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.

An evolutionary theory killer

How to create biologically uninformed theorists

Summary: On March 2, 2018, Philip C. Ball and Nick Lane started making claims about proton gradients. Their claims are based on my model of quantized energy as information. This post includes added support for what is known to all serious scientists about the light-activated endogenous substrates that link molecular epigenetics to RNA-mediated autophagy.
See first: Energy as information and constrained endogenous RNA interference (audio/visual aid 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.

Added support for the light-activated molecular epigenetics of autophagy:
Light-powering Escherichia coli with proteorhodopsin (2007)

…we quantify the coupling between light-driven and respiratory proton currents… and show that light-driven pumping by PR can fully replace respiration as a cellular energy source in some environmental conditions.

Structure of the Deactive State of Mammalian Respiratory Complex I (2018)

…the deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding to the NADH-reduced enzyme templates their reordering. Our structure both rationalizes biochemical data on the deactive state and offers new insights into its physiological and cellular roles.

Global collective motions in the mammalian and bacterial respiratory complex I (2018)

…we identify here transitions between experimentally resolved structures of the mammalian complex I as low-frequency collective motions of the enzyme, highlighting similarities and differences between the bacterial and mammalian enzymes. Despite the reduced complexity of the smaller bacterial enzyme, our results suggest that the global dynamics of complex I is overall conserved.

The conservation of light-powered functional structures and energy-dependent proton gradients link the deactive state in critical structures to the active state via the creation of enzymes in species from bacteria to mammals. The energy-dependent creation of the enzymes links metabolism of the energy (e.g., food energy) from pheromones to biophysically constrained viral latency in the context of the physiology of reproduction.
The pheromone-controlled physiology of reproduction in species from microbes to humans links our visual perception of energy and mass in the context of how ecological variation must be linked to energy-dependent ecological adaptations in all living genera.
See: Olfaction Warps Visual Time Perception

Our perception of the world builds upon dynamic inputs from multiple senses with different temporal resolutions, and is threaded with the passing of subjective time. How time is extracted from multisensory inputs is scantly known. Utilizing psychophysical testing and electroencephalography, we show in healthy human adults that odors modulate object visibility around critical flicker-fusion frequency (CFF)-the limit at which chromatic flickers become perceived as a stable color-and effectively alter CFF in a congruency-based manner, despite that they afford no clear environmental temporal information. The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.

See also: Odors Alter Subjective Time Experience Author: Dr. ZHOU Wen’s Research Group Update time: 2017/05/15

The brain is not a timepiece. Whereas it is equipped with senses like vision, audition, touch, smell, and taste, it has no direct access to or measure of the physical time (unless you read from a clock). Rather, it constructs the subjective “time” of an event from the dynamic multisensory inputs associated with that event. Yet different senses come with different temporal precisions. For instance, when standing near an apple tree, you can detect the falling of an apple much better with your eyes or ears than the nose. How does the brain coordinate multisensory signals entering different brain regions with different temporal resolutions, and come up with the subjective time?

A team at the Institute of Psychology at Chinese Academy of Sciences tackled this issue using odors and images. Specifically, Dr. Bin Zhou, the study’s lead author, and his colleagues examined whether odors could modulate one’s temporal sampling and subjective duration of visual objects. In their study, participants viewed two series of flickering isoluminant images in red and green (Figure 1A). One of the series contained opposite images of an apple or bananas; the other contained only images of red and green fields. When the images alternated at a frequency beyond 20 Hz, the participants started to have difficulty reporting which series contained an object. Indeed, for most people, chromatic flicker fusion frequency (CFF), the limit at which alternating colors become perceived as a stable fused color, falls somewhere between 20 and 25 Hz. Interestingly, the participants’ object detection accuracies around CFF were improved under the exposure of a congruent, as opposed to an incongruent, odor. In other words, the participants detected a rapidly flickering apple better when they smelled an apple odor rather than a banana odor, and vice versa (Figure 1B, left panel). In effect, the presence of a congruent odor facilitated the brain’s temporal sampling of a visual object and elevated its CFF (Figure 1B, right panel). Based on electrical activities recorded from the participants’ scalp, the researchers found that the integration between smell and vision strengthened the signals of the corresponding object in a brain region heavily implicated in object representations called the right temporal cortex, about 150-300 ms after object onset. They further showed that such integration lengthened one’s subjective duration of the corresponding object in a duration comparison task. The researchers concluded that subjective time is warped by the neural energy involved in representing multisensory inputs at subsecond scales.

Until Philip C. Ball mentioned that Nick Lane believed proton gradients came before the energy-dependent creation of RNA, I did not realize how little they knew about this link from differences in the energy of photons to consciousness.
See: What Affective Neuroscience Means for Science Of Consciousness (2013)

The coupling of the two circuits promotes an endogenous feedback that supports conscious processes. Within this framework, we present the defence that detailed study of both affective and cognitive processes, their interactions, as well of their respective brain networks, is necessary for a science of consciousness.

The coupling of the two circuits links differences in the energy of photons from the proton motive force to the light-activated endogenous feedback loops and Feedback loops link odor and pheromone signaling with reproduction.
It is extremely difficult for intelligent people to not link this experimental evidence to biophysically constrained viral latency in the context of reports that claim “Creatures’ Adaptability Begins with Their Sensors.”
But, see for comparison: David Attenborough on creationsim May, 2015

My comment on his nonsense: First steps to neutralizing Zika: How highly potent antibody neutralizes Zika infection discovered

This is framed within the context of energy-dependent changes in pH, which facilitate receptor-mediated entry of nutrients or viruses into specific cell types of species-specific tissues via stress-linked changes in hydrogen-atom transfer in DNA base pairs.

Virus-driven energy theft has been linked to all pathology in all living genera via the conserved molecular mechanisms of RNA-mediated polycombic protein folding chemistry compared to the hecatombic evolution of pathology manifested first in the differences between archaea and bacteria. Admitting that Carl Woese was wrong about the different domains of life is the first step towards understanding the difference between healthy longevity and the evolution of all virus-driven pathology.

Carl Woese was wrong

God did not create the viruses. He created the anti-entropic virucidal energy of sunlight, which protects all organized genomes from virus-driven entropy. Only the choices of our ancestors could have led to the increasing amout of virus-driven pathology during the past ~6000 years that pseudoscientists place into the context of millions of years of evolution. Then, they blame God, like these two pseudoscientists do. Darwin knew they would do that, which is why he insisted that others put conditions of life before natural selection. But they bastardized his theory anyway and taught their revision to anyone who was foolish enough to believe in it. It’s called the “Modern Synthesis” and was based on de Vries 1902 definition of “mutation.”

Celebrate Your Inner Virus

It is important that we understand the design present in viruses because God made them.

It is no wonder that Sir David Attenborough and many others like Philip C. Ball and Nick Lane are confused about the energy-dependent creation of healthy longevity and consciousness. Even some young earth creationists have failed to link the creation of the sun’s anti-entropic virucidal energy from changes in electrons to ecosystems via the proton motive force. That leaves every aspect of creation to be placed back into the context of ridiculous theories. The theories start with the virus-driven theft of quantized energy as information. The energy theft links mutations to all virus-driven pathology. The theft of quantized energy as information cannot be linked by serious scientists from beneficial mutations to the evolution of one species from another.
For comparison, pseudoscientists have no problem touting this confusing nonsense:
Sign of selection on mutation rate modifiers depends on population size (
1)  Genetic variation—the raw material for evolution—is ultimately generated by mutation.
2). …beneficial alleles never become deleterious and deleterious alleles never become beneficial.
Conclusion:

Whether these phenomena can be united in a single theoretical framework remains an open question that we are actively exploring. In any case, our results add to a growing appreciation of nonclassical population size dependence in evolution by natural selection (41, 42).

Funding for research that attempts to link natural selection to evolution via mutation-driven genetic variation should be used to link food odors and pheromones from the physiology of reproduction to biophysically constrained viral latency and ecological adaptations. It is time to stop creating more biologically uninformed theorists.

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

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.

 

5th-6th Sept 2018 Dublin, Ireland

Diet-driven RNA interference and mental health (3)

Discover’s “My Science Shop” now advertises the games that led to development of the cell biology game: “Cystosis,” which is a neo-Darwinian evolutionary theory-killer. Cytosis links the creation of anti-entropic viruidal light to all biodiversity on Earth via the physiology of reproduction and biophysically constrained viral latency.

See the dumbed-down version of that fact: Missing Mutations Suggest a Reason for Sex

Summary: A good model with a good model organism predicts. The mouse-to-human model of biophysically constrained viral latency 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 for example: A Conserved MicroRNA Regulatory Circuit Is Differentially Controlled during Limb/Appendage Regeneration

…we employ next-generation sequencing to identify shared, differentially regulated mRNAs and noncoding RNAs in three different, highly regenerative animal systems: zebrafish caudal fins, bichir pectoral fins and axolotl forelimbs.

See for comparison: Mutation, Not Natural Selection, Drives Evolution also reported as: We are all mutants (March 2014)

In 1972, he devised a now widely used formula, Nei’s standard genetic distance, which compares key genes of different populations to estimate how long ago the groups diverged. In the early ’90s, Nei was a co-developer of free software that creates evolutionary trees based on genetic data. Two decades later, Molecular Evolutionary Genetics Analysis, or MEGA, remains one of the most widely used and cited computer programs in biology.

But it’s his natural selection-busting theory, which Nei developed in the ’80s and expanded on in the 2013 book Mutation-Driven Evolution, that the researcher wants to see embraced, cited and taught in schools.

That’s not going to happen except in the context of teaching students the difference between a ridiculous theory and facts about ecology!
See: Israeli Middle Schools School to Include Theory of Evolution

…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.

See also: Asymmetric Auxin Distribution is Not Required to Establish Root Phototropism in Arabidopsis

…we conclude from our current data that the phototropic response in Arabidopsis roots is induced by an unknown mechanism…

No intelligent person on Earth is going to teach students that any phototropic response is induced by an unknown mechanism.
See for comparison: Overexpression of microRNA408 enhances photosynthesis, growth, and seed yield in diverse plants and Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis
Instead, students who are 10 years old or older will learn cell biology in the context of accurate representations of how what organisms eat biophysically constrains viral latency in the context of the physiology of reproduction. Students who learn to play the games that led to the development of the game “Cytosis” can start with the creation of microRNAs in plants and link the creation of sunlight to all biodiversity via the physiology of reproduction in plants and animals.
They will learn that embracing a ridiculous theory of mutation-driven evolution led to acceptance of  evolutionary trees based on mathematical models of genetic data. They will learn how biophysically constrained top-down causation links RNA-mediated fixation of amino acid substitutions to all cell type differentiation in all living genera via what is known to serious scientists about sensing and signaling in the context of quantitative proteomics.
Ras/ERK-signalling promotes tRNA synthesis and growth via the RNA polymerase III repressor Maf1 in Drosophila

These findings suggest that stimulation of tRNA synthesis may be one way that Ras promotes mRNA translation to drive cell and tissue growth.

The light induced stimulation of tRNA synthesis links sensing and signaling from energy-dependent protein biosynthesis and degradation in the context of microRNA-mediated switches that are “flipped” by the availabilty of nutrients, water, and oxygen. Oxidative phosphorylation is required to link the switches to the energy-dependent stability of supercoiled DNA, which protects all organized genomes from the virus-driven degradation of messenger RNA.

See: Quantitative proteomics identifies redox switches for global translation modulation by mitochondrially produced reactive oxygen species (open access)

Reported as: Nano-switches in the cell: A team with researchers has discovered a new mechanism for the regulation of protein synthesis.

..increased levels of reactive oxygen species inhibit protein synthesis. Using biochemical and cell biological methods, she showed that damaged mitochondria can signal their metabolic state to the protein synthesis machinery via reactive oxygen species and, thereby, slow down cellular protein synthesis. It is assumed that the temporary reduction of the protein synthesis rate under oxidative stress has a positive effect on the survival of the cells as it is believed to help to restore cellular homeostasis. This also prevents the cell from synthesizing proteins that cannot be taken up by damaged mitochondria, which, as a consequence, accumulate in the cytoplasm and thus need to be degraded.

Anyone who knows anything about energy-dependent microRNA-mediated autophagy will recognize the ridiculous representation and claim about the discovery of a new mechanism for the regulation of protein synthesis. The creation of the sun’s anti-entropic virucidal energy links the creation of ATP to the creation of enzymes and microRNAs. The microRNAs regulate protein biosynthesis and degradation. There is nothing new about that. Yoshinora Ohsumi won the 2016 Nobel Prize in Physiology and Medicine for details about autophagy in the context of a published work from 1998.
He was the senior author of A protein conjugation system essential for autophagy

This conjugation can be reconstituted in vitro and depends on ATP. To our knowledge, this is the first report of a protein unrelated to ubiquitin that uses a ubiquitination-like conjugation system. Furthermore, Apg5 and Apg12 have mammalian homologues, suggesting that this new modification system is conserved from yeast to mammalian cells.

The modification system is ATP-dependent and microRNA-mediated.
See: The tipping point (revisited): 68,000 publications
See also: The tipping point (revisited): 69,000 publications
For updates, see: MicroRNA at PubMed
Moving forward, it is time to link the creation of microRNAs from fixation of RNA-mediated amino acid substitutions to mental health.
See: Diet-driven RNA interference and mental health (4)

5th-6th Sept 2018 Dublin, Ireland

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

Summary: Theorists and most science journalists have failed to link the anti-entropic energy of sunlight from physical constraints on the creation of new galaxies to the biophysical constraints of ultraviolet light on viral latency. Viral latency prevents mutation-driven evolution in the context of the energy-dependent creation of ATP, microRNAs, RNA and established links from base editing to microRNA editing and RNA editing. Every aspect of energy-dependent editing links alternative splicings of pre-mRNA (microRNAs) from light-activated endogenous substrates to the pheromone-controlled physiology of reproduction. Feedback loops link food odors and pheromones to all biodiversity via what has been known or suspected about biophysically constrained feedback for more than 50 years.
A whirling plane of satellite galaxies around Centaurus A challenges cold dark matter cosmology Feb 2, 2018
Reported as:

This is inconsistent with more than 99% of comparable galaxies in simulations. Centaurus A, the Milky Way, and Andromeda all have highly statistically unlikely satellite systems. This observational evidence suggests that something is wrong with standard cosmological simulations.Science, this issue p. 534; see also p. 520

See also: Synchronized Galactic Orbit Challenges Our Best Theory of How the Universe Works Feb 1, 2018
Thanks to Dan Winter for his comment.

“… kind of funny when they fail to recognize a simple picture of phase conjugate (opposing cones) doing ‘4 wave mixing’ – which is how gravity is stabilized- AND emerges into self organization (negentropy)-those who are basically clueless to why objects fall to the ground- have no hope of understanding that the phase conjugate cause of gravity- (www.fractalfield.com/conjugategravity ) is ITSELF the path out of the entropy (belief in inevitable chaos) those fatalists try to infect us with…”

See also: A measurement of the z = 0 UV background from Hα fluorescence

This value is consistent with transmission statistics of the Lyα forest and with recent models of a UVB that is dominated by quasars.

Reported as: Universe’s ultraviolet background could provide clues about missing galaxies

Simulations show that there should be more small galaxies in the Universe, but UV radiation essentially stopped them from developing by depriving them of the gas they need to form stars.

Theorists and most science journalists have failed to link the anti-entropic energy of sunlight from physical constraints on the creation of new galaxies to the biophysical constraints of ultraviolet light on viral latency. Viral latency prevents mutation-driven evolution in the context of the energy-dependent creation of ATP, microRNAs, RNA and established links from base editing to microRNA editing and RNA editing. Every aspect of energy-dependent editing links alternative splicings of pre-mRNA (microRNAs) from light-activated endogenous substrates to the pheromone-controlled physiology of reproduction. Feedback loops link food odors and pheromones to all biodiversity via what has been known or suspected about biophysically constrained feedback for more than 50 years.
Serious scientists are beginning to wonder when pseudoscientists and all science journalists will report findings in the context of top-down causation and energy-dependent constraints. Thankfully, we are about to see constraints placed on the amount of pseudoscientific nonsense reported.
See for examples: 
Co-author, John E. Walker is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018
Structure of the mitochondrial ATP synthase from Pichia angusta determined by electron cryo-microscopy

Living cells need fuel in the form of adenosine triphosphate, or ATP, to stay alive. This fuel is generated by a molecular machine made of two motors joined by a rotor. One generates rotation by using energy provided by oxidative metabolism or photosynthesis; the other uses energy transmitted by the rotor to make ATP molecules from its building blocks, adenosine diphosphate, or ADP, and inorganic phosphate. The structure has been determined of a fungal machine, isolated from its cellular power stations, the mitochondria, where the machine operates. It provides unsuspected details of the blueprint of the machine and how it works. The working principles of the fungal machine apply to similar machines in all species.

Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase

Mitochondria generate the cellular fuel ATP to sustain complex life. 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). Disruption of the IMM, dissipation of the pmf, and cell death occur if the concentration of calcium ions inside mitochondria is sufficiently elevated to open a pore in the IMM. The identity of the pore is disputed. One proposal is that the pore is in the enzyme that makes ATP. Here, we show that proteins in the enzyme’s peripheral stalk are not involved in the formation or regulation of the pore.

Co-author, Susumu Tonegawa is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018

Tagging activated neurons with light

Two new protein tools translate neuronal activity into gene expression during a light-defined time window.

Co-author,Ada E. Yonath is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus

…we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.

Co-author, John O’Keefe is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018

The honeycomb maze provides a novel test to study hippocampal-dependent spatial navigation

Rats learn rapidly and their choices are influenced by three factors: the angle between the two choice platforms, the distance from the goal, and the angle between the correct platform and the direction of the goal. Rats with hippocampal damage are impaired in learning and their performance is affected by all three factors.

Co-author, Linda Buck is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018
Feedback loops link odor and pheromone signaling with reproduction

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

The levels of complexity include everything known to serious scientists about energy-dependent niche construction and changes in the fixation of RNA-mediated amino acid substitutions that differentiate the cell types of all individuals of all species.
See for example: Hypothalamic microRNAs flip the switch for fertility (2017); The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression (2014); and the section on molecular epigenetics from our 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior

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

See for contrasting ignorance:Universal Alternative Splicing of Noncoding Exons (2018)

We propose that noncoding exons are functionally modular, with alternative splicing generating an enormous repertoire of potential regulatory RNAs and a rich transcriptional reservoir for gene evolution.

See also: (Co-author, Linda Partridge is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018)
Drosophila as a model for ageing

Drosophila melanogaster has been a key model in developing our current understanding of the molecular mechanisms of ageing. Of particular note is its role in establishing the evolutionary conservation of reduced insulin and IGF-1-like signaling in promoting healthy ageing.

Sense and antisense RNA are not toxic in Drosophila models of C9orf72-associated ALS/FTD

We confirmed that these RNA foci are capable of sequestering endogenous Drosophila RNA-binding proteins, and that the production of dipeptide proteins (poly-glycine-proline, and poly-glycine-arginine) is suppressed in our models. We find that neither cytoplasmic nor nuclear sense or antisense RNA are toxic when expressed in adult Drosophila neurons, suggesting they have a limited role in disease pathogenesis.

Schrödinger (1944) “What is LIfe?”  placed energy-dependent biophysical constraints on viral latency into the context of light-activated endogenous substrates and ecological adaptations via the physiology of reproduction in species from soil microbes to humans.

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

See for comparison: Mutation-Driven Evolution (2013) and my refutation of that pseudoscientific nonsense in Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which was published on the same day.
See also for a brief video review: “What is life when it is not protected from virus driven entropy”

 

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

From base editing to RNA editing

Base Editing Now Able to Convert Adenine-Thymine to Guanine-Cytosine

“Nature conveniently provides us with cytosine deaminase enzymes that operate on DNA,” Liu tells The Scientist.

The creation of quantized energy in sunlight links energy as information from electrons to ecosystems via the physiology of reproduction in all living genera. The claim that “Nature” provides us with cytosine deaminase enzymes makes it seem that the enzymes emerged and automagically evolved to become purposeful and meaningful in the context of ridiculous theories about mutation-driven evolution.
See for comparison: All about that base (video parody)
See also: RNA Editing Possible with CRISPR-Cas13

Introducing specific sequence changes into RNA molecules could allow researchers to answer questions about alternative splicing mechanisms, translation, and even editing, he says. “There’s a lot of scope.”

The entirety of that scope was addressed in the context of energy-dependent RNA-mediated cell type differentiation in our section on molecular epigenetics from this 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior
Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.
All biophysically constrained RNA-mediated energy-dependent cell type differentiation has since been linked from the pheromone-controlled physiology of reproduction to supercoiled DNA via the fixation of amino acid substitutions and chromosomal rearrangements.
The facts about the amino acid substitutions in the context of transgenerational epigenetic inheritance link electrons to ecosystems via the cryo-EM technology that won the 2017 Nobel Prize in Chemistry.
See: Chemists know (video parody)
See also:

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

Cytosis

Loss of energy as information (1)

Summary: Koonin claims that the theories of population geneticists have replaced what he calls the just-so stories of adaptationists with testable predictions. He claims that serious scientists should attempt to falsify the ridiculous theories touted by people like him, so that the ongoing use of ridiculous mathematical models can improve our understanding of evolution.
I think Koonin may be attempting to address the concerns brought forward after another biologically uninformed science idiot claimed that my refutation of neo-Darwinian pseudoscientific nonsense was “…an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research.”
See for comparison: In modern discourse, …[Bonini’s] paradox was articulated by John M. Dutton and William H. Starbuck[2]

“As a model of a complex system becomes more complete, it becomes less understandable. Alternatively, as a model grows more realistic, it also becomes just as difficult to understand as the real-world processes it represents” (Computer Simulation of Human Behaviour, 1971).

The difficulty of understanding “real-world” processes has since been placed into the context of:  Building Blocks of Life May Have Formed in Water Droplets
From the journal article: Abiotic production of sugar phosphates and uridine ribonucleoside in aqueous microdroplets

…we show that sugar phosphates and a ribonucleoside form spontaneously in microdroplets, without enzymes or an external energy source.

My comment to The Scientist:

Something seems to be missing from what others may believe about the anti-entropic virucidal energy-dependent creation of life.

See for instance: 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.

That suggests there is no such thing as “abiotic production.” It is more likely that Schrodinger (1944) was correct:

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

See also: Olfaction Warps Visual Time Perception

The authors linked the quantized energy-dependent creation of the sense of smell in bacteria from the physiology of pheromone-controlled reproduction to all biophysically constrained biodiversity in the context of the space-time continuum and our visual perception of energy and mass.

See also: October 18, 2017 Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths
Excerpt:

…our results unequivocally show that duplication of protein segments happens both above and below the domain level among amino acid segments of diverse lengths. Indeed, we show that significant evolutionary information is lost when the protein is approached as a string of domains.

Duplication of protein segments is energy-dependent.
Concluding sentence:

“…the principles presented here and the computational pipeline could facilitate the detection of such peptides. Relating themes to biological functions, such as binding of ligands, nucleic acids, and proteins, may also facilitate this effort, offering a perspective on the evolution of protein function.”

Protein function is energy-dependent. No experimental evidence of biophysically constrained biologically-based cause and effect suggests that protein function “evolved” outside the context of what is known about the sun’s energy. The detection of all energy-dependent links from electrons to ecosystems via peptides has shown that the functional structure of supercoiled DNA is RNA-mediated and biophysically constrained by the physiology of pheromone-controlled reproduction.

The physiology of pheromone-controlled reproduction biophysically constrains the virus-driven degradation of messenger RNA that serious scientists have linked from mutations to all pathology.

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

For a perspective on the coevolution of protein function and speciation during the past 6000 years, see: Genome divergence and diversification within a geographic mosaic of coevolution
 
Our results further characterize a striking example of coevolution driving speciation within perhaps as little as 6000 years.
 

Did coevolution (aka ecological adaptation, aka evolutionary adaptation) drive all speciation during the past 6000 years? If so, what drove adaptive evolution?

See: January 10, 2013 Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

We estimate that approximately 73% of all protein-coding SNVs and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000–10,000 years. The average age of deleterious SNVs varied significantly across molecular pathways, and disease genes contained a significantly higher proportion of recently arisen deleterious SNVs than other genes.

If protein function “evolved,” what limited the number of deleterious mutations that arose in the past 5,000–10,000 years?

For the most likely answer, see: Base-pair opening dynamics of the microRNA precursor pri-miR156a affect temperature-responsive flowering in Arabidopsis

If the base-pair openings and closings of dynamic microRNA precursor pri-miR156a processing can be linked to all energy-dependent healthy longevity during the past 6,000 years via the physiology of reproduction in plants, will cryo-EM imaging reveal the overwhelming amount of pseudoscientific nonsense touted by neo-Darwinian theorists and other biologically uninformed science idiots?

See also: Cryo-EM imaging suggests how the double helix separates during replication

Replication is food energy-dependent, and current technology now attests to the comment Richard Feynman made about “human idiocy.”

INFORM YOURSELF

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

Cryo-EM: More than a suggestion

 
Details in the structure not previously seen reveal how various protein subunits of the twin hexamers latch on to the double helix, via tiny loop-like structures.

What are the subunits of protein?

The subunits of proteins are called amino acids.

I will not stop saying that cryo-EM links what is known about energy-dependent changes in the microRNA/messenger RNA balance from electrons to ecosystems via fixation of amino acid substitutions in the context of the pheromone-controlled physiology of reproduction, which has been linked to all biophysically constrained viral latency and all biodiversity.

 

And, obviously, serious scientists are not going to stop confirming that fact.

See: Noguchi Y et al, “Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model” appears in Proceedings of the National Academy of Sciences the week of October 23, 2017.

See also:

RNA-mediated molecular epigenetics and virus-driven entropy

The Origin of Information (2)

RNA mediated molecular epigenetics and virus driven entropy (video)

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

Proteins "evolve" (revisited)

Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths

Reported by Jay R. Feierman to the evolutionary psychology Yahoo Group as: Recycling at the molecular level: Protein evolution

Reuse patterns in protein space reflect 3.7 billion y of evolution (58), restrained by the underlying physicochemical qualities of covalently linked amino acids.

Autophagy links chirality from energy-dependent changes in electrons to ecosystems. For comparison, their claim is consistent with ridiculous misrepresentations of food energy-dependent biophysically constrained pheromone-controlled RNA-mediated amino acid substitutions and cell type differentiation. The truth about energy-dependent cell type differentiation is missing from this claim from Jordan et al., (2005) 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.

But wait, what happened to the claims about restraints by the underlying physicochemical qualities of covalently linked amino acids? Covalent bonds are energy-dependent. If you accept the claim that proteins “evolve,” you will probably accept whatever pseudoscientific nonsense is touted by any theorist. If you are a serious scientist, you already know that the physicochemical qualities of covalently linked amino acids have been detailed in the context of links from energy-dependent changes in electrons to ecosystems via the 2017 Nobel Prize winning technology referred to as cryo-EM.

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

Figure 6 “Codon optimality code” in vertebrates provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

“The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes…”

Simply put, natural selection for energy-dependent codon optimality links RNA-mediated amino acid substitutions in organized genomes from the physiology of reproduction to biophysically constrained viral latency via protein folding chemisty. That fact has never been addressed by neo-Darwinian theorists and probably never will be.

The fact that proteins have an energy-dependent atomic structure may never have occurred to an evolutionary theorist. If it had, a “Big Bang” cosmologist may have told the evolutionary theorist that the energy “emerged” from nothing, and that fact seems to be acceptable to all theorists.

See for comparison: Subatomic

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 enabling players to pay energy to shuffle through their deck quicker, or to offset the cost of more powerful deck building cards.

If you do not ask where the protons, neutrons and electrons come from, you can link atoms to ecosystems in all living genera outside the context of the energy[-dependent pheromone-controlled physiology of reproduction and RNA-mediated cell type differentiation.

See also: Atomic structure reveals how cells translate environmental signals

Translation is energy-dependent and the pheromone-controlled physiology of reproduction biophysically constrains virus-driven energy theft.