5th-6th Sept 2018 Dublin, Ireland

2018 March for Science vs microRNAs (2)

The anti-entropic virucidal energy of sunlight on contact with water has been linked from the creation of ATP synthase to the creation of ATP and to the creation of RNA. Energy-dependent RNA-mediated DNA repair has been linked to biophysically constrained viral latency via the creation of microRNAs and feedback loops linked to the food energy-dependent microRNA-mediated physiology of reproduction. The physiology of energy-dependent pheromone-controlled reproduction biophysically constrains viral latency in the context of the creation of the innate immune system and autophagy.
See: miRNA regulation of innate immunity (4/14/18)
None of the facts about the energy-dependent creation of the microRNAs or the microRNA-mediated regulation of innate immunity are included in: The Transcription Factor Runx3 Establishes Chromatin Accessibility of cis-Regulatory Landscapes that Drive Memory Cytotoxic T Lymphocyte Formation (4/17/18)
The regulatory landscape that drive memory cytotoxic T lymphocyte formation might just as well be framed in the context of magic or in the equally ridiculous context of gene-centric theories.
See this report: Your immune system holds the line against repeat invaders, thanks to this molecule

Runx3’s control of T cell differentiation is important because when our bodies fight off viruses and cancers—and our T cells burst into action—the vast majority tend to become effector cells. These effector cells are short-lived and do not persist once the infection resolves.

The control of all cell type differentiation is energy-dependent, RNA-mediated and biophysically constrained by the physiology of reproduction in all living genera. The cell biology game “Cytosis” for ages 10+ teaches the facts that link Schrödinger (1944) What is Life? to Schrödinger at 75 – The Future of Biology – September 2018
In 1944, Schrödinger wrote:

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

See for comparison (this gene-centric pseudoscientific nonsense):
– Part I: FINDING THE CODE (Run time: 12:10
The race to sequence the human genome was also billed as a race to end disease. What happened?

– Part II: FIXING THE CODE (Run time: 13:07)
CRISPR — and the promise and pain of gene therapy that came before it. 

– Part III: SELLING THE CODE (Run time: 10:55)
Genetic testing has moved out of the labs into the masses. But even with your genome in hand, what can you believe?
The gene-centric pseudoscientific nonsense does not start with the creation of energy.  But every aspect of biophysically constrained life on Earth starts with the quantized energy-dependent creation of microRNAs. The epigenetically effected energy-dependent microRNA-mediated creation of the “Code” and the microRNA-mediated fixing of the “Code” is missing from the claims of biologically uninformed theorists who link beneficial mutations from natural selection to evolution. They have sold their gene-centric pseudoscientific nonsense to many people.
For example, some gene-centric biologically uninformed theorists share beliefs about abiogenesis for comparison to quantized energy-dependent microRNA biogenesis in articles like this: DNA Denaturing through UV-C Photon Dissipation: A Possible Route to Archean Non-enzymatic Replication

Many of the fundamental molecules of life, those common to all three domains; bacteria, eukaryote, and archea, including RNA and DNA, amino acids, enzymes, vitamins, cofactors, and protoporphyrins, absorb photons in the UV-C 1. RNA or DNA in complexes with these molecules act as acceptor quenchers, providing the electronically excited pigment donor molecule with an extremely rapid (sub picosecond) non-radiative dexcitation channel, through internal conversion into vibrational energy of the nucleic acid and surrounding water molecules2.

See John Hewitt’s comment: You have just described the founding principle and thermodynamic function of life
In a classic example of human idiocy (See Feynman: food energy), biologically uninformed science idiots linked the dissipation of quantized energy to the origin of life via abiogenesis. The creation of biophysically constrained biophotonicaly based life in the context of the energy-dependent creation of microRNAs was reported in the context of photon dissipation and entropy as: Abiogenesis: A Theory on The Origins of Life

By now, we all know how evolution works. At least, most of us have a basic understanding of how it functions. At its most fundamental level, evolution is change over time. More specifically, it is changes within a biological population over successive generations.

Ultimately, biological complexity is one of the most important things to come out of evolution. Things started simple. Then genes mutated, cells interacted with their environment, mitochondria stopped being living organisms and started being part of a cell and—Tada—complex life.

A conflict arose between John Hewitt’s accurate representations of biophysically constrained life in The vibrational theory of olfaction for the win  and few months ago, Hewitt blocked me from seeing his tweets.

The same kinds of amino acid substitutions that control the separations and interactions of side chains in fluorescent proteins also play an essential role in tuning the proposed mechanism for vibration detection—inelastic electron tunneling. Life literally runs on electron tunneling through the respiratory chain complexes in mitochondria. These proteins employ complicated mechanisms including esoteric-soundings things like electron bifurcation and confurcation to pump protons across the mitochondrial inner membrane. When mitochondria go dark, cells can often continue to run for a short while, but it is only in the dim glow of the battery backup metabolism.

Here are some links to the reason for the conflict. Simply put, John Hewitt put everything known to serious scientists about energy-dependent microRNA biogenesis back into the context of abiogenesis.
2005 MicroRNA biogenesis: coordinated cropping and dicing
2015 Dysregulation of microRNA biogenesis and gene silencing in cancer
2015 RNA-mediated degradation of microRNAs: A widespread viral strategy?
Claims about abiogenesis exemplify what Richard Feynman referred to as human idiocy. So does John Hewitt and anyone else who believes in Michaelian’s pseudoscientific nonsense.
See other examples of Michaelian’s pseudoscientific nonsense and human idiocy by clicking here.
The energy-dependent creation of one domain of life links the physiology of reproduction in bacteria to biophysically constrained viral latency. The virus-driven degradation of messenger RNA is linked to the destruction of all life on Earth.
The degradation of messenger RNA links mutations to the creation of archaea and L-forms via entropy, which clearly links the weakening of the proton motive force to the elimination of the cell wall in L-forms (the last remnants of creation).
See also: Past 5,000 years prolific for changes to human genome
If you cannot link the miRNA regulation of innate immunity to all extant biodiversity via the physiology of pheromone-controlled reproduction and fixation of energy-dependent microRNA-mediated amino acid substitutions, thank a biologically uniformed science idiot.

Alternative splicing of pre-mRNA

Thanks again for asking about DNA methylation

Re: RNA-directed DNA methylation (1996) See: From Fertilization to Adult Sexual Behavior

Molecular epigenetics. It is now understood that certain genes undergo a process called “genomic or parental imprinting.” Early in embryonic development attached methyl groups become removed from most genes. Several days later, methyl groups are reattached in appropriate sites. Fascinatingly, some such genes reestablish methylation patterns based upon whether the chromosomal segment carrying the gene came from maternal or paternal chromosomes.

See also: RNA-directed DNA methylation: an epigenetic pathway of increasing complexity (2014)
See also:  Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity (2017) reported as: Humans and sponges share gene regulation
See also: Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability
Reported 10/2/17 as: Unexpected findings uncover new understanding of gene expression

What is it about the whole body of the enzyme itself that functions in development and its mutations that can result in cancer?

Thanks again for asking. It is the fact that RNA-directed DNA methylation is energy-dependent and the fact that virus-driven energy theft causes the degradation of messenger RNA, which serious scientists have linked to all pathology.
Everything known to serious scientists about energy-dependent increasing organismal complexity has been portrayed by pseudoscientists in the context of mutation-driven evolution.
The pseudoscientists are not going to stop until serious scientists force them to start helping those who are “Combating Evolution to Fight Disease.”
See for comparison: Relating protein functional diversity to cell type number identifies genes that determine dynamic aspects of chromatin organisation as potential contributors to organismal complexity

…there is evidence that some of the selected genes may contribute to the formation of different cell types. One route might be through the modification of stem cell activity in response to a greater functional diversity of the proteins that modulate epigenetic status to either maintain or promote differentiation [35,36].

Beneath the surface of what you see reported about organismal complexity in the mainstream media, you can see: Eligo Bioscience Secures $20 Million Series A from Khosla Ventures and Seventure to Bring Precision Medicine to the Microbiome

A growing body of research shows that the microbiome, made up of the ten trillion bacteria residing within and on the human body, sits “at the interface of health and disease.”

The company’s approach uses the innate immune system of bacteria (CRISPR) to edit the genetic material of antibiotic-resistant bacteria.  The microRNAome links the virus-driven degradation of messenger RNA in bacteria from the energy-dependent pheromone-controlled physiology of reproduction to all pathology biodiversity via changes in the healthy microbiome. The concept of endogenous RNA interference is rapidly replacing the nonsense about virus-driven gene editing, which has not yet earned a Nobel Prize for pseudoscientific representations of cause and effect.
See: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression (2014)

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

This is what one of my former Facebook friends called “bullspit.” It is about “bull sperm.” It is not what other former Facebook friends say “nobody cares” about. It is the link from energy-dependent changes in soil bacteria to all biophysically constrained life on Earth. It is also what other researchers who are biologically uninformed science idiots tell you is the link from virus-caused mutations to evolution.
See for comparison: 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!

See for comparison: Nobel Prize in Medicine Awarded to Circadian Rhythm Researchers
I do not expect anyone who has not already linked what is known about quantum physics to quantum souls to understand why this year’s Nobel Laureates in Physiology or Medicine have abandoned all experimental evidence of biophysically constrained top-down causation to continue touting their ridiculous gene-centric theories.
Do you? But, I understand why they do not want to admit to the facts.

Military-related trauma tied to eating disorder symptoms

…when they controlled for other trauma types, military-related trauma was the only trauma type that was uniquely associated with eating disorder symptoms. Examination of different types of military-related trauma indicated that the association was not driven by exposure to combat.

Predictably, it was an exposure-driven association with the stress-linked failure to adapt to virus-driven changes in gut microbiome and behavior that lead veterans who have served overseas to commit suicide.

See also: Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms

Reported as: The dust storm microbiome

The researchers found that during a dust storm the concentration of bacteria and the number of bacterial species present in the atmosphere rise sharply, so people walking outdoors in these storms are exposed to many more bacteria than usual.

Greg Bear put this into the perspective of Homeland Security in his techno thriller “Quantico.” At times, all that serious scientists can do is laugh about the pseudoscientific nonsense touted by theorists. Bear checked the facts from “Darwin’s Children” with me before he sent the manuscript for publication. And then came this interview with Jon Stewart.

See for comparison the simple-minded misrepresentations of human ethologists in Human Ethology Bulletin » 2017 »
HEB 32(3)
For example: “Y/Our Vocal Sounds – Towards an Ethological Classification of Human Vocalizing Behavior and Sounds
by Jay R. Feierman 

This article is a first attempt at an ethological classification of human vocalizing behaviors and the sounds they make. Lastly, how human ethologists could study these two different types of human vocalizing behaviors, using the sounds they make as proxies, will be discussed.

Summarized in part in Ourselves Explained link opens pdf

A Review of the book


The key to this book’s 18-word title can be summed up in five: Cumulative culture drives
human evolution.

The failure of this book to explain any aspect of biophysically constrained biologically-based cause and effect can be summed up in seven words. No species evolved from any other species.
Energy-dependent RNA-directed DNA methylation links ecological variation from biophysically constrained viral latency to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.


Light-activated feedback loops vs self-organization of ecosystems

John Lieff has been trying to update his ridiculous misrepresentations of biologically-based cause and effect to match the accurate representations we made in a section on molecular epigenetics in our 1996 Hormones and Behavior review.

From Fertilization to Adult Sexual Behavior

Nothing can stop him, but this will provide the next source for material that he must borrow as if he learned about it somewhere else.

Apoptosis analysis guide | Free ebook download

Virus-driven energy theft causes apoptosis, which releases cell contents for recycling in the context of autophagy, which helps to ensure food energy-dependent pheromone-controlled RNA-mediated DNA repair in species from microbes to humans.

Gene bivalency at Polycomb domains regulates cranial neural crest positional identity

Journal article abstract excerpt (figure: Epigenetic regulation of cranial NC cell identity.)

A Polycomb-dependent poised chromatin organization underlies the positional plasticity of cranial premigratory NC cell progenitors. This chromatin prepattern is maintained through migration. In response to local cues encountered by the NC cells during or after their migration, the regulatory elements (E) and promoters (P) of differentially expressed genes switch from a poised to an active chromatin state, establishing transcriptional identities specific to subpopulations of NC cells.

The use of the term “chromatin prepattern” must be linked from endogenous RNA interference to all all biodiversity via transgenerational epigenetic inheritance. Watch closely as all pseudoscientists, atheists and other biologically uninformed theorists finally realize there is no such thing as mutation-driven evolution except in the context of virus-driven energy theft, apoptosis, and the evolution of pathology. Virus-driven energy theft causes degradation of messenger RNA in the absence of nutrient energy-dependent pheromone-controlled RNA-mediated amino acid substitutions and DNA repair.

MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos

Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We discovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability.

Reported as: The role of tiny RNA in genetic diversity March 28, 2017

All species, from zebrafish to humans, possess a genetically diverse collection of traits that allow them to adapt to changing environments. Yet scientists do not fully understand how organisms reach a state of optimal diversity—just enough variability to respond to environmental risks but not too much to function properly.

Natural selection for energy-dependent codon optimality is the link to optimal diversity. Conserved molecular mechanisms of nutrient-dependent pheromone-controlled biodiversity have been linked from quorum sensing in bacteria to all cell type differentiation in all individuals of all species.
See: Feedback loops link odor and pheromone signaling with reproduction

These studies reveal a complex interplay between reproduction and other functions in which GnRH neurons appear to integrate information from multiple sources and modulate a variety of brain functions.

Escherichia coli and the peppered moth typically are typically used by biologically uninformed theorists as examples of mutation-driven evolution.
See: The Man Who Bottled Evolution
See the refutation: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

…this system enables us to understand the adaptive process in detail at the genetic and phenotypic level [over the weekend]. We identified a tractable model for gene network evolution and observed, in real time, the rewiring of gene networks to enable the incorporation of a modified component (NtrC′) creating a novel regulatory function by a highly repeatable two-step evolutionary pathway with the same point mutations often recurring in independent lineages.

They failed to differentiate between the term mutation and what occurs in the context of energy-dependent pheromone-controlled changes in the microRNA/messenger RNA balance via fixation of RNA-mediated amino acid substitutions in supercoiled DNA.
See: 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: Helicoverpa armigera images

Identification and Evaluation of Suitable Reference Genes for Normalization of MicroRNA Expression in Helicoverpa armigera (Lepidoptera: Noctuidae) Using Quantitative Real-Time PCR

…10 candidate genes of H. armigera were selected and analyzed for their expression stability under different biotic and abiotic conditions….  miR-9 and U6 snRNA for developmental stages, miR-100 and U6 snRNA for larval tissues, miR-100 and miR-305 for adult tissues, miR-9 and miR-279 for parasitic treatment, miR-998 and U6 snRNA for nuclear polyhedrosis virus infection, miR-9 and U6 snRNA for insecticide treatment, miR-92a, miR-100, and miR-279 for temperature treatment, miR-92a, miR-305, and miR-998 for starvation treatment, miR-9 and miR-279 for light treatment, miR-305 and miR-998 for hormone treatment, and there was not one reference gene suitable for all samples.

Nutrient-dependent pheromone-controlled reproduction in this moth species links the works of Karlson and Luscher (1959) Pheromones: a new term for a class of biologically active substances to the Bruce McEwen’s works on stress via Effects of Carnitine on Fatty-Acid Oxidation by Muscle (1959) and Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

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

Taken together, these works are linked to energy-dependent Normalization of MicroRNA Expression. The anti-entropic virucidal energy of sunlight is the obvious link from the de novo creation of microRNAs to the ATP-dependent biosynthesis of messenger RNA and healthy longevity.  Virus-driven energy theft clearly links the degradation of messenger RNA, which would otherwise link the creation of microRNAs from sunlight to the nutrient energy-dependent pheromone-controlled biosynthesis of ATP and all cell type differentiation in all living genera.

For example see: Genetic 3’UTR variation is associated with human pigmentation characteristics and sensitivity to sunlight

To our knowledge, this is the first time that these two 3’UTR SNPs have been associated with sun-sensitivity traits. We state the potential implication of these SNPs in human pigmentation and sensitivity to sunlight, possibly as a result of changes in the level of gene expression through the disruption of putative miRNA-binding sites.

See also:: Race-dependent association of sulfidogenic bacteria with colorectal cancer

reported as: Study links sulfide-producing bacteria and colon cancer in African-Americans

“These bacteria are using nutrients associated with an animal-based diet,” Gaskins said.

For information on the biophysically constrained energy-dependent origins of race-dependent associations see:

Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism

…precursors of amino acids glycine, serine, alanine and threonine, are inevitable by-products of this RNA assembly chemistry…

Like all chemistry, this can be placed into the context of how quantum physics must be linked from quantum chemistry to quantum biology via food as energy.

The link from food enery to the nutrient-dependent pheromone-controlled physiology of reproduction and racial differences in colon cancer was predicted based on difference in diet and links from the National Microbiome Initiative to the Precision Medicine Initiative.

See for comparison: Sonny Williams

Re: … much ado about nothing — Jay R. Feierman.

SONNY [NEW]: As we’ve discussed many times, I reject your criteria for judging the merits of a scientific observation.  Arguing that something is “much ado about nothing,” if “the results can’t be predicted by common sense or by simple observation and deductive reasoning,” is exceptionally poor reasoning.  Frankly, I’m bewildered that someone like you would cling to it.  I’ll repeat:  any judgment that includes an evaluation based on “common sense” is DOA.  It’s useless.  Whose “common sense” do you intend to use?

More importantly, the authors DID establish a pre-observation “prediction.”

They predicted that young children will show the same variation in temperament as adults, and which is associated with the various BDNFval/66met polymorphisms.  They wrote, “To the best of our knowledge, there are no studies investigating the role of BDNFval66met with regard to individual differences in temperament during infancy, a period in which genetically-based behavioral traits are hypothesized to be more easily observed (Posner & Rothbart, 2009; Rothbart et al., 2000). Hence, the purpose of the current study was to explore the association between the BDNFval66met polymorphism and individual differences in temperament in a sample of healthy 4-month-old full-term infants.”

Moreover, the authors did a far better job than you did in discussing limitations.

They wrote as follows: “The current study had some limitations. First of all, due to sample size findings cannot be generalized and future studies with larger samples are needed in order to differentiate the impact of met-homozygous and heterozygous profiles of BDNFval66met genotype. Second, infants’ temperament was measured through a parent-reported measure. A more direct account of the effects of BDNF met allele on observed temperament and regulatory behavior is warranted to be investigated in future research. Finally, single polymorphism studies are at risk of underrepresenting the role of environmental conditions, including maternal caregiving behavior. As the quality of early caregiving has been found to regulate BDNF transcriptional functioning (Unternaehrer et al., 2015), we suggest that upcoming studies should target gene x environment interactions using genetic and epigenetic approaches.

To the best of our knowledge, this study is unique in providing evidence of an association between the BDNFval66met polymorphism and infants’ temperament at 4 months of life. The present study adds to previous genetic association research on temperament in infants looking at other polymorphisms (Auerbach et al., 2001; Ivorra et al., 2011), preliminarily suggesting a further genetic factor involved in temperament. Future research is warranted to investigate the BDNF-temperament association in greater populations of infants at low- and high-risk (e.g., preterm infants) and assuming a gene-x-gene and gene-x-environment approach (Papageorgiou & Ronald, 2013).”

Sonny Williams and Jay R. Feierman are antagonists who ignore the facts that link our predictions to all energy-dependent biophysically constrained biodiversity from our 1996 Hormones and Behavior. Our predictions were based on Bruce McEwen’s advice to start with the activation of genes. That is why we included a section on molecular epigenetics.

From Fertilization to Adult Sexual Behavior

All predictions have since been linked from the anti-entropic virucidal energy of sunlight to biophysically constrained RNA-mediated biodiversity by changes in base pairs linked from amino acid substitutions to differences in morphological and behavioral phenotypes during the development of moths and humans. The epigenetic effects of sunlight were predicted in the context of the nutrient energy-dependent de novo creation of microRNAs.
Anything ever linked to the gene-centric theories of neo-Darwinists has been replaced by what is known about energy-dependent endogenous RNA interference and all biophysically constrained biologically-based biodiversity on Earth. For example, pheromones biophysically constrain the physiology of reproduction in all living genera. They protect against virus-driven entropy by linking what organisms eat to the species-specific pheromone-controlled transgenerational epigenetic inheritance of species from microbes to humans.
See also: Epigenetic regulation of face formation
See also: Explaining the accelerating expansion of the universe without dark energy

See also: A distinct role for Lgr5+ stem cells in primary and metastatic colon cancer
Reported by Genentech as: Cancer stem cells have long been thought to influence tumor growth, but a clear link has been difficult to show. Now, in a new study in Nature, our scientists show for the first time that removing cancer stem cells in a model of colorectal cancer can indeed reduce tumor growth. See how these findings could help guide new therapies aimed at targeting cancer stem cells.
What took them so long to link virus-driven energy theft from messenger RNA degradation to the negative supercoiling of DNA via G protein-coupled receptors?
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.



RNA-mediated theory killers (2)

RNA-mediated theory killers…

This is a continuation that will become a series that links the million dollar paradox to the $100,000 prize offered for finding the origin of information at Evolution 2.0, which obviously will be a continuation of Schrodinger’s claims and Dobzhansky’s claims along with the claims of others I have repeatedly mentioned here.
Critical Role of Histone Turnover in Neuronal Transcription and Plasticity
Reported as: Lifelong learning is made possible by recycling of histones

“Histones and their modifications can play an important role in switching genes on and off—a type of epigenetic control. This research uncovers an epigenetic mechanism, involving one slightly-modified, “variant” histone, that makes learning possible by facilitating the genetic changes necessary for neurons to form connections,” says study author C. David Allis.

My comment: The recycling of histones links nutrient-dependent microRNAs to the stability of supercoiled DNA in organized genomes via a single amino acid substitution during the life history transition from adolescence to adulthood.
My phys.org comment:

They have linked the nutrient-dependent pheromone controlled chemistry of RNA-mediated protein biosynthesis and degradation from the epigenetic landscape to the physical landscape of DNA in the context of metabolic networks and genetic networks that link the life history transitions of honeybees (and other invertebrates) to the life history transitions of vertebrates, mammals, and primates including humans, via the conserved molecular mechanisms of biophysically constrained RNA-mediated amino acid substitutions and protein folding that differentiate all cell types of all individuals of all genera.
For an example of the link from nutritional epigenetics to pharmacogenomics testing for a single amino acid substitution linked to life-history transitions in human behavior, see: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

For the link from nutritional epigenetics to pharmacogenomics testing for a single amino acid substitution, which may be the most obvious overlooked link between RNA-mediated amino acid substitutions and to cancer.
Clipping proteins that package genes may limit abnormal cell growth in tumors

“What we found was that histone H3.3 and its clipped form, which lacks 21 amino acids of the histone tail and associated modifications, prevents normal cells from dividing. Clipped H3.3 may be a marker of cells that stop proliferating and has implications for cancer, in particular cancers like melanoma that have a senescence phase.”

My comment: For the most obvious link from the theft of nutrient energy by viruses to life history transitions in behavior and life history transitions linked to cancer via age-related changes in immune system changes, see: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution. My published comment on the fact that no evolution of the virus could have occurred because the amino acid substitution is nutrient-dependent and thereby biophysically constrained by everything currently known to serious scientists about protein folding chemistry was replaced with this comment from the authors.

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

Nutrient energy-dependent base pair changes and RNA-mediated amino acid substitutions link everything currently known to serious scientists about cell type differentiation during the development of morphological and behavioral phenotypes in all living genera. The facts have been placed into the context of this parody. But, most people still have not recognized the links from viruses to perturbed protein folding.

And see also, this parody.

If you are a biologically informed medical practitioner, you are probably already aware of how pharmacogenomics links the conserved molecular mechanisms of biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry during life history transitions that are manifested in healthy longevity or virus-driven pathology.
See, for example:

Would you like to ensure that your treatment regimen meets the current standards of exceptional care that are based on the Precision Medicine Initiative. You and your patients or loved ones do not need to become study participants, although the option may soon become available if the US government funds the testing of all people, not just patients with Medicare coverage. The funding will remain an issue that can be compared to what has been known to some medical practitioners about the links from metabolic networks to genetic networks.
See: Metabolic typing from the 1930’s and Table of Pharmacogenomic Biomarkers in Drug Labeling 150 markers
Many researchers have already joined the ranks of those who are fighting pathology by learning more about why the honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli. Testing is already available that will help you to find what may be the perfect drug.

A Test That Finds the Perfect Drug?


“There is a huge downside: It’s called suffering, time, and money.” “Psychiatry remains the only discipline of medicine that has no test to predict treatment response,” said Evian Gordon, the founder of one such company, Brain Resource. “This is providing, for the first time, an objective step as to which drug might be responsive.”

See also:
DNA methylation and single nucleotide variants in the brain-derived neurotrophic factor (BDNF) and oxytocin receptor (OXTR) genes are associated with anxiety/depression in older women
Neuroendocrine mechanisms underlying behavioral stability: implications for the evolutionary origin of personality
Tracking the Brain’s Functional Coupling Dynamics over Development
Dopaminergic, serotonergic, and oxytonergic candidate genes associated with infant attachment security and disorganization? In search of main and interaction effects
Abstract excerpt:

…specific tests revealed evidence for a codominant risk model for COMT Val158Met, consistent across both samples. Children with the Val/Met genotype showed higher disorganization scores (combined effect size = .22, CI = .10–.34, < .001). Gene-by-environment interaction effects were not replicable across the two samples.

Conclusions:  This unexpected finding might be explained by a broader range of plasticity in heterozygotes, which may increase susceptibility to environmental influences or to dysregulation of emotional arousal. This study is unique in combining the two largest attachment cohorts with molecular genetic and observed rearing environment data to date.

My comment: More than 45,000 published journal articles are indexed on PubMed that mention the role of nutrient-dependent microRNAs, with or without mention of the fact that they link cell adhesion proteins to supercoiled DNA and the stabibility of organized genomes in all living genera. Many of the indexed articles are not likely to mention where the nutrient-dependent microRNAs come from because they link the morphological and behavioral phenotypes of all individuals of all species from metabolic networks to genetic networks. That fact presents a problem to anyone in the medical profession who was taught to believe in the emergence and evolution of pathology via mutations and natural selection.

For example, that is obviously what these researchers were taught to believe or what they want you to believe.

Additive Gene–Environment Effects on Hippocampal Structure in Healthy Humans

Abstract excerpt:

Observed effects were additive by nature and driven by both recent as well as early life events. A consecutive analysis of hippocampal subfields revealed a spatially distinct profile for each genetic variant suggesting a specific role of 5-HTTLPR for the subiculum, BDNF Val66Met for CA4/dentate gyrus, and COMT Val158Met for CA2/3 volume changes. The present study underscores the importance of G × E interactions as determinants of hippocampal volume, which is crucial for the neurobiological understanding of stress-related conditions, such as mood disorders or post-traumatic stress disorder (PTSD).

See also:
The catechol-o-methyltransferase Val158Met polymorphism modulates the intrinsic functional network centrality of the parahippocampal cortex in healthy subjects
Abstract excerpt:

…our findings may provide plausible implications regarding individual differences in the genetic contribution of COMT Val158Met to the brain network and cognition.

My comment: Do they not know that Val158Met represents an nutrient-dependent RNA-mediated amino acid substitution?
The question arises: What are some good books on molecular biology?

Dennis Mitton, Science and technical writer. Uber evolutionist. Deeply agnostic.

I suppose you will have as many choices as respondants.

My comment: Fortunately, no other respondents chose any other outdated (2007) books. Only someone who describes himself as an “Uber evolutionist” who is “Deeply agnostic” would recommend such ridiculous choices.

Description excerpt:

The Third Edition of this landmark text offers an authoritative, accessible, and engaging introduction to modern, genome-centered biology from its foremost practitioners.

My comment: Genome-centered biology and gene-centric theories about mutation-driven evolution have been virtually eliminated from consideration by serious scientists. The pseudoscientists who still tout them failed to integrate any aspect of what is known about physics, chemistry, and the conserved molecular mechanisms of biophysically constrained RNA-mediated protein folding chemistry. Why bother to read any books written by authors like that?

See also: Underlying Mechanisms of Gene–Environment Interactions in Externalizing Behavior: A Systematic Review and Search for Theoretical Mechanisms


…we argue that one way to help resolve this problem is the development of theory-driven a priori hypotheses on which biopsychosocial mechanisms might underlie cG × E. Such a theoretically based approach can help us specify our research strategies, create more comparable findings, and help us interpret different findings between studies. In accordance, we describe three possible explanatory mechanisms, based on extant literature on the concepts of (1) emotional reactivity, (2) reward sensitivity, and (3) punishment sensitivity. For each mechanism, we discuss the link between the putative mechanism and externalizing behaviors, the genetic polymorphism, and family adversity. Possible research strategies to test these mechanisms, and implications for interventions, are discussed.

My comment: I argue that anyone who is still taking a theoretically-based approach to links from ecological variation to nutrient-dependent healthy longevity or to pathology in the context of life history transitions via hormone-organized and hormone-activated behaviors in all invertebrates and vertebrate will not still be practicing medicine by the end of this decade. If they are still practicing, they will probably lose any accumulated wealth in the context of malpractice after they lose their malpractice insurance because they have not kept up with current practice guidelines, which link atoms to ecosystems in all living genera via their nutrient energy-dependent physiology of reproduction.

Excerpt 2)

Another issue concerning cG × E is that there is a lack of insight into biopsychosocial mechanisms that underlie such interactions (see also Battaglia 2012; Dodge 2009; Salvatore and Dick 2015). At present, looking at cG × E findings is like looking at a “black box,” in that we are only aware of what goes in and what comes out. However, insights into how these G × E interactions work (i.e., “how genes get outside the skin,” Reiss and Leve 2007) is of great empirical and clinical importance.

My comment: Brain on stress: How the social environment gets under the skin explains how G × E interactions work, and the Correction for McEwen, Brain on stress: How the social environment gets under the skin is a clear indicator that medical practitioners must learn to distinguish between epigenetic effects on hormones and the affects of hormones on behavior during life history transitions that link the honeybee model of morphological and behavioral diversity during life history transitions to all other animal models via a single amino acid substitution.

Excerpt 3)

The COMT polymorphism is a SNP (rs 4680) resulting in a valine (i.e., Val) to methionine (i.e., Met) mutation.

My comment: That ridiculous claim makes the need for continuing education perfectly clear. If someone who is nicer than I am tells you to please become biologically informed, I hope you will take the opportunity to do so.

Excerpt 1)

But to make proteins, first the DNA genomic information must be transcribed with complete fidelity, chemical letter by letter into an intermediary molecule, called messenger RNA, or mRNA. In what is known as the central dogma of biology, DNA makes RNA, which makes protein.”

Excerpt 2) “Small RNAs, called micro RNAs (miRNAs), work to pair with a UTR to block translation, killing the message, and thus, silencing a gene. Uncovering the interplay between miRNA and their specific UTRs have become a hot area in biology, and big business.”

My comment: Obviously, someone needs to tell the folks in ASU’s Center for Evolution, Medicine and Public Health that they are about to be forced off the campus via the works of a science fiction author and serious scientists who have since linked atoms to ecosystems across all living genera.

Evolutionary medicine, or Darwinian medicine, is the application of modern evolutionary theory to understanding health and disease.

Attempt to apply any theories to the practice of medicine have failed miserably and caused more suffering and death that could ever be imagined until after viruses kill more people than ever before. Perhaps they will kill us all. If so, the deaths will be attributed to neo-Darwinian evolutionary theory.

 Today, Perry Marshall appeared on the CBS station in Richmond Virginia, WTVR Channel 6, talking about Evolution 2.0! Perhaps Randy Nesse will ask him to speak at ASU sometime soon. After all, the Hippocratic Oath supposedly is one of the oldest binding documents in history.