5th-6th Sept 2018 Dublin, Ireland

The eternal significance of microRNAs (8)

Use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation and aging has been replaced by the use of model systems of biological processes.  Biological processes can be compared to so-called “evolutionary processes” to show that only biological processes need to be considered in the context of Darwin’s “conditions of life” or answers to the the question  What is Life? Schrödinger (1944).
K. L. Mettinger et al. (eds.), Exosomes, Stem Cells and MicroRNA, Advances in Experimental Medicine and Biology 1056, https://doi.org/10.1007/978-3-319-74470-4_6

This volume provides insight into the pivotal roles of stem cells, exosomes and other microvesicles in biofunction and molecular mechanisms and their therapeutic potential in translational nanomedicine. It further highlights evidence from recent studies as to how stem cell derived exosomes and microRNAs may restore and maintain tissue homeostasis, enable cells to recover critical cellular functions and begin repair regeneration.

Chapter 2 The Emerging Roles of microRNAs in Stem Cell Aging

involved in many biological processes such as developmental timing, differentiation, cell death, stem cell proliferation and differentiation, immune response, aging and cancer. Accumulating studies in recent years suggest that miRNAs play crucial roles in stem cell division and differentiation. In the present chapter, we present a brief overview of these studies and discuss their contributions toward our understanding of the importance of miRNAs in normal and aged stem cell function in various model systems.

Chapter 6  MicroRNAs, Regulatory Messengers Inside and Outside Cancer Cells

…like hormones, miRNAs can be secreted and regulate gene expression in recipient cells. Altered expression levels of miRNAs in cancer cells determine the acquisition of fundamental biological capabilities (hallmarks of cancer) responsible for the development and progression of the disease.

Model systems link the energy-dependent creation of microRNAs from microRNA biogenesis to the regulation of all cancer hallmarks. The virus-driven degradation of messenger RNA has been linked to all cancers and all other pathology in species from microbes to humans. Natural selection for energy-dependent codon optimality has been linked to healthy longevity.
See: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See for comparison:  The Neutral Theory in Light of Natural Selection May 2, 2018

…50 years after its introduction by Kimura. We argue that the neutral theory was supported by unreliable theoretical and empirical evidence from the beginning, and that in light of modern, genome-scale data, we can firmly reject its universality. The ubiquity of adaptive variation both within and between species means that a more comprehensive theory of molecular evolution must be sought.

The ubiquity of adaptive variation attests to the facts about how the creation of quantized energy is linked to biophysically constrained viral latency. Adaptive variation links energy-dependent changes from angstroms to ecosystems in all living genera  via the physiology of their food energy-dependent pheromone-controlled reproduction.

For comparison to mRNA stability during the maternal-to-zygotic transition, see: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

The energy-dependent molecular mechanisms of recombination clearly link microRNA biogenesis to the stability of organized genomes during the life histories of all genera. Serious scientists object to the use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

…it is tiresome to raise the same objections repeatedly, wondering why researchers have not fulfilled some of the basic requirements for establishing the occurrence of an autophagic process.

 

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.

Polymaths and paradigm shifts: from Asimov to Bear (2)

Polymaths and paradigm shifts: from Asimov to Bear (1)
See also: Search results for virus-driven energy theft
Summary: The creation of enzymes, such as ATP synthase is energy-dependent. The energy biophysically constrains viral latency via the creation of microRNAs and RNA-mediated amino acid substitutions that differentiate the cell types of all living genera.
Modifying Other’s Originality without Quote is an Act of Piracy

A writer who does not cite the sources in h/h feature article is committing piracy. Piracy is plagiarism… high level quality requires originality and creativity… these inattentions…should be strongly condemned… Accordingly, the originally contributing author may preserve the honor worthily and endeavor to further contribution in scientific study.

See for comparison: Here’s how viruses inactivate the immune system, causing cancer

It’s no new news that viruses cause cancer.

The full text of the article is free: DNA Tumor Virus Regulation of Host DNA Methylation and Its Implications for Immune Evasion and Oncogenesis

…virus-associated cancers show highly increased levels of DNMT expression [75,76,77,85,94,95,96,97,98,99]. In HBV-associated hepatocellular carcinoma (HCC), DNMT expression is inversely correlated with levels of tumor suppressor microRNAs (miRNAs), including miR-152 targeting DNMT1 [97] and miR-101 targeting DNMT3A [99]. Virus-induced DNA hypermethylation is commonly found on several tumor suppressor genes…

RNA-directed DNA methylation links the energy-dependent microRNA-mediated creation of tumor suppressor genes to biophysically constrained viral latency via the proton motive force. The proton motive force links differences in the energy of photons from hydrogen-atom transfer in DNA base pairs in solution to the light-activated endogenous substrates of RNA-mediated DNA repair.
See also: “There is no honor among thieves” is a pithy saying that captures Solomon’s observation concerning the wicked and those who choose their company.
A Twitter search returned several interesting comments related to what is known to serious scientists about the proton motive force and the claim that “There is no honor among thieves.” For instance, writers who modify the claims and questions about the proton motive force are plagiarists and/or thieves. See:

  1. 12 Sep 2010

What do proton motive force driven multidrug resistance transporters have in common?

2. 19 Jun 2010

The H+ gradient is called the proton-motive force. This force drives the H+ back across the membrane through H+ channels. ATP synthases aids

The creation of enzymes, such as ATP synthase is energy-dependent. The energy biophysically constrains viral latency via the creation of microRNAs and RNA-mediated amino acid substitutions that differentiate the cell types of all living genera.

 Philip Ball @philipcball Mar 2

This was filmed tonight, so you’ll soon get to see why Nick Lane thinks the key to the origin of life is not amino acids or RNA but proton gradients. (I think he may be right.)

See for comparison: snippet from our June 24, 2017 conversation about the claims of Philip C. Ball.

See also: The legacy of Frankenstein: A series of events celebrating 200 years of Frankenstein

The origin of life

Dr Frankenstein aimed to create new life from inanimate parts. But how did life first arise on Earth? Join Nick Lane in conversation with Phil Ball as they discuss the latest ideas, from warm ponds to space rocks and hydrothermal vents.

Ask when Nick Lane and/or Philip C. Ball first learned about proton gradients. See how much longer it takes them to link the creation of sunlight  from differences in the energy of photons to biophysically constrained viral latency and all biodiversity via the physiology of reproduction and this model: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013)

Conclusion:

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

See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

Abstract:

This angstroms to ecosystems model of ecological adaptation links nutrient energy-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements via the physiology of reproduction in species from microbes to humans. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity. Species-specific pheromones link quorum-sensing in microbes from chemical ecology to the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection for codon optimality links nutritional epigenetics to the behaviors that enable ecological adaptations. All biodiversity is an ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. Simply put, olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of supercoiled DNA in the organized genomes of species from microbes to man during their development.

See for comparison: On the Difference between Physics and Biology: Logical Branching and Biomolecules

In my model, microRNAs are the biomolecules that link the creation of sunlight to all energy-dependent biophysically constrained viral latency. Viral latency is required to link the physiology of reproduction to all biologically-based diversity in all species.

Claims about proton gradients that link physics to biology without starting with the creation of sunlight are made by biologically uninformed theorists.

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.

Mouse morphs and primate diversity in 50 years

Excerpt:

Analysis of the crystal structure of deer mouse Hb at 1.8 Å resolution (24, 25) revealed that each of the eight rHb mutants is characterized by a unique constellation of hydrogen bonds within and between subunits (Table 2 and fig. S2). Additional hydrogen bonds between subunits of the same αβ dimer are formed in the presence of β128Ser (an L-type residue; fig. S2), which contributes to the observed epistasis between allelic α- and β-chain variants.

———————————
Energy-dependent RNA-mediated biophysically constrained viral latency (i.e., silencing of viral elements) protects all organized genomes from the degradation of messenger RNA that links mutations to all pathology. The mutations are caused by nutritional stress and/or social stress. That fact has been known to all serious scientists for at least 50 years. But see:
Silencing of viral elements: A cure for schizophrenia? ARTICLE Provisionally accepted

1. The problem.
Scientific evidence for various infectious agents as cause for psychosis in schizophrenia is not robust. Many pathogens that influence brain development might play a role in disease causation. It has been shown that influenza exposure before birth(Brown, 2012), exposure to herpes simplex during birth(Brown et al., 2011) or exposition to Toxoplasma gondii and other pathogens (Arias et al., 2012) increases risk for schizophrenia and/or compromises cognition. During psychosis viral and also ancient retroviral elements become may activated in the brain(Karlsson et al., 2001; Perron et al., 2012). The implication of this research for use in clinical practice is ambiguous, because a robust virus test is lacking.

Examples of human idiocy are the problem. See for comparison:

QuEBS workshop has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has been developed in Lithuania for more than 20 years already. The beginnings could be associated with a series of “Light-harvesting Physics” international conferences, which were held in Lithuania (in Preila, 1992 and 1994, and in Birštonas, 1996). During these conferences, discussion of notable scientists and pioneers of Quantum Biology, such as Graham R. Fleming, Shaul Mukamel, Rienk van Grondelle, Richard Cogdell, Alfred Holzwarth and others, established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.

Every aspect of biophysically constrained energy-dependent RNA-mediated life on Earth has refuted the pseudoscientific nonsense about emergence and evolution.

As climate warms, mice morph

Biologists document changes in teeth and skull structure in two species in southern Quebec over past 50 years

The ridiculous claim that the fixed amino acid substitutions were adaptive mutations proves how little the authors understand about biophysically constrained viral latency.

Excerpt 1)

“Biologists document changes in teeth and skull structure in two species in southern Quebec over past 50 years

Excerpt 2)

“These changes may be related to a dietary shift caused by climate change, combined with competition for food resources between the two species of mice, according to the researchers.”

All serious scientists know that food energy biophysically constrains the pheromone-controlled physiology of reproduction, which links the fixation of RNA-mediated amino acid substitutions to cell type differentiation in all living genera.
 
We have now arrived at the claims of biologically uninformed science idiots who tell us that two different species evolved in 50 years.
 

Excerpt 3)

“One question that remains to be settled is whether the changes are genetic, and will be passed on to future generations — actual evolution — or whether they represent “plasticity,” the capacity of some species to adjust to rapid environmental change.”

The facts about the transgenerational epigenetic inheritance of healthy longevity for comparison to virus-driven pathology have been exquisitely detailed. All serious scientists have dispensed with the nonsense that questions the capacity of some species to adjust to rapid environmental change. Ecological variation must be linked from the physiology of pheromone-controlled reproduction in all living genera via the conserved molecular mechanisms of RNA-mediated cell type differentiation that link fixation of amino acid substitutions to the morphological and behavioral phenotypes of all individuals and all species on Earth.

See for instance, on the same day that my 2013 refutation of Nei’s pseudoscientific nonsense about Mutation-driven evolution was published, this also was published: Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin

Epistasis is food energy-dependent. The energy must be biophysically constrained in the context of the physiology of pheromone-controlled transgenerational epigenetic inheritance. The creation of energy in a hydrogen atom was linked from the anti-entropic virucidal effect of sunlight to the stability of the organized genome of mice by hydrogen-atom transfer in DNA base pairs in solution and differences in the hemoglobin molecule of ecologically adapted species.

Analysis of the crystal structure of deer mouse Hb at 1.8 Å resolution (24, 25) revealed that each of the eight rHb mutants is characterized by a unique constellation of hydrogen bonds within and between subunits (Table 2 and fig. S2). Additional hydrogen bonds between subunits of the same αβ dimer are formed in the presence of β128Ser (an L-type residue; fig. S2), which contributes to the observed epistasis between allelic α- and β-chain variants.

See also:

…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.

The fact that every Angstrom is dynamic and the fact that energy-dependent changes in the microRNA/messenger RNA balance have been linked to biophysically constrained viral latency and all biodiversity was placed into the context of this parody:

 See also:


The Mechanical Properties of DNA are food energy-dependent and RNA-mediated

The elastic properties of the DNA molecule determine how it supercoils during replication, how it packs into confined biological structures and how it interacts with proteins during gene expression.

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

Nutrient-dependent atomic-level changes may determine the nucleotide changes in a specific base pair. The nucleotide changes appear to link nutrient-dependent single nucleotide polymorphisms (SNPs) from the availability of fruits and vegetables or fermented milk products to individual differences and to species differences in the need for certain vitamins. For example, cell type determination and differentiation are associated with the nutrient-dependent 3D distribution of amino acid substitutions as they accumulated during a history of ecological adaptations [32] in flies [9] and in humans [33]. Sex differences in behavior also appear to arise from the single-molecule and single cell levels in flies, which suggests that adaptive changes in behavior can be explained in the context of nutrient-dependent pheromone-controlled genome-environment interactions that alter circuit plasticity via amino acid substitutions [34].

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

The companion papers [162-163] told a new short story of ecological adaptations. In the context of climate change and changes in diet, the story began with what probably was a nutrient-dependent base pair change and a variant epiallele that arose in a human population in what is now central China. Apparently, the effect of the epiallele was adaptive and it was manifested in the context of an effect on sweat, skin, hair, and teeth. In another mammal, such as the mouse, the effect on sweat, skin, hair, and teeth is probably due to a nutrient-dependent epigenetic effect on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones appear to control the nutrient-dependent epigenetically-effected hormone-dependent organization and hormone-activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates and in microbes as previously indicated.

The ecological adaptations, which appear to be manifested in the human population are detailed in these two reports [162-163]. The ecological adaptations are likely to be nutrient-dependent and pheromone-controlled. If so, ecological variation probably leads to ecological, social, neurogenic, and socio-cognitive niche construction, which is manifested in increasing organismal complexity and species diversity. If not, there may be something as yet unknown about mutations and evolution that makes sense in the light of what is known about nutritional epigenetics and the molecular biology of species from microbes to man.

See for comparison: The evolution of H2
Biohydrogen production from hyperthermophilic anaerobic digestion of fruit and vegetable wastes in seawater: Simplification of the culture medium of Thermotoga maritima
Mechanism of Nitrogenase H2 Formation by Metal-Hydride Protonation Probed by Mediated Electrocatalysis and H/D Isotope Effects
The claims that energy emerged or that differences in hydrogen and differences in species evolved outside the context of the energy-dependent creation of enzymes are among the most ridiculous examples of human idiocy that any serious scientist has ever encountered.
Claims about the emergence of life were again retracted on November 23, 20-17 and reported on December 5, 2017.

”Definitely embarrassing:” Nobel Laureate retracts non-reproducible paper in Nature journal

See: Comment awaiting moderation.

James V. Kohl December 7, 2017 at 4:35 am
The Science Behind the Game “Cytosis,” pits the collaborative efforts of 20 serious scientists against the pseudoscientific nonsense touted by theorists. The serious scientists know how energy-dependent RNA-mediated cell type differentiation occurs.
Resources (e.g., mRNA, ATP) are used to build enzymes, hormones, and/or receptors. Health points accumulate to show why food energy must be linked from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency.
For comparison, Szostak and other theorists have been stuck with their ridiculous misrepresentations of emergence and neo-Darwinian evolution, which failed to consider Darwin’s “conditions of life.”
“Conditions of life” are energy-dependent. The energy is Schrodinger’s anti-entropic virucidal energy. It comes from sunlight and is epigenetically “trapped” in food via the physiology of reproduction.
Board Game:
Cytosis: A Cell Biology Game
Title:
Cytosis – The Science Behind the Game https://boardgamegeek.com/filepage/155090/cytosis-science-behind-game
See also: Two retractions of human idiocy
See also: Routing gene therapy directly into the brain

Once the genetically-engineered HSCs are transplanted into the brain’s ventricles, the crucial enzyme they contain helps to metabolize the materials that were previously building up and causing tissue damage.

A new lineage of cells descended from the transplanted HSCs — a type of cell called a myeloid — begin to scavenge and consume the excess material that is responsible for neurodegeneration.

The pheromone-controlled differentiation of these cell types was predicted in the context of claims that pheromones biophysically constrain all pathology in the mouse to human model, which has been thoroughly detailed since 1994.
See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)
See also: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis

See also: Researchers Discover Key to Diseases in Mitochondrial DNA Mutations

Because the primary job of the mitochondrion is to produce energy, most of its genes are involved in pathways in the energy production process. Although it has a small genetic code, mtDNA contains the blueprints for building many of the enzymes and proteins that are needed to function in those pathways.
 
The virus-driven theft of quantized energy as information links the degradation of messenger RNA from mutations to all pathology in all living genera. The speed of light on contact with water has been linked to all energy-dependent RNA-mediated DNA repair in the context of the physiology of reproduction and the transgenerational epigenetic inheritance of healthy longevity.
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.

Exposing the 2nd Law to more ridicule (1)

Summary: Experiment demonstrates quantum mechanical effects from biological system

Schrödinger (1944) linked the anti-entropic virucidal energy of sunlight from the physiology of pheromone-controlled reproduction in soil bacteria to all biodiversity. He then began to suspect that his colleagues, who displayed human idiocy, would kill him – if ever again he reasserted the facts.

After 1944, Richard P. Feynman took a stand against the human idiocy, and lost. He was not killed, just ignored.

Ignorance prevails. It always has. The virus-driven degradation of messenger RNA ensures that organized genomes continue to become less organized and that biologically uninformed theorists continue to tout pseudoscientific nonsense.

New Genes and Functional Innovation in Mammals 21 July 2017

We identify several previously described cases of genes originated de novo from noncoding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes in mammals. Finally, we show that most young mammalian genes are preferentially expressed in testis, suggesting that sexual selection plays an important role in the emergence of new functional genes.

Reported as: Genes identified that distinguish mammals from other animals  4 December 2017

They have also identified antimicrobial peptides, which participate in the body’s defence against pathogens.

The energy-dependent creation of “…antimicrobial peptides, which participate in the body’s defence against pathogens” already was linked from the sense of smell in bacteria to the physiology of pheromone-controlled reproduction and biophysically constrained viral latency, which protects all organized genomes from the degradation of messenger RNA. False assumptions about entropy for comparison to experimental evidence of the de novo creation of genes have been placed into the context of the “arrow of time.”

Scientists Experimentally Demonstrate the “Reversal of the Arrow of Time” 
4 December 2017

Through a remarkable experiment, an international team of scientists has found that it is possible to reverse the arrow of time without violating the second law of thermodynamics.

Pseudoscientists need no longer consider anything that cannot be linked to this experimental evidence of top-down energy-dependent causation and biophysically constrained viral latency/genomic entropy. Thank God, nothing but experimental evidence of the anti-entropic virucidal energy of sunlight has ever been considered by those who have linked feedback loops from odors and pheromones to all biodiversity on Earth.
See: QuEBS workshop

…has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has been developed in Lithuania for more than 20 years already. The beginnings could be associated with a series of “Light-harvesting Physics” international conferences, which were held in Lithuania (in Preila, 1992 and 1994, and in Birštonas, 1996). During these conferences, discussion of notable scientists and pioneers of Quantum Biology, such as Graham R. Fleming, Shaul Mukamel, Rienk van Grondelle, Richard Cogdell, Alfred Holzwarth and others, established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.

Quantum effects in biological light-harvesting systems have been linked from the de novo creation of sunlight to answers about all biophysically constrained biodiversity via Schrodinger’s What is Life? (1944).

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

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.

See also: What is life when it is not protected from virus driven entropy (video) 30 Mar 2016

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.

See for comparison: On causal roles and selected effects: our genome is mostly junk December 5, 2017

The idea that much of our genome is irrelevant to fitness—is not the product of positive natural selection at the organismal level—remains viable.

Conclusion:

That is to say, many of our uniquely human traits are probably the contingent products of drift and historical accidents—they make us us, but were not selected to have that, or necessarily any, effect. So we are back to Ohno’s conundrum. If lungfishes have junk, or at the least extraordinarily weakly or diffusely functional DNA in their genomes, why is it that we think we do not?

The concept of “junk DNA” is inconsistent with anything known to serious scientists about energy-dependent biophysically constrained viral latency.  Feedback loops link top-down causation to the pheromone-controlled physiology of reproduction via RNA-mediated fixation of amino acid substitutions in the organized genomes of all living genera.
See: Understanding and accounting for relational context is critical for social neuroscience
My comment: New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.
“Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”

— Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors Socioaffective Neuroscience & Psychology 2012 http://www.ncbi.nlm.nih.gov/pubmed/24693349

George F R Ellis This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: [Top-down causation: an integrating theme within and across the sciences?] http://rsfs.royalsocietypublishing.org/content/2/1.toc 25 Apr 2014 at 07:49am
See also: What Bacteria Can Tell Us About Human Evolution December 5, 2017

See for comparison: Learning from Bacteria about Natural Information Processing
The link from biological light-harvesting systems to the pheromone-controlled physiology of reproduction in species from microbes to humans exemplifies everything known to serious scientists about biophysically constrained viral latency, which links ecological variation to ecological adaptations in the context of physics, chemistry, and molecular epigenetics. The facts refute all neo-Darwinian nonsense and the nonsense touted by “Big Bang” cosmologists.
Sunlight is quantized energy as information and it is virucidal.
See also: Generation of photonic entanglement in green fluorescent proteins

…our prepared state is free from environmental decoherence because of the protective β-barrel structure that encapsulates the fluorophore in the protein. Our photonic entanglement generation and characterization indicate that the SFWM process in EGFP is a promising quantum process for developing quantum spectroscopic techniques and quantum-enhanced measurements in biological materials.

Reported as: Experiment demonstrates quantum mechanical effects from biological system

Nearly 75 years ago, Nobel Prize-winning physicist Erwin Schrödinger wondered if the mysterious world of quantum mechanics played a role in biology.

Schrödinger (1944) linked the anti-entropic virucidal energy of sunlight from the physiology of pheromone-controlled reproduction in soil bacteria to all biodiversity. He then began to suspect that his colleagues, who displayed human idiocy, would kill him.
After 1944, Richard P. Feynman took a stand against human idiocy, and lost. He was not killed, just ignored.

Ignorance prevails. It always has. The virus-driven degradation of messenger RNA ensures that organized genomes continue to become less organized and that biologically uninformed theorists continue to tout pseudoscientific nonsense.

See for comparison: Microbiome-Centric Human Health: A Call for Systems Biology
Stop calling for more microbiome-centric systems biology and link what is known about energy-dependent changes in electrons to ecosystems in all living genera via pheromone-controlled biophysically constrained viral latency.
See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] 1994

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

rp_levels-of-organization.jpg

Dietary lutein and pheromone-controlled brain development

Parahippocampal Cortex Mediates the Relationship between Lutein and Crystallized Intelligence in Healthy, Older Adults
Reported as: How Leafy Greens May Protect The Brain From Aging

“As a neuroprotective nutrient, lutein may support structure and function in neural membranes, and ultimately may support the cognitive functions that rely upon these neural membranes,” Marta Zamroziewicz, a graduate student in neuroscience and the study’s lead author, told The Huffington Post.

The link from the sun’s anti-entropic virucidal energy to lutein and cell type differentiation in all living genera was placed into the context of this review of human brain development.
The role of docosahexaenoic and the marine food web as determinants of evolution and hominid brain development: The challenge for human sustainability
The link from the sun’s anti-entropic virucidal energy to the de novo creation of olfactory receptor genes and to all biodiversity was placed into the context of this article: Feedback loops link odor and pheromone signaling with reproduction
“Evolutionary processes” fail to link docosahexanoic acid and lutein to luteinizing hormone and healthy longevity. The “processes” can be viewed in the context of what is known about energy-dependent biophysically constrained RNA-mediated protein folding chemistry. For example, energy is linked to healthy longevity in all living genera and virus-driven energy theft is linked to all pathology.
In all vertebrates, the stability of of organized genomes has been linked from the substitution of achiral glycine in position 6 of the luteinizing hormone releasing hormone (LHRH) decapeptide. The LHRH decapeptide is also referred to as the gonadotropin releasing hormone (GnRH) decapeptide.
The LHRH / GnRH decapeptide links dietary lutein to the nutrient-dependent pheromone-controlled cell type differentiation of all cell types in all vertebrates via the substitution of the achiral amino acid, glycine, and via measurements of luteinizing hormone, which initially was referred to as the “yellow hormone.”
See our section on “Tracking the Yellow Hormone” in: The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002)
See also: From hydrogen atom transfer in DNA base pairs to ecosystems (video representation)
Abstract:

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on DNA base pairs in solution and RNA-mediated amino acid substitutions to chromosomal rearrangements via pheromone-controlled changes in the microRNA / messenger RNA balance. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent & pH-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Critical limits for enhanced medical care already include what is known about the RNA-mediated physics and chemistry of biologically-based ecological, social, neurogenic and socio-cognitive niche construction. The epigenetic landscape is clearly linked to the physical landscape of supercoiled DNA and top-down causation is manifested in increasing organismal complexity in species from microbes to humans. In all vertebrates and invertebrates the reciprocal relationships of species-typical nutrient-dependent & pH-dependent morphological and behavioral diversity are enabled by microRNAs, adhesion proteins, and pheromone-controlled reproduction. Ecological variation and biophysically constrained natural selection of nutrients cause the RNA-mediated behaviors that enable ecological adaptations, which include development of the brain during life history transitions. Ideas from population genetics typically exclude ecological factors, which must be linked to cell type differentiation. Theories are integrated with an experimental evidence-based approach that establishes what is currently known in the context of this mammalian model.

See also: Understanding and accounting for relational context is critical for social neuroscience

9 Comments – James Vaughn Kohl and George F R Ellis.

James Vaughn Kohl “New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.

Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”

— Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors Socioaffective Neuroscience & Psychology 2012 http://www.ncbi.nlm.nih.gov/pubmed/24693349

George F R Ellis This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: http://rsfs.royalsocietypublishing.org/content/2/1.toc

————————————————————————————————————————————–

See for comparison, the recent attempt to replace what is known to all serious scientists about energy as information with the term “bio-functional information.”

The theorists are desperately seeking new terms that can be used to replace mutation in the context of their ridiculous theories about Mutation-driven evolution.

(1) Mutation is the source of all genetic variation on which any form of evolution is dependent. Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc. (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

Energy-dependent changes in base pairs link differences in nucleotide substitutions from insertions and or deletions to gene duplication in the context of autophagy, which links the physiology of reproduction to supercoiled DNA and chromosomal rearrangements. The energy-dependent chromosomal rearrangements were first linked to transgenerational epigenetic inheritance of all morphological and behavioral diversity by Thomas Hunt Morgan who won the 1933 Nobel Prize in Physiology or Medicine.

rp_levels-of-organization.jpg

Hypothesis free pseudoscience vs facts (4)

See first Hypothesis free pseudoscience vs facts (3)
See also: The terrorist inside my husband’s brain
Conclusion:

I know you have accomplished much already in the areas of research and discovery toward cures in brain disease. And I am sure at times the progress has felt painfully slow. Do not give up. Trust that a cascade of cures and discovery is imminent in all areas of brain disease and you will be a part of making that happen.
If only Robin could have met you. He would have loved you—not just because he was a genius and enjoyed science and discovery, but because he would have found a lot of material within your work to use in entertaining his audiences, including the troops. In fact, the most repeat character role he played throughout his career was a doctor, albeit different forms of practice.
You and your work have ignited a spark within the region of my brain where curiosity and interest lie and within my heart where hope lives. I want to follow you. Not like a crazed fan, but like someone who knows you just might be the one who discovers the cure for LBD and other brain diseases.
Thank you for what you have done, and for what you are about to do.

See also: Antibiotic Guideline for Central Nervous System Infections
My comment: Someone should tell Robin Williams’ widow that these guidelines could apply to the use of antibiotics to treat gut discomfort before virus-driven energy theft causes Lewy Body Disease to be misdiagnosed and leads to death by suicide. Perhaps she would believe someone like Dr. Jon Lieff.
See: Intelligent Lysosomes Are More than A Waste Disposal
Excerpt 1)

The lysosome is a sensory hub to determine what molecules are available, what has too much and what is needed. This includes all the molecules in metabolism of the cell such as amino acids to make proteins.

My comment: The lysosome links the energy-dependent secreting of a molecule to the sensing of the molecule, which enables the link from epistasis to homeostasis.
Excerpt 2)

The lysosome maintains a particular pH (4.5 to 5.0) as an optimal amount to hydrolyze various molecules. This is similar to the way the stomach maintains a particular acid balance. But, the lysosome maintains in a singular vesicle. It contains a very large number of particular enzymes to break down almost every type of molecule that is found.  It breaks down all large molecules (polymers).

See for example: Secreting and Sensing the Same Molecule Allows Cells to Achieve Versatile Social Behaviors with my comment to the Science site.

Re: “Evolution appears to favor efficient circuits and signaling elements that can accomplish many different tasks…”

That was inferred in our 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior. We started with the conserved molecular epigenetics of yeasts and extended nutrient-dependent genetic diversity from the metabolism of nutrients to the pheromone-controlled physiology of reproduction in species from microbes to man.

Four years later our yeast-to-mammalian model was extended by others to hormone-organized and hormone-activated invertebrate behavior, and 5 years after that to the life history transitions of the honeybee model organism.

Since then, “Signaling Crosstalk: Integrating Nutrient Availability and Sex” has linked yeasts to “Feedback loops link odor and pheromone signaling with reproduction” in other species and to “Nutrient-dependent/pheromone-controlled adaptive evolution: a model”

Placing all these published works into the context of evolution as Youk and Lim have done seems somewhat problematic for some evolutionary theorists. The conserved molecular mechanisms appear to represent adaptations to ecological variation via nutrient-dependent secretion of pheromones and the sensing of pheromones.

That links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man.

The fact that ecological adaptations occur via a nutrient-dependent signaling pathway, which regulates a pheromone-controlled signalling pathway shows how unicellular and multicellular organisms produce a coordinated response to multiple stimuli with no consideration for mutations or for natural selection of anything except food.

That does not present a problem in the context of biologically-based food odor- and social odor-driven cause and effect, but it makes mutation-driven evolution appear to be not only biologically implausible but also to not be an ecologically valid approach to species diversity.

More Nobel-Winning Research that challenges neo-Darwinian evolutionary theory was announced today.
From the comments on the 2016 Nobel Prize in Physiology or Medicine.
Malay Saha:  Autophagy is an intracellular degradation system that delivers cytoplasmic constituents to the lysosome. Despite its simplicity, recent progress has demonstrated that autophagy plays a wide variety of physiological and pathophysiological roles, which are sometimes complex..
See: Autophagy: process and function

Autophagy is an intracellular degradation system that delivers cytoplasmic constituents to the lysosome. Despite its simplicity, recent progress has demonstrated that autophagy plays a wide variety of physiological and pathophysiological roles, which are sometimes complex. Autophagy consists of several sequential steps—sequestration, transport to lysosomes, degradation, and utilization of degradation products—and each step may exert different function. In this review, the process of autophagy is summarized, and the role of autophagy is discussed in a process-based manner.

My comment: The article is available for free.
Excerpt from the 2007 conclusion:

…although autophagy is generally considered to be a tumor-suppressive process (Hippert et al. 2006; Levine 2007), the relationship between autophagy and cancer is complicated, in part because different steps of autophagy have different roles in tumor generation and tumor survival. A more quantitative view will be required to further understand the net role of autophagy in vivo. Finally, our knowledge of autophagy now seems to be ready for therapeutic application. Indeed, small molecules that can regulate autophagy seem to have great potential to modulate the clinical course of neurodegenerative diseases (Sarkar et al. 2007).

My comment: The small molecules are microRNAs, but the role that they play in linking hydrogen-atom transfer in DNA base pairs in solution to healthy longevity or from virus-driven energy theft to all pathology has not been explained in the context of how the nutrient-dependent pheromone-controlled physiology of reproduction must be linked from quorum-sensing in microbes to all biodiversity.
My comment to the FB page where the announcement of the 2016 Nobel Prize was made.

James Kohl: Let’s not discuss the fact that it must link energy-dependent changes from angstroms to ecosystems in all living genera in the context of their RNA-mediated DNA repair of virus-driven damage as manifested in the transgenerational epigenetic inheritance of Zika virus pathology. If we discuss that fact, neo-Darwinian theorists will attack.

See also:

Jon Lieff has stepped ahead of the data and linked it to biologically-based cause and effect in all living genera via the nutrient-dependent pheromone-controlled physiology of reproduction in the yeast model organism.

My comment: Jon Lieff’s timely entry was posted in Blog, Cellular Intelligence, Neuronal Plasticity and tagged Lysosomes work with autophagy, Lysosomes work with mTOR to regulate cellular molecules, Many ways to get lysosome storage diseases.
Unfortunately, it is obvious that most people will not understand the intricacies of the works that led Yoshinori Ohsumi to win the 2016 Nobel Prize for Physiology and Medicine ”for his discoveries of mechanisms for autophagy,” which must be linked to lysosome storage diseases and to healthy longevity.
Most people do not know what autophagy is. It is energy-dependent. That is the most important thing about it. Autophagy is linked to biophysically constrained RNA-mediated protein folding chemistry and cell type differentiation. It links nutrient energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of reproduction. That makes autophagy the link to all biodiversity via the physiology of nutrient-dependent pheromone-controlled reproduction in species from yeasts to humans.
See also: Yoshinori Ohsumi wins Nobel medicine prize
My comment: His works take us from hypothesis-free pseudoscience to facts about RNA-mediated cell type differentiation via experimental evidence of nutrient-dependent pheromone-controlled biophysically constrained biodiversity in species from microbes to humans.
It is hard to escape the conclusion that all biodiversity is energy-dependent in the context of autophagy, and harder still to escape the conclusion that virus-driven energy theft is the cause of all pathology.
Minimally, Yoshinori Ohsumi he has bridged the gaps from physics and chemistry to biology by placing his experimental evidence into the context of molecular epigenetics. The details already were linked from energy-dependent amino acid substitutions to all biodiversity in Dobzhansky (1973).
But now there is new light shed on what Dobzhansky referred to as the light of evolution. It’s what Schrodinger (1944) called sunlight in the context of its anti-entropic virucidal energy.
See for comparison: A reply to Alice Roberts and Mark Maslin: Our ancestors may indeed have evolved at the shoreline – and here is why…
There is literally nothing left of neo-Darwinian pseudoscientific nonsense, and yet the pseudoscientists still make the same ridiculous claims.

Filtering light through a prism to identify tissue type

Hydrogen-atom energy in DNA base pairs

See also: Consciousness is simply food rearranged
Role of Double Hydrogen Atom Transfer Reactions in Atmospheric Chemistry
Abstract excerpt: 

Hydrogen atom transfer (HAT) reactions are ubiquitous and play a crucial role in chemistries occurring in the atmosphere, biology, and industry.

My comment: The link from physics to chemistry and the conserved molecular mechanisms of biologically-based RNA-mediated cell type differentiation has been the focus my works for more than 20 years, even before I knew what I would need to explain about the energy-dependent links from angstroms to ecosystems via hydrogen-atom energy in all living genera.
See also: For first time, researchers see individual atoms keep away from each other or bunch up as pairs
Excerpt:

Different configurations of electrons give rise to specific elements, making carbon atoms, for instance, distinct from hydrogen atoms.

My comment: Without the different configurations of electrons,  energy-dependent changes in angstroms could not be linked from hydrogen-atom transfer (HAT) in DNA base pairs in solution to all biodiversity in all ecosystems. Simply put, the sun’s biological energy must be linked from atmospheric chemistry to biophysically constrained protein folding chemistry on Earth.
When these interactions are seen for the first time the experimental evidence must confirm theories. Otherwise physicists will try to come up with new untestable theories to stall scientific progress.  Serious scientists make progress when experimental evidence is accepted. Chemists typically know what to accept. So do molecular biologists.
What do evolutionary theorists or other social scientists know about physics, chemistry, or molecular epigenetics? How do pseudoscientists known what to accept when they already have accepted only theories?
For comparison, serious scientists know that angstroms measure distance, and every angstrom is dynamic in the context of energy-dependent RNA-mediated cell type differentiation. How can any serious scientist understand the claims of theorists made in the context of articles like this:
Humans and Neanderthals had sex. But was it for love? An investigation
Excerpt:

We know for sure humans and Neanderthals had sex because of a Swedish scientist named Svante Pääbo, who “more or less invented the field of paleogenetics,” Elizabeth Kolbert wrote in a terrific New Yorker article in 2011.

My comment:  Elizabeth Kolbert lied and used Svante Pääbo’s works to support her ridiculous claim:

We know for sure humans and Neanderthals had sex…

Serious scientists know that Svante Pääbo is the senior author of two articles. The two articles linked Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees and Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates.
Natural selection for the de novo creation of olfactory receptor genes and the loss of genes is not an indicator that humans and Neanderthals had sex. It is an indicator that natural selection for energy-dependent codon optimality occurred in the context of the physiology of reproduction in all primates. For contrast, all serious scientists know that members of two different species do not have sex. Chromatin remodeling and chromosomal rearrangements limit fertility among species via their nutrient-dependent pheromone-controlled physiology of reproduction and their behavior. The behavior is linked to energy-dependent codon optimality via the physiology of reproduction, not by sex between consenting humans and Neanderthals.
Is is silly to ask questions about sex for love without consideration of fertility, since the sexual interactions must be linked to survival of the species via biophysically constrained RNA-mediated protein folding chemistry in the context of the physiology of reproduction. The biophysical constraints are energy-dependent, but the theorists’ and journalists’ preference for fiction is clear.
Excerpt:

Robert Sawyer is a science fiction author who won the Hugo Award — one of sci-fi’s highest honors — for his 2002 book Hominids, a story that imagines a parallel world where Neanderthals survived and we didn’t. In the book (which spawned a trilogy), a Neanderthal physicist opens up a rift between the worlds and falls in love with a human.

For comparison, see this presentation text about Greg Bear’s novels in which he detailed for his non-technical audience how the nutrient energy-dependent pheromone-controlled physiology of reproduction is linked from RNA-amino acid substitutions to all cell type differentiation in all individuals of all species. The Darwin Code
See also: Structural and Functional MRI Differences in Master Sommeliers: A Pilot Study on Expertise in the Brain
Excerpt:

This study identified enhanced structural and functional patterns in the olfactory network of sommeliers. These findings are consistent with the learning they undergo in achieving the status of Master Sommelier. Furthermore, the volume of a region of the brain involved in olfactory memory was associated with experience, suggesting that the continued training results in morphological changes of the brain. These results speak to the plasticity of the adult brain in response to sensory expertise.

Reported as: Smelling Lots Of Wine Makes Your Brain Alzheimer’s Resistant

Overall, these differences suggest that specialized expertise and training might result in enhancements in the brain well into adulthood,” the study states. “This is particularly important given the regions involved, which are the first to be impacted by many neurodegenerative diseases.

See also:  What Sensory Receptors Do Outside of Sense Organs
My comment to the Scientist (I have posted: 361 comments so far)

20 years ago, we published: From Fertilization to Adult Sexual Behavior, which was a review of RNA-mediated cell type differentiation. We included a section on molecular epigenetic in the Hormones and Behavior review.

Unfortunately, few people realize that natural selection for energy-dependent codon optimality links the de novo creation of genes from the creation of G protein-coupled receptors to chemotaxis and to phototaxis before biophysically constrained energy-dependent biodiversity via RNA-mediated protein folding biochemistry can be linked to all biodiversity by amino acid substitutions.
When others report that mutations are linked to pathology, they seem to miss the fact that virus-driven energy theft causes the mutations. Nutrient-energy dependent viral latency has gone missing from explanations that would otherwise link what is known about biologically-based cause and effect from physics to chemistry and everything known about molecular epigenetics.
See also: Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization
My comment: Pseudoscientists could challenge representations like this if they had experimental evidence for comparison. They don’t. They have only their ridiculous theories, which they report in the story about sex between modern humans and Neanderthals. It is unadulterated pseudoscientific nonsense and nothing more than an unsubstantiated fictional account. It is not science fiction. The theorists claims are not scientifically based.
See for comparison: Role of olfaction in Octopus vulgaris reproduction and Two fatty acyl reductases involved in moth pheromone biosynthesis
Both articles cite Kohl (2013) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
See also: The Ancient Origins of Consciousness: How the Brain Created Experience
Excerpt:

12. Plotnick, Dornbos, and Chen (2010). Others who advocate smell-first are Lucia Jacobs (Jacobs, 2012), who says the building of smell maps of environmental space came first and James Kohl (Kohl, 2013), whose model says chemical ecology is the main driver of adaptive evolution.  — p. 263

My comment: Chemical ecology is the main driver of energy-dependent ecological adaptations. It is not not the driver of mutation-driven evolution, and so far there is no other model for comparison to my model of chemical ecology. I deliberately used the term adaptive evolution to see if someone would take the bait and offer another model for comparison. No one did.
See also: How Psychiatrist Jon Lieff Turned an Interest in Cellular Intelligence into Award-Winning Blogging!
My comment: Lieff still presents cellular intelligence in the context of evolution. He ignores what is known about hydrogen-atom energy in DNA base pairs in solution. That shows how successful a blogger can be if they simply fail to address what is known about biophysically constrained RNA-mediated cell type differentiation. His focus is on evolution! That means he does not need to explain anything about how evolution occurs, or explain what he thinks cellular intelligence is or where it came from!
See for comparison: Direct interrogation of the role of H3K9 in metazoan heterochromatin function
Reported as: Tight DNA packaging protects against ‘jumping genes,’ potential cellular destruction
Tight DNA is supercoiled DNA and it protects the orgnaized genomes of all living genera from virus-driven energy theft and genomic entropy. Simply put, supercoiled DNA biophysically constrains virus-driven energy theft, which is the only way to establish a link from ecological variation to ecological adaptation without inventing another ridiculous theory.

… viral latency is responsible for life-long pathogenesis and mortality risk…

Nutrient energy-dependent microRNAs are the obvious link from olfaction to biophysically constrained RNA-mediated protein folding chemistry, plasticity, and prevention of all pathology.
See for example: Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization

Supercoiled DNA is the link to viral latency, which is the link to healthy longevity.

See also, from the Neuroscience FB group “As simple as random can be”
See also:  Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
My comment: There is no experimental evidence of biologically-based cause and effect that links anything except energy or energy theft to the species-specific COMT Val158Met amino acid substitution during life history transitions and the development of morphological and behavioral phenotypes.

COMT val158met polymorphism and molecular alterations in the human dorsolateral prefrontal cortex: Differences in controls and in schizophrenia
Excerpt:

…the COMT val158met polymorphism is not found in species other than humans (Palmatier et al., 1999).

My comment: That fact makes the COMT val158met polymorphism a “smoking gun” in the context of energy-dependent de novo gene creation and virus-driven energy theft that links gene losses to loss of function via differences in G protein-coupled receptors.
Dopamine Neuron-Specific Optogenetic Stimulation in Rhesus Macaques
G protein-coupled receptor kinases as regulators of dopamine receptor functions
Subsecond Regulation of Synaptically Released Dopamine by COMT in the Olfactory Bulb
Programmable RNA-binding protein composed of repeats of a single modular unit
Excerpt from the conclusion:

… Pumby may present a simplified context in which to insert Pumilio modules to study how specific amino acids contribute to the emergent properties of modular RNA binding, independent of position-specific effects.

See also: Another gate-keeping attempt by Feierman

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Innate immunity and multiplexing

Scientists Hope to Cultivate an Immune System for Crops

by Carl Zimmer
Excerpt: The complex microbial world in the soil may protect plants much like our immune system protects our bodies.
My comment: The speed of light on contact with water links the sun’s quantized anti-antropic virucidal energy from the de novo creation of nucleic acid precursors to biophysically constrained RNA-mediated protein folding chemistry and supercoiled DNA, which protects all living genera from virus-driven energy theft and genomic entropy.
SeeWhat is Life? (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)

See also: Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B
Reported as:
1) Virus uses ‘stolen’ CRISPR to hack its host’s immune system;
2) Virus uses ‘stolen’ CRISPR to hack its host’s immune system
3) Virus Hacks Host Genome, Steals CRISPR to Protect Itself
4) Viruses Hack Their Host’s Genome with CRISPR
5) Virus uses ‘stolen’ CRISPR to hack its host’s immune system
6) Virus uses ‘stolen’ CRISPR to hack its host’s immune system
This ridiculous claim is found in all reports:

“Bacteria and their viruses have a shared evolutionary history stretching for billions of years,” says Suttle. “So at some point along the way N1 stole a defensive CRISPR array from Nostoc or a close relative.”

Someone at the LABROOTS Genetics & Genomics site is removing my posts about this attempt to include viruses in neo-Darwinian theory, which links them to billions of years of co-evolution.
On June 15, 2016 the Genetics & Genomics site reported this:

In the past decade, humans have adopted CRISPR as a genetic editing system, derived from a mechanism bacteria use to remember the pathogens they come across. It turns out that humans are not the only ones who want to “steal” the CRISPR idea – a new study uncovered a virus with a CRISPR DNA sequence.
“This is the first evidence we’ve seen that a virus can donate an immunity system via CRISPR. This is like a hacker compromising a computer system, and then immediately patching it to ensure other hackers can’t break in.”

My comment: Everything in their report is a ridiculous misrepresenation of what is known to serious scientists about biophysically contrained protein folding chemistry and RNA-mediated cause and effect, which links the energy-dependent creation and maintenance of all innate immune systems in all cell types of all living genera to ecological adaptation, or from virus-driven energy theft to all pathology.
Epigenetics and Genetics of Viral Latency
Excerpt:

viral latency is responsible for life-long pathogenesis and mortality risk…

My comment: The innate immune system biophysically constrains cell type differentiation by forcing viruses to wait for stress-induced changes in pH to enable the energy theft that facilitates viral replication. The systems complexity is beyond the grasp of most science journalists and all neo-Darwinian theorists. “Big Bang” cosmologists must learn something about biochemistry and RNA-mediated cell type differentiation before adding more pseudoscientific nonsense for the biologically uninformed masses to regurgitate.
See for example:  How Can Physics Underlie the Mind? Top-Down Causation in the Human Context
See for comparison: Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
Excerpt:

we identified a core set of more than 1000 responsive enhancers in the human genome. This TP53 cistrome is invariably used between cell types and experimental conditions, whereas differences among experiments can be attributed to indirect nonfunctional binding events.

Reported as: Cancer-preventing protein finds its own way in our DNA
Excerpt:

It’s a known fact that genes are activated when a protein binds to a specific sequence on our DNA. But how does this protein find its way in our extraordinarily complex DNA? Scientists have thus far been assuming that one protein could never locate the exact DNA sequence to activate a specific gene all by itself – at least not in human beings. However, Professor Aerts and his colleagues from the Department of Human Genetics at KU Leuven, Belgium, have now shown that some of these proteins are in fact capable of locating their targets autonomously. Furthermore, the composition of some DNA switches turns out to be unexpectedly simple.

My comment: The simplicity can be compared in the context of the forward by Roger Penrose to the reprint edition of Schrodinger (1944) What is Life?

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

My comment: The energy links hydrogen-atom transfer in DNA base pairs in solution to RNA methylation and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

See for example: One Tiny RNA Could Break the Cycle of Arterial Thrombosis  (Labroots)
Excerpt:

…a specific type of microRNA called miR-181b regularly balances the impact of both acute and vascular inflammation.

See also:  Color vision helps birds find good food and the right partner

Excerpt:

The researchers have established that chickens — just like people — have colour constancy. For birds, this means that they, in different environments and under different lighting conditions, recognise the colour of, for instance, berries and can thereby distinguish those that are ripe from those that are not. Without colour constancy, they would not be able to rely on their colour vision — they would simply see the berries in different colours as the light changed. They would certainly also not be able to recognise their own kind of species.

My comment: Species recognition is nutrient-dependent and the pheromone-controlled physiology of species specific reprodution in all vertebrates has been link linked to chromosomal rearrangements in birds and to morphological as well as behavioral diversity.  See: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes

See also: DNA in ‘unbiased’ model curls both ways

Excerpt:

“Think of the chromosome at mitosis as a bit like what would happen to a piece of sewing thread if you doubled it up and rolled it between your finger and your thumb,” he said. “Depending on how you rolled your fingers, you would get right- or left-turning structures.”
The thread itself has a helical arrangement of even smaller fibers, though the twist at one scale doesn’t necessarily determine the twist at the larger scales. “But bundles of threads usually get twisted somehow,” Wolynes said.
That “somehow” remains one of the mysteries, he said.

My comment: The fact that someone like Wolynes thinks that details of biophysically constrained RNA-mediated protein folding, supercoiled DNA, and energy-dependent chromosomal rearrangements have left us with any mysteries is a mystery. It’s as if he cannot link physics to chemistry, and stalls before linking protein folding chemistry from RNA methylation to supercoiled DNA. If he were not attempting to explain biologically-based cause and effect, he might readily explain why there is no mystery to how energy is created in physical systems.
See:Scientists using sunlight, water to produce renewable hydrogen power
Excerpt:

Hydrogen also can be made using electrolysis, which requires electricity and highly purified water to split water molecules into hydrogen and oxygen. Although this is a sustainable process (assuming the electricity is produced from a renewable energy source), the cost of materials associated with the system are expensive—a major barrier to the affordable production of renewable hydrogen.

My comment: All life on earth is hydrogen powered. Hydrogen-atom transfer in DNA base pairs in solution links the sun’s anti-entropic virucidal force to the de novo creation of receptors that link olfaction from the innate immune system to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. What prevents serious scientists from grasping the facts that must link quantized energy to physical systems or to biophysically constrained cell type differentiation?

See: Engineers discover light can stamp out defects in semiconductors for better solar panels and LED bulbs
Excerpt:

The team discovered that if you add light while firing the material in a furnace at high temperatures, the light generates extra electrons that can change the composition of the material.

My comment: The energy-changing properties of light and its effects on the composition of materials is linked from the speed of light on contact with water to the de novo creation of nucleic acid precursors and all biodiversity via supercoiled DNA.
See also: Biosensor Chip Flawlessly Detects Genetic Mutations
Excerpt:

The future of this technology is as vast as scientists’ understanding of the genetic mutations that cause certain diseases. If they know the SNP that causes a certain autoimmune disease, they can create the complementary strand and attach it to a biosensor chip to be sent into a patient suspected to have the disease or has a family history of the disease.

My comment: If they know how biophysically constrained energy-dependent RNA-mediated cell type differentiation occurs, they can link viruses from energy theft to the changes in SNPs that are link mutations to all pathology. But, even people who know that are not going to tell anyone until after their plans to make money from potent cures are secured by patents like this one.

RNA-Guided Human Genome Engineering

Excerpt:

Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

My comment: They know that energy-dependent RNA-mediated protein folding chemistry is the cure for all virus-driven energy theft and pathology. When do you think they’re going to tell you that?

See also: Pregnant women’s high-fat, high-sugar diets may affect future generations
Excerpt:

“Our data are the first to show that pregnant mouse mothers with metabolic syndrome can transmit dysfunctional mitochondria through the female bloodline to three generations,” Moley said. “Importantly, our study indicates oocytes – or mothers’ eggs – may carry information that programs mitochondrial dysfunction throughout the entire organism.”

My comment: That fact has been known to all serious scientists for at least two decades. See our section on molecular epigenetics in From Fertilization to Adult Sexual Behavior
See also: Alzheimer’s Disease: The Role of Presenilin 2
Excerpt:

Why exactly this is the case is unclear, but Ralph Nixon at NYU (who was unaffiliated with this study in Cell), suggests that it might be because the aggregation-prone Aβ42 is more resistant to the acidic environment in the lysosomes so it accumulates instead of being degraded like Aβ40.

My comment: Nutrient stress and social stress cause the pH changes the favor viral replication in specific tissue types.

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The Mind's Eyes (revisited)

Author’s copy: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences (2007)
Abstract:

The across-species genetic conservation of intercellular and extracellular chemical communication enables unicellular and multicellular organisms to functionally distinguish between self and non-self.  Non-self olfactory/pheromonal input from the social environment elicits a vertebrate neuroendocrine response.  The organization and activation of this neuroendocrine response modulates the concurrent maturation of the mammalian neuroendocrine system, the reproductive system, and the central nervous system during the development of sexual preferences that may be expressed in sexual behavior.  Psychophysiological mechanisms for the development of these sexual preferences include focus on unconscious affects that are detailed in reciprocal cause and effect relationships.  Olfactory/pheromonal conditioning elicits neuroendocrine effects accompanied by unconscious affects on the development of sexual preferences.  Integrating these unconscious affects extends to humans a developmental model of behavior that includes the development of male sexual preferences for other males.

For comparison, see: How Can Physics Underlie the Mind? Top-Down Causation in the Human Context (2016)
by George Ellis

George Ellis, FRS, is one of the world’s leading researchers in general relativity theory and cosmology. He is Emeritus Distinguished Professor of Complex Systems in the Department of Mathematics and Applied Mathematics at the University of Cape Town in South Africa. He co-authored The Large Scale Structure of Space-Time with Cambridge physicist Stephen Hawking.

Book description:

  • Addresses one of science and philosophy’s biggest puzzles:  how complex structures that emerge from atoms and molecules can become causative agent
  • Argues that the human mind and resultant social agency has a special status among complex systems
  • Is fully consistent with present day physics, but also takes into account key features of biology and how the brain functions
  • Will appeal to general and academic readers alike

Available 6/12/16 from Amazon books
Description:

Physics underlies all complexity, including our own existence: how is this possible? How can our own lives emerge from interactions of electrons, protons, and neutrons? This book considers the interaction of physical and non-physical causation in complex systems such as living beings, and in particular in the human brain, relating this to the emergence of higher levels of complexity with real causal powers. In particular it explores the idea of top-down causation, which is the key effect allowing the emergence of true complexity and also enables the causal efficacy of non-physical entities, including the value of money, social conventions, and ethical choices.

On pages 3 and 4 from my online version, look for:

In the influential book What Is Life, written in 1945, Erwin Schrödinger wrote [80, p. 81]: From all we have learnt about the structure of living matter, we must be prepared to find it
working in a manner that cannot be reduced to the ordinary laws of physics. And that not on the ground that there is any ‘new force’ or what not, directing the behaviour of the single atoms within a living organism, but because the construction is different from anything we have yet tested in a laboratory.

See for comparison:
What is Life?  in the section on ORGANIZATION MAINTAINED BY EXTRACTING ‘ORDER’ FROM THE ENVIRONMENT
Excerpt:

…the awkward expression ‘negative entropy’ can be he replaced by a better one: entropy, taken with the negative sign, is itself a measure of order. Thus the device by which an organism maintains itself stationary at a fairly high level of the orderliness ( = fairly low level of entropy) really consists continually sucking orderliness from its environment. This conclusion is less paradoxical than it appears at first sight. Rather could it be blamed for triviality. 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)

Look inside for information on the role of virus-driven energy theft. Search for viruses  on page 172 in my online version
Excerpt:

Folding of Single-Stranded DNA Sequences Following Reverse Mutations. The selection of native nucleic acid folding (an irreducible higher level variable) is an epigenetic effect,with broad implications for the evolution of plants and their viruses. The folding structure (a higher level variable) corresponds to an equivalence class of lower level sequences, and is the biologically relevant variable determining the selection that occurs. How do we demonstrate this top-down causation? This has been shown in detail experimentally by Shepherd et al. [171].
Note: “…a three-nucleotide mutation adversely affected Rep nucleic acid folding…” and a “…single-nucleotide reversion [C(601)A] restored wild-type-like folding.”

My comment: This exemplifies the difference between virus-driven energy theft, which caused the mutation, and a nutrient energy-dependent change in a base pair, which was required to restore the energy-dependent biophysically constrained protein folding.
Look inside for information on the role of pheromones, on page 424 in my online version.
Excerpt:

Hartwell et al. express the last point in the following way [104]:

Much of twentieth-century biology has been an attempt to reduce biological phenomena to the behaviour of molecules […] Despite the enormous success of this approach, a discrete biological function can only rarely be attributed to an individual molecule, in the sense that the main purpose of haemoglobin is to transport gas molecules in the bloodstream. In contrast, most biological functions arise from interactions among many components. For example, in the signal transduction system in yeast that converts the detection of a pheromone into the act of mating, there is no single protein responsible for amplifying the input signal.

My comment: Sensing and signalling of differences in cell types is energy-dependent. No one who knows that would expect to find a single protein that was involved in two different biophysically constrained functions, which must link metabolic networks to genetic networks in yeasts and humans via the innate immune system, the physiology of reproduction, RNA methylation, and learning and memory which must be linked to supercoiled DNA and all biodiversity.
But wait, Ellis cites Schrödinger, and ignores what Roger Penrose claimed in the forward of the reprint.

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?

It’s beginning to seem that George Ellis is going to tell only half of the story that he thinks explains how physics and the mind are connected, automagically. What about the energy source, George?

He is saved from ridicule only by the recognition that he may need to keep his faith in evolution despite the lack of experimental evidence of biologically-based cause and effect that could link neo-Darwinian theories to Darwin’s “conditions of life”. Clearly, he understands the need to establish the context in which his claims can be placed.

See page 141

4.1.4.2 Setting Values for Contextual Variables
Contextual variables set by the environment must lie in a suitable range. For example, the following are crucial to life as we know it:
• The environmental temperature must lie in a very narrow band.
• Oxygen and water must be available.
• A suitable energy source must be available (sunlight for a plant, food for an animal).
Without these contextual conditions being right,much life on Earth (animals, plants, and insects) would be in trouble. Other forms of life might have different sources of energy (e.g., thermal vents), but without some energy source, they will not survive.

My comment: Without a link from the contextual variables to the energy-dependent physiology of species-specific reproduction, the innate immune system could not be linked to all biodiversity. George Ellis knows that.

See also: Understanding and accounting for relational context is critical for social neuroscience
In the comments section, I wrote:
“New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.
Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”
— Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors Socioaffective Neuroscience & Psychology 2012; 2: 17338 – DOI: 10.3402/snp.v2i0.17338
George Ellis replied: This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: http://rsfs.royalsocietypublishing.org/content/2/1.toc
George Ellis also responded: Great links, thanks. I’m intrigued by your work on pheromones. It is just possible it might relate to the issue of primordial emotional systems, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3540967/
See also:

I added: It’s interesting to look at how our works fit, which they must do if our findings correctly represent biophysically constrained ecological adaptations manifested in morphological and behavioral phenotypes. Others are quickly eliminating any perceived incongruities. For example, see: Maternal nutrition at conception modulates DNA methylation of human metastable epialleles http://dx.doi.org/10.1038/ncomms4746. This takes physics and chemistry to the one-carbon metabolism level of DNA methylation, which links ecological variation to ecological adaptations via micronutrients and macronutrients.

Since you are familiar with Panksepp’s works, I will note that my group won the seminal award in 2001 that his group won in 2002 . See Human pheromones: integrating neuroendocrinology and ethology http://www.ncbi.nlm.nih.gov/pubmed/11600881 and Comparative approaches in evolutionary psychology: molecular neuroscience meets the mind http://www.ncbi.nlm.nih.gov/pubmed/12496741. Evolutionary theorists have since ignored or denied the role of nutrient-dependent species-specific pheromone production, which controls the physiology of reproduction, and continued to tout their ideas about mutations, natural selection and evolution.
Here we are more than a decade later and others are just now learning that the molecular mechanisms of signaling and sensing are conserved across species from yeasts to humans, which means the conserved molecular mechanisms must be the basis for emotional systems. At least one Nobel Laureate already has attested to that fact. See Feedback loops link odor and pheromone signaling with reproduction” http://www.ncbi.nlm.nih.gov/pubmed/16290036. “Indications that GnRH peptide plays an important role in the control of sexual behaviors suggest that pheromone effects on these behaviors might also involve GnRH neurons.” (p 683).
Start with yeasts: Signaling Crosstalk: Integrating Nutrient Availability and Sex http://stke.sciencemag.org/cgi/content/abstract/sigtrans;6/291/pe28 The nutrient-dependent production of the alpha mating pheromone exemplifies cell type differentiation at the advent of sexual reproduction, and when concentrated it elicits a luteinizing hormone (LH) response from the cultured pituitary cells of a mammal, the rat.
The mammalian GnRH-directed LH response has been the focus of my works for more than 2 decades since someone told me my mammalian model had to start with gene activation in hormone-secreting nerve cells of the brain. However, in 2010 , Richard Doty published a book an claimed that mammalian pheromones don’t exist. Simply put, they can’t — if you’re a social scientist. See: A Fear of Pheromones http://dx.doi.org/10.1056/NEJM197108122850708

When more experimental evidence became available, I added Timothy W. Bredy’s group has done it again. See: Long noncoding RNA-directed epigenetic regulation of gene expression is associated with anxiety-like behavior in mice. http://www.biologicalpsychiatryjournal.com/article/S0006-3223%2815%2900095-5/fulltext

Conclusion: Experience-dependent expression of lncRNAs plays an important role in the epigenetic regulation of adaptive behavior, and the perturbation of Gomafu may be related to anxiety and the development of neuropsychiatric disorders.

The most obvious correlation with what is now being discussed in the context of top-down causation and 4-D genome make-up that changes during life history transistions is: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults. http://dx.doi.org/10.1007/s00429-014-0895-5
It shows the difference that a single amino acid substitution can make during experience-dependent RNA-mediated life history transitions that link metabolic networks to genetic networks.

——————————————-

George Ellis left our brief discussion, perhaps to work on the misrepresentations of biologically-based cause and effect he just included in his book. In the book, he links information on the energy-dependent pheromone-controlled physiology of reproduction to the energy-dependent pheromone-controlled physiology of reproduction in primates via Dobzhansky’s claims from Nothing in Biology Makes Any Sense Except in the Light of Evolution.

Excerpt: 

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

My comment: Others have since shown that Feedback loops link odor and pheromone signaling with reproduction and that the energy-dependent changes linked from food odors to the pheromone-controlled physiology of reproduction are also linked to the Structural diversity of supercoiled DNA. 

Many serious scientists have joined the ranks of others who are Combating Evolution to Fight Disease by linking everything known about physics and chemistry to the molecular mechanisms of energy-dependent brain development from the origin of the nervous system in nematodes to the glorious representations that have been placed into the context of the energy-dependent de novo creation of nucleic acids, cell type differentiation, and biodiversity in the context of our 1996 Hormones and Behavior review, From Fertilization to Adult Sexual Behavior, my book chapter in The Handbook of the Evolution of Human Sexuality, and this 2013 review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

George Ellis has set the stage for others to accept, deny, or ignore everything Schrödinger probably long-ago expected to be linked from the anti-entropic energy of sunlight to all biodiversity.

See for instance: Epigenetics and Genetics of Viral Latency
Excerpt:

…viral latency is responsible for life-long pathogenesis and mortality risk…

See also: Viral Nucleic Acids
Abstract excerpt:

…viral nucleic acids can be DNA or RNA, double-stranded or single-stranded, monopartite or multipartite, linear or circular, as short as 2 kb or up to 2500 kb long. The goal of a virus is to replicate itself. To do so, viruses have evolved various strategies to replicate their genomes…

See also: Applications of nucleic acid testing in diagnosis and therapy

1) Nucleic acid testing or nucleic acid amplification testing, often abbreviated as NAT or NAAT… has been associated with blood screening for some time. It was first introduced by the German Red Cross in 1997 for blood screening to reduce the risk of transfusion-transmitted viral infections due to the failure of serologic screening tests to detect recently infected donors in the pre-seroconversion “window” phase of infection.1

2) NAT is extensively used to detect and identify organisms for proper diagnosis, prognosis, and treatment of diseases.

3) Nucleic acid testing helps to identify genetic variations and predicts predisposition to cancer, alters diagnostic categories, enhances treatment strategies, enables early detection and prevention, and improves outcomes for cancer patients. Nucleic acid testing has led to the emergence of precision and personalized medicine—that is, the tailoring of treatment based on the individual’s genetic make-up.

The emergence of nucleic acid testing led to the emergence of precision and personalized medicine. Persoalized medicine has since led to the emergence of attempts that will link Cracking the Olfactory Code  from the National Microbiome Initiative to a series of  successful attempts that led others to report on Cracking the epitranscriptome.

Excerpt:

…advances in recent years have dramatically expanded our toolkit for studying m6A and have begun to expose different levels at which RNA methylations are associated with phenotypic and molecular consequences.

George Ellis attempts to put everything known to physicists, chemists, and molecular biologists about the links from angstroms to ecosystems back into the context of the evolution of the human mind. But he waited to do that until after others cracked the epitranscriptome. That cracks me up. His sense of humor is as dry as Dobzhansky’s and hit wits are still sharp.

I’m almost certain the George Ellis is joking because he mentions Feynman’s works several times, but fails to put them into the context of Schrodinger’s anti-entropic force of sunlight; Dobzhansky’s “light of evolution;” or Roger Penrose’s question. “How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?

For comparison, see:

Periodic Scarred States in Open Quantum Dots as Evidence of Quantum Darwinism

A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution.

If you’re not sure whether or not George Ellis is joking about the evidence of quantum Darwinism or the theory about docosahexanoic acid in energy-dependent cell type signaling that links the underlying physics from chemistry to the molecular epigenetics of brain development and the human mind, ask him a few questions. Does he know how my works on RNA-mediated amino acid substitutions linked the works of Luca Turin, Anna Di Cosmo, Eugene Daev, Bruce McEwen, the late Robert L. Moss, and Timothy W. Bredy to everything currently known about biophysically constrained energy-dependent RNA methylation and cell type differentiation in all living genera?

Physics

Creating gravity, nucleic acids, receptors, and supercoiled DNA

Liveblog: Scientists to announce major gravitational wave finding

My comment: If they link gravitational waves and changes in the speed of light on contact with water, they will be one less step away from linking the creation of gravity to the creation of nucleic acids and the de novo creation of olfactory receptor genes and supercoiled DNA that protects organized genomes from virus-driven entropy.

A new method furthers understanding of evolutionary genetics

Excerpt:

Since Darwin, evolutionary biologists have been fascinated by how different organisms are from one another. The ultimate goal is to understand how mutations in DNA, the genetic blueprint, shape the growth and behavior of animals, plants, and microbes around us.

My comment: The ultimate goal of all serious scientists is to continue to use experimental evidence of biologically-based cause and effect to support Darwin’s links from “conditions of life” to all biomass and all biodiversity. Neo-Darwinists have held their advantage over the heads of all serious scientists. They need only make claims like this:

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

My comment: The ridiculous claims of neo-Darwinists can then be placed into the context of experimental evidence like this:
Polygenic evolution of a sugar specialization trade-off in yeast
Excerpt:

In hybrids formed by mating S. cerevisiae with other Saccharomyces species6, we noted a pattern of coherent cis-regulatory variation in the seven genes of the galactose metabolic pathway.

My comment: Hybrid sterility is typically the result of such matings. None have been linked to the evolution of one species from another. For comparison, UV light-induced hydrogen-atom transfer in DNA base pairs in solution links the speed of light on contact with water to the de novo creation of nucleic acids, changes in microRNAs, RNA-mediated amino acid substitutions, adhesion proteins, and supercoiled DNA, which protects organized genomes from virus-driven entropy.
The nutrient energy-dependent RNA-mediated physiology of pheromone-controlled reproduction links sex differences in the cell types of brewers yeast to human sexual orientation via biophysically constrained differences in the morphological phenotypes and the behavioral phenotypes of all living genera.
Evolutionary biologists ignore Darwin’s “conditions of life” and focus their efforts on differences in organisms instead of similarities.
I reiterate the claim from: A new method furthers understanding of evolutionary genetics
Excerpt:

Since Darwin, evolutionary biologists have been fascinated by how different organisms are from one another. The ultimate goal is to understand how mutations in DNA, the genetic blueprint, shape the growth and behavior of animals, plants, and microbes around us.

My comment: Evolutionary biologists may continue to link mutations to differences instead of linking gravity and/or the speed of light to similarities via RNA-mediated amino acid substitutions that differentiate the cell types of all individuals of all species. After today’s announcement, however, they will probably continue to be laughed at by serious scientists who link atoms to ecosystems via what is currently known about physics, chemistry, biology and molecular epigenetics.