5th-6th Sept 2018 Dublin, Ireland

The eternal significance of microRNAs (8)

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in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation and aging has been replaced by the use of model systems of biological processes.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

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

Chapter 2 The Emerging Roles of microRNAs in Stem Cell Aging

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

Chapter 6  MicroRNAs, Regulatory Messengers Inside and Outside Cancer Cells

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

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

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

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

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

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

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

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

 

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

Autophagy in health and disease (1)

Novel Treatment Strategies for the Nervous System: Circadian Clock Genes, Non-coding RNAs, and Forkhead Transcription Factors

Each of these pathways have an intimate relationship with the programmed death pathways of autophagy and apoptosis and share a common link to the silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1) and the mechanistic target of rapamycin (mTOR). Circadian clock genes are necessary to modulate autophagy, limit cognitive loss, and prevent neuronal injury. Non-coding RNAs can control neuronal stem cell development and neuronal differentiation and offer protection against vascular disease…

The author includes what is known about the links from biophysically constrained RNA-mediated energy-dependent pheromone-controlled reproduction in yeasts to mammals.
See also this comment by Frank Xavier on Eat Yourself to Live: Autophagy’s Role in Health and Disease

Amino acids are not all the same, EAA and NEAA messages epigenetically control sometimes univocal responses, but more often they rule opposing effects.

I wrote:

Thanks for mentioning that. In a recent interview about his forthcoming book, Carl Zimmer claimed

…we need to be much more skeptical about other forms of heredity, like epigenetics.

(edited) Food energy-dependent biophysically constrained viral latency has been linked to healthy longevity in all living genera via autophagy, in the context of fixation of RNA-mediated amino acid substitutions and game play in Cytosis, for ages 10+.

In that context, we included a section on molecular epigenetics in this 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior

Our claims have since been supported at every level of examination that now links the sun’s anti-entropic virucidal energy from electrons to ecosystems via cryo-EM technology and the creation of microRNAs.

See: Regulation of Luteinizing Hormone Receptor mRNA Expression in the Ovary: The Role of miR-122 and Regulation of FSH expression by differentially expressed miR-186-5p in rat anterior adenohypophyseal cells and Modulation of miRNAs by Vitamin C in Human Bone Marrow Stromal Cells
The microRNA-mediated link from Vitamin C to ecological adaptations in a modern human population in China established the facts about alternative splicings of pre-mRNA that we included in our 1996 review. See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
See also:  Reproductive role of miRNA in the hypothalamic-pituitary axis
See also: Chemistry at the nexus of water and energy

Our ability to harness reactions that absorb or release energy is often contingent on water as a mediator. We can appreciate this simply by considering the steam that drives our electricity-generating turbines, the rivers that flow through our hydroelectric plants, and the freshwater–saltwater interface from which we can harvest blue energy. Whether we split water (as plants do), make it (as a product of combustion) or just drink it, this compound is inexorably tied to energy. Chemistry is at the heart of these topics and this collection brings together content from across Nature Research that focuses on the chemistry of energy production and water treatment.

Philip C. Ball and Carl Zimmer continue to display their overwhelming ignorance of cell biology in two books:
Beyond Weird

We now realise that quantum mechanics is less about particles and waves, uncertainty and fuzziness, than a theory about information…

See for comparison: Life is physics and chemistry and communication and What is life when it is not protected from virus driven entropy
See also: She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity

We need a new definition of what heredity is…

Both so-called science journalists have ignored everything known to serious scientists about biophysically constrained viral latency. They reach a very large target audience of others who are biologically uninformed.
In the context of those who are equally uninformed, so-called science journalists have the power to contribute to increasing amounts of  unnecessary suffering and premature deaths. Only the emergence of Timothy J. Cunningham as director of the CDC is likely to stop them. May God help us all if Timothy J. Cunningham has somehow vanished without a trace and fails to return to put pseudoscientists and their idiot minions into their proper place.

Lethal virus kills 5 billion people?

Until death: Virus-driven failure of multisensory integration (2)

Summary: The virus-driven degradation of messenger RNA is clearly linked to frontotemporal dementia (FTD) by altered language, personality, behavior, cognition and motor function. What causes FTD? If the virus-driven degradation of messenger RNA causes all pathology, I would expect to find a link from microRNAs to the pathology and to the effective treatment.

The social and economic burden of frontotemporal degeneration

Reported as: Study reveals staggering economic burden of dementia in younger people

Frontotemporal degeneration (FTD) accounts for 20 to 50 percent of dementia cases in people under the age of 65. FTD ravages an individual’s quality of life by dramatically altering their language, personality, behavior, cognition and motor function.

FTD alters language, personality, behavior, cognition and motor function. What causes FTD? If the virus-driven degradation of messenger RNA causes all pathology, I would expect to find a link from microRNAs to the pathology and to the effective treatment.
See for instance: Tumour necrosis factor-α (TNF-α) and miRNA expression in frontal and temporal neocortex in Alzheimer’s disease and the effect of TNF-α on miRNA expression in vitro
See also: miR-106b inhibits tau phosphorylation at Tyr18 by targeting Fyn in a model of Alzheimer’s disease
The facts that link the virus-driven degradation of messenger RNA to all pathology have also been placed into the context of this report: Global Sensory Impairment Predicts Morbidity and Mortality in Older U.S. Adults
I mentioned before that this was reported in the news as: Problems with senses may predict older adults’ overall health, ability to function

Researchers have mainly focused on what happens after people lose one or two of their senses. However, we know that losing more than two senses occurs frequently for older adults. Until now, no studies have examined how losing multiple senses affects older adults.

I also mentioned that the virus-driven loss of G protein-coupled receptors has been linked to the loss of multiple senses in all organisms at all ages.
See: Olfaction Warps Visual Time Perception
For comparison, pseudoscientists reported Brain wiring affects how people perform specific tasks

“Individuals organize themselves into densely interconnected communities, like the dormitories and sports teams, though individuals within these groups also have connections with people outside of those groups. Brains are the same way: Brain regions are organized into communities with lots of connections between regions in the community and fewer connections to regions outside of the community. But people’s brains are different. Some people have brains that are better described as having rigid community structure—or higher modularity—while other people have brains without such rigid community structure—or lower modularity.”

The individuals of all species must find food to reproduce. That’s how the individuals become part of a species. Their pheromone-controlled physiology of reproduction has been linked to all biodiversity in all genera. The claim “Individuals organize themselves…” is foolish. Claims about higher or lower modularity could be linked to the pseudoscientific nonsense touted in reports like this: The fusiform face area and occipital face area show sensitivity to spatial relations in faces
See also: The Blur of Pleasure: Appetitively Appealing Stimuli Decrease Subjective Temporal Perceptual Acuity
Reported as:  Appetizing imagery puts visual perception on fast forward

“Our research shows that emotionally-charged stimuli, specifically positive and negative images, may influence the speed, or the temporal resolution, of visual perception…”

See for comparison: Supercool Protein Imaging Gets the Nobel Prize

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

See for comparison: How childhood trauma affects the brain

The researchers’ conclusion is that experiencing abuse in early life “may lastingly disrupt” the connectivity between the areas of the brain that are key in cognitive and emotional processes.

Receptor mediated epigenetic effects on hormones are the link to affects on behavior via energy-dependent RNA-mediated cell type differentiation in the context of the creation of enzymes and the physiology of pheromone-controlled reproduction. See anything ever published by Bruce McEwen for examples of how a single amino acid substitution predicts differences in behavioral development.
 
Keep in mind that “Bump stock” is not a person. It’s an invention that can be examined in the context of cryo-EM to explain why someone would use reports on the “bump stock” technology to obfuscate the facts about the cryo-EM technology. The facts about cryo-EM and supercoiled DNA can be used to eradicate all virus-driven pathology.
 
For example, the ability to examine virus-driven changes in the transfer of energy in DNA base pairs can be linked to what is known about food energy-dependent RNA-mediated amino acid substitutions in organized genomes. The substitutions typically stabilize the organized genomes of people like Stephen Paddock.
 

See also: Irreversibility and the Arrow of Time in a Quenched Quantum System

Reported as: Physicists confirm thermodynamic irreversibility in a quantum system

“Our experiment shows the irreversible nature of quantum dynamics, but does not pinpoint, experimentally, what causes it at the microscopic level, what determines the onset of the arrow of time,” coauthor Mauro Paternostro at Queen’s University in Belfast, UK, told Phys.org. “Addressing it would clarify the ultimate reason for its emergence.”

For comparison, see: Charles Darwin’s 150-year-old theory of how life on earth emerged gets thumbs-up from scientists

Their ridiculous theories can be placed into the context of Lewis Carrol’s attribution of this thought process to “Humpty Dumpty.”

 

“Emergence” and “evolution” are meaningless terms outside the context of ridiculous theories and pseudoscientific nonsense touted by researchers who are biologically uninformed science idiots. They seem to think that they can put the pieces of biophysically constrained life on Earth back into their theories as if “Humpty Dumpty” exemplified a creature with an evolved shell.

Cryo-EM has helped to pinpoint why the nature of quantum dynamics is irreversible. At the microscopic level of hydrogen-atom transfer in DNA base pairs in solution, the creation of energy as information has been linked to healthy longevity in all living genera. Virus-driven energy theft has been linked from the degradation of messenger RNA to all pathology.

See also: Neuropathology of suicide: recent findings and future directions

“…the unravelling of the unique epigenetic processes that occur in the brain has opened promising avenues in suicide research.”

Reported without citation in the context of: How childhood trauma affects the brain

What led my former FB friends to claim that my life’s works and efforts toward suicide prevention were “bullspit” or that “nobody cared?” The Nobel Prize in Chemistry just validated my model in the context of what is known about cryo-EM.
 

What led researchers who are biologically uninformed science idiots to criticize my model? Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

Who will be the first to apologize for the role they played in the suicide death of Stephen Paddock and the unnecessary suffering and death of his victims?

Moving forward, what role will “apologetics” play in consoling the victims of virus-driven energy theft and all pathology?

See: Celebrate Your Inner Virus 

…we seek to highlight the strengths of what makes a virus on this Virus Appreciation Day.

Answers in Genesis is an apologetics ministry, dedicated to helping Christians defend their faith and proclaim the gospel of Jesus Christ.

Virus appreciation is interesting in the context of claims this group made since 1999.

See: Did God Make Pathogenic Viruses? (1999)

Without viruses, the genetic revolution we are now experiencing would be impossible. They also serve numerous beneficial functions that we are just beginning to research and understand.

Viral Genome Junk Is Bunk (2015)

…mammalian viruses may not have existed at all before the Curse, but after mankind’s sin may have been allowed to develop from DNA sequence already present in the now-fallen people and animals of the earth. Again, cutting-edge genome research confirms the Genesis account of origins.

I agree, but the Genesis account of origins puts the Curse before the creation of viruses, which have been linked from the virus-driven degradation of messenger RNA to mutations and all pathology during the past 5-10,000 years.

See: 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

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.

Stress has different effects on different people.

See for comparison: Epigenetic Regulation of the Kappa Opioid Receptor by Child Abuse

…this receptor may be epigenetically regulated by stressful experiences, in particular as a function of early social life.

See also: Cell stress response sheds light on treating inflammation-related cancer, aging

A Traumatic Experience Can Reshape Your Microbiome

The stress-linked reshaping of  your microbiome has repeatedly been linked from the virus-driven failure of multisensory integration to suicide.

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

Energy-dependent physical and biophysical constraints (7)

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

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

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

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

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

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

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

Cytosis: Biology Content

 

Help Me Write Some Biology Content

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

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

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

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

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

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

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

Details for other serious scientists:

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

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

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

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

See: Combating Evolution to Fight Disease

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

See also: Carl Woese, Evolution’s Golden Revolutionary

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

— Carl Woese and physicist Nigel Goldenfeld

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

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

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

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

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

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

See also:

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

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

— Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors Socioaffective Neuroscience & Psychology 2012


    17 Apr 2014 at 03:07am

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

See also:

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

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

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

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

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

Harvard researchers support young earth creationism

A conserved NAD+ binding pocket that regulates protein-protein interactions during aging March 24, 2017 (Science)
Reported as:

Also reported as:  It’s Happening: Scientists Can Now Reverse DNA Ageing in Mice
Excerpts:

When we’re born, all of our cells have the ability to repair DNA damage, which we experience constantly through random mutations when our cells divide, or whenever we go out in the sun.

But as we get older, our ability to patch up this damage declines, and our cells being to age.

Before we get too excited, we need to keep in mind that many, many studies in mice are not replicated in humans.

So until the results of these early clinical trials in people begin to trickle in, there’s no promise that NMN will help protect human DNA.

DNA repair is energy-dependent and RNA-mediated in the context of the pheromone-controlled physiology of reproduction in all living genera. The physiology of reproduction links food odors and pheromones to the energy-dependent biophysically constrained RNA-mediated cell type differentiation.
See for comparison: Johns Hopkins researchers support mutation-driven evolution.

rp_levels-of-organization.jpg

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!

3/27/17 My comment:

On March 24, 2017 this article was published in ‘Science.’ A conserved NAD+ binding pocket that regulates protein-protein interactions during aging

The article linked virus-driven energy theft from hydrogen-atom transfer in DNA base pairs in solution to all pathology.

On March 24, 2017 this article also was published in ‘Science.’ Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention

The authors failed to link the anti-entropic virucidal energy of sunlight to all biophysically constrained biodiversity via protection of organized genomes manifested in supercoiled DNA.

It seems likely that without “Cytosis,” another generation of biologically uninformed researchers would fail to link top-down causation from quantum physics to all energy-dependent healthy longevity via endogenous RNA interference.

Without “Cytosis” the unnecessary suffering and premature deaths caused by the virus-driven degradation of messenger RNA might never be stopped by serious scientists who known how cell type differentiation occurs.

Are you planning to develop a game about “Photosynthesis” to show others how to link physics and chemistry from molecular epigenetics to all biophysically constrained cell type differentiation via the physiology of reproduction? If so, I could help with some of the more technical aspects.

Physics

Virus-driven energy theft: definition?

The FB group antagonists at “Creationism” complain that I am the only one who uses the term “virus-driven energy theft.” They want a definition, and they demand that I tell them my religious beliefs. Young-earth creationist, or not? It’s one of the “False Flag” FB groups, where impersonators claim to be well-educated experts from different disciplines, who then tout their expertise when they attack creationists at every level including denigration of published works and personal denigration of people’s worth.

The impersonators and antagonists cannot understand why serious scientists do not typically use definitions and assumptions to set forth a case for creationism or an alternative to it,  such as mutation-driven evolution. And, as everyone who understands the concept of the “False Flag” in movies about pirates, the pirates in the Creationism will steal all your energy and claim your intellectual property has always belonged to them.

See for example: Replace the Modern Synthesis (Neo-Darwinism): An Interview With Denis Noble

Excerpt:

[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another….  Assumptions, made but not verified, were taught as fact.

Do I owe the impersonators and antagonists  a definition of “virus-driven energy theft” that they can compare to the definition of evolution and their assumptions. Of course not, but let me explain why. First, virus-driven energy theft is a fact. Cells use energy to reproduce, but viruses must steal that energy to replicate. That fact explains why there are different death rates in archaea compared to bacteria in the oceans and everywhere else.

The bacteria and all other living genera have an innate immune system that links what they eat to the physiology of reproduction via energy transfer. For example, the sun’s biological energy can be used for photosynthesis, but ultraviolet (UV) light is virucidal.

I’ve reported that fact here repeatedly in the context of what is known about UV light and RNA-mediated DNA repair, which exemplifies how quantized energy protects all organism from virus-driven energy theft.

Recently, a report in Science linked virus-driven energy theft to the creation of so called oncohistones.  An oncohistone deranges inhibitory chromatin.

See: Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape

Excerpt:

Missense mutations (that change one amino acid for another) in histone H3 can produce a so-called oncohistone…

They invented the so-called oncohistone because they needed a word to link energy-dependent changes in amino acids from mutations to cancer. RNA-mediated amino acid substitutions link nutrient energy dependent changes from angstroms to ecosystems and healthy longevity in all living genera.

The authors needed a word they could use to link virus-driven energy theft to loss of function histone mutations via the amino acid substitutions that typically differentiate the cell types of all living genera. For example, they linked these four amino acid substitutions to cancer instead of linking virus-driven energy theft from the mutations to the cancer.

1) lysine 27–to–methionine (K27M)
2) glycine 34–to–arginine/valine (G34R/V)
3) glycine 34–to–tryptophan/leucine (G34W/L)
4) lysine 36–to–methionine (K36M)

They invented a word that could be used to link the mutation to cancer without acknowledging the fact that cancer is caused by virus-driven energy theft. Viruses cause the change of one amino acid for another. To prevent virus-driven energy theft, an anti-entropic force must be linked from sunlight to energy-dependent cell type differentiation. They do not want people to learn that energy is the anti-entropic force that prevents cancer. But information about that fact is not hard to find. Neither is the souce of the energy.

For example, see: Food-derived sensory cues modulate longevity via distinct neuroendocrine insulin-like peptides

Excerpt:

The team discovered that the smell or taste of food can directly shorten lifespan by affecting sensory neurons that produce insulin-6, an insulin hormone-like factor. They also showed that insulin-6 from sensory neurons alters the action of FOXO in various tissues. Their findings were published in Genes & Development as the cover article

They then attempted to turn on the function of only a pair of food-sensing sensory neurons by a blue light, a technique called optogenetics, to mimic the taste of food.”

My comment: They linked the speed of light on contact with water from hydrogen atom transfer in DNA base pairs in solution to the de novo creation of G protein-coupled olfactory receptor genes via energy-dependent changes in microRNA flanking sequences which link adhesion proteins from the innate immune system to supecoiled DNA, which protects the organized genomes of all living genera from the virus-driven energy theft that other researchers just linked to the creation of oncohistones and pathology.

Blue light optogenetics links a specific quantized energy level to the de novo creation of genes and virus-driven energy theft links mutations (so-called oncohistones) to all pathology.

In that context virus-driven energy theft would need to be defined as the opposite of what happens when what is known about optogenetics links a specific quantized energy level to the de novo creation of genes. By using words properly in the context of de novo gene creation, the need to define virus-driven energy theft is negligible.  If you don’t understand how a term is used in context,  you will need to invent a word to use out of that context. Mutation was the word that was invented and defined to take everything know about energy-dependent de novo gene creation out of context.

The taste or smell of foods can affect aging Here’s what the report of the article took out of context.
Animals can perceive changes in many environmental factors such as temperature and the taste or smell of foods. This is achieved by specialized nerve cells called sensory neurons. Interestingly, sensory neurons have been known to control the rate of aging in various animals, including the tiny free living roundworm C. elegans.
The impairment of sensory neurons has been known to delay aging by switching on the action of a well-known anti-aging protein called FOXO. FOXO then turns on the gene’s encoding proteins that protect cells and repair damages in various body parts. However, how sensory neurons influence the activity of the anti-aging FOXO proteins in an entire animal has remained a mystery.
Researchers hypothesized that the smell or taste of food acts on sensory neurons, which may produce a type of aging hormone. This aging hormone may be delivered to various body parts and may affect the action of FOXO proteins. The team discovered that the smell or taste of food can directly shorten lifespan by affecting sensory neurons that produce insulin-6, an insulin hormone-like factor. They also showed that insulin-6 from sensory neurons alters the action of FOXO in various tissues. Their findings were published in Genes & Development as the cover article.
They then attempted to turn on the function of only a pair of food-sensing sensory neurons by a blue light, a technique called optogenetics, to mimic the taste of food. Authors discovered that blue light itself can decrease the lifespan of animals through producing insulin-6 hormone that leads to the reduction of FOXO action without food taste or smell.
It has been shown that perception of food increases the level of blood insulin hormone levels in humans. In addition, many biological processes related to aging are similar in C. elegans and mammals which include humans. Therefore, the team concluded that it is unsurprising to find that food smell or taste play similar roles in the aging of mammals via sensory neurons and hormones like insulin.
See also: A Family of non-GPCR Chemosensors Defines an Alternative Logic for Mammalian Olfaction
Excerpt:

Insects and mammals use similar molecular mechanisms to detect light, heat, and several gases, suggesting that solutions to common sensory problems are often conserved (Caterina, 2007; Dhaka et al., 2006; Terakita, 2005).

Conclusion:

Future investigation of the functional role of Ms4a gene families across chordates—and the relevance of interactions between MS4A proteins and ethologically relevant cues like pheromones and fatty acids—will reveal both common and species-specific roles of the MS4As in processing information from the chemical environment.

For a historical record of publications that linked ethologically relevant cues from fatty acids and pheromones to behavior in all invertebrates to all vertebrates, see:
Effects of Carnitine on Fatty-Acid Oxidation by Muscle (1959)
DEPENDENCE OF RNA SYNTHESIS IN ISOLATED THYMUS NUCLEI ON GLYCOLYSIS, OXIDATIVE CARBOHYDRATE CATABOLISM AND A TYPE OF “OXIDATIVE PHOSPHORYLATION” (1964)
Human pheromones: integrating neuroendocrinology and ethology (2001)
Feedback loops link odor and pheromone signaling with reproduction (2005)
The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences (2007)
Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors (2012)
Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013)

See also, today’s OP in an attempt to discuss this on the “Creationism” FB group
human-evolution

Ecological adaptations you cannot live without

Follow up to: Stress-perturbed mitochondrial dysfunction
Summary: Bruce McEwen and others are taking the concept of RNA-mediated amino acid substitutions in cell type differentiation to a new level. They will force neo-Darwinian theorists to differentiate between mutations and amino acid substitutions. After February 14, 2016, if you still don’t know the difference, you may be subjected to ridicule by serious scientists who know how to link atoms to ecosystems in the context of biologically-based cause and effect.
Also, the “Precision Medicine Initiative” links metabolic networks and genetic networks via RNA-mediated amino acid substitutions. Virus-perturbed mitochrondrial energy function cannot be linked from mutations to increasing organismal complexity, and neo-Darwinian theorists appear to have no fall-back position. They seem to have bet everything on de Vries definition of mutation and their assumptions about how long the accumulation of mutations might take to cause the evolution of a new species. If you are in the USA and were not taught to believe in that pseudoscientific nonsense, you will have a nicer Valentine’s Day.
——————————-
Evidence of a genetic ‘fountain of youth’ discovered is the most recent story about biologically-based RNA-mediated cell type differentiation, which is linked to life extension and increased vitality via nutrient energy-dependent RNA-mediated amino-acid substitutions. The coordinating author of the recently published study is a “Professor of Energy Metabolism at ETH Zurich.” Nutrient energy-dependent metabolic networks are linked to genetic networks via RNA-mediated events linked from gene duplication and gene expression to cell type differentiation and ecological speciation via the physiology of reproduction.

Excerpt:

it is helpful to have a basic understanding of how genes are expressed. A measure of gene expression can be found in the number of its mRNA molecules present in an animal’s cells. When the mRNA of a certain gene is widespread, that gene is being upregulated and when it is scarce, the expression of the gene is minimal. Using statistical models, the researchers looked for the intersection of genes that were regulated in the same manner across the different life stages of all three animals. Out of 40,000 genes shared by the organisms, the researchers identified a mere 30 that were significant markers for aging.

The journal article was published as: Branched-chain amino acid catabolism is a conserved regulator of physiological ageing, which is available for free.
My comment: The article shows that branched-chain amino acids (BCAAs) alter a nutrient-dependent neuroendocrine signal, which impacts lifespan via receptor-mediated events. The amino acids clearly link the innate immune system via microRNAs, heat shock proteins, and cell adhesion proteins to the de novo creation of the receptors that protect organized genomes from virus-driven entropy in an experience-dependent cell type non-autonomous manner. Transcription factors control epistatic synergy, which is how the transcription factors modulate physiological aging.
Extended nutrient-dependent healthspan is linked from the pheromone-controlled life history transitions of nematodes across species from microbes to humans via the RNA-mediated amino acid substitutions that differentiate the cell types of all individuals of all species.
Journal article excerpt:

Lastly and consistent with previous findings in rodents, nutritional supplementation of BCAAs extends nematodal lifespan. Taken together, BCAAs act as periphery-derived metabokines that induce a central neuro-endocrine response, culminating in extended healthspan.

Journal article conclusion (with my emphasis):

Since daf-7 is expressed in ASI neurons only30, while its receptors daf-1 and daf-4 act in the periphery49, daf-7/TGFβ may now be considered to act cell-non-autonomous as a neuro-endocrine hormone that impairs lifespan in otherwise healthy animals in response to evolutionary conserved pathways and amino acid signals derived thereof (Fig. 9g).

My comment: The obvious need to link atoms to ecosystems via nutrient energy-dependent life was removed when they placed their experimental evidence into the context of “evolutionary conserved pathways.” Instead of conserved molecular mechanisms, they claim that evolutionary conserved pathways automagically link atoms to ecosystems in the context of population genetics and ridiculous theories based on neo-Darwinian concepts. Neo-Darwinists also link accumulated mutations to the evolution of different species.
De Vries 1904 definition of “mutation” is typically included in articles that clearly link what is known about biophysically constrained RNA-mediated protein folding chemistry to nutrient-dependent amino acid substitutions. The substitutions link the epigenetic landscape to the physical landscape of supercoiled DNA via microRNAs and cell adhesion proteins that stabilize organized genomes in all living genera.
Neo-Darwinists seem unable to grasp the fact that there are obvious differences between mutations, which linked to pathology and amino acid substitutions, which are linked to nutrient-dependent healthy longevity.

See: What is Life?

Excerpt:

We know definitely, today, that Darwin was mistaken in regarding the small, continuous, accidental variations, that are bound to occur even in the most homogeneous population, as the material on which natural selection works. For it has been proved that they are not inherited.

My comment: More than 70 years later, all serious scientists know that the accidental variations, which are still called mutations, contribute to virus-driven genomic entropy. Viruses steal the energy that is required for nutrient-dependent RNA-mediated cell type differentiation in the context of the physiology of reproduction in all living genera. Simply put, viruses are linked to loss of function and the loss of genes. Human life appears to involve the nutrient-dependent de novo creation of at least a few thousand genes that we cannot live without.

The 3230 genes you can’t do without

Excerpt: 

Among all those genes, the researchers found 10 million variants—places within genes that varied from person to person.

My comment: A report about the nutrient-dependent substitution of achiral glycine in position six of the GnRH decapeptide links the substitution from the epigenetic effects of food odors and pheromones on the physiology of reproduction to the stability of vertebrate genomes via metabolic networks, genetic networks, and supercoiled DNA, which probably protects organized genomes from virus-driven entropy.
See:Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor
Excerpt (with my emphasis):

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

My comment: What he calls “coordinated evolutionary selection of amino acids” requires fixation of nutrient-dependent RNA-mediated amino acid substitutions in organized genomes, which occurs only in the context of the physiology of reproduction. It will be interesting to see how many essential genes from the forthcoming report can be placed into the context of this report:  Feedback loops link odor and pheromone signaling with reproduction.
Excerpt:

At least 10,000 neurons in 26 different brain areas appear to transmit signals directly to GnRH neurons.

My comment: Nutrient-dependent pheromone-controlled fixation of RNA-mediated amino acid substitutions must have occurred in many of the neurons that transmit signals directly to GnRH neurons. If fixation had not occurred, the stability of organized vertebrate genomes could not have been achieved.
For comparison, if the 10 million variants in the 10,000 neurons in these 26 different brain areas linked mutations to the development of the human brain, biologically uninformed science idiots could claim that the human brain evolved via a series of mutations in the genes of microbes that also led to the evolution of human morphological and behavioral diversity. However, no information that links biologically-based cause and effect includes experimental evidence that links mutations to the 10 million variants in the 10,000 neurons in these 26 different brain areas. All experimental evidence of biologically-based cause and effect links Schrodinger’s claims from 1944 to non-Darwinian cell evolution. which exemplifies ecological adaptation.
Indeed, the latest articles to report on non-Darwinian cell evolution in cancer tissues, links nutrient-dependent supercoiled DNA to protection from virus-driven genomic entropy and pathology.
Virus-driven pathology: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity
Protection from virus-perturbed protein folding Structural diversity of supercoiled DNA
My comment: Nutrient-dependent microRNAs link supercoiled DNA from mitochondrial function via metabolic networks and genetic networks:
See: Mitochondrial functions modulate neuroendocrine, metabolic, inflammatory, and transcriptional responses to acute psychological stress
Excerpt (with my emphasis):

In mice with WT mitochondria, stress significantly decreased circulating levels for 13 (65%) of the 20 amino acids investigated (Fig. S3).

My comment: The stress is readily linked to the proliferation of viruses. The viruses steal the nutrient energy that is required for DNA repair and biophysically constrained RNA-mediated protein folding chemistry. Perturbed thermodynamic cycles of protein biosynthesis and degradation link the viruses from energy theft to decreased levels of circulating amino acids, which are essential to the stability of organized genomes in all living genera. The microRNA/messenger RNA balance is linked from RNA-mediated protein folding chemistry to supercoiled DNA and protection of organized genomes except when stress alters the molecular mechanisms that are required for DNA repair.
For example, see: MicroRNAs: From Female Fertility, Germ Cells, and Stem Cells to Cancer in Humans
See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
My comment: Despite what is known about the links from branch-chained amino acids to mitochondria-driven metabolic and genetic networks, the fact that a single amino acid substitution is linked to the virulence of viruses via the theft of energy seems to be ignored.
See: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution
Excerpt: The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
My comment: Nutrient-dependent microRNAs are linked to RNA-mediated via DNA repair, which is linked to ecological adaptations that you cannot live without.
 

achiral-glycine

Seemingly futile cycles are not thermodynamically futile

Scientists discover an on/off switch for aging cells

The switch controls the growth of telomeres, the timekeepers of cells

Excerpt: Understanding how this “off” switch can be manipulated–thereby slowing down the telomere shortening process–could lead to treatments for diseases of aging (for example, regenerating vital organs later in life).”
My comment: Seemingly futile thermodynamic cycles of protein biosynthesis and  degradation appear to be confusing. I’m somewhat certain that the folks at Salk realize that cycles of biophysically-constrained nutrient-dependent RNA-mediated protein folding limit how the switches are epigenetically-effected by olfactory/pheromonal input. I’m unsure that what they know is being conveyed to others.
This news report says nothing about how the conserved molecular mechanisms of nutrient-dependent, RNA-mediated, pheromone-controlled cell type differentiation via amino acid substitutions differentiates cell types in species from microbes to man during their life-cycle transitions.See for example:

The journal article is behind a paywall. I have requested it from the corresponding author and may be able to link “Regulated assembly and disassembly of the yeast telomerase quaternary complex” to the thermodynamics of protein structure and function from what they say about “The balance between the assembly and disassembly pathways, which dictate the levels of the active holoenzyme in the cell…” and homeostasis. Obviously, homeostasis is manifested in organism-level thermoregulation.
Hopefully, I can match what is known about biophysical constraints on light-induced amino acid substitutions to nutrient-induced amino acid substitutions in plants and animals via Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins. The rest of the story can then be compared to the ‘Just-So’ stories of evolutionary theorists who left physics and chemistry out of their ridiculous theories based on population genetics.
An open access article places the thermodynamic cycles of protein biosynthesis and degradation into the context of my model.  Thermodynamics with continuous information flow.
See: “FIG. 2. Bipartite examples” They use the terms from biology to link the sun’s biological energy to the de novo creation of light-induced amino acid substitutions and enzymes. They link nutrient-dependent RNA-directed DNA methylation from the enzymes to receptor-mediated cell type behavior.
Excerpt: “Measurement and feedback is performed through a nonautonomous process that simultaneously flips the bits, while switching the energy landscape. By biasing uphill potential flips with a nonequilibrium force (not shown), the particle can be driven preferentially uphill in order to extract work.”
My comment: The “nonequilibrium force (not shown)” is probably the anti-entropic “force” of the sun, which altered the equilibrium of cell from the time of their energy-dependent creation. The “flips”probably are base pair flips, which are linked from differences in hydrogen bond energies to cell type differentiation via amino acid substitutions in my model of nutrient-dependent  ecological adaptations.
Excerpt: “Researchers recently rediscovered a nutrient-dependent epigenetic variant that links vitamin C to what is probably a glucose and glucose dehydrogenase-dependent base pair change. The base pair change results in addition of a methyl group to a cytosine base, which takes on a hydroxyl group to form different 5-hydroxymethylcytosines (5hmCs). Different 5hmCs are associated with differences in cell types that have the same genetic backgrounds. Nutrient-dependent epigenetically-marked bases help to explain how hundreds of cell types in the human body and in the brain (Kriaucionis & Heintz, 2009) are differentiated and how they maintain their glucose-dependent and other nutrient-dependent receptor-mediated identities (Wu et al., 2014).”
Again See: “FIG. 2. Bipartite examples”
Excerpt: “…the enzyme, through a sequence of reactions (purple dotted), speeds up the removal of bound methyl groups M (purple). This feedback loop shifts the enzyme’s stability, so as to maintain it in the same adapted distribution…
My comment: The adapted distribution is nutrient energy-dependent RNA-directed via DNA methylation. Ecological adaptations occur via amino acid substitutions that stabilize RNA-mediated protein folding during thermodynamic cycles of protein biosynthesis and degradation that are RNA-mediated and perturbed by mutations.  These facts link physics from chemistry to the conserved molecular epigenetics of RNA-mediated cell type differentiation in all genera.
Obviously, more physicists should be taught to understand the accurate representations made of biologically-based cause and effect in “Life as physics and chemistry: A system view of biology.” However, most of them seem unwilling to abandon the pseudoscientific nonsense of their ridiculous theories and would rather prevent scientific progress than admit that they didn’t realize that the link to life from the sun’s biological energy was a more important consideration than mutations, natural selection, and evolutionary theory could ever become — even if serious scientists were not Combating Evolution to Fight Disease.