Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Is meat protein unhealthy? (2)

See also: Microbiome-Grade DNA Extraction Kits

…the thermal and chemical methods effectively lyse the gram-negative organisms and boost their population in the final profile, amplifying the bias.

This suggests that all links from food energy-dependent de novo creation of the pheromone-controlled biophysically constrained bull sperm microRNAome have been misinterpreted in the context of virus-driven fescue toxicosis.

The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

…the miRNA profile of mature ejaculated sperm may in fact have downstream consequences upon embryonic development. The potential for sperm miRNA affecting zygote development has recently been reported in the literature [18] and has interesting implications for the use of sperm miRNA profiles as indicators of potential male fertility.

Fescue toxicosis links the virus-driven creation of enzymes to the degradation of messenger RNA in bull sperm and to the transgenerational epigenetic inheritance of mutations, which all serious scientists have linked from damage to supercoiled DNA to all pathology in humans and other species.

Eating the meat from other animals that have not ecologically adapted to the virus-driven theft of quantized energy has been linked from the viruses in their genomes to human pathology via the degradation of messenger RNA in bacteria that become archaea and L-forms.

See also: Dobzhansky (1973)

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

See also: The Breadth of Viruses in Human Semen

The presence of viruses in semen is probably more widespread than currently appreciated, and the absence of virus in genital secretions should not be assumed for traditionally non–sexually transmitted viruses. The investigation of virus detection and persistence in semen across a range of viruses is useful for clinical and public health reasons, in particular for viruses that lead to high mortality or morbidity rates or to epidemics.

No serious scientist has ever reported a link from the Virus-mediated archaeal hecatomb in the deep seafloor to the evolution of anything except pathology. All serious scientists have, for comparison, linked ecological variation to food energy-dependent  polycombic ecological adaptations via biophysically constrained viral latency in species from microbes to humans.

From Fertilization to Adult Sexual Behavior (1996)

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…

See also: Cytosis: A Cell Biology Board Game for ages 10+

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

5th-6th Sept 2018 Dublin, Ireland

Is meat protein unhealthy? (1)

Patterns of plant and animal protein intake are strongly associated with cardiovascular mortality
Reported as: Meat protein is unhealthy, but protein from nuts and seeds is heart smart

In the context of everything known about how the creation of anti-entropic virucidal light must be linked to all biodiversity on Earth, watch this ridiculous misrepresentation of the honeybee model organism. Food energy-dependent microRNA-mediated pheromone-controlled biophysically constrained viral latency is portrayed as if visual input was most important.

Bee swarms work like giant brains

See instead:

RNA-mediated nutritional psychiatry

RNA-mediated nutritional psychiatry (2)

Psychophysical Laws of Biology: RNA-mediated nutritional psychiatry (3)

Learn how to prevent more school shootings via what is known about how the “Psychophysical Laws” of Biology are linked to food energy-dependent biophysically constrained behaviors via microRNA-mediated cell type differentiation and the fixation of RNA-mediated amino acid substitutions like COMT Val158Met during the transition from adolescence to adulthood.

Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults (Epub Oct 16 2014)

Alternative splicing of pre-mRNA

Pseudoscientists hate what science explains! (3)

See also: Pseudoscientists hate what science explains (2)
Summary: In addition to germline silencing via information transfer to the physical landscape of supercoiled DNA, multicopy transgene arrays are linked from changes in the microRNA/messenger RNA balance to variation in their somatic expression level. That fact helps to establish the difference between healthy longevity and pathology across generations.
Problems with DNA replication can cause epigenetic changes that may be inherited for several generations
My summary: The polycomb repressive complex 2, additional chromatin- and small RNA–related pathways carry quantized energy as information from the epigenetic landscape. The information causes changes in microRNAs that modify histones, which links the energy to the transgenerational epigenetic inheritance of morphological and behavioral phentypes in the nematode model organism.
In addition to germline silencing via information transfer to the physical landscape of supercoiled DNA, multicopy transgene arrays are linked from changes in the microRNA/messenger RNA balance to variation in their somatic expression level. That fact helps to establish the difference between healthy longevity and pathology across generations.
The difference is food energy-dependent, RNA-mediated, and biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera.
See for comparison: From Fertilization to Adult Sexual Behavior (1996)

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…. 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.

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

We propose that CNEs [conserved non-coding elements] represent the ‘hard-wired’ sequence traces of these core animal group-specific GRNs [gene regulatory networks]. The alternative core GRNs of different animal lineages are reflected in their having alternative CNEs. However, because of their co-evolution from a common metazoan ancestor, the core GRNs of different animal groups often utilize the same regulatory genes. As a result, distinct yet parallel sets of CNEs have become irreversibly associated with the same genes that coordinate core developmental networks in diverse animal groups. Indeed, this evolution of regulatory elements may underlie the astounding diversification of animal body plans that was seen during the Cambrian period approximately 550 million years ago.

No experimental evidence suggests that regulatory elements evolved.
Predicting phenotypic variation in yeast from individual genome sequences
No experimental evidence predicts a link from gain of function mutations to evolution
Differential DNA mismatch repair underlies mutation rate variation across the human genome
All experimental evidence links natural selection for energy-dependent codon optimality to mutation rate variation across species and to individual differences in the human genome via the pheromone-controlled physiology of reproduction.

3D structures of individual mammalian genomes studied by single-cell Hi-C

Reported as: Scientists have determined the 3D structures of intact mammalian genomes from individual cells, showing how the DNA from all the chromosomes intricately folds to fit together inside the cell nuclei. The research is published in Nature this week. http://go.nature.com/2n6psaw

My comments:

See also: 3D RNA and Functional Interactions from Evolutionary Couplings “…the ongoing explosion of available sequence data means that the outlook for elucidating functional interactions in mRNAs, lncRNAs, and viral genomes, as well as their protein-binding partners, is promising.” http://dx.doi.org/10.1016/j.cell.2016.03.030

Virus-driven energy theft causes the degradation of messenger RNA in all organized genomes. That fact threatens anyone who has ever reported results in the context of mutations, natural selection and evolution because natural selection occurs only for energy-dependent codon optimality.

It would be even more amazing if they told the truth about energy-dependent amino acid substitutions that stabilize supercoiled DNA, which links chromosomal rearrangement to all biodiversity via the physiology of reproduction in species from microbes to humans. See: http://science.sciencemag.org/content/355/6328/910

See other comments to this Nature Facebook page
Addendum: Say goodbye to mutation-driven evolution. Everything known to serious scientists about biophysically constrained endogenous RNA interference and the pheromone-controlled physiology of reproduction has been linked from the de novo creation of nucleic acids to energy-dependent amino acid substitutions that differentiate all cell types in all living genera via fixation in organized genomes.
See: Transgenerational transmission of environmental information in C. elegans
They link diet- and stress-induced changes in heterochromatin from repressed repetitive elements that escape epigenetic reprogramming to phenotypic variation in mammals. It is obvious that heterochromatin provides the link from the molecular mechanisms of biophysically constrained protein folding chemistry to the epigenetic transmission of information between generations. But they speculate that the transgenerational epigenetic inheritance of environmentally triggered changes in expression from repressed chromatin may be linked to ecological adaptations.
See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

 …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’.

Ben Lehner and his co-authors have consistently tried to sneak up from behind and link explanations of energy-dependent top-down causation from mutations to evolution.
Others are also ignoring the experimental evidence that links energy-dependent changes in microRNAs to healthy longevity or from virus-driven energy theft to all stress-linked pathology.
See: Stress-induced changes in miRNA biogenesis and functioning
See for comparison: I am not a story

Reported as: Life is not a neat narrative, it’s a patchwork of competing, even contradictory, forces. Sensations are too spurious and memory too fickle for the formation of reliable storylines. Reject the impulse to narrativise. Summer Reads from the Aeon archive: http://ow.ly/bLd430ekoJn

Re: Sensations are too spurious and memory too fickle for the formation of reliable storylines.

My comment: Too late for more of this nonsense. See: Olfaction Warps Visual Time Perception

 

The sense of smell in bacteria has been linked from the physiology of pheromone-controlled reproduction to our visual perception of mass and energy in the context of the space-time continuum via food energy.

See for comparison: Quantum common sense

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

My comment: No, it’s Santa Claus who sees you when your sleeping; He knows when you’re awake. And he knows if you’ve been bad or good, so be good for goodness sake.

Filtering light through a prism to identify tissue type

Respiration-dependent endogenous RNA interference

If you are a theorist, please take a deep breath before beginning to read this.

The speed of light on contact with water has been linked from the level of oxygen on Earth to all biodiversity via the physiology of pheromone-controlled reproduction and the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes in all living genera.

15h15 hours ago  It’s “game over” for all theorists. There’s a new game in town. It’s an evolutionary theory killer.

12h12 hours ago Epigenetically-effected nucleosome repositioning sheds Dobzhansky’s light on evolution

Why are many mRNAs translated on or nearby mitochondria?

15h15 hours agoThanks for asking. Because otherwise one species could evolve into another species via natural selection for virus-driven energy theft.

35m35 minutes ago Replying to @jvkohl

how many times might a typical eukaryotic mRNA get translated? is it eventually degraded by RNAases? eroded from the ends?

Yes. Thanks for asking. Virus-driven energy theft degrades messenger RNA in the context of respiration and changes in pH in all cell types.

15m15 minutes ago The change to supercoiled DNA was energy-dependent. Where did the lost energy go? I need it back to support Schroedinger’s claims from 1944.

Re: Schodinger’s claims about sunlight: Practical application of the concept of energy as information sunlight.

Vitamin C is a natural antihistamine. It destroys the molecular structure of histamine, which decreases the amount of histamine in the blood. A diet that included the ingestion of leaves from the sago palm might have helped modern human populations in what is now Central China to ecologically adapt via energy-dependent changes in base pairs that link single nucleotide polymorphisms from natural selection for codon optimality to endogenous RNA interference and DNA repair via what is know about respiration in the context of the citric acid cycle.

See also: I forgot Wendy’s last name. She was a friend from Las Vegas, Nevada who died from lung cancer at an early age (38?).  We belonged to a public speaking group, which I was forced out of by my marriage in 1992, ~25 years ago.

The group was for single people only. Lung cancer has since caused the unnecessary suffering and premature death of many others because few people have learned that one energy-dependent base pair change can be linked from a single amino acid substitution to all RNA-mediated healthy longevity or from virus-driven energy theft to all pathology.

See for another example: Lkb1 inactivation drives lung cancer lineage switching governed by Polycomb Repressive Complex 2

The researchers linked sex differences in cell types to differences in the types of lung cancers. The differences were placed into the context of the nutrient energy-dependent metabolism of one amino acid, methionine. They suggest that methionine is essential to cell type differentiation in humans without placing that fact into the context of virus-driven energy theft, which links the degradation of messenger RNA from mutations to all pathology in all cell types of all living genera. It makes me very angry that they will not tell the truth about how energy-dependent endogenous RNA interference protects all organized genomes from virus-driven energy theft and genomic entropy. I’m beginning to wonder whether something more than ignorance is causing the misrepresentations of biologically-based cause and effect that are linked to the prevention and/or cure of cancer and all other pathology via nutritional epigenetics and the pheromone-controlled physiologoy of reproduction in all genera

.…one possibility is that metabolism of methionine is a link between LKB1 and EED. Studies with an inhibitor of S-adenosyl homocysteine hydrolase have demonstrated that decreased methionine metabolism can cause destabilization of the PRC2 components at the protein level61. Future studies will focus on identifying the link between the cellular genotype and the epigenetic identity of lung cancer cells from different subtypes of lung cancer…

Reported as: New study proves one lung cancer subtype can switch to another

“Now that we have a glimpse into the molecular mechanism of lineage switching, we can begin to learn how to manipulate this phenomenon for better therapeutic outcomes,” said Brainson.

My comment: In our 1996 Hormones and Behavior review we linked energy-dependent “lineage switching” to healthy longevity via alternative splicings of pre-mRNA and Polycomb.

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: Thanks to everyone who helped fund the end of neo-Darwinian pseudoscientific nonsense and the end of the “Big Bang” theory. Viral latency is energy-dependent, RNA-mediated, and endogenous RNA interference is biophysically constrained by the physiology of pheromone-controlled reproduction.

The anti-entropic virucidal energy of the sun will be placed into its proper context by anyone who plays this game.

`6650 backers will receive the games and the number of biologically informed serious scientists will grow exponentially.
Anyone who plans to “March for Science” on Earth Day (April 22, 2017) is likely to be asked this embarrassing question. “Where did the energy in a hydrogen atom come from?”
Their answer will lead to a second question. “Where does the energy go when it no longer sustains the life of the organism?”
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.

Biology to a Physicist

Coulombic interactions facilitate polycombic adaptation

RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly
Summary: Everything known to serious scientists about energy-dependent biophysically constrained RNA-mediated protein folding chemistry is attributed to “Nature” and evolution with no consideration for where the energy came from or where it goes when viruses use it for their replication.

See also: War Games: False Flag Terrorism (2)

I baited Sean Ovis, and caused him to join a discussion on “The Battlefield.Sean Ovis regurgitated parts of my model when he wrote:
Excerpts:

  1. This scenario is explored fully within my model which links virus-driven energy theft and genomic entropy in all ecosystems on Earth to energy-dependent RNA-mediated amino acid substitutions via olfaction and the innate immune system in the context of the physiology of reproduction, and is fully known to all serious scientists.
  2. In this model all organized genomes in all tissues of all living genera are linked to nutrient-dependent RNA-mediated amino acid substitutions via symbiosis and the pheromone-controlled physiology of nutrient-dependent reproduction in biochemically-based ecosystems which protects energy-dependent ecological adaptations from virus-driven energy theft and genomic entropy. The model was about to be published when due to an unfortunate accident, I tripped and the only copy of the manuscript fell out of my pocket and was eaten by a small dog.

My reply: Please note: After my last encounter with Sean Ovis, he wrote:

“If you are a creation scientist, you can take comfort in the fact that as you get older, the control of these viral fragments is considerably weakened, and eventually one or more of these jumping genes will be let loose in your body to wreak havoc on your DNA. When that happens, you can thank God, because they will have brought you closer to him.”

Addendum: That will remain as one of the most vicious of all atheistic attacks on my model.

I’ve since added information on coulombic interactions to help others link angstroms to ecosystems in all living genera via the physiology of reproduction and fixation of RNA-mediated amino acid substitutions in supercoiled DNA, which protects all organized genomes from virus-driven entropy.

Sean Ovis bastardized the discussion of Quantum Consciousness, so I ended comments on the threat after attempting to get him and others to start their own OP.

See: James Kohl

Was Hitchens a self- described marxist-trotskyist who regarded the materialist conception of history as legitimate for explaining the human condition?

Sean Ovis “Language is elitist,” says Marx; however, according to la Tournier , it is not so much language that is elitist, but rather
the rubicon, and some would say the defining characteristic, of language. Bataille’s analysis of neocultural textual theory states that consciousness may be used to marginalize minorities. Thus, Lacan suggests the use of postsemantic feminism to challenge hierarchy.
If one examines dialectic nationalism, one is faced with a choice: either accept postsemantic feminism or conclude that the task of the poet is social comment, given that culture is interchangeable with sexuality. The within/without distinction which is a central theme of Tarantino’s Pulp Fiction emerges again in Reservoir Dogs, although in a more mythopoetical sense. Therefore, if Lacanist obscurity holds, we have to choose between subpatriarchialist narrative and the capitalist paradigm of discourse.

In an attempt to move forward, I started a new OP based on the claims in: Peptides design based on transmembrane Escherichia coli’s OmpA protein through molecular dynamics simulations in water-dodecane interfaces

It seems futile to continue to address questions about the transfer of energy as information, when people cannot seem to grasp the fact that transfer must be biophysically constrained in the context of RNA-mediated protein folding chemistry that links coulombic interactions to polycombic adaptation, which prevents the hecatombic evolution of all virus-driven pathology.

Matthew Hunt, who is the co-author of “Electrostatic effects on linear and nonlinear waves in hanging film flows” (link opens pdf paper) continued to ask questions like this: You talk about the transfer of energy, but what is physically being transferred?

One of the administrators, Larry Kinser Jr., began to provide vague answers. His vague answers and proselytizing are all that I’ve seen come from the administrators of the group.

James Kohl Thanks for asking. Energy as information is being physically transferred as in the context of the Laws of Physics, which must be linked from the fundamentals of what is known about organic chemistry to Kohl’s Laws of Biology or Darwin’s ‘conditions of life,” which God established in the context of His Creation. Chemists know that — see for example:


See also: Gianmarc Grazioli YouTube Channel for Chemistry AND Guitar Tutorials!
See also: m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs
Excerpt:

These observations provide a mechanism for disrupting RNA structure through post-transcriptional modifications. The different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help cells meet the opposing requirements of maintaining genome stability, on the one hand, and of dynamically modulating the structure of the epitranscriptome, on the other.

My comment: For several years, others have also attempted to portray what they think are novel mechanisms of RNA-mediated cell type differentiation in the context of the epitranscriptome and epitranscriptomics. Their attempts seem to be nothing more than attempts to obfuscate the facts that have been known about the molecular epigenetics of RNA-mediated cell type differentiation for at least two decades.
See for example:  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: See also this report on “m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs”
DNA’s dynamic nature makes it well-suited to serve as the blueprint of life
Excerpt:

“For something as fundamental as the double helix, it is amazing that we are discovering these basic properties so late in the game,” said Al-Hashimi. “We need to continue to zoom in to obtain a deeper understanding regarding these basic molecules of life.”

Excerpt:

“The team believes that RNA doesn’t form Hoogsteen base pairs because its double helical structure (known as A-form) is more compressed than DNA’s (B-form) structure. As a result, RNA can’t flip one base without hitting another, or without moving around atoms, which would tear apart the helix.” That means fixation of RNA-mediated amino acid substitutions is the basis of life and all biodiversity.

My comment: That fact means DNA cannot serve as the “blueprint of life” outside the context of biophysically constrained energy-dependent fixation of RNA-mediated amino acid substitutions that differentiate all cell types in all living genera. Science journalists continue to twist the facts to support the pseudoscientific nonsense of neo-Darwinian theories.
For musical fun with those who cannot link energy-dependent changes from angstroms to ecosystems in all living genera, see what intelligent people are doing with their experimental evidence of biologically-based cause and effect, which must start with changes in base pairs and link hydrogen-atom transfer from natural selection for energy-dependent codon usage to RNA-mediated amino acid substitutions in supercoiled DNA, which protects all organized genomes from virus-driven entropy.
 

To be continued.
 

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

Chromatin: The structure of DNA

Update on Inflammation and Degenerative Brain Disease

Excerpt:

While mapping connections of neurons has become the holy grail of current neuroscience, it is clear that communication of neurons with many other types cells is, also, vitally important to every aspect of brain function.

My comment:

Understanding dementia was placed into the context of understanding how virus-driven energy theft alters the de novo creation of olfactory receptor genes and causes the loss of function that is linked to all pathology via chromatin remodeling. The energy-dependent chromatin remodeling is linked from alternative RNA splicing to supercoiled DNA via the innate immune system and nutrient-dependent RNA-mediated amino acid substitutions.

An example of what is known about biologically-based cause and effect was placed into the context of two very different patent applications. One addresses prevention, the other is referred to as Church’s “billion dollar baby.”
For prevention see: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis (2011)
For contrast, this is the billion dollar baby: RNA-Guided Human Genome Engineering (2015)
My comment: Nutrient-dependent pheromone-controlled codon optimality links natural selection for food to RNA-mediated cell type differentiation via amino acid substitutions in all cell types of all individuals of all living genera. Transgenerational epigenetic inheritance is the link to energy-dependent ecological adaptations.
Continuing to place the facts about cell type differentiation into the context of cellular intelligence and evolution, which is what Jon Lieff has done for several years, is a misrepresentation of what is known about biologically-based cause and effect. The facts about cell type differentiation place the experience-dependent energy-dependent de novo creation of olfactory receptor genes first.
The creation of new genes is the holy grail of biology. Misrepresentation of virus-driven energy theft, which causes all inflammation and pathology, is the link to replacing the holy grail of biology with the holy grail of neuroscience: mapping connections among neurons. Even when all the connections are mapped, most serious scientists agree that consciousness will not be found among the connections, and that only epigenetic effects on the connections will be linked to degenerative brain disease via chromatin structure and epigenetically-effected supercoiled DNA.
See: From Fertilization to Adult Sexual Behavior
Excerpt (with my emphasis):

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 the context of  our section on molecular epigenetics and sex differences that must be linked to alternative splicings of otherwise identical genes via chromosomal rearrangements in sex chromosomes, we included that fact that energy-dependent chromatin remodeling was the link from the alternative splicings to cell type differentiation via chromatin structure. Should we have specifically mentioned that what organisms eat determines the structure of chromatin?
What caused the 20 year-long delay between reporting what was known about role of epigenetically-effected chromatin in RNA-mediated cell type differentiation and what is being reported now in the context of mapping connections of neurons, which Jon Lieff refers to as the holy grail of current neuroscience? How did the holy grail of biology become the holy grail of neuroscience with the change from de novo gene creation to mapping the effects of new genes and the effects of gene losses in different cell types?
See:

Many researchers have reported the link from epigenetically-effected chromatin remodeling to gene regulation. Most have reported the link outside the context of energy-dependent chemical ecology and changes that must link angstroms to ecosystems in all living genera. The alternative is to dismiss everything known to physicists, chemists, and molecular biologists who have already done that.
See for example: Structural diversity of supercoiled DNA  Can you dismiss supercoiled DNA?
See also: Excess of Deleterious Mutations around HLA Genes Reveals Evolutionary Cost of Balancing Selection Can you dismiss what is known about the innate immune system and codon optimality?
See also: Direct interrogation of the role of H3K9 in metazoan heterochromatin function Can you dismiss the role of H3K9?
Reported as: Tight DNA packaging protects against ‘jumping genes,’ potential cellular destruction
Excerpt: 

Scientists discovered that the major developmental function of heterochromatin — a form of tight DNA packaging found in chromosomes — is likely the suppression of virus-like DNA elements known as transposons or ‘jumping genes,’ which can otherwise copy and paste themselves throughout the genome, potentially destroying important genes, and causing cancers and other diseases.

What will be the next think that pseudoscientists are forced to dismiss if they continue to try to support their ridiculous theories?
See also: Grand project to unify global efforts to understand the brain
Excerpt:

As brainy gatherings go, it takes some beating. Neuroscientists are meeting in New York today to agree on a global mission to understand the workings of the human brain and how to fix it when something goes wrong.
The lofty aim of the Coordinating Global Brain Projects meeting is to unify worldwide efforts to study the brain, in the same way that international collaborations have spurred on astronomy, physics and genetics.
“Neuroscience is coming of age, and it’s now ready for big science,” says Rafael Yuste at Columbia University in New York, who organised today’s meeting with Cori Bargmann at Rockefeller University, also in New York. “This is the first real meeting with all the players in the same room together,” says Yuste.

I mentioned the award that Cori Bargmann won in the narrative of this poster presentation, which was published to Youtube March 2, 2016.
See:  RNA mediated molecular epigenetics and virus driven entropy

In two weeks, Cori Bargmann will receive an award that links a single neuron to all works on the lifespan and behavior of the nematode, C. elegans. That neuron integrates information from multiple chemical cues including food, oxygen and pheromones. The integration of the cues controls the expression of social behavior in the context of changes in pH. She is scheduled to present: “Genes, neurons, circuits and behavior: an integrated approach in a compact brain.

Perhaps she realizes there is no further need for her integrated approach, since energy-dependent RNA-mediated pheromone-controlled cell type differentiation has been linked from species of microbes to humans. Others do not seem to be aware of that fact.
See the discussion on the Neuroscience FB group
For example: Misha Zilberter is the first author of Dietary energy substrates reverse early neuronal hyperactivity in a mouse model of Alzheimer’s disease (2013). His work can be compared in the context of my model: Nutrient-dependent/pheromone-controlled adaptive evolution: a model and also this 2016 report on A Genetically Encoded Probe for Live-Cell Imaging of H4K20 Monomethylation
Excerpt:

Critical amino acids for the stability and/or folding of the mintbody were revealed.

Reported as: New Probe Detects Histone Modifications in Live Cells
Excerpt:

Using genetic analysis and X-ray crystallography, the new work has also identified amino acids that are critical to the solubility and conformational stability of the H4K20me1-mintbody. Aberrant folding of the antibody fragments in the cellular cytoplasm usually causes solubility problems, but a potential solution has been found. As such, the researchers have overcome challenges to the performance of antibody fragments in live cells due to solubility issues.

For insight on what might prevent discussion of facts about RNA-mediated amino acid substitutions and cell type differentiation in all living genera, see:

Thanks to Anna Di Cosmo for calling attention to this. (Although he uses foul language to make his point, it is a point that needs to be made.)
 
Unfortunately, using Bill Nye to represent scientists may cause serious scientists to laugh along with anyone among the lay audience who does not believe what people like Bill Nye claim about evolution.
 
Like serious scientists, they may be waiting for Nye to present experimental evidence that links energy-dependent changes from angstroms to ecosystems in all living genera. Only then are they likely to believe that hydrogen-atom transfer in DNA base pairs in solution is contributing to the loss of species via climate warning.
If changes in the pH of the ocean are not considered, what experimental evidence that links ecological variation to ecological adaptation will be considered by those who think the “Science Guy” is biologically uninformed? Why, from his perspective on evolution, aren’t species simply acquiring more beneficial mutations to evolve —  if that’s what theorists want you to believe in?

See also this discussion of As simple as random can be
See also this discussion of  Four things you should know about brain research
What can anyone expect to come from any Grand project to unify global efforts to understand the brain.  All past grand projects have failed to link what is known about biophysically constrained RNA-mediated protein folding chemistry to cell type differentiation in all living genera via what is known about chromatin, which links energy-dependent changes in the microRNA/messenger RNA balance to biophysically constrained cell type differentiation in all living genera, including those with the primitive brain of a nematode or the brain of a conscious human.
Most the grand projects seem designed to support the ridiculous theories of the project organizers.

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.