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

Exome Sequencing Impact in Routine Care

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

US Air Force Studying Impact of Exome Sequencing in Routine Care

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

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

I was trained to become a medial laboratory scientist during the last 4 years of my 7 years in the United States Air Force (Dec. 1970-Aug. 1977).  I worked in the laboratory and examined the experimental evidence reported in published works, I learned that all pathogenic variants are caused by the virus-driven degradation of messenger RNA. I also learned that pharmacogenomic profiles have already been linked to effective treatments for virus-driven energy theft via my model of nutrient-dependent pheromone-controlled biodiversity.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Conclusion:

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

My model refuted every aspect of neo-Darwinian pseudoscientific nonsense, which may be why some doctors never heard about it, or why some of them don’t want to admit to what they know about effective treatments for all pathology.
During suicide prevention month, the National Commander of the American Legion focused on efforts to help reduce the number of suicides among veterans, which occur at ~ 22 each day. I was surprised to see how little response from the general public there has been since then. It’s as if no one has learned about experimental evidence of biologically-based cause and effect such as this:
Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity

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

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

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

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

Abstract:

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

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

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

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

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

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

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

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

Cytosis

Your indifference is killing you and others (4)

Summary:
I suspect that Subatomic, like Cytosis, will help link atoms to ecosystems via my model of nutritional epigenetics and the pheromone-controlled visual perception of mass and energy, which has been linked from the sense of smell in bacteria across the space time continuum via olfaction.
From 7 years ago.
Published 7 years ago on 15 Aug 2010 by James V. Kohl of Pheromones.com, RNA-mediated.com, and Autophagy.pro
Kohl is the co-author of “The Scent of Eros” and he is the creator of: The Scent of Eros and The Mind’s Eyes human pheromone-enhanced products. This is an excerpt from his presentation at the 2010 Annual Gathering of Mensa (i.e., the “high IQ” society).

Pheromones have since been linked from suicide prevention to the prevention of all neurodegenerative diseases and the prevention of all other pathology, which includes cancer prevention.

See for examples:

 
 
 

Everything known to serious scientists about biophysically constrained energy-dependent RNA-mediated cell type differentiation and viral latency in the context of quantum physics and the space time continuum will soon be known to everyone older than 10 who plays the game “Cytosis” and the game “Subatomic.”

In less than 3 hours of play-time, it will become clear that the virus-driven theft of quantized energy causes the degradation of messenger RNA, which links mutations to all pathology.

Suzan Mazur: What is your definition of life?

Eviatar Nevo: Our understanding of origin of life is very slim. . . . [First] life didn’t fossilize. The best we can know about origin of life may be from viruses we are looking at. They could have been at the origin of life before they parasitized it, or became symbionts in prokaryotes and eukaryotes. . . .

Young earth creationist / scientists put the virus-driven parasitism of life into the perspective of perfect creation in: Viral Genome Junk Is Bunk

“The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6

The fact that viruses got their genes from their hosts became clear in the context of what is known about natural selection for energy-dependent codon optimality.

The extent of codon usage bias in human RNA viruses and its evolutionary origin (2003)

Revealing the determinants of codon usage bias is central to the understanding of factors governing viral evolution. Herein, we report the results of a survey of codon usage bias in a wide range of genetically and ecologically diverse human RNA viruses. This analysis showed that the overall extent of codon usage bias in RNA viruses is low and that there is little variation in bias between genes. Furthermore, the strong correlation between base and dinucleotide composition and codon usage bias suggested that mutation pressure rather than natural (translational) selection is the most important determinant of the codon bias observed. However, we also detected correlations between codon usage bias and some characteristics of viral genome structure and ecology, with increased bias in segmented and aerosol-transmitted viruses and decreased bias in vector-borne viruses. This suggests that translational selection may also have some influence in shaping codon usage bias.

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

Synopsis

Embedded Image

In addition to spelling out protein sequence, mRNA codon triplets contain translation‐dependent regulatory information that influences transcript stability and contributes to controlled turnover of maternal mRNAs in frogs, mice, and flies.

  • Codon optimality forms a regulatory code within the genetic code that controls mRNA stability and translation efficiency.

  • Codon composition shapes maternal mRNA clearance during the maternal‐to‐zygotic transition in zebrafish, frog, mouse, and fly in a translation‐dependent manner.

  • Amino acid composition also influences mRNA stability in vertebrates.

  • Codon optimality correlates with codon bias, suggesting that codon optimality shapes steady‐state mRNA levels in homeostasis.

Excerpt:

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

Reported as: A code within a code: how codons influence mRNA stability

The sequence changes in the amino acid optimality code link energy-dependent changes in base pairs to fixation of amino acid substitutions in supercoiled DNA via the physiology of reproduction. The substitutions protect all organized genome from the virus driven degradation of messenger RNA that links mutations to all pathology.

See also: Kinetic Rain | Art + Com

The level of creativity required to link physics to chemistry and the conserved molecular mechanisms that link kinetic energy and food energy to RNA-mediated cell type differentiation via quantum mechanics and amino acid substitutions is exemplified in this moving sculpture and ignored by theorists who might unknowingly attribute all the interactions to mutations and evolution.

See also: The  Critical Thinking Cafe

The group has been archived. No more comments will be added by those who lack the critical thinking skills required to link what organisms eat to the physiology of pheromone-controlled reproduction and all biodiversity.

It should be even clearer that two games “Cytosis” and “Subatomic” will put an end to any theoretical nonsense about mutations and evolution.

I suspect that Subatomic, like Cytosis, will help link atoms to ecosystems via my model of nutritional epigenetics and the pheromone-controlled visual perception of mass and energy, which has been linked from the sense of smell in bacteria across the space time continuum via olfaction.
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

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

Energy-dependent physical and biophysical constraints (7)

See first: Energy-dependent physical and biophysical constraints (6)
Stems Cells in the Hypothalamus Slow Aging in Mice
My comment to The Scientist

Cai says microRNAs could be a potential mechanism by which hypothalamic neural stem cells have such wide-ranging effects on aging, yet he believes that neurogenesis may also be involved.

See also: Feedback loops link odor and pheromone signaling with reproduction

At least 10,000 neurons in 26 different brain areas appear to transmit signals directly to GnRH neurons.  GnRH neurons appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.

More than 63,000 indexed articles on PubMed link energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity. Many of them also link the virus-driven theft of quantized energy from mutations to pathology such as John McCain’s glioblastoma. He will probably be treated with microRNAs, but that fact may not be reported because the effective treatment is a refutation of neo-Darwinian pseudoscientific nonsense about mutations, natural selection, and evolution.

Cytosis

Epigenetic effects of stress by Bruce McEwen (2)

Summary:

…rapid mRNA turnover starts with the energy-dependent de novo creation of microRNAs and ends with the virus-driven degradation of messenger RNA, which links mutations to all pathology.
 
This was reported in the following context: “RNA molecules live short lives” July 12, 2017

See also: Epigenetic effects of stress by Bruce McEwen (1)

Summary:

In the early 1990’s, Bruce McEwen inspired my life’s works, which link the epigenetic effects of nutrient-stress and/or social stress to the fact that RNA biosynthesis is ATP-dependent. That fact helped all serious scientists link the virus-driven energy theft of quantized energy to the degradation of messenger RNA, which links mutations to all pathology.

Pseudoscientists refuse to accept that fact.

New research uncovers the secrets of photosynthesis that could help develop computer technology

Energy and charge transfer is what drives photosynthesis and any solar-to-chemical or electrical-to-chemical energy conversion.

That fact links the anti-entropic virucidal energy of sunlight from the de novo creation of microRNAs to all biodiversity. Bruce McEwen published on the role that microRNAs play in: Characterization of the vulnerability to repeated stress in Fischer 344 rats: possible involvement of microRNA-mediated down-regulation of the glucocorticoid receptor (2008)

We also identified that microRNA (miR)-18a inhibited translation of GR mRNA in cultured neuronal cells and that increased expression of miR-18a in the PVN was observed in F344 rats compared with SD rats. These strain differences in GR protein levels were not found in the hippocampus and prefrontal cortex, and the expression of miR-18a was much lower in these brain regions than in the PVN. Our results suggest that F344 rats could be a useful animal model for studying vulnerability to repeated stress, and that miR-18a-mediated down-regulation of GR translation may be an important factor to be considered in susceptibility to stress-related disorders.

See also: Early Life Stress Enhances Behavioral Vulnerability to Stress through the Activation of REST4-Mediated Gene Transcription in the Medial Prefrontal Cortex of Rodents (2010)

Figure 3.

Expression analyses of mRNAs of RE-1-containing genes and brain-enriched pre-microRNAs in the mPFC of the maternally separated rats. A, B, The expression of mRNAs (A) and pre-microRNAs (B) of a variety of RE-1-containing genes in the mPFC of AFR, HMS15, and HMS180 rats at P14 were quantified by Q-PCR (n = 6 for all groups). C, D, The expression of mature microRNAs in the mPFC of AFR, HMS15, and HMS180 rats at P14 were quantified by Northern blotting analysis (n = 5–6 for each group). E, The mRNA and pre-microRNA expression of RE-1-containing genes in the mPFC of adult AFR, HMS15, and HMS180 rats were quantified by Q-PCR (n = 6 for all groups). *p < 0.05.

Bruce McEwen subsequently linked what is known about energy-dependent changes in single nucleotide polymorphisms to effects of hormones on behavior in mice and humans via a food energy-dependent biophysically constrained amino acid substitution.

See: Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity (2015)

Excitatory amino acids play a key role in both adaptive and deleterious effects of stressors on the brain, and dysregulated glutamate homeostasis has been associated with psychiatric and neurological disorders. Here, we elucidate mechanisms of epigenetic plasticity…  In WT mice after CRS and in unstressed mice with a BDNF loss-of-function allele (BDNF Val66Met), we show that the epigenetic activator of histone acetylation, P300, plays a pivotal role in the dynamic up- and down-regulation of mGlu2 in hippocampus via histone-3-lysine-27-acetylation (H3K27Ac) when acute stressors are applied. These hippocampal responses reveal a window of epigenetic plasticity that may be useful for treatment of disorders in which glutamatergic transmission is dysregulated.

See also: Multiplexed gene control reveals rapid mRNA turnover (open access)

The rapid mRNA turnover starts with the energy-dependent de novo creation of microRNAs and ends with the virus-driven degradation of messenger RNA, which links mutations to all pathology.
 
This was reported in the following context: “RNA molecules live short lives” July 12, 2017
“Sometimes it is hard to believe that scientists could have unknowingly worked with methods that produce inconsistent results for almost 30 years”, says Becskei.
 
Becskei adds insult to the injury, unnecessary suffering, and the premature death caused by misrepresentations of biologically-based cause and effect. An accurate representation was reported in 1964 as: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” 
 

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

The fact that some researchers still do not know that the synthesis of RNA is energy-dependent makes it impossible for them to link virus-driven energy theft from the degradation of messenger RNA to mutations and all pathology in all living genera.

It will soon become “child’s play” for anyone over 10 years old. See: Cytosis: A Cell Biology Board Game

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

terrarium-eco-system

The emergence of light as energy from a life-giving star

The Sun – our steady, reliable companion – tells a very different story up close

“…a mesmerising, perspective-shaking glimpse at Earth’s life-giving star.” (video)

Questions:
1) Did the energy in this life-giving star create itself?
2) How is hydrogen-atom transfer in DNA base pairs in solution biophysically constrained.
3) Who created the feedback loops that link the solar analemma from the time-space continuum to representations of biophysically constrained life and free will in the Mobius strip.
4) Was Linda Buck the first Nobel Laureate to establish the link from the food energy-dependent pheromone-controlled physiology of reproduction to biodiversity in all living genera?
5) Are biologically uninformed theorists capable of answering any questions about the energy of life or how virus-driven energy theft causes the degradation of messenger RNA that links constraint-breaking mutations to all pathology?
The Mobius strip and the solar analemma exemplifie biophysical constraints on life history events.

The Mobius strip (above) is a visual aid for those who do not understand the concept of how free will is connected to the conserved molecular mechanisms of biophysically constrained energy-dependent RNA-mediated cell type differentiation in all living genera. If you cannot answer all 5 questions about energy in the context of the visual aid, which links the solar analemma to choices between quantized energy-dependent life and death, please search for microRNA on PubMed. The sun’s anti-entropic virucidal energy is biophysically constrained in microRNAs at every level of examination from angstroms to ecosystems.
If you cannot find the answers to any of the five questions about energy, ask a theorist to answer the first question. Alternatively, see: Computational identification of mutually homologous Zika virus miRNAs that target microcephaly genes

…ZIKV may modulate the action of various miRNAs, and miR-1304 in particular, resulting in microcephaly.

ZIKV – driven degradation of messenger RNA is linked to microcephaly. See also: Absolute Biophysical Characterization with Multi-Angle and Dynamic Light Scattering

A SEC-MALS-RI or UV with DLS system extends the characterization range of biomolecules to glycoproteins, PEGylated proteins, hydrophobic proteins, biopolymers, and other biomolecules.

My summary: The “Brownian” motion of molecules links dynamic light-scattering (DLS) from ecological variation to ecological adaptations via Ultraviolet-visible (UV-Vis) spectroscopy. Detection of energy as information has been placed into the context of virucidal light as energy.

Dynamic light scattering [DLS]

Dynamic light scattering (DLS) is a technique in physics that can be used to determine the size distribution profile of small particles in suspension or polymers in solution.[1] In the scope of DLS, temporal fluctuations are usually analyzed by means of the intensity or photon auto-correlation function (also known as photon correlation spectroscopy or quasi-elastic light scattering).

See also: Detection Limits of DLS and UV-Vis Spectroscopy in Characterization of Polydisperse Nanoparticles Colloids
My summary: Ultraviolet-visible (UV-Vis) spectroscopy links the the food energy-dependent pheromone-controlled physiology of reproduction to the weekend resurrection of the bacterial flagellum in P. fluorescens, which responds to the light-activated chemistry of life with fluorescence even after the “knock-out” of the gene for its mobility, which was resurrected over the weekend as reported in: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The resurrection in this organism, links its fluorescence to quantized energy-dependent exosome-delivered microRNAs, which have been reported to be Ultraconserved Elements in the Human Genome. When theorists use terms like ultraconserved elements outside the context of the conserved energy in microRNAs, it is clear that theorists are attempting to obfuscate this fact: The energy-dependent de novo creation of microRNAs has been linked to all biodiversity in all living genera via the physiology of pheromone-controlled reproduction.
See for example: All in the (bigger) family I wrote:

The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made since the 2013 ecological epigenetics symposium. For example, since then authors claimed “…ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” http://dx.doi.org/10.1038/nature13400

Six months later, other authors traced signaling factors found in vertebrates to the origin of nerve cell centralization via the diffuse nerve net of animals like the sea anemone. http://dx.doi.org/10.1038/ncomms6536 That fact suggests ecological variation is linked to ecological adaptations in morphological and behavioral phenotypes via signaling protein concentrations that differentiate various cell types in body axes and the central nervous system.

Links across species from the epigenetic landscape to the physical landscape of DNA in organized genomes appear to have their origins in the conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated protein folding. Two weeks after the publication that refuted ideas about independently evolved neural systems or muscle specification — and perhaps refuted the independent evolution of anything else, SICB presenters linked crustaceans to insects.

Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.

Why were they left with any questions about how crustaceans and insects could all be part of one big family? They linked RNA-mediated cell type differentiation to what we described in our section on molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior

See for comparison: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

The interactions of these small noncoding RNAs in such primitive species have wide-reaching effects, from increasing viral and bacterial proliferation, better responses to stress, increased virulence, to manipulation of host immune responses…

The small non-coding RNAs are energy-dependent microRNAs, which are the same thing as Ultraconserved Elements in the Human Genome..
Here’s a way to make that fact perfectly clear. When it becomes available, play this game: Cytosis: A Cell Biology Board Game

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

Stop playing the ridiculous games of theorists who have failed to link the Creation of the sun’s quantized energy to all biodiversity on Earth. Theorists also failed to link the virus-driven degradation of messenger RNA from mutations to all pathology. Instead, they have used definitions of terms and definitions of species that are not limited to that fact that all organisms on Earth must eat or they fail to reproduce.
See for examples of pseudoscientific nonsense: New Research Problem of Species Definitions

Darwin first noted that there is no one definition of species, and not much has changed since then.

All species-specific behavior is food energy-dependent and RNA-mediated cell type differentiation biophysically constrains it in the context of the physiology of pheromone-controlled reproduction in all living genera. Darwin presciently included that fact in his “conditions of life.” He warned others that they could not start with natural selection, but many others have consistently ignored Darwin’s warnings. They also ignore the consistency of biological facts that link what organisms eat to the survival of all species via the pheromone-controlled physiology of reproduction. That forces them to ignore the consequences of virus-driven energy theft.
See: Virus-mediated archaeal hecatomb in the deep seafloor

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

See for support of the fact that virus-archaea interactions play a central role in global biogeochemical cycles: Feedback loops link odor and pheromone signaling with reproduction
The feedback loops link natural selection for energy dependent codon optimality from RNA-mediated amino acid substitutions in supercoiled DNA to all biodiversity on Earth via the exosome-mediated delivery of microRNAs.
See also: The phylogenetic utility and functional constraint of microRNA flanking sequences

…the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

The assembly of all organized genomes is food energy-dependent. Without food energy there is no energy for assembly of anything. Exosomes mediated the delivery of the food energy in microRNAs.
See also: Exosome Mediated Delivery of miR-124 Promotes Neurogenesis after Ischemia.

The intrinsic ability of neurogenesis after stroke has been proven weak, which results in insufficient repair of injury in the nerve system. Recent studies suggest multiple microRNAs (miRNAs) are involved in the neuroremodeling process. Targeted miRNAs delivery for amplification of neurogenesis is promising in promoting the prognosis after ischemia. Here, we showed that modified exosomes, with rabies virus glycoprotein (RVG) fused to exosomal protein lysosome-associated membrane glycoprotein 2b (Lamp2b), could efficiently deliver miR-124 to the infarct site. Systemic administration of RVG-exosomes loaded with miR-124 promoted cortical neural progenitors to obtain neuronal identity and protect against ischemic injury by robust cortical neurogenesis. Our study suggests that RVG-exosomes can be utilized therapeutically for the targeted delivery of gene drugs to the brain, thus having great potential for clinical applications.

The fact that “…multiple microRNAs (miRNAs) are involved in the neuroremodeling process…” makes the role of food energy-dependent RNA-mediated DNA repair perfectly clear to all serious scientists. For comparison, use of virus-assisted delivery has been linked to the predictable horror of gene editing technology.
See: Unexpected mutations after CRISPR-Cas9 editing in vivo
See for comparison: Cell proliferation in the subventricular zone by synthetic murine pheromones

The elucidation of the mechanisms by which specific compounds influence cell proliferation and neurogenesis, and eventually reproductive conditions in males and females should provide further insight as to how the odor environment controls and modulates the reproductive activities of animals.

See also: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
Clearly, researchers who use viruses to stimulate neurogenesis have not learned that all cell type differentiation is energy-dependent and controlled by feedback loops. Their use of viruses will continue ot link virus-driven energy theft from the degradation of messenger RNA to all pathology via the constraint breaking mutations the Masatoshi Nei, and many other biologically uninformed theorists have included in their stories about Mutation-Driven Evolution.

Exosome-delivered microRNAs modulate the inflammatory response to endotoxin 6/18/16

The functional relevance of exosomes in many different biological systems, including the immune system, is beginning to be demonstrated5,6,7,8,9,10,11.

See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, ; Duvarci, Nader, & LeDoux, ; Griggs et al., ; Monahan & Lomvardas, ) in adaptive evolution will certainly be discussed in published works that will follow.

See also: Humans Fit All Of The Government Criteria For ‘Endangered Species’ and Past 5,000 years prolific for changes to human genome
See for comparison: Independent and Stochastic Action of DNA Polymerases in the Replisome

It has been assumed that DNA synthesis by the leading- and lagging-strand polymerases in the replisome must be coordinated to avoid the formation of significant gaps in the nascent strands.

Reported as: Close-Up View of DNA Replication Yields Surprises

What looks like coordination is actually the outcome of a random process of starting, stopping and variable speeds. Over time, any one DNA polymerase will move at an average speed; look at a number of DNA polymerases synthesizing DNA strands over time, and they will have the same average speed.

See for comparison: The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity

…the metabolic enzyme, pyruvate kinase muscle (PKM), interacts with sub-pools of endoplasmic reticulum (ER)-associated ribosomes, exerting a non-canonical function as an RNA-binding protein in the translation of ER-destined mRNAs.

Metabolism is food energy-dependent. That fact should have eliminated all the pseudoscientific nonsense about the random process of starting, stopping and variable speeds. For example, autophagy is quantized energy-dependent and the energy from food protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA that links mutations to all pathology.
See also: The evolution of ecosystem ascendency in a complex systems based model
Abstract conclusion:

Our findings support the validity of ecosystem ascendency as a meaningful measure of ecosystem organisation, which increases over evolutionary time scales and significantly drops during periods of disturbance. The results suggest a general trend towards both higher integrity and increased stability driven by functional and structural ecosystem coadaptation.

Ecosystem ascendancy is food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera.
Attempts to model general trends towards the increased stability of functional and structural ecosystems without linking the anti-entropic virucidal energy of sunlight to the physiology of reproduction are examples of what Richard Feynman referred to as human idiocy.

Richard Feynman was a Nobel prize winning Theoretical Physicist who popularized physics with his entertaining lecture style. This snippet is taken from one of his lectures in the series “The character of Physical Law” where he complains about all the different units that are used to measure the single concept of Energy.
See also: Structural diversity of supercoiled DNA

Six decades after the elucidation of its double helical structure, DNA continues to surprise us by revealing new information. Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

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.
7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
See also:These groups are moderated by Robert Karl Stonjek, who is an example of human idiocy. He knows nothing about biophysically constrained energy-dependent cell type differentiation and consistently displays his ignorance by limiting ability to explain the role that the virus-driven degradation of messenger RNA plays in all pathology.
Psychiatry and Clinical Psychology
Neuroscience
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On his FB group for discussion of Sensescence on 6/16/17 I wrote:

All death is caused by trauma or the virus driven degradation of messenger RNA

On 6/17/17 Robert Karl Stonjek wrote (with my emphasis):

Or viruses, or bacteria, or degenerative disease, or genetic disease (there are many), or substance abuse (there are many), or obesity, or….the only one I can’t find in the regular literature is virus driven degradation of messenger RNA.

And then: Robert Karl Stonjek turned off commenting for this post. Can you die from old age?
The pervasive ignorance of those who moderate or censor the comments made by serious scientists via social media has overwhelmed all attempts to present what is known about the virus-driven degradation of messenger RNA, which causes the mutations that have been linked to all pathology.
See for comparison:

Theorists will cause the death of us all. Who will be the next of your loved ones to unnecessarily suffer and prematurely die from the ignorance of theorists?
America’s Dominance In The Scientific World Is shrinking

…while Chinese-born scientists who trained in the United States used to stay here to work, they are now going back to China after their education is over.
 

Denise Chen’s student, Wen Zhou did that. See: Olfaction Warps Visual Time Perception

Had she stayed in the United States, she would have been subjected to pseudoscientific nonsense like this:

Still, even in fruit flies, other sensory input besides pheromones — acoustic, tactile, and visual stimuli — play a role in sexual attraction, and sex specific responses to these stimuli appear to be innate rather than learned by association [36.]. We simply don’t know where the boundary between prespecified attraction and learned association lie in our own species, nor do we have compelling evidence for the primacy of one sense over another.” — Simon LeVay (2011) in his comments on my award-winning model – after it won a second award in 2007. See: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences

See also:

… chemosignal enthusiasts point to a variety of studies in which sniffing body secretions or substances purified from secretions appears to have some psychological effect…” — Simon LeVay (2016)

He cited the review that won the first award (Kohl et al., 2001). Human pheromones: integrating neuroendocrinology and ethology

It does not surprise me that senior author Wen Zhou has since linked the sense of smell to the time-space continuum. She was the most promising student I ever met, and I was sad to see her return to China after developing her expertise in the context of what she learned from Denise Chen, who learned about olfaction and pheromones from Martha McClintock.
 
Earlier this year, Wen Zhou’s group showed that olfaction alters the perception of the space-time continuum, which also is warped by the distribution of mass and energy. She has helped to show how food energy and the pheromone-controlled physiology of reproduction are linked to energy-dependent subjective time. For comparison, theorectical physicists have failed to explain anything in the context of multisensory inputs. That is why I frequently refer to biologically uninformed theoretical physicists in the same context as the biologically uninformed neo-Darwinian theorists who have failed to link quantized energy to all healthy longevity and failed to link virus-driven energy theft from the degradation of messenger RNA to mutations and all pathology.
 
Simply put, the multisensory inputs link quantized energy as information from the epigenetic landscape to the physical landscape of DNA at subsecond scales via neural energy and RNA-mediated amino acid substitutions.
 

The subsecond scales links femtosecond blasts of UV light to DNA repair, which is required to link quantum physics to quantum souls. That is the topic of my next interview with J.A. Parker, who sent me the questions in advance, so that I could try to keep the jargon to a minimum.

Until I am sucessful, see: Analysis sheds light on how metaphors like ‘sheds light’ evolved

Words that originally had only concrete or external meaning have grown to also have meaning in the realms of the abstract and internal.

Who else besides Schrodinger in “What is Life? (1944) and J.A. Parker of Quantum Souls knew that Dobzhansky’s “light of evolution” would be traced back to “Let there be Light” in Biblical Genesis via what is known about the anti-entropic virucidal energy of sunlight?

MicroRNAs GnRH and the failure of sex research

Summary: “The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression” accurately represents what is known about food energy-dependent RNA-mediated cell type differentiation in species from soil microbes to humans. MicroRNAs are not new players in the hypothalamic control of fertility and the effects of food odors and pheromones on microRNAs link energy-dependent changes in hormones to behavior. That fact was detailed two decades ago in our Hormones and Behavior review.

Now see: [MicroRNAs: new players in the hypothalamic control of fertility]

MicroRNAs are small non-coding RNAs that modulate gene expression post-transcriptionally. Discovered more than 15 years ago, their functions start to be unraveled. Increasing evidence points to an important functional role of microRNAs in brain development. In particular, miRNAs have recently been established to play a vital role in the mechanisms underlying the infantile rise in gonadotropin-releasing hormone (GnRH) production by neurons in the hypothalamus, a phenomenon necessary for the onset of puberty in mammals.

The anti-entropic virucidal energy of ultraviolet light links the de novo creation of of microRNAs from flanking sequences that biophysically constrain all biodiversity by protecting the organized genomes of all living genera from the virus-driven degradation of messenger RNA, which links mutations to all pathology.

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

After scanning the article that accurately represents what is known about RNA-mediated cell type differentiation in species from soil microbes to humans, see this pseudoscientific nonsense for comparison:

Prenatal Influences on Human Sexual Orientation: Expectations versus Data. Breedlove SM. Arch Sex Behav. 2017 Feb 7. doi: 10.1007/s10508-016-0904-2.

Human Sexual Orientation: The Importance of Evidentiary Convergence. Balthazart J, Court L. Arch Sex Behav. 2017 May 12. doi: 10.1007/s10508-017-0997-2.

A Bird’s Eye View. Adkins-Regan E. Arch Sex Behav. 2017 May 10. doi: 10.1007/s10508-017-0998-1

Proceed with Caution: Interpreting Evidence for Prenatal Influences on Sexual Orientation. LeVay S. Arch Sex Behav. 2017 May 8. doi: 10.1007/s10508-017-0996-3

On Possible Hormonal Mechanisms Affecting Sexual Orientation. McFadden D. Arch Sex Behav. 2017 May 5. doi: 10.1007/s10508-017-0995-4

Reconsidering Prenatal Hormonal Influences on Human Sexual Orientation: Lessons from Animal Research. Baum MJ, Bakker J. Arch Sex Behav. 2017 May 4. doi: 10.1007/s10508-017-0994-5

Each published work represents the failure of the sex researchers to link energy-dependent RNA-mediated cell type differentiation from the pheromone-controlled physiology of reproduction to all biodiversity via the section on molecular epigenetics from our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior

In our section on molecular epigenetics, we linked the quantized energy-dependent de novo creation of microRNAs from fertilization to adult sexual behavior via this claim.

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

The alternative splicing techniques of pre-mRNA are quantized energy-dependent and they link microRNA flanking sequences to all biodiversity via hydrogen-atom transfer in DNA base pairs in solution. The hydrogen-atom transfer was place into the context of the biophysically constrained physiology of reproduction and the role of microRNAs in this published work:

The phylogenetic utility and functional constraint of microRNA flanking sequences

Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

Genomes do not automagically assemble themselves. Placing the energy-dependent de novo creation of microRNAs into the context of the speed of evolution is a horrid error in logic that extends across all disciplines, which is the only way it can continue to be placed into the pseudoscientific claims of sexuality researchers.

See also: Feedback loops link odor and pheromone signaling with reproduction

At least 10,000 neurons in 26 different brain areas appear to transmit signals directly to GnRH neurons. GnRH neurons appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

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

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

If you take any time at all to review the published works of sex researchers, you will learn why Feynman referred to all social scientists as pseudoscientists.

See also:

Richard Feynman was a Nobel prize winning Theoretical Physicist who popularized physics with his entertaining lecture style. This snippet is taken from one of his lectures in the series “The character of Physical Law” where he complains about all the different units that are used to measure the single concept of Energy.

The human sexualilty researchers whose works were recently published in the Archives of Sexual Behavior represent the worst of pseudoscience. They skip past the facts about food energy and pheromones and link behavior to anything except the role that microRNAs (pre-mRNAs) play in energy-dependent RNA-mediated cell type differentiation, which links quantized energy from angstroms to ecosystems in all living genera via the sense of smell in bacteria.
Scientists investigate how the sense of smell works in bacteria

…the signaling and inactive states differ only very slightly at the nitrate-binding site – by 0.5-1 angstroms, which is approximately one fifth of the size of the ion itself (1 angstrom is 10-10 meters). However, when this ion binds to the sensor, it causes huge changes in the protein: The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.

See also this: Animation of a particle where the Helicity matches the Chirality.
This appears to be a match made in Heaven so far as young earth creationists are concerned. It links the creation of the sun’s anti-entropic energy to all biodiversity on Earth via the physiology of food energy-dependent pheromone-controlled reproduction in the context of what is known about autophagy (Yoshinhori Ohsumi) and chromosomal inheritance (Thomas Hunt Morgan).
But now, all the works of Nobel Laureates can be placed into the context of works by people like Lukin MD
See for example: Symmetry-protected collisions between strongly interacting photons and Lukin MD microRNA no entries found, for comparison
People like Lukin are not going to link microRNA-mediated cause and effect from the sun’s anti-entropic virucidal energy to all biodiversity on Earth via food energy and the pheromone-controlled the physiology of reproduction and transgenerational epigenetic inheritance. They are like the biologically uninformed sex researchers who have failed to make sense of anything known to serious scientists.
If symmetry protects collisions between strongly interacting photons, the virus-driven theft of quantized energy clearly can be linked to the assymetry manifested it in conditions where the degradation of messenger RNA can clearly be linked to all pathology via the sense of smell.
See Hormonal correlates of women’s mid-cycle preference for the scent of symmetry

When women are fertile in their cycles, in comparison with when they are in the luteal phase, they are more attracted to masculine facial features (Johnston, Hagel, Franklin, Fink, & Grammer, 2001; Penton-Voak & Perret, 2001; Penton-Voak et al., 1999), darker facial skin color (Frost, 1994), lower voice pitch (Feinberg et al., 2006; Puts, 2005), masculine body odor (Grammer, 1993), the scent of men who are socially dominant (Havlicek, Roberts, & Flegr, 2005), the scent of men displaying developmental stability/bilateral symmetry (Gangestad & Thornhill, 1998a; Rikowski & Grammer, 1999; Thornhill & Gangestad,1999; Thornhill et al. 2003), masculine (or dominant) behavioral displays (Gangestad, Garver-Apgar, Simpson, & Cousins, 2007; Gangestad, Simpson, Cousins, Garver-Apgar, & Christensen, 2004; Gangestad, Thornhill, & Garver-Apgar, 2008), masculine or muscular bodies (Gangestad et al., 2007; Little, Jones, & Burriss, 2007) and creative men (Haselton & Miller, 2006; see Thornhill & Gangestad, in press, for a critical review of these and other cycle effects). Substantial evidence indicates that these shifts are specific to women’s preferences for men evaluated as sex partners and not to their preferences for men as long-term, investing mates (e.g., Gangestad et al.,2004, 2007; Haselton & Miller, 2006; Penton-Voak et al., 1999; Puts, 2005).

All these preferences can be framed in the context of what is known about the sense of smell and the substitution of achiral glycine in position 6 of the GnRH decapeptide. One substitution stabilizes the organized genomes of all vertebrates by preventing nearly all the virus-driven degradation of messenger RNA, which has been linked to all pathology in all living genera.
See: Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

It is possible that GnRH has an early origin in life history as a regulator of reproduction, since yeast α mating factor has 80% amino acid homology with mammalian GnRH and stimulates gonadotropin release from the mammalian pituitary (Loumaye et al., 1982; King and Millar, 1995). There is a question whether the structure of the GnRHs and their receptors in invertebrates conserved their structure during evolution in a sufficient degree to support the homology with the structure of GnRHs and their receptors in vertebrates.

There is no longer any question about the conserved molecular mechanisms of biophysically constrained RNA-mediated cell type differentiation in all living genera. The mechanisms are light energy-dependent in the context of food energy and the pheromone-controlled physiology of reproduction.
When will all researchers learn to search PubMed for more information about the role of microRNAs before continuing to tout their pseudoscientific nonsense? What do serious scientists say, for comparison?
See: MicroRNA Items: 1 to 20 of 61842
For example: Computational identification of mutually homologous Zika virus miRNAs that target microcephaly genes.

Conclusions We suggest that following infection of fetal neurons ZIKV may modulate the action of various miRNAs, and miR-1304 in particular, resulting in microcephaly.

In reality, they suggest that all theorists are examples of human idiocy, which is the source of all virus-driven pathology.
 
 

Cytosis

God's shrinking role in salvation

God’s shrinking role in salvation can temporarily be placed into the context of what serious scientists are reporting for comparison to the claims of pseudoscientists.
See: Quantum Simulation (free download)

It presents several examples of experiments using both density and momentum imaging and quantum gas microscopy to study the motion of atoms in optical lattices.

The energy-dependent motion of atoms must be linked to ecosystems by the physiology of pheromone-controlled reproduction in all living genera. That fact requires extended consideration of helicity, chirality, autophagy, and hydrophobicity in supercoiled DNA
Helicity – the projection of the spin onto the direction of momentum. ie. spin direction depends on direction of motion;
Chirality – not identical to its mirror image, ie. left-handed vs right-handed;
Cool animation of a particle where the Helicity matches the Chirality.

I’m not sure how to start an attempt to finalize ongoing comments on what has been learned during the past century about  energy-dependent RNA-mediated cell type differentiation, which is manifested in the complexity of the animation. I would like to move forward without the redundancy of explaining everything each time a new finding links quantized energy from physics to chemistry and the facts link molecular epigenetics to the biologically-based energy-dependent creation of microRNAs and RNA-mediated cause and effect.
The energy-dependent creation of microRNAs is missing in this representation of energy-dependent internal motion in DNA.
DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid

The internal motions of DNA appear to be governed by strong internal forces arising from being crowded into the small space of the nucleoid.

God’s shrinking role in salvation can be placed into the context of works published by those who fail to link the creation of energy as information to the packed nucleoid via DNA internal motion in the context of the creation of microRNAs.
See for example: microRNA
Everything known to serious scientists about the creation of microRNAs links the sun’s anti-entropic virucidal energy from the solar analemma to representations of the time-space continuum in a Mobius strip and to this solution to the grandfather paradox, which is based on quantum entanglement, which includes quantum entanglement in DNA.
The solution to the grandfather paradox links quantized energy from quantum entanglement to energy-dependent changes in the structure and function of supercoiled DNA, which helps to ensure the survival of individuals and species, but only if the anti-entropic virucidal energy of sunlight was created before anything else.
The creation of quantized energy also must be biophysically constrained by the physiology of reproduction in all living genera.
See: Light Modulates the Biosynthesis and Organization of Cyanobacterial Carbon Fixation Machinery through Photosynthetic Electron Flow, which was reported as: Illuminating the inner ‘machines’ that give bacteria an energy boost
See also: Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes, which was reported as: Nanotechnology reveals hidden depths of bacterial ‘machines’ and subsequently placed into the context of the nonsense touted by theorists on June 8, 2017 as  Revealing the Structure of Bacterial Machines
The structure and function of the bacterial machines depends on the innate ability of the species to find enough food. If an organism fails to find food, it cannot adapt to ecological variation and reproduce in the context of the pheromone-controlled physiology of reproduction. For example, this species finds food that it metabolizes to create a uranium isotope.
See: A new twist on uranium’s origin story, by CSU scientists

…using new techniques including synchrotron radiation-based spectroscopy and isotope fingerprinting. They found that up to 89 percent of the uranium from their 650-foot-deep samples wasn’t crystalline uraninite at all, but rather, a non-crystalline uranium that was bound to organic matter or inorganic carbonate. Most of the uranium they found in that unmined site is estimated to be 3 million years old, and formed via reduction by microorganisms – microbes that respire not on oxygen, but on uranium.

The energy-dependent creation of the isotope exemplifies how the energy of sunlight is biophysically constrained in the context of quantum physics and the physiology of energy-dependent reproduction, which Richard Feynman linked to the creation of the atomic bomb — even though he did not know where the energy in a hydrogen atom came from. I have asked others where the energy came from, but the question has not been answered.
The estimate that the uranium was formed by bacteria 3 million years ago is based on pseudoscientific nonsense touted by neo-Darwinian theorists and “Big Bang” cosmologists. Taken together those who are biologically uninformed are now attempting to separate everything known to serious scientists about the energy-dependent creation of all life on Earth from the quantized energy required for creation and the physiology of reproduction.
If quantized energy is not information, the loss of energy from the sun via thermal entropy could create life and all biodiversity, at least in theory. But who believes in theories that are this ridiculous?
See: Information entropy and thermal entropy: apples and oranges

…the change of information entropy and the related change of thermal entropy can be separated in space and time leading to the break of Brillouin’s negentropy principle. iv) The information entropy can increase without triggering any change of the thermal entropy indicating that information erasure does not necessarily require energy dissipation.
v) There is no case where Landauer’s principle of erasure dissipation is even seemingly valid because erasing of the memory does not yield change in the information entropy. vi) The information entropy can violate the Third Law of Thermodynamics.

When theorists are allowed by others who are biologically uninformed to tout the amount of pseudoscientific nonsense contained in this excerpt (above), everyone who believes that the Laws of Thermodynamics can be violated is an example of what Feynman claimed is a form of human idiocy.

See also, from 2-3 years ago in the science news:

The first ever photograph of light as both a particle and wave 3/2/15

Scientists see ripples of a particle-separating wave in primordial plasma 6/10/15

Scientists find genetic basis of brain networks seen in imaging studies 6/11/15
Cell density remains constant as brain shrinks with age 6/12/15
This Nifty Infographic Is a Great Introduction to Neuroplasticity and Cognitive Therapy
New immunoregulation and biomarker 6/12/15

Cell type stability is receptor-mediated and biophysically constrained.

DNA data explosion lights up the Bronze Age 6/10/15

Quantized energy-dependent amino acid substitutions are still being reported as if they are mutations.

See for comparison: The Molecular Nutrition of Amino Acids and Proteins, 1st Edition

See also: The Ancient Origins of Consciousness: How the Brain Created Experience 3/25/16
See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model 6/14/13 My review is cited in the context of:

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

The concept of smell-first was linked from energy-dependent changes in angstroms to ecosystems in all living genera.
Scientists investigate how the sense of smell works in bacteria

…the signaling and inactive states differ only very slightly at the nitrate-binding site – by 0.5-1 angstroms, which is approximately one fifth of the size of the ion itself (1 angstrom is 10-10 meters). However, when this ion binds to the sensor, it causes huge changes in the protein: The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.

The signal transmission was linked from the physiology of reproduction in soil bacteria to fertility in mammals via changes in the bull sperm microRNAome. See: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
Outside the context of the creation of quantized energy and the de novo creation of genes linked to increasing organismal complexity, there is no need to discuss God’s shrinking role in salvation. You can, instead, link the Stepwise Evolution of a Buried Inhibitor Peptide over 45 My from the de novo evolution of genes and the novel proteins they encode to the innovations that automagically contribute to the diversity of life via The evolution of social behavior in microorganisms.
See also: Metabolism and the evolution of social behavior

…using experimental evolution, we followed the joint evolution of the genome, the metabolome and the social behavior as swarming re-evolved. New variants emerged spontaneously with mutations that reorganized the metabolome and compensated in distinct ways for the disrupted metabolic prudence. These experiments with a unicellular organism provide a detailed view of how metabolism—currency of all physiological processes—can determine the costs and benefits of a social behavior and ultimately influence how an organism behaves towards other organisms of the same species.

Simply put, the quantized energy of the smell-first model of energy-dependent ecological adaptation in species from microbes to humans can be compared to the metabolism-first theory of de novo gene evolution. Both can be compared in the context of the joint evolution of the genome, the metabolome and the evolution of social behavior, which is portrayed as swarming in the bacterium Pseudomonas aeruginosa. The swarming behavior re-evolved in an evolution experiment.
The re-evolved ability to swarm can be compared to the report on the weekend resurrection of the bacterial flagellum in Pseudomonas fluorescens.
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The weekend resurrection of the bacterial flagellum suggests that virtually any change in an organized genome can be linked to the pheromone-controlled the physiology of reproduction. If not, the claims about evolution can be linked from the wrong choice of food to the virus-driven degradation of messenger RNA, which links mutations to all pathology. But claims about the virus-driven degradation of messenger RNA are rarely made by theorists.
When the missing information about the virus-driven degradation of messenger RNA is placed into the context of the the solar analemma, a Mobius strip, and the solution to the grandfather paradox, quantum entanglement appears to link all changes in the amount of quantized energy that comes from sunlight to biophysically constrained energy theft and viral latency, which prevents pathology.
For comparison, see: A New RNA Synthesis of Cells: A Possible End of Birth Defects

…an estimation of these two above elements [nitrogen and phosphorus] as a chemical compound leads a human’s birth defect to have the correct amino acid sequence as previously mentioned and then become a normal trait. With the correct calculation of the compound of nitrogen and phosphorous for an unstable RNA messenger, which is traced to a birth defect, a researcher can discover the ideal growth rate for its stability as an RNA messenger and then its end as a birth defect.

The quantized energy-dependent biosynthesis of RNA is food energy-dependent and pheromone-controlled in species from microbes to humans and virus-driven energy theft appears to cause the degradation of messenger RNA, which has been linked to all pathology. The report of the evolutionary resurrection of flagellar motility clearly exemplifies how energy-dependent changes in RNA-mediated amino acid substitutions are linked to survival of the species outside the context of the “magic traits.” The “magic traits” do not link nutrient-dependent pheromone-controlled cell type differentiation to all biodiversity in reports like this one: Magic traits in speciation: ‘magic’ but not rare?
The “magic traits” have been linked to rapid speciation in bacteria and vertebrates
See: Extraordinarily rapid speciation in a marine fish

We evaluated different possible evolutionary scenarios under the approximate Bayesian computation framework and estimate that the speciation process started in allopatry ∼2,400 generations ago, following the colonization of the Baltic by the demersal lineage. This is faster than most known cases of ecological speciation and represents the most rapid event of speciation ever reported for any marine vertebrate.

Reported as:“Evolution on the fast lane—One flounder species became two” May 30, 2017

“The answer may lay in so called magic traits, meaning traits that are under selection which at the same time cause reproductive isolation as a byproduct. In theory, selection on such traits could play a central role in rapid speciation events. The mating strategies and reproductive traits of the two flounder species could act as magic traits,” clarifies Momigliano.

Quantum Physics News (see for discussion on this group)
The Quantum Physics News was created by Robert Karl Stonjek, whose atheistic pseudoscientific nonsense is pervasively distributed among several other Facebook groups and yahoo groups. His influence has caused the unnecessary suffering and premature death of millions of people who think God’s shrinking role in salvation can best be viewed in the context of the “magic traits” of neo-Darwinian theorists.
 

Alternative splicing of pre-mRNA

Viruses in pathogenic variants disrupt alternative splicings (2)

Autophagy is activated by virus-driven energy theft. Click on the term “Autophagy” That fact is clear in the diagram of systems complexity and in my model.

See for contrast:  Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors

A key question in virology, that is potentially answerable using paleovirological analyses, is what caused the elimination of extinct viral lineages?

Conclusion:

The selection pressures acting on hsaHTenv, its orthologs and progenitors might have been complex. Loss of fusogenicity but retention of receptor binding activity are, in a sense, opposing influences in terms of maintenance of the ORF and its function. Moreover, although some purifying selective pressure (low dN/dS) can be detected in hsaHTenv and its orangutan ortholog, a relaxation of those forces might be expected to have occurred after HERV-T extinction, perhaps leading to reduced antiviral activity observed in modern hsaHTenv. Finally, as MCT-1 is a moncaboxylate transporter that is upregulated in human cancers (Halestrap, 2013), the ability of hsaHTenv to deplete MCT1 from cell surfaces may suggest an additional or alternative metabolism-related cellular or even anti-tumor functions and selective pressures. Such an activity might have continued to shape hsaHTenv sequence independent of anti-HERV-T activity. In either case, this study highlights the potential importance of ERV proteins as raw material for the innovation of new functions in human ancestors.

All energy-dependent cell type differentiation is receptor-mediated. The nutrient energy-dependent de novo creation of receptors in cell types links metabolic networks to genetic networks via RNA-mediated protein folding chemistry, which biophysically constrains virus-driven energy theft. The energy theft links viral replication to the degradation of messenger RNA and mutations, which are linked to all pathology.

Reported as: Virology: Pushing the envelope

My comment:
Rarely do we see this degree of prescient raw insight displayed by a non-scientist who predicted the claims about viruses in the manuscript reviewed.
Please see: Evolution rising from the grave http://dx.doi.org/10.1038/3… Excerpt: “Reactivation of a dormant message signals the dawn of a new humanity.”
See also: Living with the Neanderthals http://www.nature.com/natur…

My competing interests include ownership of domains that disseminate accurate information about energy-dependent biologically-based cause and effect, which is biophysically constrained. My publication history extends across twenty years during which I have refuted every aspect of neo-Darwinian nonsense.
The nonsense places claims about evolution into the context of what is known to serious scientists about the links from angstroms to ecosystems in all living genera. Serious scientists start with hydrogen-atom transfer in DNA base pairs in solution.
The potential of hydrogen is referred to as pH. Virus driven energy theft links changes in pH to the degradation of messenger RNA and the mutations that are linked to pathology in all living genera.
My comments are rarely published here.
—————————————————-
See, for comparison, my comment to Greg Bear’s FB page:
Darwin’s Radio and Darwin’s Children (revisited)
“Viral Fossils Reveal Immune Capabilities of Our Ancestors”
http://buff.ly/2nT1osY
Hi Greg. Nutrient energy-dependent pheromone-controlled RNA-mediated viral latency became the focus of my published works and presentations after you linked pheromones to ecological adaptations in a new human subspecies.
My 2017 Labroots Precision Medicine presentation is an extension of facts you helped to detail for your target audience.
https://www.youtube.com/watch?v=cdtsfweO5SQ
“Energy as information and constrained endogenous RNA interference” is being ignored because it refutes every aspect of pseudoscientific nonsense that has ever been touted by neo-Darwinian theorists. I continue to be amazed by those who claim to be scientists who cannot begin to understand what you understood at the time you wrote “Blood Music.” Like others, I am also somewhat scared of what you predicted in “Quantico.”

Cytosis: Biology Content

 

Help Me Write Some Biology Content

Project Update #5: Cytosis: A Cell Biology Board Game by John Coveyou (Genius Games)

Many of you have mentioned that you’d like to have an explanation of the biology behind Cytosis available… and I think that is an AWESOME plan. Every time I’ve taught the game to non-science players in the past, they say gameplay made even more sense (and was so much more enjoyable) when I explained the science as well. This way they knew WHY they were doing what they were doing!

If you’ve got a strong background in biology, love explaining complexities in a way that someone unfamiliar with biology could understand, and would be interested in volunteering to help me write a page or two of science explanatory content for the rulebook, please shoot me an email… with the subject line “Cytosis Biology Explanations – [Your Name]” and we can start discussing!

I wrote: Kohl’s Laws of Biology may help. See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

1) Life is nutrient-dependent. See for review [2, 31]. The physiology of reproduction is pheromone-controlled. See for review [30].

In the context of the game “Cytosis,” Kohl’s Laws link the epigenetic effects of food odors and pheromones to changes in the mitochondria of all cell types. The energy-dependent changes in the mitochondria are linked to healthy longevity.
If the epigenetic effects of food odors and pheromones did not clearly link cytosis to healthy longevity, we would be left with only the link from virus-driven energy theft to all pathology. The explanation for all pathology involves more complexity than most people are willing to examine even when it is placed into the context of a book for a general, albeit educated, target audience.
See: The Scent of Eros: Mysteries of Odor in Human Sexuality

This is science at its best, with adventure, ideas, and lots of facts. — Helen Fisher

Details for other serious scientists:

The synthesis of RNA is nutrient energy-dependent. From 1964 Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

The anti-entropic virucidal energy of sunlight has since been linked to all biophysically constrained human cell type differentiation via representations in Feedback loops link odor and pheromone signaling with reproduction

The feedback loops link Dobzhansky’s claims about amino acid substitutions and RNA-mediated cell type differentiation from natural selection for energy-dependent codon optimality to the pheromone-controlled biodiversity of all living genera.

See: Combating Evolution to Fight Disease

…transient errors in mRNA synthesis can also cause heritable non-DNA-based phenotypic change. This is observed when low-abundance transcriptional regulators are affected by transcription errors. This disruption can cause a cell to alter its gene expression, resulting in a phenotype that may be heritable (2).

See also: Carl Woese, Evolution’s Golden Revolutionary

…there is probably no other scientist but Carl Woese who could write about having “no use for natural selection” and have Nature magazine respond with a Nobel endorsement. It is Carl Woese who first identified the Archaea and introduced us to horizontal gene transfer.

Virus-driven energy theft causes the degradation of messenger RNA, which links negative supercoiling of DNA in bacteria to the creation of archaea and links the conserved molecular mechanisms from archaea to the evolution of all pathology. For comparison, horizontal gene transfer links the nutrient energy-dependent de novo creation of genes from the pheromone-controlled fixation of RNA-mediated amino acid substitutions to supercoiled DNA, which prevents virus-driven energy theft from causing more degradation of messenger RNA.

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

This invited review of nutritional epigenetics includes a model that links nutrient energy-dependent changes from atoms to ecosystems. Most theorists have been caught with their pants down because they are still making claims about mutations and evolution. How can serious scientists compete with pseudoscientists who make claims that link mutations to millions of year of evolution?  Most serious scientists know how to link quantized energy from chemistry to biologically-based cause and effect. Most biologically uninformed people accept the claims of pseudoscientists, atheists, and other theorists.

Some Harvard researchers are still trying to hide facts that link research on the synthesis of mRNA to all biophysically constrained biodiversity on Earth via hydrogen-atom transfer in DNA base pairs in solution and RNA-mediated amino acid substitutions in supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. ATP-dependent cell type differentiation is placed into the context of conserved NAD+ and protein-protein interactions.

See:  A conserved NAD+ binding pocket that regulates protein-protein interactions during aging

See for contrast: Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention

It is now widely accepted that cancer is the result of the gradual accumulation of driver gene mutations that successively increase cell proliferation (1–3).

Johns Hopkins researchers framed everything known to serious scientists about cell type differentiation into the contest of cancer as ‘bad luck” as if cytosis was not energy-dependent and healthy longevity arose in the context of mutation-driven evolution — if species were lucky enough to evolve into other species.
No serious scientist has ever accepted that ridiculous claim.

See for comparison: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

…we characterize two distinct p120-associated complexes with antagonistic functions and we describe a microRNA (miRNA)-mediated mechanism through which the ZA suppresses transformed cell growth.

Backers and players of the game “Cytosis” will learn how the energy-dependent function of mitochondria must be linked to every aspect of healthy longevity or be linked from virus-driven energy theft to all pathology. They will be prepared to learn from the next game: “Photosynthesis,” which will link the sun’s anti-entropic virucidal energy to all biophysically constrained biodiversity via what is known to all serious scientists. They will not need to learn anything more than is required for them to reject the pseudoscientific nonsense of neo-Darwinian theories.

See what’s happened after 20 days of comments to this society. 

The information has been shared more than 450 times. The number of biologically informed students will force the biologically uninformed professors to stop playing the evolution game until they can begin supporting their ridiculous claims with facts. The facts must link ecological variation to ecological adaptations via what is known to serious scientists about hydrogen-atom transfer in DNA base pairs in solution.

Clearly, the facts tell us that all individuals of all species that live on Earth must eat and reproduce or they become extinct. None mutate and evolve into other species.

Thus, we regard as rather regrettable the conventional concatenation of Darwin’s name with evolution, because there are other modalities that must be entertained and which we regard as mandatory during the course of evolutionary time.

— Carl Woese and physicist Nigel Goldenfeld

I encourage others to support the development of games that teach what pseudoscientists do not want an interested target audience to learn. With enough support for an easy way to learn about energy-dependent cytosis compared to virus-driven pathology, the facts about RNA-mediated cell type differentiation will become clearer.

See also our section on molecular epigenetics in this review from 1996: From fertilization to adult sexual behavior

Every aspect of cytosis is food energy-dependent and RNA-mediated. Virus-driven energy theft cause all pathology. That fact makes sense in the context of all claims made by serious scientists. See for example:

 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)

— with forward by Roger Penrose who co-authored with George F.R. Ellis and Stephen Hawking

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

See also:

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


    17 Apr 2014 at 03:07am

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 also:

…every angstrom is dynamic from the 5 prime to the three…

See also: Genetic 3’UTR variation is associated with human pigmentation characteristics and sensitivity to sunlight

Sunlight exposure induces signalling pathways leading to the activation of melanin synthesis and tanning response. MicroRNAs (miRNAs) can regulate the expression of genes involved in pigmentation pathways by binding to the complementary sequence in their 3′-untrastaled regions (3’UTRs).

Top-down causation starts from the creation of the sun’s anti-entropic virucidal energy. Hydrogen atom transfer in DNA base pairs in solution links energy-dependent changes in the microRNA/messenger RNA balance from microRNA flanking sequences to RNA-mediated amino acid substitutions that alter the stability of supercoiled DNA in the context of the physiology of reproduction.

One base pair change and a single amino acid substitution makes the difference between healthy longevity and pathology during life history transitions. See for example: Epigenetic Regulation of BDNF Gene during Development and Diseases
See also: Δ133p53 Functions to Maintain Redox Homeostasis in Response to Low ROS Stresses
https://www.omicsgroup.org/articles-images/single-cell-signaling-response-oxidative-stresses-5-154-g001.png
See also: Keep science a priority. Stand with ASCB at the March for Science rally April 22.
Amino acid modification FA_Epigenetics_Table1

Thinking about energy is not radical re-thinking

The brain: a radical rethink is needed to understand it

…Optogenetics, a technique that uses genetic modification of neurons so that their electrical activity can be controlled with light pulses – can help us to explore their specific contribution to brain function.

Optogenetics links the speed of light on contact with water to what is known about all energy-dependent cell type differentiation in all individuals of all living genera. Serious scientists, for example, have linked angstroms to ecosystems in all living genera because they know that brain function is experience-dependent and RNA-mediated.

Even in organisms that have no brain, cell type differentiation occurs in the context of biophysically constrained RNA-mediated protein folding chemistry. All chemistry is energy-dependent quantum chemistry and chemistry links quantum physics from the de novo creation of G protein-coupled receptors to the biological basis for all biodiversity on Earth.
For example, food odors link natural selection for energy-dependent codon optimality to the metabolism of food to pheromones. Biophysically constrained RNA-mediated feedback loops link the metabolism of food from the physiology of reproduction to supercoiled DNA, which protects all organized genomes from virus-driven entropy.
Simply put, quantum physics, quantum chemistry, and energy-dependent quantum biology prevent virus-driven entropy, which links everything known to serious scientists about niche construction to consciousness.
The Penrose Institute was established to link that fact to human consciousness in the context of everything known about cell type differentiation to everyone since the time that Lewis Thomas began making claims olfaction and smell.
A Fear of Pheromones (1971)
On Smell (1980)

The act of smelling is remarkably like the act of thinking itself.

See also:

I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece, all the mysteries.  —  as cited in The Scent of Eros: Mysteries of Odor in Human Sexuality

In 1991, Roger Penrose, summarized what was known about all the mysteries in his forward to the reprint of Schrodinger’s “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?

For comparison, see this comment by “Sonny” Williams to the International Society for Human Ethology’s yahoo group:

The empirical evidence is overwhelming that the brain is composed of highly specialized regions, whose neuronal members are unique in their cytoarchitecture (down to the molecular level).  Moreover, empirical evidence reveals that genes have directed these neural variations during corticogenesis; that is, most specialized neurons are differentiated early during development and directed to their place in the brain by intrinsic cues, and not activity-dependent cues.  This fact does not preclude later “rewiring,” or changes that are activity-dependent (plasticity), but this range of plasticity is constrained by the genetically derived regions.

Thus, the metaphor that the brain is “modular” is as accurate as any other metaphor.  HOWEVER, “modular” and functionally specialized regions has always included the fact that functional outcomes require a widely distributed network of specialized regions.  That is, modules do not exist in isolation, as islands of specialized function, but rather there existence as a specialized region is predicated upon their iterative communication with many other equally specialized regions.

I cannot recall any comment by Clarence “Sonny” Williams that might ever have made sense to a serious scientist. He is, in my opinion, a biologically uninformed science idiot. I once wondered who could have taught anyone to believe what biologically uninformed people believe in, or why they think what they were taught makes sense to serious scientists.
Then, I tried to discuss what I know about the energy-dependent links from angstroms to ecosystems in all living genera with the senior author of Complex Spike Patterns in Olfactory Bulb Neuronal Networks by Alister U Nicol, Anne Segonds-Pinchon, and Magnus S. Magnussen. It was also published as a book chapter in Discovering Hidden Temporal Patterns in Behavior and Interaction: T-Pattern Detection and Analysis with THEME™
Background:

T-pattern analysis is a procedure developed for detecting non-randomly recurring hierarchical and multiordinal real-time sequential patterns (T-patterns).

CONCLUSIONS:

We conclude that such sequences are an important physiological property of the neural system studied, and suggest that they may form a basis for encoding sensory information.

My summary: They link everything known to serious scientists about energy as information to non-randomly recurring patterns of biophysically constrained RNA-mediated protein folding chemistry and “…characterize these patterns in light of their putative role in processing sensory information.”
They ignore the fact that sunlight is the anti-entropic virucidal source of the energy that prevents genomic entropy via the pheromone-controlled physiology of reproduction in all living genera.
Apparently, like other biologically uninformed theorists, they did not realize what Dobzhansky (1973) did when he linked the light of evolution to all biophysically constrained biodiversity via the nutrient energy-dependent pheromone-controlled physiology of reproduction.
Dobzhansky was one of the first self-declared Creationists to level the playing field with his joke about evolution as if it occurred over billions of years.

I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation. Creation is not an event that happened in 4004 B.C.; it is a process that began some 10 billion years ago and is still under way.

Anyone who followed Dobzhansky’s works probably got the joke. He knew there was experimental evidence of God’s Creation. For example, he linked sensory input from what organisms eat and their physiology of reproduction to amino acid substitutions that differentiate all cell types in all living genera. He also knew that theorists had not found experimental evidence of biologically-based cause and effect that supported their claims about millions to billions of years of evolution.
All serious scientists were made aware of Dobzhansky’s rabbinical form of debate in 1964. He began by referring to theorists as bird-watchers and butterfly collectors.  A rather well known form of rabbinical begins with: “Thou fool….”
Dobzhansky was far less damning when he started his address with this:

The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.

Dobzhansky probably was referring to himself in the third person when he made the claim about the unidentified Professor of Zoology. Still, to avoid ridicule by biologically uninformed theorists, he tempered the claim.

Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.

Clearly, Dobzhansky knew that his claims about amino acid substitutions would be accepted by serious scientists and rejected by pseudoscientists, who have continued to reject the claims of all serious scientists. That’s what pseudoscientists have always done.
See for instance:

3/09/17 Jay Feierman: One can’t have Darwinian evolution by natural selection without either “random” mutations or directional selection. They are both necessary, proximate, contributing causes for genes and the proteins they code for changing in frequency over time in a population and by which the population becomes adaptively configured to the current environment.

3/17/17 Jay R. Feierman [NEW]: We are adaptively configured to the current environment because we are the most successful mammal on earth by any measure. There are 7 billion of us and we inhabit every continent on earth. We accomplished this by Darwinian natural selection adaptively influencing the structural design features we call genes and the proteins they make as well as the extra-genetic structural design features developed through our creativity and ingenuity where we pass the instructions on how to make them across generations by social learning. An iPhone is an example today and an obsidian arrow head was an example in the past.

My comment:  After attempts to discuss energy-dependent biophysically constrained RNA-mediated cause and effect with Magnus S. Magnusson, I was not surprised to find support for some of Feierman’s claims about human adaptations in:

Complex spike patterns in olfactory bulb neuronal networks

Indeed, adaptations occur. But, in the same article, they failed to support Feierman’s claims that the adaptations randomly occur.

Abstract excerpt:

BACKGROUND:

T-pattern analysis is a procedure developed for detecting non-randomly recurring hierarchical and multiordinal real-time sequential patterns (T-patterns).

Conclusion: We conclude that such sequences are an important physiological property of the neural system studied, and suggest that they may form a basis for encoding sensory information.

My conclusion: People like Jay R. Feierman should try to support their assertions about adaptations with experimental evidence of biologically-based cause and effect like the evidence that was cited in the article linked above.

Any claims about how a population becomes adaptively configured to the current environment are not true outside the context of what is known about energy as information and biophysically constrained RNA-mediated protein folding chemistry. If those ridiculous claims were true, the experimental evidence of top-down causation that theorists think support the claims could be used to convince serious scientists that something besides natural selection for energy-dependent codon optimality and the physiology of pheromone-controlled reproduction could replace facts to support theories about mutation-driven evolution.

See also 3/18/17: [MODERATOR NOTE: I’m posting this submission even though it misquotes Feierman, who did not ever say or imply that “adaptations randomly occur.” jrf]
See alson 3/18/17: [MODERATOR NOTE: Adaptations and mutations are not synonyms. An adaptation is a mutation acted upon by natural selection to configure a population to the current environment. It would be an oxymoron to say that “adaptations randomly occur.” By definition, adaptations are mutations that have been acted upon by natural selection by which their frequency is increased in a population over time in a specific environment. jrf]