Witzhany2018

Sympatric speciation vs pseudoscientic nonsense (2)

This is how intermittent fasting protects us from viruses in the context of using stored fat for quantized energy-dependent RNA-mediated DNA repair.
Fat cells converted into stem cells can repair any damaged tissues (video 3:48)
Some whales use the molecular mechanisms of quantized energy-dependent RNA-mediated DNA repair during their migration, which is when they may not eat anything until after completing their route.
See for details: Energy as information and constrained endogenous RNA interference (video 6:46)

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution.

The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

Whales are often reported to be the largest creatures on Earth. Some some whales eat large amounts of small creatures. That fact links the sympatric speciation of microbes to the sympatric speciation of all life on Earth via the biophysically constrained energy of sunlight and physiology of reproduction in cyanobacteria.
Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).

Long-range coherence and energy storage in biological systems (1968) Published in: International Journal of Quantum Chemistry

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

This notice just appeared in my email inbox with the new title from Aeon: Weekend Reads: Quantum biology and what life wants.
See for comparison: What life wants (2012)

…given that this sense of purposefulness is how we identify life in the first place, perhaps we should resist conclusions that seem to wave it away too easily.

I don’t pretend to have answers to any of these questions. On the other hand, the speed of progress in fields that cross the boundaries between natural sciences – not least quantum biology – makes me optimistic that we will get some, sooner or later.

Aeon magazine continues to attempt to obfuscate their history of horrid misrepresentations exemplified in articles like this:
Quantum common sense (2017)

To turn quantum to classical, we don’t need a conscious mind to measure or look; we just need an environment full of stuff. With or without us, the Universe is always looking.

See the sidebar:

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

See also: Schrödinger at 75 – The Future of Biology – September 2018
See also: 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.

5th-6th Sept 2018 Dublin, Ireland

RNA-mediated nutritional psychiatry (2)

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

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

Neo-Darwinian theorists dispense with Darwin’s food energy-dependent  “conditions of life.” They link mutations and disease to evolution via mathematical models. They exemplify human idiocy.
See for example: Neopterygian phylogeny: the merger assay
Reported as: Adaptive radiations in the Mesozoic

Bony fishes are the most diverse of all extant vertebrate groups. A comprehensive phylogenetic analysis of the group now provides new insights into its 250-million-year evolutionary history.

The claim about the 250-million-year evolutionary history can be compared to what happens when food energy-dependent fixation of a single RNA-mediated amino acid substitution occurs across a vertebrate lineage.
See: Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

It is very surprising and fascinating that the coordinated evolutionary selection of amino acids participating in binding GnRH has resulted in such perfection, that no substitution with a natural amino acid in any position improves binding potency.

Evolution does not select amino acids. Natural selection for food energy-dependent pheromone-constrained viral latency links the substitution of achiral glycine in position 6 of the GnRH decapeptide to the biodiversity of all morphological and all behavioral phenotypes in all vertebrates.
See also: Handbook of Biologically Active Peptides (2013) Chapter 106 GnRH (LHRH)
Page 794 Figure 2 shows that food energy-dependent substitution of achiral glycine at position 6 stabilizes the folded conformation; increases binding affinity; and decreases metabolic clearance.

This feature is incorporated in all agonist and antagonist analogs.

Simply put, the substitution of achiral glycine in the GnRH decapeptide biophysically constrains viral latency in the context of ligand-receptor interactions and the physiology of pheromone-controlled reproduction.
See also: Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

Kohl (2013) is Nutrient-dependent/pheromone-controlled adaptive evolution: a model
The facts that link vertebrates to invertebrates via olfaction and the 2013 model will almost undoubtedly be restated when Tuning Insect Odorant Receptors is published.
Until then, see:Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity (2005)
Biophysical constraints link feedback loops from odors and pheromones to the functional structure of the GnRH decapepetide via achiral glycine in position 6. The link from food to the de novo creation of energy-dependent receptors is required in all organisms. They must select the right food, which helps to ensure their ability to reproduce.

5th-6th Sept 2018 Dublin, Ireland

RNA-mediated nutritional psychiatry

Summary: Young Genes are Highly Disordered as Predicted by the Preadaptation Hypothesis of De Novo Gene Birth
Stop this nonsense about de novo gene birth and you will help to stop the school shootings without more gun control.
See my presentation at the 2017 Precision Medicine Virtual Conference (2/15/17) Energy as information and constrained endogenous RNA interference
See also: Pat Sweeney et al (3/13/2017) Protein misfolding in neurodegenerative diseases: implications and strategies. 

A notable development is the creation of collaborative ecosystems that include patients, clinicians, basic and translational researchers, foundations and regulatory agencies to promote scientific rigor and clinical data to accelerate the development of therapies that prevent, reverse or delay the progression of neurodegenerative proteinopathies.

For consideration of protein folding in the context of my life’s works, see: From de novo to “de nono”: most novel protein coding genes identified with phylostratigraphy represent old genes or recent duplicates

Claudio Casola refers “… to the putative de novo genes that failed to pass the validation criteria as the ‘de nono’ genes.” Use of the term ‘de nono’ to refute Pat Sweeney’s neo-Darwinian pseudosceintific nonsense is brilliant! For instance, all serious scientists know that protein folding chemistry is energy-dependent.
 
 

The structural diversity biophysically constrains viral latency and the constraints are referred to in the context of RNA-mediated autophagy. Autophagy clearly makes “de novo” gene creation a no-no term. That is why serious scientists are not likely to use the term de novo. It is like claiming that something automagically occurs.

In the context of what is known about energy-dependent cell type differentiation, see also:

Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis (2011)

and

Formulation and evaluation of anti-suicidal nasal spray of Thyrotropin releasing hormone (2017)
The fact that food odors and pheromones biophysically constrain physical and mental pathology via alternative splicings of RNA has been addressed in published works since 1990.
See for a recent example: RNA splicing is a primary link between genetic variation and disease (2016)
See for examples of constraints:
Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults (E-pub 2014)
The catechol-o-methyltransferase Val158Met polymorphism modulates the intrinsic functional network centrality of the parahippocampal cortex in healthy subjects (2015)
Subsecond Regulation of Synaptically Released Dopamine by COMT in the Olfactory Bulb (2016)
The COMT Val158Met polymorphism exerts a common influence on avoidant attachment and inhibited personality, with a pattern of positive heterosis (2017)
In the context of energy-dependent constraints, the COMT VaL158Met amino acid substitution exemplifies the facts detailed in the context of: Hydrogen bonds directly detected for the first time (2017). The facts about hydrogen-atom transfer in DNA base pairs in solution have since been linked to all energy-dependent pheromone-controlled biodiversity in: Principles of Transgenerational Small RNA Inheritance in Caenorhabditis elegans (2017)
See also: Catechol O-methyltransferase (COMT) functional haplotype is associated with recurrence of affective symptoms: A prospective birth cohort study (1/15/2018)
Analysis of COMT Val158Met polymorphisms and methylation in Chinese male schizophrenia patients with homicidal behavior (2/20/2018)
Adjunctive nutrients in first‐episode psychosis: A systematic review of efficacy, tolerability and neurobiological mechanisms (3/21/18)
Reported as: Antioxidants and amino acids could play role in the treatment of psychosis 3/22/2018
See for comparison: March for Our Lives 3/24/18

Theme Gun violence awareness
Support of gun control

The focus on support of gun control ignores everything known to all serious scientists about biophysically constrained mental health and the virus-driven constraint-breaking mutations in the killers with guns. The future of school shootings depends on mental health treatment.

Why nutritional psychiatry is the future of mental health treatment

…29 clinical trials of antidepressant use in young people found no benefits at all. These trials revealed that instead of relieving symptoms of anxiety and depression, antidepressants caused children and young people to feel suicidal.

See for comparison: 7/25/13 Jay R. Feierman:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

My understanding of biology is linked to my understanding of physics and chemistry via 40 years testing experience as a medical laboratory scientist (ASCP emeritus). Simply put, all organisms must eat and reproduce or species do not survive. The discovery of bacteria that eat electrons and create uranium ore was place into the context of this news:
Biologists discover electric bacteria that eat pure electrons rather than sugar, redefining the tenacity of life (2017)
The link from eating electrons to hydrogen-atom transfer in DNA base pairs in solution appears in the context of energy delivery to all cell types in organisms that have blood in their circulatory system. The claim that the human circulatory system evolved incorporates ‘de nono’ gene creation.
There is no such thing as de novo gene creation and ‘de nono gene creation’ can now be used in the context of post-publication ridicule of this model:
Basic Science Model of Blood as an Electron-Delivery Circuit Describes the Evolution of the Human Circulation (2017)
The anti-entropic virucidal energy of sunlight is the link from ecological variation to ecological adaptation in the context of the physiology of reproduction and biophysically constrained viral latency. Pseudoscientists will not stop trying to place that fact into the context of ridiculous neo-Darwinian theories.
Thankfully, ages 10+ can learn how energy-dependent life is biophysically constrained by playing the cell biology game “Cytosis” and the game that links energy-dependent changes from electrons to ecosystems in all living genera: “Subatomic“.
See my attempt to deliver that message in: There is no such thing as de novo control of electrons or the self-assembly of genes. (11/21/17)
But see: Young Genes are Highly Disordered as Predicted by the Preadaptation Hypothesis of De Novo Gene Birth
Stop this nonsense and you will help to stop the school shootings without more gun control.

Caption: Contemporary analyses of cell metabolism have called out three metabolites: ATP, NADH, and acetyl-CoA, as sentinel molecules whose accumulation represent much of the purpose of the catabolic arms of metabolism and then drive many anabolic pathways. Such analyses largely leave out how and why ATP, NADH, and acetyl-CoA (Figure 1) at the molecular level play such central roles. Yet, without those insights into why cells accumulate them and how the enabling properties of these key metabolites power much of cell metabolism, the underlying molecular logic remains mysterious. Four other metabolites, S-adenosylmethionine, carbamoyl phosphate, UDP-glucose, and Δ2-isopentenyl-PP play similar roles in using group transfer chemistry to drive otherwise unfavorable biosynthetic equilibria. This review provides the underlying chemical logic to remind how these seven key molecules function as mobile packets of cellular currencies for phosphoryl transfers (ATP), acyl transfers (acetyl-CoA, carbamoyl-P), methyl transfers (SAM), prenyl transfers (IPP), glucosyl transfers (UDP-glucose), and electron and ADP-ribosyl transfers (NAD(P)H/NAD(P)+) to drive metabolic transformations in and across most primary pathways. The eighth key metabolite is molecular oxygen (O2), thermodynamically activated for reduction by one electron path, leaving it kinetically stable to the vast majority of organic cellular metabolites

Ecological adaptation: A new definition of heredity (3)

Excerpt:
Moving forward: Novel and Haplotype Specific MicroRNAs Encoded by the Major Histocompatibility Complex

…these data suggest that a subset of the identified novel miRNAs may contribute to the pathophysiology of numerous diseases, laying the groundwork for future studies to elucidate the functional connections of miRNAs to the numerous diseases associated with sequence variants within non-coding regions of the MHC.

OMCD: OncoMir Cancer Database

Dysregulation of miRNAs is commonly observed in cancers and it largely cancer dependent.

The virus-driven theft of quantized energy as information has been linked from changes in the microRNA/messenger RNA balance to all pathology. That fact replaces the circular logic that links cancer-dependent dysregulation of miRNAs to cancer.  Simply put, the proliferation of viruses cause cancer. The proliferation of viruses is energy-dependent in the context of established links from atoms to ecosystems in all living genera.
See: Subatomic: An Atom Building Board Game

A deck-building game where particle physics & chemistry collide! Use quarks to build subatomic particles & particles to build Atoms!

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

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements.

Moving forward: Novel and Haplotype Specific MicroRNAs Encoded by the Major Histocompatibility Complex

…these data suggest that a subset of the identified novel miRNAs may contribute to the pathophysiology of numerous diseases, laying the groundwork for future studies to elucidate the functional connections of miRNAs to the numerous diseases associated with sequence variants within non-coding regions of the MHC.

My “Disqus” comment (and nearly 2000 others): Gene expression is energy-dependent, RNA-mediated, and biophysically constrained.
See: FUS Regulates Activity of MicroRNA-Mediated Gene Silencing.

MicroRNA-mediated gene silencing is a fundamental mechanism in the regulation of gene expression.

MicroRNAs do not create themselves.
See also:  Energy as information and constrained endogenous RNA interference
8 of my 9 most recent comments to Disqus have been removed.
See for comparison: Incomplete host immunity favors the evolution of virulence in an emergent pathogen
Reported as: In nature, an imperfect immune system drives the evolution of deadly pathogens

…birds that eat at feeders are more likely to be infected with the disease, which causes red, swollen eyes and often blindness that results in death.

…lower virulence strains could be their own worst enemies, creating a population of hosts that are resistant to them but not the higher virulence strains that remain.

By removing my Disqus comments, the moderators limit discussion of the facts about virus-driven energy theft, which links mutations to all pathology.  That allows the biased reporting on preprints that continue to try to support the ridiculous concept of neo-Darwinian evolution.
It also prevents the realization of goals by serious scientists who have linked the biogenic creation of uranium ores to the prevention of radiation sickness via microRNA therapy. See, for examples: miRNA-mediated therapies
A miRNA-145/TGF-beta1 Negative Feedback Loop Regulates the Cancer-Associated Fibroblast Phenotype

…miR-145 is a key regulator of the CAF phenotype, acting in a negative feedback loop to dampen acquisition of myofibroblastic traits, a key feature of CAF associated with poor disease outcome.

See also: Microhomology-assisted scarless genome editing in human iPSCs

Gene-edited induced pluripotent stem cells (iPSCs) provide relevant isogenic human disease models in patient-specific or healthy genetic backgrounds. Towards this end, gene targeting using antibiotic selection along with engineered point mutations remains a reliable method to enrich edited cells. Nevertheless, integrated selection markers obstruct scarless transgene-free gene editing. Here, we present a method for scarless selection marker excision using engineered microhomology-mediated end joining (MMEJ). By overlapping the homology arms of standard donor vectors, short tandem microhomologies are generated flanking the selection marker. Unique CRISPR-Cas9 protospacer sequences nested between the selection marker and engineered microhomologies are cleaved after gene targeting, engaging MMEJ and scarless excision. Moreover, when point mutations are positioned unilaterally within engineered microhomologies, both mutant and normal isogenic clones are derived simultaneously. The utility and fidelity of our method is demonstrated in human iPSCs by editing the X-linked HPRT1 locus and biallelic modification of the autosomal APRT locus, eliciting disease-relevant metabolic phenotypes.

Reported as: Gene Editing Is Now Precise Enough to Modify a Single Letter of DNA

To make these very precise edits, an SNP modification is first inserted alongside a fluorescent reporter gene that helps researchers to identify modified cells. The researchers engineered a duplicate DNA sequence known as a microhomology (hence the technique’s name) on each side of the fluorescent gene, targeting sites for CRISPR to go in and cut DNA. The researchers were then able to use a DNA repair system known as microhomology-mediated end joining (MMEJ) to remove the fluorescent gene. That left only the single-base edit, in the form of an SNP, behind.

See also: Inhibition of the Host Translation Shutoff Response by Herpes Simplex Virus 1 Triggers Nuclear Envelope-Derived Autophagy
Nuclear envelope-derived autophagy (NEDA) appears to be a cellular stress response, which is triggered late during HSV-1 infection. An energy-dependent single nucleotide repeat (SNR) might compensate for the viral alteration of the macroautophagic response. At this level of hydrogen-atom energy transfer in DNA base pairs in solution, the link to supercoiled DNA and viral latency becomes increasingly important.
Theorists are angry because they have been left behind. They know very little about what is important. That was expected by all serious scientists, especially those who have accumulated decades of testing experience while working in medical laboratories.
See for example: Applications of ligation-mediated PCR

Using a molecular energy source (which differs depending on the enzyme source organism), DNA ligase reforms the missing covalent bond and the strand is whole again. Two aspects of this are critical:

The nick to be repaired occurs on a single strand but in the context of a double-stranded molecule.
The bases of the nicked strand, and particularly those directly flanking the nick site, must be properly base-paired to the opposite (un-nicked) strand.

It’s not hard to imagine why this is: the base pairing is required to hold the two parts (sugar 3′ -OH and the next phosphate) in place for the ligase enzyme active site to catalyze joining them. If either one of these isn’t base-paired down and is flopping about with thermal motion, the reaction geometry doesn’t occur, and no new bond can be made.

Biologically uninformed theorists cannot even speak the same language. They do not start with a molecular energy source for base pairing and microRNA-mediated amino acid substitutions that differentiate all cell types. Instead, mutations are linked to increasing organismal complexity via the magic of evolution.

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.

Quantized energy-dependent viral trophism (3)

Summary: If the pathway is ancestral, how and when did it evolve to protect species from microbes to humans from the virus-driven degradation of their messenger RNA?

Peer-Reviewed Science: A “Mathematical Proof of Darwinian Evolution” Is Falsified

The theorem addresses only the effects of natural selection. Fisher did not directly address any other effect (mutation, genetic drift, environmental change, etc.) as he considered them to be insignificant. Later mathematicians took issue with Fisher’s lack of rigor, some at considerable length. But the omission of the effects of mutation got the most attention.

The effects of mutation are revisited in: Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus
The automagical creation of receptors is an important determinant of viral tropism. A comparison of amino acid frequencies is linked to ecological adaptation in the virus without concern for the fact that all ecological adaptations are quantized energy-dependent. The authors seem to know nothing about the energy-dependent creation of enzymes and receptors.
See also: Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasite Leishmania
Again, where did the energy come from for the adaptations to viruses by these organisms? Is the diversity caused by mutations and evolution in:

…fungi, green algae, diatoms, slime molds, oomycetes, dinoflagellates, apicomplexans, kinetoplastids, diplomonads, and trichomonads…

The authors cite: The evolution of RNAi as a defence against viruses and transposable elements. (2009) and claim that the RNAi pathway is “believed to be ancestral to all eukaryotes.”
If the pathway is ancestral, how and when did it evolve to protect species from microbes to humans from the virus-driven degradation of their messenger RNA?
See: Virus-mediated archaeal hecatomb in the deep seafloor

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

Viruses (aka bacteriophages) kill bacteria. That is how they control archaeal dynamics. Viruses steal the quantized energy from bacteria, which causes bacteria to become archaea and cells out walls (L-forms). Bacteria, for comparison, use the sun’s anti-entropic virucidal energy to ecologically adapt. All life on Earth depends on the anti-entropic virucidal energy of sunlight. The virus-driven degradation of messenger RNA links mutations to all pathology. Theorists may be unable to understand that fact, because they never learned how to link sunlight to error-free RNA-mediated DNA repair via endogenous RNA interference.
See: Energy as information and constrained endogenous RNA interference (6:46)

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection. This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes minutes.

Something has gone horribly wrong among pseudoscientists, and that fact  is being exposed.
PNAS Editor-in-Chief Placed on Leave

… I recognize the sensitivities present in this current environment and have far too much esteem for NAS to risk the possibility that events related to Salk would in any way distract from the Academy’s extraordinary work…
 

Let’s put this into perspective of the extraordinary example of pseudoscientific nonsense published by researchers at Johns Hopkins who have a “bad luck” theory of cancer.

 

They published in “Science”. No charges have been filed for discrimination against intelligent serious scientists.

 
 
 

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

Exome Sequencing Impact in Routine Care

Summary: They placed the pseudoscientific nonsense about selection for beneficial mutations into the context of positive selection for mutations, which are caused by the virus-driven degradation of messenger RNA. The mutations have been linked to all pathology. It’s as if all theorists want to become known as “biologically uninformed science idiots” via their associations with others who have touted claims about “beneficial mutations.”

US Air Force Studying Impact of Exome Sequencing in Routine Care

Who, among my fellow veterans, and especially among others from The American Legion and The American Legion Riders, did not anticipate that the US Air Force would lead the way forward to prevention of all virus-driven pathology via the use of this technology?

The doctors will receive an educational primer in genomics and on-site genetic counseling support. After exome testing is performed on patients, their doctors will get a report listing the pathogenic and likely pathogenic variants related to dominant and recessive monogenic conditions, risks for complex diseases, and response to drugs. These results will be entered into the service members’ electronic medical records.

I was trained to become a medial laboratory scientist during the last 4 years of my 7 years in the United States Air Force (Dec. 1970-Aug. 1977).  I worked in the laboratory and examined the experimental evidence reported in published works, I learned that all pathogenic variants are caused by the virus-driven degradation of messenger RNA. I also learned that pharmacogenomic profiles have already been linked to effective treatments for virus-driven energy theft via my model of nutrient-dependent pheromone-controlled biodiversity.
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 model refuted every aspect of neo-Darwinian pseudoscientific nonsense, which may be why some doctors never heard about it, or why some of them don’t want to admit to what they know about effective treatments for all pathology.
During suicide prevention month, the National Commander of the American Legion focused on efforts to help reduce the number of suicides among veterans, which occur at ~ 22 each day. I was surprised to see how little response from the general public there has been since then. It’s as if no one has learned about experimental evidence of biologically-based cause and effect such as this:
Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity

Differences in miRNA expression or structural gene variants were not detected. Results lend further support for models in which deficits in microglial, endothelial (blood-brain barrier), ATPase activity and astrocytic cell functions contribute to MDD and suicide, and identify putative pathways and mechanisms for further study in these disorders.

The only obvious link from from energy-dependent ATPase activity to cell type function in all cell types of all living genera is the anti-entropic virucidal energy of sunlight, which biophysically constrains viral latency in the context of the pheromone-controlled physiology of reproduction. That fact suggests exome sequencing data must be linked to routine case via the creation of energy, the creation of ATP and the creation of RNA.
See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

If the role of microRNAs is not examined in the context of virus-driven energy theft, the degradation of messenger RNA cannot be linked to all pathology. The suicide rate may never change, or it may not change until the virus-driven degradation of messenger RNA is linked to cancer and all other pathology in species from microbes to humans.
See also: exome sequencing microRNA  for examples like this:
Whole exome sequencing and single nucleotide polymorphism array analyses to identify germline alterations in genes associated with testosterone metabolism in a patient with androgen insensitivity syndrome and early-onset colorectal cancer.
If you do not agree that exome sequencing is the key to understanding the difference between energy-dependent healthy longevity and virus-driven pathology, please explain what you don’t like about the scientific approach to effective treatment and/or prevention of all pathology in the context of Precision Medicine.
See also: Energy as information and constrained endogenous RNA interference from the Labroots: Precision Medicine Virtual Conference February 22-23. 2017
Narrative: The term microRNA has been used in 58,000 indexed works. All the works support claims that link the anti-entropic virucidal energy of sunlight from endogenous RNA interference to biophysically constrained protein folding chemistry and cell type differentiation.

Abstract:

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

The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes.

For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

See for comparison: Evolutionary Analysis Reveals Number, Nature of Mutations Under Positive Selection in Cancer

The research shows that “across cancer types a relatively consistent small number of mutated genes is required to convert a single normal cell into a cancer cell, but that the specific genes chosen differ according to cancer type,” Sanger Institute Director Michael Stratton, a co-author on the study, said in a statement.

…the researchers identified almost 200 mutated genes under positive selection in cancer — a collection that included known cancer contributors and genes not previously implicated as cancer driver candidates.

They placed the pseudoscientific nonsense about selection for beneficial mutations into the context of positive selection for mutations, which are caused by the virus-driven degradation of messenger RNA. The mutations have been linked to all pathology. It’s as if all theorists want to become known as “biologically uninformed science idiots” via their associations with others who have touted claims about “beneficial mutations.”

Lethal virus kills 5 billion people?

Entertaining yourself to death

Summary: Food energy is required for the creation of enzymes that metabolize the food, which links the metabolism to the pheromone-controlled physiology of reproduction in species from microbes to humans via alternative splicings of pre-mRNAs, which are now called microRNAs in more than 65,000 published works. The horrid tradjedy of of yet another preventable death by suicide extends those works to preventing the cause of death of those killed by Stephen Paddock.
Vegas gunman transferred $100K, set up cameras at hotel room
Excerpts with my emphasis:

Lombardo said he is “absolutely” confident authorities will find out what set off Paddock, a 64-year-old high-stakes gambler and retired accountant who killed himself….

…speculated that there was “some sort of major trigger in his life — a great loss, a breakup, or maybe he just found out he has a terminal disease.”

…a “psychological autopsy” may be necessary to try to establish the motive. If the suicide didn’t destroy Paddock’s brain, experts may even find a neurological disorder or malformation

He said there could be a genetic component to the slaughter…

“The genetics load the gun, personality and psychology aim it, and experiences pull the trigger, typically,” Clemente said.

He later worked for a defense contractor.

“No affiliation, no religion, no politics. He never cared about any of that…

Two former facebook friends are among those who claim that “nobody cares” that I have detailed the facts about the virus-driven cause of death for Stephen Paddock and his victims. When will others learn why there was no obvious motive to his madness?
The excerpts above clearly indicate that virus-driven epigenetic drift led to the deadly constraint-breaking mutations via everything known to serious scientists about epitranscriptomics and biophysically constrained viral latency.
Simply put, like most people, Stephen Paddock failed to protect himself from the virus-driven degradation of messenger RNA that serious scientists have linked to all pathology in all living genera. Psychiatrist/antagonist Jay R. Feierman put that fact into the context of this post to the “Evolutionary Psychology” Yahoo Group.

168958 Origin and Evolution of RNA-Dependent RNA Polymerase OPEN ACCESS

I find this article interesting because of the “object of study.” We are used to thinking about evolution at hierarchical levels above that of protein enzymes. Yet, protein enzymes are “structural design features” and follow the same principles of evolution by natural selection as structural design features at higher hierarchical levels, such as certain kinds of behaviors and even species. Compared to other kinds of evolution, protein enzyme evolution is very conservative in that it does not change much through phylogeny. We essentially have the same enzymes for metabolizing glucose as do bacteria and other single cell animals.

The death of Stephen Paddock and his victims can now be attributed to medical professionals, like Jay R. Feierman, and anyone else who claims: “We are used to thinking about evolution at hierarchical levels above that of protein enzymes.”
The creation of protein enzymes requires an energy source. That fact refutes every aspect of the pseudoscientific nonsense touted by biologically uninformed science idiots. [An idiot is someone with no professional expertise: A biologically uninformed science idiot is someone like Feierman, who has professional expertise but no common sense.] Feierman linked to this article: Origin and Evolution of RNA-Dependent RNA Polymerase (with my emphasis)

With the emergence of a variant with properties of reverse transcriptase, and subsequently a DNA polymerase, a fundamental step occurred to originate the first genomes based in DNA, being the bridge to move from a RNA/Protein World to a DNA/RNA/Protein World (Gilbert, 1986; Müller, 2006). When DNA molecules emerged, by variation, other classes of polymerases appeared. With the complexification of the biological system, functions such as replication, repair, and recombination emerged, very high error rates were selected against, and the new variants arose to work in specific processes.

My summary: The authors eliminate the energy-dependent creation of enzymes (1) reverse transcriptase and (2) a DNA polymerase. In the second act of their tragic comedy routine, they eliminate the biophysical constraints that link the physiology of pheromone-controlled reproduction from natural selection for energy-dependent codon optimality to the creation of enzymes and food energy-dependent RNA-mediated DNA repair via feedback loops.
See: Feedback loops link odor and pheromone signaling with reproduction
The feedback loops link the sense of smell in bacteria from the physiology of their pheromone-controlled reproduction to our visual perception of energy and mass in the context of the space-time continuum.
See: Olfaction Warps Visual Time Perception

The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.

Virus-driven degradation of messenger RNA links alterations in the timing of multisensory events to the suicide of Stephen Paddock and to the unnecessary suffering and premature death of his victims. That fact was placed into the context of Feierman’s thinly veiled attack on the practice of Precision Medicine.
See: Energy as information and constrained endogenous RNA interference, which was presented during the Labroots: Precision Medicine Virtual Conference February 22-23. 2017
Description:

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

Stephen Paddock killed 59 people and more than 500 people were injured. On 10/4/17, there were only 637 views of my 7 minute-long presentation. With release of the cell biology game “Cytosis,” which is scheduled to be available later this month, everyone who is not dead yet will be able to learn how to protect themselves from the cause of death by suicide: viruses. The virus-driven degradation of messenger RNA will also be the cause of death for people who have not learned the difference between energy-dependent healthy longevity and the virus-driven energy theft that will kill them either directly or indirectly.

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

See also this comment to the human-ethology Yahoo group (reproduced below)

See for comparison: Transcription factor clusters regulate genes in eukaryotic cells

Attempts continue to link epigenetic drift and epitranscriptomics to RNA-mediated cell type differentiation outside the context of natural selection for energy-dependent codon optimality and the biophysically constrained pheromone-controlled physiology of reproduction. All past attempts have failed.

The reason for those attempts and the reason all past attempts have failed may require more clarification from people like Jay R. Feierman. Others realize that the enzymes linked from metabolism to survival of all species did not create themselves and did not evolve, which means that no species evolved via natural selection for beneficial mutations. Pseudoscientists have been left behind with their hypothetical scenarios.’

See for example: Origin and Evolution of RNA-Dependent RNA Polymerase

“Based in the present results, we suggest a hypothetical scenario where initially a ribozyme with polymerase activity could have enhanced its activity by the binding of a simple cofactor, as magnesium (Shechner et al., 2009; Horning and Joyce, 2017), thus, exerting the functions of replication of some information stored on RNA molecules (Kim and Higgs, 2016; Tagami et al., 2017).”

See for comparison: Lipid Encapsulation of Self Replicating Ribozymes

“Despite their challenges, ribozymes have made an interesting niche for themselves in the field of abiogenesis. The evolution of a successful RNA polymerase ribozyme is a lofty goal. While its discovery would not be the be-all and end-all of abiogenesis research, it would represent an important stepping stone between prebiotic chemistry and life. The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection. Based on progress in current research, it is only a matter of time before that ribozyme is discovered.”

I have discussed the claims about abiogenesis and ribozymes in the context of “…a system of heredity and evolution through natural selection…” with scientists who have repeatedly assured me that the claims are nothing more than examples of what Richard Feynman placed into the context of “human idiocy.” Food energy is required for the creation of enzymes that metabolize the food, which links the metabolism to the pheromone-controlled physiology of reproduction in species from microbes to humans via alternative splicings of pre-mRNAs, which are now called microRNAs in more than 65,000 published works.

See for example: miRNA as viral transcription tuners in HPV-mediated cervical carcinogenesis

Discovery of microRNAs (miRs) in recent years and differential expression of a set of specific miRs in HPV infection and cervical lesions indicate that among various regulatory mechanisms, role of these differentially expressed miRs in the post-transcriptional control is pivotal.

When will people like Feierman and Jones begin to examine the extant literature that links energy-dependent biophysically constrained biologically-based cause and effect as detailed in the molecular epigenetics section of our 1996 review:
From Fertilization to Adult Sexual Behavior
How many more people will needlessly suffer and/or die prematurely due to the ignorance and arrogance of biologically uninformed science idiots?

Lethal virus kills 5 billion people?

Predicting who wins the 2017 Nobel Prizes (2)

Summary: Endogenous RNA interference is the energy-dependent epigenetic link from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency. The stress-linked virus-driven degradation of messenger RNA has been linked to all pathology.
Three Americans win Nobel medicine prize for body rhythm work [But they failed to link Americanism to Creationism]
I predicted that Wen Zhou would win for linking the energy-dependent creation of G protein-coupled receptors to all biodiversity via olfaction and the space-time continuum in the context of RNA-mediated cell type differentiation via the physiology of pheromone-controlled reproduction. See: Olfaction Warps Visual Time Perception. 
She returned to China after training in the United States of America, but is a good example of someone who appears to practice Americanism, which is an ideology that appears to be integrated into her research. I do not know what people in China refer to in the context of this ideology.

In the words of Theodore Roosevelt, “Americanism is a question of spirit, conviction, and purpose, not of creed or birthplace.”[3]

After Ben Feringa (Chemistry/chirality) and Yoshinora Ohsumi (Physiology or Medicine/autophagy) won last year, I thought that all gene-centric nonsense would be eliminated. It became perfectly clear that energy-dependent changes in chirality must be linked to autophagy, which protects all organized genomes from the virus-driven degradation of messenger RNA.
Instead, see:

Excerpt 1) The awardees’ work stems back to 1984, when Rosbash and Hall, who was then also at Brandeis, along with Young isolated the “period gene” in fruit flies. Hall and Rosbash found that a protein encoded by the gene accumulated during the night and degraded during daytime. A decade later, Young discovered another “clock gene.”

Excerpt 2) “The paradigm-shifting discoveries by the laureates established key mechanisms for the biological clock,” the Nobel Assembly said in its prize statement.

See for comparison: The Nobel Prize in Physiology or Medicine 1973 Karl von Frisch, Konrad Lorenz and Nikolaas Tinbergen

for their discoveries concerning organization and elicitation of individual and social behaviour patterns.

The organization and elicitation of individual social patterns of behavior is energy-dependent and it links what organisms eat to the metabolism that links the energy to the physiology of pheromone-controlled reproduction in species from microbes to humans.
Since 1973,  and especially during the past 13 years, there has not been a gene-centric theory that has successful been linked to a paradigm shift. For example, all paradigm-shifting Nobel Prizes in Physiology or Medicine during the past 13 years have linked the energy-dependent creation of ATP and the creation of messenger RNA to protection from the virus-driven energy theft that serious scientists have linked from the degradation of messenger RNA to all pathology.
See for examples:
2016: Yoshinori Ohsumi of Japan for his work on autophagy—a process whereby cells “eat themselves”—which when disrupted can cause Parkinson’s and diabetes.
2015: William Campbell (US citizen born in Ireland) and Satoshi Omura (Japan), Tu Youyou (China) for unlocking treatments for malaria and roundworm.
2014: John O’Keefe (Britain, US), Edvard I. Moser and May-Britt Moser (Norway) for discovering how the brain navigates with an “inner GPS”.
2013: Thomas C. Suedhof (US citizen born in Germany), James E. Rothman and Randy W. Schekman (US) for work on how the cell organises its transport system.
2012: Shinya Yamanaka (Japan) and John B. Gurdon (Britain) for discoveries showing how adult cells can be transformed back into stem cells.
2011: Bruce Beutler (US), Jules Hoffmann (French citizen born in Luxembourg) and Ralph Steinman (Canada) for work on the body’s immune system.
2010: Robert G. Edwards (Britain) for the development of in-vitro fertilisation.
2009: Elizabeth Blackburn (Australia-US), Carol Greider and Jack Szostak (US) for discovering how chromosomes are protected by telomeres, a key factor in the ageing process.
2008: Harald zur Hausen (Germany), Francoise Barre-Sinoussi and Luc Montagnier (France) for work on the viruses causing cervical cancer and AIDS.
2007 Mario R. Capecchi, Sir Martin J. Evans and Oliver Smithies for their discoveries of principles for introducing specific gene modifications in mice by the use of embryonic stem cells.
2006 Andrew Z. Fire and Craig C. Mello for their discovery of RNA interference – gene silencing by double-stranded RNA.
2005 Barry J. Marshall and J. Robin Warren for their discovery of the bacterium Helicobacter pylori and its role in gastritis and peptic ulcer disease.
2004 Richard Axel (US) and Linda Buck (US) for their discoveries of “odorant receptors and the organization of the olfactory system.
Endogenous RNA interference is the energy-dependent epigenetic link from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency. The stress-linked virus-driven degradation of messenger RNA has been linked to all pathology.
Addendum 1)
This morning I spoke with a 10-year veteran who had served in Iraq. He was not happy with the treatment for PTSD that he was receiving from the VA because he and his wife know he is getting worse (e.g., hyper-vigilance and more nightmares).

He has a 20% disability and my antagonists are causing it to get worse with their claims that my life’s works are “bullspit” and/or that “nobody cares.”
 
How can anyone convince a veteran that people care at a time when most will not take the time to watch a short video like this one?  Superbugs, Bacteriophages and Phage Therapy: An Interview with James Kohl Published on 17 May 2017
 
See for comparison:3/09/17 Jay Feierman: One can’t have Darwinian evolution by natural selection without either “random” mutations or directional selection. They are both necessary, proximate, contributing causes for genes and the proteins they code for changing in frequency over time in a population and by which the population becomes adaptively configured to the current environment.
 
Adaptations are food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans.The claim that populations are adaptively configured are nothing more than pseudoscientific nonsense.
 

If you let our veterans, as individuals, continue to think they are less than human because a mutation or something else causes their failure to adapt to the challenges of life after returning from military service overseas, how will you convince yourself that you are not contributing to the death rate by suicide?

Addendum 2) Las Vegas Shooting: Live Updates (with video)

Other lawmakers woke up to the news and offered thoughts and prayers. Governor Brian Sandoval of Nevada called the shooting a “heinous act of violence.”

All heinous acts of violence are caused by the virus-driven degradation of messenger RNA, not by the natural selection for mutations as claimed in Mutation-Driven Evolution

(2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation.

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’.

For God and Country

Life and death via chemical effects on photosynthesis

Summay: “…chemosignals are a promising approach both to modeling posttraumatic stress disorders in humans [36] and to searching for mehods of their treatment.”
Serious scientists linked the sense of smell in bacteria from the physiology of pheromone-controlled reproduction in all living genera to our visual perception of energy and mass in the context of the space time continuum.
The fact that food odors and pheromones biophysically constrain cell type differentiation in mammals was first placed into the context of [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] (1994)


For evidence of the link from the anti-entropic virucidal energy of sunlight to all biodiversity, see also: 1994 Effect of atrazine herbicide on growth, photosynthesis, protein synthesis, and fatty acid composition in the unicellular green alga Chlorella kessleri

Sublethal atrazine concentrations induced a general inhibition on growth, photosynthesis, and dark respiration in the green alga Chlorella kessleri….. Progressive reduction in protein synthesis was associated with increasing herbicide concentration at all experimental periods. The herbicide had preferential effect on the associated fatty acid composition of total and phospholipids. After 24 and 48 hr the herbicide stimulated fatty acids synthesis at concentrations where photosynthesis was inhibited. Meanwhile, stearic and miristic acids disappeared at 15 μM after 24 hr and the total polyunsaturated fatty acids were not affected after 48 hr. Fatty acid synthesis was sensitive to treatment at 72 hr by 5 and 10 μM atrazine, whereas the total saturated fatty acids were completely inhibited.

Sublethal effects of  chemicals on protein biosynthesis and degradation have been linked to all pathology via the virus-driven degradation of messenger RNA, which links changes in the microRNA/messenger RNA balance to mutations and all pathology. For example, this is what must happen to link the sun’s anti-entropic virucidal energy from electrons to ecosystems via the chemistry and physiology of pheromone-controlled reproduction in all living genera.

A dietary difference in nematodes links their chemistry of metabolism from what they eat to the pheromone-controlled physiology of reproduction in C. elegans and the ecological adaptations manifested in P. pacificus, a predatory nematode with teeth.
See other information on biophysically constrained biologically based cause and effect in Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

The epigenetic effects of nutrients on evolved differences in the diet and starch digestion of dogs and wolves (Axelsson et al., ) were detailed at the same time differences in the socialization of these subspecies were attributed to explorations involving only chemosensory input in 3 to 4-week-old wolf pups. For comparison, differences in starch digestion and exploration involving multisensory input in dogs begin a mere 2 weeks later (Lord, ). The differences in nutrient-dependent pheromone-controlled socialization, however, extend across a life-time of more aggressive behavior in wolves that have not been domesticated because less digested starch from their diet genetically predisposes infants to first respond to olfactory/pheromonal cues as they initially explore their postnatal environment.

See also: Dogs Recognize Themselves in Test Based on Smell, Not Sight

But, she said, her test and the mirror tests “all show that there’s this selective sensory investigation of something that comes from yourself, but is changed.”

The link from a light-induced change in an endogenous substrate — that comes from yourself — to the physiology of reproduction is changed by the pheromone-controlled physiology of reproduction, which is linked to all biodiversity.
That fact and facts about intelligence in different species started to become clear when Schrodinger (1944) wrote:

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)

Perfect clarity was achieved among all intelligent serious scientists when McEwen et al, (1964) wrote; Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation

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

Nothing in life happens outside the context of the ATP-dependent creation of RNA.
Decades later, 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?” (Roger Penrose 8 August 1991)

See also: Olfaction Warps Visual Time Perception
The authors linked the sense of smell in bacteria from the physiology of pheromone-controlled reproduction in all living genera to our visual perception of energy and mass in the context of the space time continuum.
The fact that food odors and pheromones biophysically constrain cell type differentiation in mammals was first placed into the context of [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] (1994) in Russian
Abstract excerpt (in English)

The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

See also: [Cytogenetic effect of volatile components of urine of sexually mature animals on bone marrow cells of young female house mice Mus musculus L] (1996) in Russian

Effects of volatile components of the urine (VCU) of mature male and female CBA/LacStoRap mice on proliferating bone marrow cells in young females of the same line were analyzed.

In 2005,  a 2004 Nobel Laureate and her co-authors caught up to what researchers in Russia had already been claiming for 20 years. See: Feedback loops link odor and pheromone signaling with reproduction
See also: Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain (2014) with my emphasis

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

[46] is Kohl, J.V., Atzmueller, M., Fink, B., and Grammer, K., Human pheromones: integrating neuroendocrinology and ethology, Neuroendocrinol. Lett., 2001, vol. 22, pp. 309–321.
See also: Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems (2015)

Genetic monitoring of the environment is an important component in the analysis of the status of the biosystems. Its efficiency depends on the correct choice of (a) natural bioindicator species; (b) appropriate signs reflecting the state of the environment; and (c) appropriate statistical analysis. The assessment of genomes’ integrity plays the key role in the studies of mutagenicity in a polluted environment. We present a step-by-step recommendations for the analysis of the cytogenetic data and discuss the prospects of applying genetic tests for ecological monitoring, based on the example of analysis using crustacean species.

The nutrient energy-dependent pheromone-controlled ecological adaptations in all invertebrates and vertebrates were reviewed in the context of: Role of olfaction in Octopus vulgaris reproduction

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000). — p. 61

See for comparison 1): Riding the Evolution Paradigm Shift With Eugene Koonin

“[T]he entire ideology of personalized medicine should be taken with many grains of salt. It’s not useless, it’s useful to sequence thousands of genomes. It’s useful to sequence everyone’s genome. It’s useful and desirable — yet, it’s wrong and to some degree dangerous to think that, by peering into the sequence of the A, G, T, and Cs in your genome, your family doctor is going to tell you how to treat all your conditions and what conditions you are going to develop, and which ones you are not going to develop, and so on.” — Eugene Koonin

See also for comparison 2): Riding the Evolution Paradigm Shift With Eugene Koonin

“The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…” — Eugene Koonin

The entire ideology of personalized medicine is based on what is known about how the anti-entropic virucidal energy of sunlight must be linked from endogenous RNA interference and foraging behavior to the physiology of biophysically constrained pheromone-controlled reproduction in species from microbes to humans. See this 7 minute representation from my Precision Medicine virtual conference presentation. Energy as information and constrained endogenous RNA interference (2017)
Do not be surprised if you cannot track the historical record of scientific advances in nutritional epigenetics from 1994 Effect of atrazine herbicide on growth, photosynthesis, protein synthesis, and fatty acid composition in the unicellular green alga Chlorella kessleri to the current representations of top-down causation and energy-dependent biophysically constrained biologically-based cause and effect. There are many pseudoscientists who will do everything possible to prevent you from learning that their ridiculous theories have never been supported by experimental evidence.
See for example: 7/25/13
Jay R. Feierman: “Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.”
See also: One crank dies, another rises to take his place by PZ Myers

I was asked to look at a string of comments left on a science article by a fellow going by the pseudonym JVK, and all the Davison traits were there. Pretentious phrasing. Repetition: if the audience didn’t get it the first time, just say the same thing again, twice. A kind of sneering anger that people don’t understand how smart he is. An obsession with one narrow idea, which is his, which explains all of evolution and proves that everyone else is wrong.
Behold James Vaughn Kohl.

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.

Ecological adaptations are food energy-dependent and biophysically constrained in the context of biologically based chromosomal inheritance via the pheromone-controlled physiology of reproduction. There is only one model for that.
It’s my model:
Nutrient-dependent/pheromone-controlled adaptive evolution: a model
See for comparison: Interactome analysis reveals ZNF804A, a schizophrenia risk gene, as a novel component of protein translational machinery critical for embryonic neurodevelopment
Reported as: Gene associated with schizophrenia risk regulates neurodevelopment

A gene associated with the risk of schizophrenia regulates critical components of early brain development, according to a new study led by researchers from Penn State University. The gene is involved in the translation of proteins from RNA and in the proliferation and migration of neurons in the brain.

Gene regulation is energy-dependent and RNA-mediated. That fact is twisted into this misrepresentation: “The gene is involved in the translation of proteins from RNA and in the proliferation and migration of neurons in the brain.”

What they claim, in the most twisted way possible, is that the energy-dependent RNA-mediated translation of proteins must be linked to ecological adaptations via the proliferation and migration of neurons in the brain.

For God and Country

Sci-Hub vs limits on the dissemination of information

The ideology of “Americanism” is not consistent with the tactics of academics and politicians that constrain release of accurate information about  biologically-based cause and effect.

Americanism is an ideology, or belief in devotion, loyalty, or allegiance to the United States of America, or to its flag, traditions, customs, culture, symbols, institutions, or form of government.[2] In the words of Theodore Roosevelt, “Americanism is a question of spirit, conviction, and purpose, not of creed or birthplace.”[3]

Americanism has two different meanings. It can refer to the defining characteristics of the United States and can also signify loyalty to the United States and a defense of American political ideals. These ideals include, but are not limited to self-government, equal opportunity, freedom of speech, and a belief in progress.

Scientific progress has been hindered by publishing companies whose corporate purpose is financial gain for stockholders, not the dissemination of freecinformation that is required to make scientific progress by serious scientists who are Combating Evolution to Fight Disease.
Rarely do the efforts of serious scientists get noticed because there is too much pseudoscientific nonsense that gets published in peer-reviewed journals. The nonsense overwhelms the ability to discern between facts and story-telling. Evolutionary theorists, for example, are story-tellers.
For an attempt to resolve the problem with theorists, see: Publishers’ Legal Action Advances Against Sci-Hub

Based on data from Google Trends, researchers found that the suits against Sci-Hub led to brief spikes in visits to the site.

The publishers contribute to the theft of information because most people do not care how they acquire it. People want the information on biologically based cause and effect for free, and many of them will use it to make scientific advances such as those that have linked energy-dependent changes in microRNAs to all pathology.
A PubMed search for “microRNA” reveals that nearly 65,000 indexed published works have already established facts that link virus-driven energy theft to all pathology. Most the publications are behind “pay walls.”
That means most researchers will be unable to access all of them. Anyone outside the specific discipline that is the focus of the article will not be likely to integrate the information across disciplines and accurately represent what is known about biophysically constrained biologically-based cause and effect.
For an example of the level of integration that is required, request a copy from the corresponding author and wait to see the information in this “pay-walled” publication: Olfaction Warps Visual Time Perception.
By the time you get it, there will probably be several hundred more publications that link the food energy-dependent physiology of pheromone-controlled reproduction in bacteria to our visual perception of energy and mass in the context of the space-time continuum.
See also:

Alternatively, see: Energy as information and constrained endogenous RNA interference
Cited works:
1) ATP hydrolysis by UPF1 is required for efficient translation termination at premature stop codons
2)  Evolutionary drivers of thermoadaptation in enzyme catalysis
3). Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans
4) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
5) Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
6) Metabolic theory predicts whole-ecosystem properties
7) The phylogenetic utility and functional constraint of microRNA flanking sequences
8) Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression
9) MicroRNA analysis in mouse neuro-2a cells after pseudorabies virus infection
10) microRNA-binding proteins: specificity and function
11) RNA in extracellular vesicles
12) Structural diversity of supercoiled DNA
13)  Communication between viruses guides lysis–lysogeny decisions
14) The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters
15) Prevalence and architecture of de novo mutations in developmental disorders
16) All about the base
17) Chemists know.
18) Dynamic control of chirality and self-assembly of double-stranded helicates with light
19) The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes
20) RNA-Guided Human Genome Engineering
21) What is Life?
22) Arginine 66 Controls Dark-State Formation in Green-to-Red Photoconvertible Fluorescent Proteins
23) Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor
24) A Big Bang in spliceosome structural biology
The works cited above have been placed into the context of the cell biology game “Cytosis.”

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

See for comparison: 2017 Royal Society Insight Investment Science Book Prize

The perfect science book marries scientific breakthrough with elegant, engaging communication. Reading these books side-by-side, we were struck by how creative and unique each voice was, and the varied ways these writers tackle their subjects, using metaphors and personal stories as much as scientific facts.

The perfect science book marries what is known about the creation of energy as information with the biophysically constrained physiology of pheromone-controlled reproduction, which prevents the virus-driven degradation of messenger RNA.

Biophysically constrained viral latency prevents all pathology. This year’s Prize winner linked testosterone to “gender” differences in behavior.

For comparison, see: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences

Excerpt:

…this model incorporates a logical pathway that directly links sensory input from the social environmental to the development of sexual preferences and to the development of sexual behavior.

The five-step logical pathway that directly links sensory input from the social environment to the development of sexual preferences and sexual behavior is gene→cell→tissue→organ→organ system. Failure to incorporate any of the steps in this pathway makes it impossible to directly connect to sexual preferences and sexual behavior, a logical sequence of events that must somehow and somewhere begin with the effect of sensory input from the social environment.

See also: Intelligent Design – Science & Philosophy: discussion thread

Antagonist, Timothy Kershner wrote:

I have a PhD in Psychology and a minor degree in Microbiology and personally funded many Bacterial Consciousness studies between 2008 and 2012 and mentored directly under James Shapiro from 2009 to 2011.

Shapiro already is laughing at you and others as he tries to recover from teaching you to become biologically uninformed science idiots who believe in evolution outside the context of energy-dependent ecological adaptations that are biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera.

See: Biological action in Read-Write genome evolution

Coincidentally, ‘non-coding’ RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.

Shapiro’s latest is part of a Theme issue ‘New trends in evolutionary biology: biological, philosophical and social science perspectives’ organized by Denis Noble, Nancy Cartwright, Patrick Bateson, John Dupré and Kevin Laland.

See for comparison: How life changes itself: The Read-Write (RW) genome

Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA.

See also: Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution

and UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

All cell-mediated processes are energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans.

Energy dependent life does not change itself. RNA-mediated events must be linked to the stability of organized genomes. The organized genomes cannot come first. The details of energy-dependent cell-mediated RNA-directed DNA methylation clearly link the virucidal energy of sunlight from microRNAs in plants to the microRNAome of all mammals. All humans are included.

RNA interference occurs in plants, animals, and humans. It is of great importance for the regulation of gene expression, participates in defense against viral infections, and keeps jumping genes under control. RNA interference is already being widely used in basic science as a method to study the function of genes and it may lead to novel therapies in the future.

Naturally occurring endogenous RNA interference links what organisms eat from their physiology of pheromone-controlled reproduction to all energy-dependent biodiversity on Earth via biophysically constrained viral latency. For example, see:

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

MicroRNA present in mature sperm appears to not only be left over from spermatogenic processes, but may actually serve important regulatory roles in fertilization and early developmental processes. Further, our results indicate the possibility that environmental changes may impact the expression of specific miRNA.

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.

See for comparison: Alnylam’s rare disease drug shines in trial, paving way for a brand-new class of medicines

RNA interference, or RNAi, a technology that uses snippets of genetic code to shut down disease-causing genes. The scientists who invented RNAi were awarded the Nobel Prize for Medicine in 2006. Many years and more than $1 billion in research later, Alnylam is finally on the cusp of proving that RNAi can be transformed into a medicine that helps patients.

Scientists did not invent RNAi. They discovered that it links what organisms eat to their biophysically constrained pheromone-controlled physiology of reproduction. That fact links RNAi to all biodiversity without the pseudoscientific nonsense touted by evolutionary theorists. The cost of any RNAi drug that is approved will almost assuredly bankrupt the person who needs the drug and the cost will probably destroy the economy of the United States of America via the impact on the costs of Medicare and/or other insurance.
This is not Amercanism: Alnylam Data Puts a Nobel Discovery One Step Closer to Approved Drug

Shares of Alnylam soared more than 51 percent and closed at $113.84 apiece on Wednesday.