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

Ecological adaptation: A new definition of heredity (3)

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

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

OMCD: OncoMir Cancer Database

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

5th-6th Sept 2018 Dublin, Ireland

Ecological adaptation: A new definition of heredity (1)

Excerpt: ” …long-standing presumptions led to the claims made by biologically uninformed theorists who failed to link biophysically constrained viral latency to the recent origin of most protein-coding variants via the physiology of pheromone-controlled reproduction in species from microbes to humans…”
She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity May 29, 2018 | 672 Pages
From the description of the book:

1) We need a new definition of what heredity is…

2) …Zimmer ultimately unpacks urgent bioethical quandaries arising from new biomedical technologies, but also long-standing presumptions about who we really are and what we can pass on to future generations.

The long-standing presumptions led to the claims made by biologically uninformed theorists who failed to link biophysically constrained viral latency to the recent origin of most protein-coding variants via the physiology of pheromone-controlled reproduction in species from microbes to humans. For comparison to the long-standing presumptions, see:
Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants May 11, 2012
Evolution and functional impact of rare coding variation from deep sequencing of human exomes May 17, 2012
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants
Reported as: Past 5,000 years prolific for changes to human genome November 28, 2012

Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report. 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years. More broadly, the results suggest that humans are carrying around larger numbers of deleterious mutations than they did a few thousand years ago. But this doesn’t mean that humans now are more susceptible to disease, says Akey. Rather, it suggests that most diseases are caused by more than one variant, and that diseases could operate through different genetic pathways and mechanisms in different people.

Akey dismissed everything known about the epigenetic effects of food energy and the metabolism of food to pheromones, which biophysically constrains viral latency in the context of the physiology of reproduction in species from microbes to humans.
See for comparison: A third of Americans don’t believe in evolution January 1, 2014
My comment:

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.

That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

When food energy-dependent pheromone-controlled autophagy (see: Autophagy.pro) fails to protect organized genomes from the virus-driven degradation of messenger RNA, organisms pass on mutations to future generations. Clear evidence of that fact was published in the context of this article: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants January, 2013.

Establishing the age of each mutation segregating in contemporary human populations is important to fully understand our evolutionary history1, 2 and will help to facilitate the development of new approaches for disease-gene discovery3.

The facts about the age of all mutations have since been placed into the context of:
Sperm epigenetics and influence of environmental factors February, 2018

… epigenetic variation may be genetically selected [41], which is in contradiction with the opposite model in which epigenetic variation is a cause of genetic variation. While both models can cooperate, more experimental evidence, other than computationally-based, should be provided to address the mutagenicity of regions subjected to environmentally-induced epigenetic variation and the evolutionary implications.

Conclusion:

Future research efforts may be able to identify a unified epigenetic remodeling response to lifestyle stress across species. Understanding the role of environmentally-driven epigenetic changes in gametes on the phenotype of the offspring constitutes not only a fascinating biological question on its own but also represents a moral obligation for the health of future generations.

See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression December, 2014

MicroRNA present in mature sperm… may actually serve important regulatory roles in fertilization and early developmental processes.

To see how much experimental evidence of biophysically constrained food energy-dependent pheromone-controlled biologically-based cause and effect has been ignored during the past two decades, see: From Fertilization to Adult Sexual Behavior December 1996

…we focus directly on molecular events themselves. Here the “environment” involved can be that within a DNA segment. We also expand the notion of “biologically based sex differences.” Although many, and perhaps most, important sex differences arise from gonadal and hormonal development, also important are sex differences which are neither gonadal nor hormonal. All these factors affect the internal workings of the individual and intervene in structuring how the social environment might or might not modify sexual behavior. This discourse calls attention to features that are central to the so-called nature-nurture discussion.

Our section on molecular epigenetics may have been the first to detail what is now being reported in the context of the cryo-EM technology, which links energy-dependent changes from electrons to ecosystems in all living genera via what is known about pre-mRNAs. Pre-mRNAs are now also referred to as microRNAs in more than 70,000 published works.
See: microRNA and/or pre-mRNA 
Clearly, what is known to all serious scientists about biophysically constrained viral latency and healthy longevity has forced Carl Zimmer to suggest that “We need a new definition of what heredity is…”
See also:
7/31/16 From hydrogen atom transfer in DNA base pairs to ecosystems
7/31/16 RNA-mediated physics, chemistry, and molecular epigenetics
7/30/16 What is life when it is not protected from virus driven entropy
7/29/16 RNA-mediated molecular epigenetics and virus-driven entropy
4/10/14 Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
8/8/13 Nutrient-dependent / pheromone-controlled adaptive evolution
3/8/13 Nutrient-dependent / Pheromone–controlled thermodynamics and thermoregulation
2/17/13 Nutrient-dependent / Pheromone-controlled Adaptive Evolution
Watch for Philip C. Ball’s newest book: Beyond Weird  March 22, 2018

Over the past decade or so, the enigma of quantum mechanics has come into sharper focus. We now realise that quantum mechanics is less about particles and waves, uncertainty and fuzziness, than a theory about information: about what can be known and how.

See: 5/8/17 Energy as information and constrained endogenous RNA interference May 8, 2017
See also: New Giant Viruses Further Blur the Definition of Life

“The gap between cellular organisms and viruses is starting to close,” Deeg said. “Which then brings us back to: What is a virus, and what is life?”

Has anyone else linked biophotonics to the energy-dependent proton motive force via the cryo-EM technology?
See for instance: Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase.
And preview, Schrödinger at 75 – The Future of Biology – September 2018
Nobel Laureates, Linda Buck, Ben Feringa, Michael Rosbash are among other Nobel Laureates who are scheduled to present.
See also: Are Humans “Smeller Underachievers?” Not So Fast…

…they will share their data and experience on the psychological influences on eating and behavior, the chemosensory properties of food and how we experience them, the role of food as medicine, and the history and evolution of flavor and flavor perception.

No experimental evidence of energy-dependent biophysically constrained top-down causation suggests that flavor perception “evolved.”  See: Feedback loops link odor and pheromone signaling with reproduction

Exemplifying human idiocy

MicroRNAs biophysically constrain behavior (2)

Excerpt:

Researchers, like Shunsuke Suzuki, who cannot link photonic coupling from quantum physics to biophysically constrained atomic energy via classical physics and quantum chemistry prevent scientific progress, They are limited to asking questions that have already been answered by serious scientists.

MicroRNA 1-20 of more than 70,400
The fact that the energy-dependent creation of microRNAs links RNA-mediated cell type-differentiation to biophysically constrained viral latency and all morphological phenotypes has been established.
See: PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers

…using nascent RNA capture sequencing, we identify 1145 temporally expressed S-phase-enriched lncRNAs. Among these, 570 lncRNAs show significant differential expression in at least one tumor type across TCGA data sets.

Reported as: RNA-based therapy cures lung cancer in mouse models

By turning down the activity of a specific RNA molecule researchers at Sahlgrenska Academy, Sweden, have cured lung tumors in mice by 40-50 percent. The results, published in Nature Communications, represent the tip of the iceberg in an extensive research project in which 633 new biomarkers for 14 types of cancer have been identified.

Ongoing support for my model of Energy as information and constrained endogenous RNA interference continues to link RNA-mediated differences in human populations to biophysically constrained viral latency and survival. Why haven’t others accepted the fact that there must be a link from the RNA-mediated differences to behavior? Morphological and behavioral phenotypes are energy-dependent and receptor-mediated.
See: Vital Signs: Racial Disparities in Age-Specific Mortality Among Blacks or African Americans — United States, 1999–2015
See also:
1) Vascular Endothelial Growth Factor Receptor 3 Controls Neural Stem Cell Activation in Mice and Humans (2015)
2) Delayed Dopamine Signaling of Energy Level Builds Appetitive Long-Term Memory in Drosophila (2015)
Reported as: Fruit flies remember a good meal, Blood growth factor activates neural stem cells

…the fruit fly brain is wired to remember and crave sweeter, energy-rich foods. After smelling and consuming a meal, such as a glob of sugar, information about the food’s energy content is relayed via dopaminergic neurons to a fruit fly’s olfactory long-term memory center.

The ability to remember a good meal is linked to a single amino acid substitution in one or more receptors.
3) A Single Amino Acid Substitution in the Activation Loop Defines the Decoy Characteristic of VEGFR-1/FLT-1 (2006)
The link from the food energy-dependent creation of microRNAs and the creation of enzymes to the single amino acid substitution that controls receptor-mediated neural step cell activation in mice and humans may not be obvious. For instance, the acronym VEGFR might not be linked to other reports on Vascular Endothelial Growth Factor Receptors.
The likelihood of establishing facts about top-down causation and biophysically constrained viral latency is reduced as each step towards neo-Darwinian pseudoscientific nonsense brings another level of obfuscation. See for example:

Identification of Multiple Forms of RNA Transcripts Associated with Human-Specific Retrotransposed Gene Copies (2016)

Duplicated genes are abundant in eukaryotic genomes and thus are presumed to play important roles in evolution.

Duplicated genes do not create themselves. The de novo creation of genes is energy-dependent and receptor-mediated. That fact establishes all the links from top-down causation to biophysically constrained viral latency and ecological adaptations via the creation of RNA and energy-dependent fixation of RNA-mediated amino acid substitutions.
If serious scientists understand the facts about food energy-dependent pheromone-controlled ecological adaptations in species from microbes to humans, questions like this are not likely to arise. VEGF165b elevation in pulmonary arterial hypertension patients, causative or adaptive? (4/1/18)
No reply is required. But see: VEGF165b elevation in pulmonary arterial hypertension patients, causative or adaptive? -Reply. (4/1/18)
Shunsuke Suzuki is a co-author of the reply. I am not interested in reading about questions or replies that are placed into the context of ridiculous theories, or attending meetings on Epigenetics & Chromatin where discussion of the emergence of novel CpG islands and genomic imprinting in mammalian evolution are discussed.
See for comparison: Direct Photonic Coupling of a Semiconductor Quantum Dot and a Trapped Ion (2015)
Understanding the key role played by single atoms and ions in the context of elementary quantum information processing protocols is required to answer questions about top-down causation and adaptation. Researchers, like Shunsuke Suzuki, who cannot link photonic coupling from quantum physics to biophysically constrained atomic energy via classical physics and quantum chemistry prevent scientific progress, They are limited to asking questions that have already been answered by serious scientists.
See Frohlich (1968) Long-range coherence and energy storage in biological systems

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

See also: Schrödinger at 75 – The Future of Biology – September 5-6, 2018
The future of biology lies in the understanding of how the creation of the sun’s anti-entropic energy links RNA-mediated top-down causation via natural selection for energy-dependent codon optimality in the context of novel CpG islands and genomic imprinting. The RNA-mediated genomic imprinting must be linked to biophysically constrained viral latency. It is ridiculous to link the systems complexity of cell type differentiation and cancer prevention to mammalian evolution without consideration of how behavior could be linked to biophysically constrained cell type differentiation.
See for instance: CpG islands microRNA

5th-6th Sept 2018 Dublin, Ireland

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (5)

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (3)


The list of those scheduled to present has changed. Michael Rosbash has been added. John E. Walker is not scheduled, which suggests that everyone else already knows that the creation of the sun’s anti-entropic virucidal energy is the link from the creation of ATP to the creation of RNA and all biophysically constrained viral latency via feedback loops and the physiology of reproduction.
Rosbash, as all serious scientists know,  started with energy-dependent changes in cycles of RNA biosynthesis. Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990). Pseudoscientists failed to link the energy from feedback to biophysically constrained viral latency.
But see: Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase

Production of ATP depends on the oxidation of energy-rich compounds to produce a chemical potential difference for hydrogen ions, the proton motive force (pmf), across the inner mitochondrial membrane (IMM).

Other serious scientists have consistently linked photophosphorylation from oxidative phosphorylation to all biodiversity via the physiology of pheromone-controlled reproduction in species from soil bacteria to humans
Speakers (new copy-protected list)
Speakers (old list)
See also: Viral Resistance Project
The differences in innate immunity and ecological adaptation are obviously nutrient energy-dependent and transgenerationally inherited in the context of the epigenetically-effected physiology of pheromone-controlled reproduction and the affects of hormones on behavior. For instance, pheromones biophysically constrain viral latency via the fixation of amino acid substitutions.
See for comparison: Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses
There are several neo-Darwinian theorists who are scheduled to present, which means they may be ready to accept the ridicule from serious scientists.
See for example: A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

See also: Why I got rid of my friends
Some of my former friends kept dumping their garbage about evolution on others in the same way that I. King Jordan and Eugene Koonin did it with their comment about the evolution of the amino acid composition of proteins. See for comparison: All About that Base (Meghan Trainor Parody) 12/10/14 and Energy as information and constrained endogenous RNA interference 2/15/17
Help others who are Combating Evolution to Fight Disease

5th-6th Sept 2018 Dublin, Ireland

Light-activated carbon fixation did not evolve (4)

Summary: Dobzhansky was joking about the time it would take for the creation of light to cause the energy-dependent fixation of RNA-mediated amino acid substitutions, which link food energy to the creation of enyzmes that metabolized food. His joke extends from the creation of sunlight — as the “light of evolution” — to the species-specific pheromone-controlled physiology of reproduction and cell type differentiation in chimpanzees and humans compared to gorillas via one amino acid substitution. The joke was played on theorists who, in 1973, still believed that mutations could be linked to evolution despite the claims in Schroedinger: What is Life? (1944).
See: Light-activated carbon fixation did not evolve (3),(2),(1) and RNA mediated molecular epigenetics and virus driven entropy and The origin of information (2)
For comparison, see: Genome editor CRISPR’s latest trick? Offering a sharper snapshot of activity inside the cell

…this tool can record exposure to light, antibiotics, and viral infection or document internal molecular events.

The “tool” links the anti-entropic virucidal energy of sunlight to the creation of enzymes, which link the metabolism of food energy to the physiology of reproduction in the context of autophagy and viral latency.

The facts about autophagy and biophysically constrained viral latency have been placed into the context of phage-activated continuous evolution (PACE) by people who do not want others to learn the facts about how autophagy protects all organized genome from the virus-driven degradation of messenger RNA.
See: Evolution in Action – Literally

The idea is that you use bacteriophage as your vehicle for evolving proteins, because of their extremely short generation time. These infect E. coli bacteria, and the two of them are modified in this system so that you can use selection pressure to get to a protein with specific binding properties. It’s been used to look at protease inhibitor resistance and DNA-binding specificity, and now it’s put to work for a protein-protein interaction.

All protein-protein interactions are energy-dependent, RNA-mediated and biophysically constrained in the context of the physiology of reproduction and transgenerational epigenetic inheritance.
See for contrast: Church Speaks George Church [2.14.18]

  1. Maybe it would help if the very top scientists believed in neo-Darwinism or something.
  2. We found the enzymes that occur in nature, which was not obvious, and both companies have patents on making those alkanes.

Top scientists who believe in neo-Darwinism are more likely to believe Church’s claim that the anti-entropic energy of sunlight was not the obvious link to the creation of enzymes and all biophysically constrained life on Earth. The creation of enzymes was required to biophysically constrain viral latency.

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: Regulation of the unfolded protein response by noncoding RNA
See: Endoplasmic reticulum stress signaling: the microRNA connection
See also: ER homeostasis and autophagy

The endoplasmic reticulum (ER) is a key site for lipid biosynthesis and folding of nascent transmembrane and secretory proteins. These processes are maintained by careful homeostatic control of the environment within the ER lumen. Signalling sensors within the ER detect perturbations within the lumen (ER stress) and employ downstream signalling cascades that engage effector mechanisms to restore homeostasis. The most studied signalling mechanism that the ER employs is the unfolded protein response (UPR), which is known to increase a number of effector mechanisms, including autophagy.

Place the unfolded protein response (UPR) into the context of how virus-driven energy theft links the degradation of messenger RNA from mutations to all pathology. Link femotosecond blasts of ultraviolet light to the creation of enzymes and energy-dependent RNA-mediated DNA repair to complete the picture of creation vs neo-Darwinism.
See: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair
If you are a top scientist who believes in neo-Darwinism, retire as soon as possible to avoid the ridicule that will be linked to the lack of funding for your so-called research.
See also: miRs-103/107 regulate autophagy in the epidermis

We found that antagomir-107 treatment in epidermis: (i) depleted endogenous miR-107; (ii) increased GFP-LC3 puncta in epidermal basal layers of GFP-LC3 transgenic mice, indicative of an accumulation of autophagosomes; (iii) inhibited LC3 turnover and increased p62, suggesting an inhibition of autophagy flux; and (iv) increased phosphorylated dynamin (p-dynamin, an inactive form), a key enzyme in end-stage autophagy. Conversely, miR-107 mimic treatment in mouse epidermis: decreased GFP-LC3 puncta in basal layer as well as p62 protein levels; and diminished p-dynamin, indicative of activation of this enzyme.

See also: CCPG1: A new breed of autophagy cargo receptor: 3:00pm GMT / 10:00am EST / 7:00am PST on Thursday 1st March
The anti-entropic energy-dependent creation of receptors is enzyme-dependent and RNA-mediated in the context of the physiology of reproduction and autophagy, which biophysically constrains viral latency.
The overwhelming complexity prevents most attempts to link quantum physics from quantum chemistry to the molecular mechanisms of epigenetically-effected cancer prevention and treatment. Despite that fact, prevention and effective treatments will continue to link the speed of light on contact with water from hydrogen-atom transfer in DNA base pairs in solution via the creation of microRNAs linked to biophysically constrained viral latency.
Do you remember what Barry J. Marshall did to link H. pylori to prevention of gastric cancer?
See: Neutrons identify critical details in bacterial enzyme implicated in gastric cancer

Ronning’s team focused on H. pylori’s use of a unique biosynthetic pathway to synthesize vitamin K2, which aids in the electron transfer processes, or chemical reactions, of all organisms.

Ronning’s team linked Barry J. Marshall’s energy-dependent changes (e,g., hydrogen-atom transfer in DNA base pairs in solution) from electrons to ecosystems and healthy longevity in all living genera via the physiology of pheromone-controlled reproduction in species from microbes to humans.
I asked the evolutionary theorist, John Hewitt (a so-called science journalist): “Are you still planning to do that by starting with the magical creation of selenocysteine?”
I’ve heard nothing from him, since then.
See also: Is Maternal Food Security a Predictor of Food and Drink Intake Among Toddlers in Oregon? (2012)

CDC Disclaimer: The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.

The 35-year-old author works as a team lead for the CDC’s Division of Population Health.

Authorities say he called in sick on February 12, 2018 and has not been heard from since.

In 2014 he was the first author of: Sex-specific relationships between adverse childhood experiences and chronic obstructive pulmonary disease in five states

This work adds to a growing body of research suggesting that ACEs may contribute to health problems later in life and suggesting a need for program and policy solutions.

The link from the anti-entropic virucidal energy of sunlight to healthy longevity and the link from stress-induced biophysical constraint-breaking mutations reaffirms that suggestion.
Cunningham’s brother, Anterio Cunningham, does not want to assume the worst, yet he is worried something horrible has happened for him to leave his family and prized job with no notice.
The CDC did not immediately respond to ABC News’ request for comment.

Anyone with information is urged to call 911 or the Atlanta Police Homicide/Adult Missing Persons Unit at 404-546-4235.

The need for program and policy solutions at the CDC could bring the current practice of medicine to an end. The end requires all practitioners to acknowledge the facts about disease control. The facts link the creation of sunlight from fixation of light in cyanobacteria to the physiology of reproduction in humans and to all biodiversity via biophysically constrained viral latency.
See also: Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

 I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation.

Dozhansky supposedly assumed that:

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.

But he may also have been joking. He wrote:

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

Dobzhansky was joking about the time it would take for the creation of light to cause the energy-dependent fixation of RNA-mediated amino acid substitutions, which link food energy to the creation of enyzmes that metabolized food. His joke extends from the creation of sunlight — as the “light of evolution” — to the species-specific pheromone-controlled physiology of reproduction and cell type differentiation in chimpanzees and humans compared to gorillas via one amino acid substitution. The joke was played on theorists who, in 1973, still believed that mutations could be linked to evolution despite the claims in Schroedinger: What is Life? (1944).
Anyone who places Dobzhansky’s claims from 1964 and the claims of McEwen et al. (1964) into the context of Frohlich’s assertions in 1968 would close the door on evolutionists in three steps.
Dobzhansky compared theorists to bird watchers and butterfly collectors.
McEwen et al., (1964) linked the creation of ATP to the creation of RNA.
Frohlich (1968) linked the creation of RNA to all biophysically constrained biodiversity.
The cell biology game “Cytosis” can be used to teach people like George Church about cell biology. Alternatively, Church could ask a serious scientist what was known about the energy-dependent creation of naturally occurring enzymes.
For comparison, retracted works by Jack Szostak’s group are the only works that might make that fact not obvious (e.g., to other theorists). Serious scientists know that all enzymes naturally occur in the context of their energy-dependent microRNA-mediated creation. If George Church shared Dobzhanky’s creationist beliefs, he might have avoided the shame that comes from his claim that it was not obvious where all naturally occurring enzymes come from.
See: Retraction Watch Also reported as: Oops! Scientific retraction a major blow to evolution theory

Szostak’s study reopens what is perhaps the largest hole in evolutionary theory, as scientists remain unable to explain how the building blocks of life were “spontaneously” created.

Jack W. Szostak—a professor of chemistry and chemical biology at Harvard University,  shared the 2009 Nobel Prize in Physiology or Medicine. It seems likely that he influenced the works by George Church — also at Harvard, and the claims Church made about the “not obvious” creation of naturally created enzymes.
See for comparison: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
Reported as: Researchers may have solved origin-of-life conundrum

…the conditions that produce nucleic acid precursors also create the starting materials needed to make natural amino acids and lipids. That suggests a single set of [light activated] reactions could have given rise to most of life’s building blocks simultaneously.

The difference between George Church’s neo-Darwinian approach, and the approach that serious scientists have taken, may be as simple as the difference between a creationist and an evolutionary theorist.
 
For comparison, see: What is life when it is not protected from virus driven entropy Published on 30 Mar 2016

Poster: The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

Witzhany2018

The tipping point (revisited): 70,000 publications

Excerpt:

This new empirically based perspective on the evolution of genetic novelty will have more explanatory power in the future than the „error-replication“ narrative of the last century.

Simply put, all serious scientists have always known that the “error-replication” narrative of the 20th century was a ridiculous misrepresentation of what Darwin placed into the context of his “conditions of life.”

The tipping point?: 50,000publications (May 16, 2016)
See also: The tipping point (revisited): 69,000 publications (January 20, 2018)
Nearly 1000 more published works have been added to the 69,000 on microRNAs that had already been published by last month.
All experimental evidence has been placed into the context of 12,000 more published works on microRNAs, since the time of this presentation (February 15, 2017):

Energy as information and constrained endogenous RNA interference

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: Transposons: a blessing curse (open access) with my emphasis
Conclusion:

The circumstances of transposon bursts, preferences of insertion sites, and the life cycle of many elements are not fully understood. Like in classical mutagenesis with chemical or physical treatments, unwanted side effects are likely and cannot be excluded, and new TE-related phenotypes must be thoroughly tested for genetic and epigenetic stability. However, detrimental and beneficial events can teach us both principles, and well-established advantageous interactions between TEs and genes might serve as templates for more precise and targeted genome editing and breeding.

Pseudoscientists continue to put what is known into the context of their ridiculous theories about evolution:
See for comparison (from the same issue): Despacito: the slow evolutionary changes in plant microRNAs (paywalled) with my emphasis

…this review describes the processes by which new miRNAs are hypothesized to have emerged. Two major models describe miRNA origins, firstly, de novo emergence via inverted duplication of target gene fragments, and secondly, the expansion and neofunctionalization of existing miRNA families. The occasional acquisition of target sites by previously un-targeted genes adds further dynamism to the process by which miRNAs may shift roles during evolution. Additional factors guiding miRNA evolution include functional constraints on their length and the importance of precursor conservation that is observed in regions above or below the mature miRNA duplex; these regions represent recognition sites for components of biogenesis machinery and direct precursor processing. Insights into the mechanisms of miRNA emergence and divergence are important for understanding plant genome evolution and the impact of miRNA regulatory networks.

No experimental evidence of biophysically constrained biologically-based cause and effect suggest that microRNAs emerged or that plant genomes evolved. All experimental evidence consistently has shown that the anti-entropic virucidal energy of sunlight creates microRNAs in the context of photophosphorylation.
See: Energy limitation of cyanophage development: implications for marine carbon cycling
Photophosphorylation is obviously:

…a mechanistic link between diurnal changes in irradiance and observed community level responses in metabolism, i.e., through an irradiance-dependent, viral-induced release of dissolved organic matter (DOM).

Simply put, photophosphorylation links the anti-entropic virucidal energy of sunlight to all biophysically constrained biodiversity via oxidative phosphorylation and the physiology of reproduction in all living genera. That fact has been suspected or established in the context of all works published by serious scientists since the publication of What is Life? (1944)

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

See also: Gene Expression Patterns during Light and Dark Infection of Prochlorococcus by Cyanophage
For extension of the research from cyanobacteria to humans see:
Quantification of microRNA expression with next-generation sequencing 2013 (coauthored by George M. Church)
Differential expression of microRNAs in the normal skin of the Han and Uyghur populations in Xinjiang Province (2018)
Any additional claims about the emergence of microRNAs and the evolution of genomes can be placed into the context of what will be presented at the forthcoming conference on “Genetic Novelty/Genomic Variations by RNA Networks and Viruses,” or the cell biology board game “Cytosis” for ages 10+.

This new empirically based perspective on the evolution of genetic novelty will have more explanatory power in the future than the „error-replication“ narrative of the last century.

Simply put, all serious scientists have always known that the “error-replication” narrative of the 20th century was a ridiculous misrepresentation of what Darwin placed into the context of his “conditions of life.”
See for instance: 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. Experiments are described which show that the required ATP is produced by reactions associated with glycolysis, the citric acid cycle, and a type of oxidative phosphorylation.

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

George Church refutes theistic evolution (4)

See: George Church refutes theistic evolution (February 9, 2017)
See also: Energy as information and constrained endogenous RNA interference (February 15, 2017)

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: Church Speaks  George Church (February 14, 2018)

[Arctic grass and] cyanobacteria, on the other hand, they fix [carbon]. Cyanobacteria turn carbon dioxide, a global warming gas, into carbohydrates and other carbon-containing polymers, which sequester the carbon so that they’re no longer global warming gases. They turn it into their own bodies. They do this on such a big scale that about 15 percent of the carbon dioxide in the atmosphere is fixed every year by these cyanobacteria, which is roughly the amount that we’re off from the pre-industrial era. If all of the material that they fix didn’t turn back into carbon dioxide, we’d have solved the global warming problem in a year or two. The reality, however, is that almost as soon as they divide and make baby bacteria, phages break them open, spilling their guts, and they start turning into carbon dioxide. Then all the other things around them start chomping on the bits left over from the phages.

The anti-entropic virucidal quantized energy of sunlight links the creation of ATP to the creation of microRNAs and changes in the energy-dependent microRNA/messenger RNA balance, which link what organisms eat to RNA-mediated fixation of amino acid substitutions that differentiate all cell types in all individuals of all living genera. Simply put, sunlight, food energy, and pheromones biophysically constrain the DNA damage that is done by phages.
Release of the cell biology game “Cytosis” and the forthcoming conference Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses (4 – 8 July 2018 Salzburg – Austria) have forced George Church and others like him to begin telling the scientific truth about how the virus-driven theft of quantized energy is either biophysically constrained, or linked from the virus-driven degradation of messenger RNA to mutations and all pathology.

Preliminary List of Confirmed Speakers (41)
Chantal Abergel >
Aix-Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Marseille, France
Gustavo Caetano Anolles >
Department of Crop Sciences, Evolutionary Bioinformatics Laboratory, University of Illinois at Urbana-Champaign Urbana, USA.
Marlene Belfort >

Department of Biological Sciences and RNA Institute, University at Albany, New York, USA
Felix Broecker >
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
Department of Chemistry & Biochemistry, University of California, Santa Barbara, USA
Julian Chen >
Department of Chemistry and Biochemistry, Arizona State University, Tempe, USA
Jean-Michel Claverie >
Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille, France
Bryan Cullen >
Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, USA
Valerian Dolja >

Department of Botany and Plant Pathology, Oregon State University, Corvallis, USA
Cedric Feschotte >
Department of Human Genetics, University of Utah, School of Medicine, Salt Lake City, USA
Matthias Fischer >
Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Heidelberg, Germany
David Gilmer >
Institut de biologie moléculaire des plantes, Integrative virology, Strasbourg, France
Reynald Gillet >
Université de Rennes 1, Translation and Folding Team, Rennes cedex, France Institut Universitaire de France
Jordi Gomez >
Instituto de Parasitología y Biomedicina ‘López-Neyra’ (CSIC), Granada, Spain
Matti Jalasvuori >

Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Finland
I.King Jordan >
School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
Eugene Koonin >
National Center for Biotechnology Information, National Library of Medicine, Bethesda, USA.
Dusan Kordis >
Department of Molecular and Biomedical Sciences, Josef Stefan Institute, Ljubljana, Slovenia
Mart Krupovic >

Unit BMGE, Department of Microbiology, Institut Pasteur, Paris, France
Erez Levanon >
Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
German Martinez >
Dept. of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
John Mattick >
Garvan Institute of Medical Research, Darlinghurst, Australia
Jeff Miller >
California NanoSystems Institute, University of California, Los Angeles, USA
Karin Moelling >
Max Planck Institute for molecular Genetics, Berlin, Germany
Sabine Müller >
Universität Greifswald, Institut für Biochemie , Greifswald , Germany
Ulrich Müller >
Department of Chemistry & Biochemistry, University of California, San Diego, USA
Mariusz Nowacki >
Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
David Prangishvili >
Department of Microbiology, BMGE, Institut Pasteur, Paris, France
Lennart Randau >
Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
Forest Rohwer >
Department of Biology, San Diego State University, San Diego, CA, USA
Corrado Spadafora >
Institute of Translational Pharmacology, CNR, Rome, Italy
James Shapiro >
Department of Biochemistry and Molecular Biology , University of Chicago , IL , USA
Jason Shepherd >
Biochemistry and Ophthalmology & Visual SciencesUniversity of Utah, School of Medicine Salt Lake City, USA
Ravindra Singh >
Department of Biomedical Sciences, Iowa State University, Ames, USA
Keizo Tomonaga >
Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
Peter Unrau >
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
Luis P. Villarreal >
Center for Virus Research, University of California, Irvine, Irvine, CA, USA
Andreas Werner >
RNA biology group, Institute for Cell and Molecular Biosciences, Newcastle University, UK
Eric Westhof >
Architecture and Reactivity of RNA, Institute of Molecular and Cellular Biology of the CNRS, University of Strasbourg, France
Bojan Zagrovic >
Department of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna, Austria
Steven Zimmerly >
Department of Biological Sciences, University of Calgary, Calgary, Canada

 

An evolutionary theory killer

Conceptual critique: Innateness vs the death gene (2)

Excerpt: Martie Haselton notes

“…there’s a hidden adaptive intelligence that has been shaped over eons. Martie Haselton places that ecological adaptation into the context of the claim that “…our bodies are designed to fight off invaders, whether they take the form of a cold virus… (p 73.) and she mentions the link from the designer to one theory about menstruation: “female bleeding serves to flush out “bad” sperm that may carry bacteria, viruses and other pathogens.” (p. 84)

See also: Conceptual critique: Innateness vs the death gene (1)
Re: Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases

This approach may help limit seasonal influenza epidemics, transmission of tuberculosis, as well as major pandemics.

See for comparison: Subatomic

…is a deck building game where players are competing to build a number of available atoms. Each player starts with the same small deck of cards that consist of Proton Cards, Neutron Cards, Electron Cards and Energy Cards and a beginning hand limit of 5 cards. They use these cards to build upon their current Atom, in an attempt to construct one of the available Atom Cards, and/or use their hand of cards to purchase more powerful atom building cards for later use, or increase their hand limit. The deck building cards are simple and clean, but offer a number of interesting combinations. Players also have an energy track that allows them to store energy, which introduces a “push-their-luck” type of mechanic…

See also: Cytosis: A Cell Biology Board Game

Players start out with a number of workers and on their turn, they will place one of their workers on any available location within that cell. Some of the locations provide players with resources (e.g., mRNA, ATP); some with actions (e.g., convert resources, collect cards). Resources are used to build enzymes, hormones, and/or receptors, which score Health Points.

Science Concepts: cell biology, nucleus, free ribosomes, smooth ER, rough ER, golgi apparatus, plasma membrane, mitochondria, enzymes, hormones, receptors, cell detoxification, antibodies and viruses
Alternatively, theorists may continue to ignore the Science Concepts: in the context of  The Hidden Intelligence of Hormones — How They Drive Desire, Shape Relationships, Influence Our Choices, and Make Us Wiser (Feb 13, 2018) for comparison to From Fertilization to Adult Sexual Behavior (1996)

Martie Haselton notes

“…there’s a hidden adaptive intelligence that has been shaped over eons. Martie Haselton places that ecological adaptation into the context of the claim that “…our bodies are designed to fight off invaders, whether they take the form of a cold virus… (p 73.) and she mentions the link from the designer to one theory about menstruation: “female bleeding serves to flush out “bad” sperm that may carry bacteria, viruses and other pathogens.” (p. 84)

See for comparison: Conditional expression of women’s desires and men’s mate guarding across the ovulatory cycle (2006)In 2006, it became clear to most serious scientists that Martie Haselton knew nothing about biophysically constrained RNA-mediated viral latency. Now, she places everything known back into the context of neo-Darwinian pseudoscientific nonsense and eons of evolution. Fortunately,  you can read and discuss her book in the context of what other pseudoscientists have been doing for the past two decades. Simply copy and paste from Wikipedia in attempts to promote ridiculous theories.

See for comparison: Evolution: Genetic Novelty/Genomic Variations by RNA-Networks and Viruses 2018 >

Preliminary List of Confirmed Speakers (41)
Chantal Abergel >
Aix-Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Marseille, France
Gustavo Caetano Anolles >
Department of Crop Sciences, Evolutionary Bioinformatics Laboratory, University of Illinois at Urbana-Champaign Urbana, USA.
Marlene Belfort >

Department of Biological Sciences and RNA Institute, University at Albany, New York, USA
Felix Broecker >
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
Department of Chemistry & Biochemistry, University of California, Santa Barbara, USA
Julian Chen >
Department of Chemistry and Biochemistry, Arizona State University, Tempe, USA
Jean-Michel Claverie >
Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille, France
Bryan Cullen >
Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, USA
Valerian Dolja >

Department of Botany and Plant Pathology, Oregon State University, Corvallis, USA
Cedric Feschotte >
Department of Human Genetics, University of Utah, School of Medicine, Salt Lake City, USA
Matthias Fischer >
Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Heidelberg, Germany
David Gilmer >
Institut de biologie moléculaire des plantes, Integrative virology, Strasbourg, France
Reynald Gillet >
Université de Rennes 1, Translation and Folding Team, Rennes cedex, France Institut Universitaire de France
Jordi Gomez >
Instituto de Parasitología y Biomedicina ‘López-Neyra’ (CSIC), Granada, Spain
Matti Jalasvuori >

Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Finland
I.King Jordan >
School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
Eugene Koonin >
National Center for Biotechnology Information, National Library of Medicine, Bethesda, USA.
Dusan Kordis >
Department of Molecular and Biomedical Sciences, Josef Stefan Institute, Ljubljana, Slovenia
Mart Krupovic >

Unit BMGE, Department of Microbiology, Institut Pasteur, Paris, France
Erez Levanon >
Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
German Martinez >
Dept. of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
John Mattick >
Garvan Institute of Medical Research, Darlinghurst, Australia
Jeff Miller >
California NanoSystems Institute, University of California, Los Angeles, USA
Karin Moelling >
Max Planck Institute for molecular Genetics, Berlin, Germany
Sabine Müller >
Universität Greifswald, Institut für Biochemie , Greifswald , Germany
Ulrich Müller >
Department of Chemistry & Biochemistry, University of California, San Diego, USA
Mariusz Nowacki >
Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
David Prangishvili >
Department of Microbiology, BMGE, Institut Pasteur, Paris, France
Lennart Randau >
Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
Forest Rohwer >
Department of Biology, San Diego State University, San Diego, CA, USA
Corrado Spadafora >
Institute of Translational Pharmacology, CNR, Rome, Italy
James Shapiro >
Department of Biochemistry and Molecular Biology , University of Chicago , IL , USA
Jason Shepherd >
Biochemistry and Ophthalmology & Visual SciencesUniversity of Utah, School of Medicine Salt Lake City, USA
Ravindra Singh >
Department of Biomedical Sciences, Iowa State University, Ames, USA
Keizo Tomonaga >
Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
Peter Unrau >
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
Luis P. Villarreal >
Center for Virus Research, University of California, Irvine, Irvine, CA, USA
Andreas Werner >
RNA biology group, Institute for Cell and Molecular Biosciences, Newcastle University, UK
Eric Westhof >
Architecture and Reactivity of RNA, Institute of Molecular and Cellular Biology of the CNRS, University of Strasbourg, France
Bojan Zagrovic >
Department of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna, Austria

Steven Zimmerly >
Department of Biological Sciences, University of Calgary, Calgary, Canada

For comparison to Martie Haselton’s February 13, 2018 publication of her pseudoscientific nonsense about hormonal women, see: Energy as information and constrained endogenous RNA interference from my February 15, 2017 virtual conference presentation on Precision Medicine.

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

5th-6th Sept 2018 Dublin, Ireland

Diet-driven RNA interference and mental health (4)

See: Diet-driven RNA interference and mental health (3)

Social transmission and buffering of synaptic changes after stress

Transmission from the stressed subject to the naive partner required the activation of PVN CRH neurons in both subject and partner to drive and detect the release of a putative alarm pheromone from the stressed mouse.

Reported as: Researchers discover brain cells change following close contact with a stressed individual

“There has been other literature that shows stress can be transferred — and our study is actually showing the brain is changed by that transferred stress,” says Toni-Lee Sterley, an Eyes High postdoctoral fellow in Bains’s lab and the study’s lead author. “The neurons that control the brain’s response to stress showed changes in unstressed partners that were identical to those we measured in the stressed mice.”

The researchers discovered that the activation of the neurons causes the release of a chemical signal, an “alarm pheromone,” from the mouse that alerts the partner. The partner who detects the signal can, in turn, alert additional members of the group.

This links Bruce McEwen’s works on stress to my works. It completes details of how the mouse-to-human model links nutrient stress-linked and social stress-linked mutations from the virus-driven theft of quantized energy to all pathology. It predicts that fact that human pheromone-enhanced products will continue to be used to prevent or effectively treat Alzheimer’s disease and other neurodegenerative diseases, and to prevent suicide.
See: Formulation and evaluation of anti-suicidal nasal spray of Thyrotropin releasing hormone
See also: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
The unnecessary suffering and premature deaths of ~ 22 veterans per day and many others who commit suicide or who suffer through largely ineffective treatments for cancer can be place into the context of two reviews:
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013)
and Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
In my 2014 invited review of nutritional epigenetics, I linked one food energy-dependent base pair to fixation of one amino acid substitution and the stability of organized genomes in a modern human population. The stability was clearly linked from the creation of microRNAs via ingestion of sago palm-like leaves to an increase in endogenous vitamin C.
See also: Vitamins and Hormones Volume 106 Thyroid Hormone February 2018 (paywalled)
Vitamin C links a single base pair change to one amino acid substitution (V370A) in a modern human population. That fact can now be linked from my 2013 refutation of neo-Darwinian pseudoscientific nonsense to all biodiversity on Earth via the creation of sunlight and the 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.

The model organism that best represent the facts about epigenetic regulation of biophysically constrained ATP-dependent RNA-mediated viral latency is featured here: Meet the creature that can regenerate its brain and resist cancer.

A good model with a good model organism predicts. The mouse to human model predicts that one base pair and one fixed RNA-mediated amino acid substitution link the pheromone-controlled physiology of reproduction to all vertebrate biodiversity via food odors.  Predictably, in the axolotyl (aka the “walking fish”), an iodine isotope and cryo-EM technology will soon be used to establish the facts about how the creation of sunlight must be linked from the creation of ATP and the creation of RNA to DNA repair and all biodiversity via the physiology of reproduction and healthy longevity in all living genera.

See also: Researchers ID New Mechanism for Keeping DNA Protein in Line

The actions of a protein used for DNA replication and repair are guided by electrostatic forces known as phosphate steering, a finding that not only reveals key details about a vital process in healthy cells, but provides new directions for cancer treatment research.
Electrostatic forces are not known as phosphate steering.
See: What is an Electrostatic Force?

Electrostatic force between electrons and protons is one of the strongest forces in the universe, even more powerful than gravity. A hydrogen atom, which contains only one electron and one proton, has the fundamental force of gravity keeping it together. However, each subatomic particle can develop electrostatic force as well, which becomes even stronger.

Pseudoscientists are prepared to attack serious scientists at every level of examination that includes aspects of how subatomic particles contribute to oxidative phosphorylation. Who doesn’t know about the role that subatomic particles play in biophysically constraining viral latency?
See: Subatomic: An Atom Building Game (2017)

Subatomic is a deck building game where players are competing to build a number of available Elements, which score them points. Each player starts with the same small deck of cards that consist of Proton, Neutron, and Electron Cards. They use these cards to build upon their current Atom (by playing these cards face-up as Subatomic Particles) in an attempt to construct one of the available Element Cards. Or players may use their hand of cards to purchase more powerful cards for later use (by playing them in combinations of face-down as energy and face-up as Subatomic Particles!) Subatomic introduces a unique variation on deck building with a highly accurate chemistry theme…

The fact that Discover’s “My Science Shop” does not yet include information on the game “Subatomic” can be explained because the game is not yet available. The fact that Discover’s “My Science Shop” does not mention the availabilty of “Cytosis” suggests they are not willing to admit that their past representations of neo-Darwinian pseudoscientific nonsense were removed from consideration in 1944 when Schrödinger published “What is Life?”
See: Schrödinger at 75 – The Future of Biology – September 2018
The most accurate of all chemistry themes has continued to link Schrödinger’s claims from  quantum physics and quantum chemistry to quantum biology via the conserved molecular mechanisms of biophysically constrained protein folding chemistry. The conserved molecular mechanisms link energy-dependent epigenetics to healthy longevity. The conserved molecular mechanisms also link the virus-driven theft of quantized energy to all pathology.
See also: A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution (2013)
Classical biophysics does not have a ready explanation for the role of docosahexanoic acid (DHA), which appears to be irreplaceable in the context of a light-activated endogenous substrate that functions as an electron tunnelling device. DHA provides precise quantized signals that are essential to visual accuity in the context of synaptic signaling. The link from quantum physics to classical physics helps to explain why the energy-dependent creation of photoreceptors has been linked to their counter intuitive orientation — away from the incoming light.
But, I digress. I am often forced to digress by theorists who invent new terms, such as phosphate steering, to obfuscate what is know about epigenetically-effected top-down causation, which starts with effects of sunlight linked to oxidative phosphorylation. Top-down causation does not start with phosphate steering. It starts with the creation of receptors. If any aspect of biophysically constrained life on Earth started with phosphate steering, there would be more than one citation to the claim. There is only one. See. “Phosphate steering.”
For comparison to what is known about the link from microRNAs to the brain and behavior, see:
microRNA brain and microRNA behavior
See also: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene (2011)
and Targeted expression of suicide gene by tissue-specific promoter and microRNA regulation for cancer gene therapy (2013)

See: Epigenetics study helps focus search for autism risk factors

Within the Shank3 promoter 6 region they identified a single nucleotide polymorphism (or SNP, a common type of genetic variation) known as rs6010065. Analyzing genomic data from a clinical study of 554 children with autism and 214 healthy controls, they found that rs6010065 is indeed associated with autism spectrum disorder.

I reiterate. The profiles are energy-dependent and the pheromone-controlled physiology of reproduction helps to ensure that viral latency is biophysically constrained by the dynamic processes. That fact can be compared to ridiculous claims about mutations and the “evolving profiles.”

See for example, this link from the food energy-dependent pheromone-controlled fixation of the BDNF val66met polymorphism amino acid substitution to behavior in human infants.

The BDNF val66met polymorphism and individual differences in temperament in 4-month-old infants: A pilot study

See for comparison: Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity

Reported as: Newly discovered windows of brain plasticity may help with treatment of stress-related disorders 

…they looked at mice genetically engineered to carry a genetic variant associated with development of depression and other stress-related disorders in humans [ the variant is (BDNF Val66Met)] and present in 33 percent of the population.

If you don’t know where to look, you might find where the information on the BDNF Val66Met is buried. But, if you look at the life’s works of Bruce S. McEwen, you will discover what is known to all serious scientists about stress linked RNA-mediated cell type differentiation.

Redefining neuroendocrinology: Epigenetics of brain-body communication over the life course (2017)

Heterozygous BDNF Val66Met mice are genetically susceptible to stress. The effects of stress on messenger RNA levels in wild-type mice was recapitulated but only via activation of immediate early genes when the heterozygous BDNF Val66Met mice were actually stressed. In the absence of stress, stress activated expression of immediate early genes is not worth studying. Similarly, it is not worth studying how nutrient stress is linked to social stress via c-fos activation in gonadotropin releasing hormone (GnRH) neuroscretory neurons.

However, if baseline studies had not already linked expression of the Fos protein to epigenetic effects of pheromones on luteinizing hormone in mice, the epigenetic effects of food odors and pheromones on humans might never have been linked to interethnic genetic differences in human morphology and behavior.

See: Influence of male rats on the luteinizing hormone-releasing hormone neuronal system in female rats: role of the vomeronasal organ (1993)

[Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] (1994)

Human pheromones: integrating neuroendocrinology and ethology (2001)

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

The link from diet-driven RNA interference to mental health can now be considered in the context of gene gains and losses.

For example, see: APOBEC1

  1. Catalytic component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the postranscriptional editing of a CAA codon for Gln to a UAA codon for stop in the APOB mRNA.
  2. Also involved in CGA (Arg) to UGA (Stop) editing in the NF1 mRNA.
  3. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation.

Loss of APOBEC1 RNA-editing function in microglia exacerbates age-related CNS pathophysiology

These data provide powerful evidence supporting the critical role of APOBEC1-mediated RNA editing in maintaining the balance between the homeostatic and activated immune functions of MG.

See also: Psychological Stress and Mitochondria: A Conceptual Framework (Part 1) and Psychological Stress and Mitochondria: A Systematic Review (Part 2)

Reported as: Cellular ‘powerhouses’ may explain health effects of stress

The findings are especially exciting for the field of psychosomatic medicine, with its traditional focus on re-integrating the mind (“psyche”) and body (“soma”). Emerging evidence on the role of mitochondria in translating the effects of stress on health “extend the reach of mind-body research into the cellular-molecular domain that is the core foundation of current biomedical training and practice,” Drs. Picard and McEwen write. They emphasize the need for further studies to test various elements of their model, especially in humans. “Future research should consider the dynamic bi-directional interactions between mitochondria and other important physiological systems,” the authors conclude.

See also: Mitochondrial alterations and neuropsychiatric disorders

Mitochondria are membrane-enclosed organelle found in most eukaryotic cells, where they generate the majority of the cell’s supply of adenosine triphosphate (ATP), used as a source of chemical energy. In addition, they are involved in a range of other processes, such as signalling, cellular differentiation, cell death, as well as the control of the cell cycle and cell growth. Mitochondria have been implicated in several neuropsychiatric disorders, in particular, depression, anxiety, schizophrenia, autism, and Alzheimer’s dementia. Furthermore, the presence of mutations at the level of mitochondrial or nuclear DNA (mtDNA and nDNA, respectively) has been linked to personality disorders, behavioral disturbances, thought alterations, impulsivity, learning impairment, cognitive failures until dementia. The aim of this paper is to review the literature on the relationship between psychiatric symptoms or syndromes and mtDNA mutations or mitochondrial alterations, while highlighting novel therapeutic targets for a broad range of disorders.

 

An evolutionary theory killer

Subatomic: From thermophiles to humans (3)

Summary: RNA-mediated cell type differentiation in species from insects to primates can be linked from claims about the lower percentage of food energy-dependent DNA methylation in Diet and cell size both affect queen-worker differentiation through DNA methylation in honey bees (Apis mellifera, Apidae) to the conclusion from “Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility.”
See also: Starfish reveal the origins of brain messenger molecules (February 9, 2016)

One of the neuropeptides found is similar to kisspeptin, a chemical that triggers the onset of puberty in humans.

The link from kisspeptin to GnRH helped to establish the link from food odors and pheromones to the RNA-mediated physiology of reproduction in all invertebrates and vertebrates.
Placing facts about neuropeptides into the context of human brain evolution thus seems to exemplify incredible ignorance of physics, chemistry, and molecular epigenetics.
See for comparison: The Importance of ncRNAs as Epigenetic Mechanisms in Phenotypic Variation and Organic Evolution
Conclusion:

The increasing number and diversity of these small and long ncRNAS in relation to the complexity and adaptability of living beings, explains that they have been paramount in complex biological processes and are not an evolutionary paradox.

The fact that miRNAs can be mobilized by the fluids of plants and animals, allows them to act at different distances to where they were transcribed, much like hormones or pheromones do. In addition, they can respond to environmental stimuli, favoring the adaptation of organisms through the modification of epigenetic marks and also a transgenerational inheredity and the evolution of species as part of a Neo-Lamarckian model.

There has never been a neo-Lamarkian model for the evolution of species. Lamarck put his observations into the context of Darwin’s “conditions of life.” If the conditions of life are met, ecological variation can be linked to food energy-dependent ecological adaptations. Only the bastardization of Darwin’s claims put natural selection for mutations first — when biologically uninformed theorist invented neo-Darwinian pseudoscientific nonsense.
SARCASM ALERT: Please do not tell anyone about this 2013 refutation of neo-Dawinism. Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Excerpt:

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.

Conclusion:

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

See for comparison. Others are  making the same claims:
Modulation of miRNAs by Vitamin C in Human Bone Marrow Stromal Cells

…identification of vitamin C-dependent microRNA regulation is important for understanding the basic mechanisms underlying BMSC differentiation and tissue engineering.

All cell type differentiation in all tissues of all species with tissues is energy-dependent and RNA-mediated. That fact is consistently thrown into the political ring of nonsense touted by theorists who attack the President of the United States.
See: Trump: Tell us about your flu shot

Why are so few Americans getting the flu vaccine? And why isn’t the CDC doing more to change that?

The CDC can do nothing. Intelligent people know that the flu virus adapts each season. The CDC will abandon their claims about mutations, which were linked to evolution. More people will be angry when they learn that only a single amino acid substitution can cause an adaption.
Trump-hating liberals may be forced to repurpose their anger and use it to rid the academic swamp of their idiot minions — the so-called science journalists who refused to join the serious scientists who are Combating Evolution to Fight Disease
Most of the anger will be directed toward biologically uninformed science journalists who have failed to present the facts about all virus-driven pathology. For example see: The Quest to End the Flu (2013)

New pandemics don’t come out of the blue. They evolve from viruses that infect animals—typically birds.

Pandemics “evolve” from viruses? What kind of so-called science journalist makes a claim like that?
Is Most of Our DNA Garbage? (March 5, 2015)

…junk DNA isn’t a sign of evolution’s failure. It is, instead, evidence of its slow and slovenly triumph.

The triumph is not slow and slovenly. One base pair change and fixation of one amino acid substitution is all that is required to start the process of ecological adaptation.
See for comparison: It’s time to put America’s health first

While the CDC neglected its mission here, Obama committed billions to build labs and train health personnel in Africa during the Ebola scare. Billions for a disease that killed only one person in the United States — and even he got infected elsewhere.

The so-called science journalists who also are Trump-haters have contributed to more unnecessary suffering and premature death than most people can begin to imagine. They spread their ignorance and hatred across the country and across the world. It is the pathology of their ignorance that must be removed if ever we are to put America’s health first. The first thing we must do, is rid ourselves of the unethical so-called science journalists.