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

From photons to the proton motive force (1)

Conclusion: If you would like to learn how to link quantized energy-dependent changes in atoms to ecosystems in all living genera via the physiology of reproduction, join others age 10+ who will be playing this game in September 2018.
Fly’s Blood-Brain Barrier Has Circadian Rhythms

“the anatomic characteristics of insect and vertebrate BBB structures are quite distinct.”

The molecular mechanisms are conserved.
My comment to The Scientist:

Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990)

The levels of complexity have since been placed into the context of how energy-dependent changes in the microRNA/messenger RNA balance link atoms to ecosystems in all living genera via feedback loops.

For instance, see: Feedback loops link odor and pheromone signaling with reproduction

When theorists fail to start with energy-dependent changes they are forced to use de Vries 1902 definition of mutation in attempts to link the virus-driven theft of quantized energy to evolution. Two forthcoming conferences will place that pseudoscientific nonsense into its proper perspective.

Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses

Schrödinger at 75 – The Future of Biology – September 2018

See also:  Here Comes Single-Cell Optogenetics

.. two-photon excitation with computer-generated holography (a way to precisely sculpt light in 3D) allow light to be focused tightly enough  to hit one cell.

OLYMPUS experiment sheds light on structure of protons

…most of the time, only one of the photons has high energy….

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

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

Researchers who have not linked differences in the energy of photons to the proton motive force are not likely to be among those who are presenting in September: Schrödinger at 75 – The Future of Biology
See for comparison: Subatomic

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, with the ultimate goal of building Elements to score points, but allowing many varying types of strategies.

If you would like to learn how to link quantized energy-dependent changes in atoms to ecosystems in all living genera via the physiology of reproduction, join others age 10+ who will be playing this game in September 2018.

5th-6th Sept 2018 Dublin, Ireland

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

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


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

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

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

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

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

An evolutionary theory killer

Conceptual critique: Innateness vs the death gene (2)

Excerpt: Martie Haselton notes

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

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

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

See for comparison: Subatomic

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

See also: Cytosis: A Cell Biology Board Game

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

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

Martie Haselton notes

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

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

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

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

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

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

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

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

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

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

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection. This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes

An evolutionary theory killer

A reversible TCA cycle in a thermophile

Make no mistake, pseudoscientists have stolen the soul of science for more than 20 years, with their ridiculous claims about mutations and evolution.
For comparison, see:

“…considering that we have just 3 such round Nos ‘100’ ‘1000’ ‘10000’, its just three out of all realistic possibilities, no? Admit its looks cool just bec. we calc in Dec system. History books claims was invented by ancient societies; but I think its evolution: We have 10 fingers!”

My reply (SARCASM ALERT):

Thanks. The correlations are intriguing. Templeton funding might help you prove that the numbers game of evolution is true in the context of Cosmopsychism. With enough correlations, facts that link physics and chemistry to viral latency can be dismissed.

Thanks to the Ralser lab for bringing this to my attention with a claim about:
A reductive TCA cycle in a thermophile, which uses the same citrate synthase [enzyme] both for the oxidative and the reductive directionality.

“Every day it looks more likely that primoridial and modern metabolism look similar”

A link was provided to: A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile

…raises the possibility of a facultatively chemolithomixotrophic origin of life.

Has anyone else considered that possibility?
I tried to look at it from the perspective of chemoorganoheterotrophic metabolism and electron-eating microbes that enzymatically (not automagically) create uranium isotopes, but I got side-tracked by the claims about mutations and evolution. I could not link those claims from the physiology of reproduction in microbes to claims that link the metabolism of food energy to pheromones that biophysically constrain viral latency in species from microbes to humans.

Now, the physiology of pheromone-controlled reproduction in electron-eating microbes that create uranium isotopes suggests the same thing that the Ralser lab suggested: SARCASM ALERT: “It’s turtles all the way down” (the infinite regress problem in cosmology).Unless, like the folks at the Ralser Lab,  you are a serious scientist.

The problem for pseudoscientists, theorists, and many so-called science journalists may be familiar to those at the Ralser lab. McEwen et al., (1964) reported “The synthesis of RNA in isolated thymus nuclei is ATP dependent.” All serious scientists know “ATP controls the crowd.

These findings suggest an additional way for cells to use ATP to maintain proteostasis in the crowded cytoplasm and also fine-tune the material properties of nonmembrane-bound organelles and the cell interior in general.

Obviously, there are now several groups of serious scientists that can make fun of all the pseudoscientists and so-called science journalists who have failed to link physics and chemistry to biophysically constrained viral latency via energy-dependent changes in base pairs in species from thermophiles to those that create uranium isotopes. But Kudos to the first group, or one of the first, to do that:

12/10/14 All about that base and Structural diversity of supercoiled DNA 10/12/15

Sarcasm Alert: I hope that claims about the emergence of energy and mutation-driven evolution did not confuse others as much as they confused so-called science journalists such as John Hewitt, Philip C. Ball, Carl Zimmer, and many others.
When you see the facts reported by an intelligent science journalist, please tell others about the claims that link the creation of energy from the game “Subatomic” to biophysically constrained viral latency in “Cytosis.” Comparisons will be made. It will become clearer that pseudoscientists, theorists and many others have lost their games.
See for example: Attacked from All Sides: RNA Decay in Antiviral Defense

…RNA decay machinery plays important roles in antiviral defense. This can involve either direct effects on vRNA stability or indirect regulation of the intracellular milieu. Furthermore, an emerging theme suggests that many RNA binding proteins can be repurposed from their endogenous roles in the nucleus to antiviral roles in the cytoplasm. Future studies are necessary to further elucidate how these RNA binding…

…proteins recognize foreign RNAs and how they interface with the RNA decay machinery to restrict vRNA replication.”

Alternatively, everyone can simply accept the fact that food energy typically restricts the virus-driven degradation of messenger RNA, and tell all the pseudoscientists and so-called science journalists where to put their pseudoscientific nonsense (e.g., where the sun don’t shine).
For example: Is the Universe a conscious mind?

Cosmopsychism might seem crazy, but it provides a robust explanatory model for how the Universe became fine-tuned for life

For comparison: A Big Bang in spliceosome structural biology and Alternative splicing and the evolution of phenotypic novelty
But remember to link the claims about the evolution of phenotypic novelty to the missing claims about behavior, and see the claims made by Bruce McEwen and Martin Picard in:
Psychological Stress and Mitochondria: A Conceptual Framework (Part 1)

Mitochondria, a subcellular organelle with its own genome, produce the energy required for life and generate signals that enable stress adaptation. An emerging concept proposes that mitochondria sense, integrate, and transduce psychosocial and behavioral factors into cellular and molecular modifications. Mitochondrial signaling might in turn contribute to the biological embedding of psychological states.

Reported as: Cellular ‘powerhouses’ may explain health effects of stress
in the same context as Psychological Stress and Mitochondria: A Systematic Review (Part 2)

Evidence from metabolomic, proteomic, and transcriptomic studies also suggest additional layers of regulation by which stressful experiences may alter mitochondrial components among rodents. Although these metabolites, protein composition, and gene expression outcomes do not reflect the functionality of mitochondria, when assessed in parallel with functional outcomes, they will help explain and refine our understanding of the mechanisms by which stress influences mitochondrial function and health. In addition, whereas functional changes should be regarded as primary indicators of MAL (21), stress-induced molecular changes within mitochondria may also reflect compensatory mechanisms or recalibrations that contribute to long-term changes in mitochondrial function and to the accumulation of MAL. [mitochondrial allostatic load (MAL)]

Review: Subatomic
See also: Self-evident: Contrary to recent opinion, there is such a thing as the self, and it is empirically amenable to scientific investigation 
It has been investigated at every level of investigation that links quantum physics from quantum chemistry to quantum souls in the context of what is known to all serious scientists about biophysically constrained energy-dependent protein folding chemistry that protects supercoiled DNA from the virus-driven degradation of messenger RNA, which links mutations to all pathology.
Conclusion (from self-evident):

The multitudinous self mediates scientific explanations of the complexity of real people with and without mental disorders. It also provides resources for enhancing the moral agency that permits people to flourish. For me, flourishing is simply the development of a person’s psychological and social skills in engagement with herself and with others, in the face of the challenges triggered by her physical, social and psychological environment. If we know the characteristics of the self, we might be able to improve the lives of those whose self-experiences are not conducive to flourishing. The self is not an idle concept, either scientifically or ethically; it organises human experience and proliferates moral possibilities. So, yes, know thyself. Every single part.

See: From Fertilization to Adult Sexual Behavior

Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995).

Make no more mistakes, pseudoscientists have stolen the soul of science for more than 20 years, with their ridiculous claims about mutations and evolution.

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”

 

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.

A null mutation and healthy longevity?

Summary: Food odors and pheromones biophysically constrain all pathology in species from microbes to humans. What kind of biologically uninformed science idiot leaves out everything known to serious scientists about the virus-driven degradation of messenger RNA and tells others they must falsify the neutral null theory that led to claims about a biophysically constrained beneficial “null mutation” in the Amish population of Berne, Indiana?
Glutamylation Regulates Transport, Specializes Function, and Sculpts the Structure of Cilia
Reported as: How to Control Traffic on Cellular Highways

Intracellular and extracellular traffic control

Reported in: How to control traffic on cellular highways http://neurosciencenews.com/enzyme-transportation-7915/

See for comparison: A null mutation in SERPINE1 protects against biological aging in humans
Reported as: Amish gene can make them live 10 years longer and avoid diabetes

A gene variant that arose decades ago in an Amish group…

All gene variants are quantized energy-dependent and the pheromone-controlled physiology of reproduction protects all organized genomes from the virus-driven degradation of messenger RNA. The degradation of messenger RNA links mutations to all pathology. Any claim that “a gene variant arose” is a claim made by a biologically uninformed science idiot. Gene variants in humans are biophysically constrained by the availability of food energy. Other humans may not know that.
Watch and listen to Richard P. Feynman presciently claim that the “null mutation” theory of healthy longevity is an example of “human idiocy.”

Help others to find any experimental evidence that suggests a “null mutation” can be beneficial and/or protect them from biological aging. See for alternative representations of biologically-based facts: Best matches for “null mutation“: and others.
If you cannot find experimental evidence of a beneficial “null mutation” see: Consciousness in the universe: A review of the ‘Orch OR’ theory They inadvertently linked quantum physics from consciousness to quantum souls.
Reported as: Anesthesia Points to Deeper Level ‘Quantum Channels’ as Origins of Consciousness subtitle “Electron resonance pervades the brain”

“Using molecular modeling, the US-Canadian team of Travis Craddock, Stuart Hameroff and Jack Tuszynski had previously shown anesthetic binding in ‘quantum channels’, non-polar arrays of amino acid pi resonance clouds, winding through microtubules.”

See also: The vibrational theory of olfaction for the win

The same kinds of amino acid substitutions that control the separations and interactions of side chains in fluorescent proteins also play an essential role in tuning the proposed mechanism for vibration detection—inelastic electron tunneling. Life literally runs on electron tunneling through the respiratory chain complexes in mitochondria.

For comparison, see the conclusion to: Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2
Beneficial “null mutations” can now be placed into the context of the creation of a universe that — with or without us — is always watching, like Santa Claus.
For a historical perspective on that pseudoscientific nonsense, see:
Splendor and misery of adaptation, or the importance of neutral null for understanding evolution

To claim adaptation, the neutral null has to be falsified.

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.

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis… — Eugene Koonin
What kind of biologically uninformed science idiot leaves out everything known to serious scientists about the virus-driven degradation of messenger RNA and tells others they must falsify the neutral null theory that led to claims about a biophysically constrained beneficial “null mutation” in the Amish population of Berne, Indiana?
Food odors and pheromones biophysically constrain all pathology in species from microbes to humans.
See for comparison: Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain

…specific, volatile, and zoosocial important chemosignals are a promising approach both to modeling posttraumatic stress disorders in humans [36] and to searching for mehods of their treatment.

Humans also have various pheromone-induced physiological effects, especially those associated with reproduction [46, 47]. This suggests that the human olfactory system is still an effective pathway for influencing environmental factors on the human nervous
system.

[46] is Kohl, J.V., Atzmueller, M., Fink, B., and Grammer, K., Human pheromones: integrating neuroendocrinology and ethology, Neuroendocrinol. Lett., 2001, vol. 22, pp. 309–321.
See also: Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems

The assessment of genomes’ integrity plays the key role in the studies of mutagenicity in a polluted environment. We present a step-by-step recommendations for the analysis of the cytogenetic data and discuss the prospects of applying genetic tests for ecological monitoring, based on the example of analysis using crustacean species.

I suspect that the manufacturer of my human pheromone-enhanced fragrance products asked to speak with me next week due to the all-to-obvious link from human pheromones to biophysically constrained viral latency and the prevention of all pathology, which was detailed in the context of the creation of sunlight, which was subsequently linked from the creation of ATP to the creation of RNA.
Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
The last time I spoke with him, he asked how to monetize the facts. Bergdhal’s pathology may have prompted renewed interest. Attempts to discuss that fact with other veterans have failed. I think that some of them would rather see him crucified rather than link the energy-dependent weekend resurrection of the bacterial flagellum in P. fluorescens to the the energy-dependent Resurrection of Christ.
Bergdhal’s pathology can also be placed into the context of the problematic transitions from adolescence to adulthood that are altered by fixation of one energy-dependent RNA-mediated amino acid substitution.
See: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
The A or Met allele is associated with lower enzymatic activity and the polymorphism is associated with many different personality traits. The USAF is leading the way forward towards effective treatment of mental disorders in veterans, which is something the psychiatrists who evaluated Bergdhal know about.  See for instance: US Air Force Studying Impact of Exome Sequencing in Routine Care
 

Light-induced-conformer-intercoversion-of-hydrogen-bond

Open Science: Closed to facts about microRNAs

See my 5-part series on: The tipping point? 50, 000 publications

Imagine how we could accelerate innovation, stimulate economic growth and all the solutions we need to live on a healthy and sustainable planet, if we were to open up our science fully and allow a free flow of scientific knowledge.” says Kamila Markram, a neuroscientist and the CEO of Frontiers, one of the largest Open Access science publishers in the world and a leader in the Open Science movement.

Talk is cheap. See: Understanding and accounting for relational context is critical for social neuroscience
I wrote:

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

Open access publication in Frontiers has not led to any discussion of facts represented since 2005 in articles like this and this one which was co-authored by 2004 Nobel Laureate, Linda Buck. Feedback loops link odor and pheromone signaling with reproduction.
See for comparison, the validation of my model and its importance in the context of integrating disparate disciplines.
George F R Ellis wrote:

“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 [Top-down causation Organized by George F. R. Ellis, Denis Noble and Timothy O’Connor]: http://rsfs.royalsocietypublishing.org/content/2/1.toc ” 25 Apr 2014 at 07:49am

See also, my comment posted to YouTube:

Talk is cheap. I am a medical laboratory scientist whose efforts to use open access publication have not led to any discussion of facts about energy-dependent biophysically constrained RNA-mediated cell type differentiation or facts about how virus-driven energy theft can be linked from the degradation of messenger RNA to mutations and all pathology in all living genera. See: Energy as information and constrained endogenous RNA interference https://www.youtube.com/watch?v=cdtsfweO5SQ

Q: What happened to the facts about energy as information?

See: A different tack for Alzheimer’s research

“Despite observations that link mitochondrial dysfunction and sporadic neurodegenerative disease, there hasn’t been a robust hypothesis that could explain the origin of mitochondrial stress associated with human aging and able to account for neurological disease observed across the entire human population,” Larsen continues. “The ‘Alu neurodegeneration hypothesis’ provides this link. Alus belong to a class of retrotransposons or mobile elements. They get the name ‘jumping gene’ because they can move about the genome and insert themselves into new locations. Alus are found only in primates, and they are abundant in the human genome (approximately 11 percent of human DNA). For a long time, they were considered junk DNA because their function was largely unknown. Only recently has the scientific community begun to appreciate how much Alu elements have influenced human evolution.”

A: The assumption that humans evolved has influenced the interpretation of any facts based on experimental evidence of energy-dependent de novo creation and/or maintenance of organized genomes. The facts have repeatedly showed that supercoiled DNA protects organized genomes from virus driven degradation of messenger RNA and that the degradation of messenger RNA links mutations to all pathology. The facts also links natural selection for energy-dependent codon optimality to the transgenerational epigenetic inheritance of all biophysically constrained biodiversity.

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

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 (Ikemura, 1982; Akashi, 1994; Akashi & Gojobori, 2002; Drummond & Wilke, 2008; Kudla et al, 2009; Novoa & Ribas de Pouplana, 2012). The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

See also: The Excitable Mitochondria by science journalist, John Hewitt.

…the brain’s logical architecture may, in the end, be familiar to us. We do not, after all, have that many models for computation.

Also, there is only one model that links what organisms eat from food energy to the biophysically constrained brain development of humans. 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.

See also: MicroRNA Items: 1 to 20 of 59836

What can be said about researchers who fail to use any model of biophysically constrained biologically-based cause and effect to link energy to supercoiled DNA and virus-driven energy theft to all pathology?

See for example: Mutation-Driven Evolution

Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation.

See also and combination of these search terms for articles that have been published about clear links to energy-dependent increasing organismal complexity and how virus-driven energy theft contributes to all pathology.

microRNA; miRNA; virus; viruses; psychiatric disorders; autism spectrum disorder; biomarkers; genetic variation; expression profiling; animal studies

Location, Location, Location

Since first proposing that a cell’s function and biology depend on its surroundings, Mina Bissell continues to probe the role of the extracellular matrix.

Virus-driven energy theft prevents the typical interactions that link the function of the extracellular matrix to healthy longevity. As predictably occurs at the time of completion for any paradigm shift, Mina Bissell and others like her will claim that they have known about the role of viruses in cell type differentiation for several decades.

Revealing literature gaps. At UCB, Bissell became interested in cell culture techniques and how viral transformation changes metabolism, working with virus-transformed chicken cells to study how glucose metabolism differs from that of normal cells in culture. She began to read the literature on the Warburg effect—the observation that cancer cells produce energy by aerobic glycolysis and lactic acid fermentation rather than through the typical ATP-producing oxidative phosphorylation cycle.

Bissell’s lab again confirmed that transformed cells rely more heavily on aerobic glycolysis for energy, but that the switch to this energy pathway did not result from the impairment of the hydrogen-transfer pathway. The results, says Bissell, went against the other half of Warburg’s hypothesis: that the reason for the increased glycolysis is impaired hydrogen transfer.

Her lab could not have confirmed anything associated with Warburg’s hypothesis (in 1976). The differences in the energy of photons had not yet been linked from hydrogen-atom transfer in DNA base pairs in solution to the biophysically constrained physiology of reproduction and all biodiversity via changes in base pairs and fixation of amino acid substitutions in supercoiled DNA that protect all organized genomes from virus-driven energy theft and genomic entropy. Since then, the Nobel Prize-winning works of Thomas Hunt Morgan (1933 Physiology or Medicine) and Schrodinger/Dirac (1933 Physics) have linked changes in atomic energy from chirality (Ben Feringa, Chemistry 2016) to autophagy (Yoshinori Ohsumi, 2016 Physiology or Medicine and chromosomal inheritance via the pheromone-controlled physiology of nutrient energy-dependent reproduction in species from microbes to humans.

According to Bissell’s ‘dynamic reciprocity’ model, signals from the ECM traveled through transmembrane receptors to a cell’s interior and nucleus, altering its gene expression.

According to my model of biophysically constrained biologically-based cause and effect Bissell’s ‘dynamic reciprocity’ model fits into the context of neo-Darwinian pseudoscientific nonsense instead of into the context of established facts.

See: Feedback loops link odor and pheromone signaling with reproduction

See for comparison:

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.