathology of α-, β- or δ-thalassemia, respectively. It would be difficult to include facts about biophysically constrained energy dependent cell type differentiation in the context of any other model that links amino acid substitutions to healthy longevity and links mutations to all pathology in all living genera.

See for example:  Criticisms of the nutrient-dependent pheromone-controlled evolutionary model 

Excerpt:

…James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research.

My comment: The claims of a biologically uninformed undergraduate student reviewer were placed into the context of modern evolutionary theory, which involves Masatoshi Nei’s simple-minded revision of neo-Darwinian pseudoscientific nonsense. Nei does not compare his theory of mutations to the facts about nutrient energy-dependent fixation of amino acid substitutions in supercoiled DNA. The problem appears to be the use of the term “mutation” in the textbook published on the same day as my 2013 review was published.

I linked the energy-dependent fixation of amino acid substitutions to all healthy longevity. Nei’s textbook misrepresentations did not link anything to healthy longevity, but linked mutations to what I claimed are nutrient-dependent pheromone-controlled polycombic ecological adaptations.

I failed to include what is known about energy-dependent codon optimality in the context of polycombic ecological adaptations because there was no experimental evidence of biologically-based cause and effect to support those claims at the time of our 1996 review or my 2013 review. For comparison, there has never been any experimental evidence of biologically-based cause and effect to support claims about mutation-driven evolution. Simply put, nothing known to serious scientists about cell type differentiation suggest that mutation-driven evolution can occur.

For comparison, see: New analysis of big data sheds light on cell functions
Excerpt:

With today’s technology, scientists are able to generate data about a cell’s or organism’s complete set of genes, proteins, RNA profiles, metabolites and much more—known as omic data. Using omic data, scientists can model complex biological interactions and gain a more holistic view of different cellular processes.

See also: Research Topic Multi-omic Data Integration

Excerpt:

Stable, predictive biomarkers and interpretable disease signatures are seen as a significant step towards personalized medicine. In this perspective, integration of multi-omic data coming from genomics, transcriptomics, glycomics, proteomics, metabolomics is a powerful strategy to reconstruct and analyse complex multi-dimensional interactions, enabling deeper mechanistic and medical insight.

My comment: Glycomics, transcriptomics, proteomics, metabolomics and genomics have established fact about the biological basis of complex multi-dimensional interactions that link the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria from quorum sensing to the molecular mechanisms that enable deeper mechanistic and medical insight in the context of the National Microbiome Initiative and Precision Medicine Initiative.

See for example: ‘Oming in on RNA–protein interactions

Excerpt:

…the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities without the need to create additional genes and without affecting existing proteins [4-6].

See for comparison: From Fertilization to Adult Sexual Behavior

Excerpt:

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…. That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

My comment: Detailed examples of how the interactions between pre-mRNA and alternative splicings create new genes in the fine-tuned energy-dependent functional structure of supercoiled DNA explain how all cell types of all individuals of all living genera are protected from virus-driven energy theft. Energy-dependent RNA-mediated amino acid substitutions are fixed in organized genomes via the physiology of reproduction, which helps to prevent the transgenerational epigenetic inheritance of nearly all pathology by linking innate immune system to supercoiled DNA.

For comparison, viruses steal the energy that is required for cell type differentiation, which is how mutations are linked to all pathology. All differences between healthy longevity and virus-driven human pathology can be explained in the context of how nutrient energy-dependent microRNAs. The nutrient energy-dependent microRNAs are carried by erythrocytes in species with circulating blood.

See: Pitfalls of analysis of circulating miRNA: role of hematocrit

MicroRNAs are are delivered to the cell types on an as needed basis. When too few nutrient energy-dependent microRNAs are available, viruses use the existing energy they steal from cells to replicate. Eventually, the replication of the viruses causes the mutations, which are linked to all pathology. That’s why it is important to revisit the facts presented in the context of this article, which was published on 10/26/16

See: Multi-omic data integration enables discovery of hidden biological regularities
I reported this here as: Polycombic ecological adaptation as a science, not a theory for comparison to Biological evolution as a philosophy, not a science.
Despite several attempts to discuss the difference between science and philosophy, no progress was made.
See for example: Evolutionary assumptions (revisited)
See also the impasse that was reached in this attempt to discuss the anti-entropic virucidal energy of the sun.
It is worth joining The Battlefield FB group to see that others would rather hold on to their theories and opinions despite the overwhelming amount of experimental evidence that I have used to support my claims. For me, it is time to move forward and focus on the rediscovery of hidden biological regularities.
Finally, others have discovered that small intranuclear proteins generate alternative splicing techniques of pre-mRNA, which is how microRNAs link hydrogen-atom transfer in DNA base pairs in solution to the conserved molecular mechanisms of energy-dependent cell type differentiation, and to all cell type differences in all individuals of all living genera.
For comparison, this is an example of how virus-driven energy theft is linked viral replication and to virulence:
Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

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

For an example of how nutrient energy-dependent RNA-mediated amino acid substitutions are linked to healthy longevity via the physiology of reproduction, see:

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).”

My comment: The facts stated above have forced theorists to invent evolutionary cell biology.
See Evolutionary cell biology: Two origins, one objective
Reported as: Why some junk DNA is selfish, but selfish genes are junk
Excerpt:

“A commonly held but incorrect stance is that essentially all of evolution is a simple consequence of natural selection.” They point out, for example, that many pathways to greater complexity of both genomes and cells don’t confer any selective fitness.

My comment: Greater complexity requires a link from ecological variation to polycombic ecological adaptation, which links supercoiled DNA to protection from the virus-driven hecatombic evolution of all pathology.
My comment: New theories are worthless if they do not include information on the role of energy in cell type differentiation or the role of virus-driven energy theft in all pathology.
See for comparison the facts about: Detection of hemoglobinopathies and thalassemias using automated separation systems
See also: In vivo correction of anaemia in β-thalassemic mice by γPNA-mediated gene editing with nanoparticle delivery
Excerpt: 

The combination of nanoparticle delivery, next generation γPNAs and SCF treatment may offer a minimally invasive treatment for genetic disorders of the blood that can be achieved safely and simply by intravenous administration.

My comment: That fact suggests all suffering and death caused by hemoglobin variants is caused by neo-Darwinian theorists who do not know how the variants link ecological variation to polycombic ecological adaptation.

Reported as: Scientists edit gene mutations in inherited form of anemia
Excerpt:

The researchers found that the technique corrected the mutation to such a degree that the mice no longer had symptoms of thalassemia. After 140 days, they tested hemoglobin levels in the animals and found them to be normal.
“The fundamental result here is that with nanoparticles containing PNAs, along with template DNA, and simple IV infusion of molecules, we achieved enough gene editing to effectively cure the anemia in mice that had thalassemia,” Glazer said.

My comment: The ability to correct the mutation requires a link from energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solutions such as blood. That’s how their IV therapy works. It changes the microRNA/messenger RNA balance and that forces the innate immune system to repair the damaged DNA.
See also:  Two novel loci, COBL and SLC10A2, for Alzheimer’s disease in African Americans
Excerpt:

Two SNPs at novel loci, rs112404845 (P = 3.8 × 10−8), upstream of COBL, and rs16961023 (P = 4.6 × 10−8), downstream of SLC10A2, obtained genome-wide significant evidence of association with the posterior liability.

Reported as: Study Identifies Two New Genes Responsible for Alzheimer’s in African Americans
Excerpt:

In 2013, a genome-wide association study of AD in more than 5,500 African Americans identified two genetic risk factors for AD. This study looked at genetic variants across subjects’ entire genome and compared their frequency in cases versus controls.
By doing so they were able to identify two new genes (COBL and SLC10A2) associated with risk of AD in African Americans.

My comment: The author’s study results link hydrogen-atom transfer in DNA base pairs in solution to energy-dependent changes in the microRNA/messenger RNA balance. The neuroscience news report claims they identified two new genes. The neuroscience news report then links the genes — instead of the energy-dependent changes — to the disease in a human population. Many African Americans are examples of how ecological variation has been linked to polycombic ecological adaptation via hemoglobin variants. The adaptations include amino acid substitutions linked to the stability of organized genomes in populations where malaria is endemic. Failed adaptations are included in examples of virus-driven energy theft linked to mutations and the pathology of Alzheimer’s disease.

My comment: The ability to edit out gene mutations clearly links RNA-mediated amino acid substitutions to supercoiled DNA and all biodiversity.
See also: Inventing neo-Darwinism
See also: Pioneering Geneticist Explains Ambitious Plan to “Write” the Human Genome

Excerpt:

…he notes that with an editing tool like CRISPR, one base out of many can be altered, but with a synthesis approach, a hundred edits could be made. This sort of change, he tells JAMA, could make a cell resistant to multiple viruses.

My comments: All the changes in base pairs may already have been linked from natural selection for codon optimality and energy-dependent changes in RNA-mediated cell type differentiation to supercoiled DNA, which links the physiology of reproduction from the innate immune system to fixation of the amino acid substitutions that differentiate the cell types of all living genera. If so, what might happen to an organized genome when a hundred edits are made?

Will anyone be able to stop the hecatombic evolution of pathology via the polycombic ecological adaptation, which links autophagy to healthy longevity via protection of organized genomes from virus-driven entropy?

See also: Yale scientists edit gene mutations in inherited form of anemia Genetics & Genomics

A new gene therapy is being tested for its ability to treat thalassemia, a form of anemia caused by genetic mutations. So far, scientists have successfully corrected gene mutations causing the disease in mice, and now researchers are interested in seeing if the same approach will work effectively in humans.
“The fundamental result here is that with nanoparticles containing PNAs, along with template DNA, and simple IV infusion of molecules, we achieved enough gene editing to effectively cure the anemia in mice that had thalassemia. We demonstrated we have extremely low off-target effects.”

See for comparison:

Product Development Pipeline

Excerpt:

Each microRNA mimic in our pipeline is designed to replicate the activity of a single tumor suppressor miRNA and regulate the expression of key oncogenes across multiple oncogenic pathways which can prevent proliferation and induce apoptosis in cancer cells.

See also: VACRC Projects

Excerpt: Future Projects

 The Influence of Carbon Dioxide Enhancement on Plant Growth
 Thermoregulation in Honey Bees
 Biochemistry and Taxonomy in Pine Trees
 The Formation of Multiple Tree Rings in Bristlecone Pine Trees

The VACRC suddenly seems willing to take everything I have claimed about RNA-mediated cell type differentiation during the past twenty years and begin to investigate the claims. This would have been a desirable outcome 20 years ago, but now it might prevent progress via use of my model. The model links energy-dependent changes from angstroms to ecosystems in all living genera, it and links virus-driven energy theft to all pathology.

The Pacific Yew Tree and production of taxol is an example of how the physi0logy of reproduction in soil bacteria can be linked from plant growth to the honeybee model organism of thermoregulation and behavior, which must be linked to the biochemistry and taxonomy of all species. That becomes meaningful via the explanatory power of a model that links RNA-mediated amino acid substitutions to all energy-dependent biodiversity via the conserved molecular mechanisms of polycombic ecological adaptation we detailed in our 1996 review.

However, when others wait too long to accept a model that may already have led to a paradigm shift, they may also realize it. That fact was addressed by Kaveli Kull in the context of next week’s meeting of the Royal Society.

See: Kalevi Kull: Censorship & Royal Society Evo Event

Excerpt:

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.

My comment: Some work by young earth creationists has been at the cutting edge since 1996, as indicated here: Where do viruses come from?

Excerpt:

‘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.”9

My comment: 9 is Holmes, B. (1996) Who Rules the Waves? New Scientist 152(2054):8-9, supp I have not read it in its entirety but the claim fits into the context of everything else I have learned about physics, chemistry, and conserved molecular mechanisms of RNA-mediated cell type differentiation, which appears to be biophysically constrained in all living genera via their nutrient-dependent pheromone-controlled physiology of energy-dependent reproduction.

Alternative splicing of pre-mRNA

80 years of causal analysis (1936 – 2016)

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

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

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

Some Principles of Causal Analysis in Genetics (1936)

Extract:

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

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

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

See for ~54,000 examples: microrna and autophagy

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

Excerpt: 

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

nature.com

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

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

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

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

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

Tweets

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

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

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

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

James Kohl

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

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

Alternative splicing of pre-mRNA

Half truths support theories without facts

How to lie by telling the truth

Excerpt:

People… trot out half-truths, in full expectation and knowledge that they will create a false impression. And then, when others act on the false impression, the “truth-telling liars” can sit back and pretend that they aren’t liars. They get the benefit of lying, without any damage to their precious self-image.

My comment: It is more difficult for others to determine who benefits from half truths when more than one individual or research group fails to link biologically-based cause and effect. When two groups use the same model organism, but no model, they are not likely to report the truth about biologically-based cause and effect, .

Craig Venter’s Synthetic Genome 3.0 Evokes Classic Experiments

Venter’s group seems to have run into a common problem with attempts to explain nutrient-dependent RNA-mediated cell type differentiation. They try to keep it constrained by evolution, which leads them to use terms like mutation instead of amino acid substitution. See their references for a link to work on viruses that should have led to recognition of the difference between the amino acid substitutions the cause changes in virulence and the mutations, which are biophysically constrained.
Dobzhansky (1973) used “amino acid” and “mutation” in the context of claims that we know can be supported only with experimental evidence that links atoms to ecosystems in all living genera via the physiology of reproduction. The nutrient-dependent physiology of reproduction is biophysically constrained by the innate immune system, which is the RNA-mediated link to supercoiled DNA. Supercoiled DNA protects all organized genomes from virus-driven entropy.
See also: A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans
Excerpt: 

Synthesis of dsRNA is required for replication of RNA viruses and transposons, and therefore dsRNA constitutes a ‘‘danger signal’’ in many organisms, including humans, where it activates the interferon response (Wang et al., 2002). As in worms, RNAi is important for anti-viral defense (Lu et al., 2005); it is possible that the mere ‘‘sensing’’ of dsRNA (for example, by pattern recognition mechanisms [Melo and Ruvkun, 2012]) is sufficient to activate the RNAi system, regardless of whether the dsRNA molecule is further processed to trigger an RNAi response or not.

My comment: Nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation in the nematodes, C. elegans and P. pacificus clearly shows how the innate immune system links metabolic networks and genetic networks to supercoiled DNA that protects the organized genome of all living genera from virus-driven entropy.
See: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
Reported as: The neurobiological consequence of predating or grazing
Excerpt:

While C. elegans feeds exclusively on bacteria, P. pacificus is able to switch its behaviour to prey on other worms if bacterial food gets scarce.

See also: Distinct Circuits for the Formation and Retrieval of an Imprinted Olfactory Memory
Excerpt:

Classical olfactory imprinting drives approach behavior, such as homing to the natal stream for salmon (Nevitt et al., 1994), bonding between mammals and their young (Lorenz, 1935), kin recognition in zebrafish (Gerlach et al., 2008), and acceptance of imprinted foods (Wilson and Sullivan, 1994). Positive imprinting to odors experienced early in life also has been described in C. elegans, although little is known about its mechanisms beyond a requirement for the orphan G protein-coupled receptor SRA-11 in AIY neurons (Remy and Hobert, 2005).

My comment: The nutrient-dependent de novo creation of G protein-coupled receptors links classical olfactory imprinting to supercoiled DNA via everything known about RNA-mediated cell type differentiation, which is controlled by the physiology of reproduction. Examples link all invertebrates to all vertebrates via the conserved molecular mechanisms we detailed in our section on molecular epigenetics in the Hormones and Behavior review.  From Fertilization to Adult Sexual Behavior
Excerpt:

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

Rechavi’s group recognizes the fact that RNA-mediated events are important for anti-viral defense. Bargmann’s group ignores the fact that virus-driven energy theft links perturbed protein folding chemistry to mutations and gene loss.
But her group does not link what nematodes eat to nutrient-dependent biodiversity via the de novo creation of olfactory receptors, which are G protein-coupled receptors. Instead, Bargmann wins another award.  McGovern Institute awards prize to neurogeneticist Cori Bargmann
Excerpt:

Building on her olfaction work, Bargmann has also studied the neural basis of social behavior, which in worms is strongly regulated by chemical cues. In one set of papers, for example, she identified a single neuron that integrates information from multiple chemical cues including food, oxygen and pheromones, to control the expression of social behavior.

My comment: Her award-winning works fail to link virus-driven energy theft from perturbed protein folding chemistry to mutations and gene loss.  Perhaps no one else but me will ever know that she could have linked the works from Rechavi’s group from what is known about how olfaction and the immune system enable the fine-tuning of metabolic networks and genetic networks, which is linked from the physiology of reproduction to supercoiled DNA.
She could have stopped the threat of the Zika virus and other viruses by acknowledging the fact that supercoiled DNA protects all organized genomes in all living genera from virus-driven entropy. Instead, her works will continue to be well-funded.
Others will be forced to increase their efforts and focus on Combating Evolution to Fight Disease.