Can protein folding chemistry be understood by theorists?

Excerpt: The researchers believe their discovery dovetails with their research on how tumor viruses and cancer mutations change a cell’s DNA structure and organization to cause uncontrolled cell growth.
Aye group discovers avenue for precision cancer treatment

One challenge is that multiple variations, or isoforms, of the same protein can all catalyze the same cellular function, “but the nuances of biology rest in how individual isoforms are regulated,” Aye said.

Natural selection for energy-dependent codon optimality regulates the creation of isoforms and all biodiversity via links from RNA-mediated amino acid substitutions in supercoiled DNA to chromosomal inheritance.

Protein folding: Much more intricate than we thought

All protein folding chemistry is energy-dependent and RNA-mediated. It must link chirality to autophagy and the physiology of pheromone-controlled reproduction or it cannot link quantum physics to quantum souls via what organisms eat in the context of niche construction.
See also: New Imaging Technique Overturns Longstanding Textbook Model of DNA Folding

The researchers believe their discovery dovetails with their research on how tumor viruses and cancer mutations change a cell’s DNA structure and organization to cause uncontrolled cell growth.

Energy-dependent protein folding chemistry is no more intricate than it was when we detailed everything known about RNA-mediated cell type differentiation in this 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior

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

THIS MODEL DETAILS HOW CHEMICAL ECOLOGY DRIVES ADAPTIVE EVOLUTION VIA: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction.

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

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction.

See also: Olfaction Warps Visual Time Perception

See for comparison: What the ctenophore says about the evolution of intelligence

The ctenophore was already known for having a relatively advanced nervous system; but these first experiments by Moroz showed that its nerves were constructed from a different set of molecular building blocks – different from any other animal – using ‘a different chemical language’, says Moroz: these animals are ‘aliens of the sea’.

Moroz tries and fails to recover from decades of touting the pseudoscientific nonsense of neo-Darwinian evolution.  See: Independent origins of neurons and synapses: insights from ctenophores

The possibility of secondary loss of neurons and synapses in the Porifera/Placozoa clades is a highly unlikely and less parsimonious scenario.

The virus-driven degradation of messenger RNA has been linked to the secondary loss of G protein-coupled receptors that link multisensory input from the sense of smell in bacteria to our visual perception of mass and energy in the context of the space-time continuum.
See also: Viral Genome Junk Is Bunk

So, where do viruses come from that essentially share the same sequences as those found in their host genomes? Perhaps the evolutionists have placed the cart before the horse on this issue, as proposed by several creationist scientists.4,6 In fact, in an ironic twist, the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6

The possibility that the virus-driven degradation of messenger RNA causes the secondary loss of neurons and synapses in the Porifera/Placozoa clades is the most likely and most parsimonious scenario. Neo-Darwinian theorists and others who have failed to link the sun’s anti-entropic virucidal energy to the biophysically constrained physiology of reproduction and all biodiversity via the chemistry of protein folding are forced to continue to ignore all experimental evidence of biologically-based cause and effect. Their only alternative is to invent new terms for “microRNA,” since energy-dependent changes in the microRNA/messenger balance have linked the physiology of reproduction from chromosomal rearrangements to viral latency and all biodiversity.
See also:  Gut viruses tied to potentially deadly complication of bone marrow transplant

…the onset of GvHD appeared to trigger the late awakening of these covert viruses, laying to rest a longstanding chicken-and-egg debate: which comes first, viral infection or GvHD? The researchers conclude that much of the viral flare they saw is due to reactivation of latent gut infections following transplantation.

The link from gut bacteria to reactivation of latent gut infections following transplantation links a change in the energy-dependent microRNA/messenger RNA balance to hematopoiesis and.cell type differentiation in all vertebrates and vertebrates.
 See also:
Mysterious children’s neurological disease is traced to a single error in one gene

The researchers found in all patients the same spontaneously occurring, non-inherited genetic change in a gene (named “UBTF”) responsible for ribosomal RNA formation.
 

The de novo creation of RNA is energy-dependent. No disease can be traced to a single gene outside the context of the virus-driven degradation of messenger RNA that causes the pathology.

See: Oligogenic basis of isolated gonadotropin-releasing hormone deficiency

The deficiency links the virus-driven degradation of messenger RNA from a single gene to every aspect of vertebrate morphology and behavior via GnRH.

The de novo energy-dependent creation of RNA has been linked to GrRH since 1964.

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

I reiterate:  Next we will learn that “Nothing in Biology Makes Sense…” outside the context of food energy-dependent pheromone-controlled RNA-mediated ecological adaptations.

NgAgo Paper Retracted

“[W]hen it comes to biology, answers are often not definitive. And when it comes to replication studies, the one thing we know is that it takes time,” it says. “In the case of NgAgo, the time has come and the data have spoken.”

Earlier today, I mentioned to my friend, Jo Rockafellor, that Bruce McEwen told me, in 1992, my model could not be validated without starting from gene activation in gonadotropin releasing hormone (GnRH) neurons. After learning from Donald Pfaff that Robert L. Moss might know something important, “Bob” Moss and I became friends. He once told me, “you know how it works, write the book.”
 
If you think I am name-dropping, you are right. These are the people that others must learn from or they are not likely to learn anything about energy-dependent biophysically constrained RNA-mediated cell type differentiation.
 
Another line of experimental evidence links publication of The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002), from Martha McClintock’s works to the claim made by Denise Chen when she introduced me to Wen Zhou.

Denise claimed that my book was responsible for her interest in the study of olfaction, and Wen Zhou has since linked quantum physics to quantum souls.

When someone like Moroz claims that “The possibility of secondary loss of neurons and synapses in the Porifera/Placozoa clades is a highly unlikely and less parsimonious scenario.” he attests to the ignorance of several generations of pseudoscientists who failed to ask how and when the energy-dependent de novo creation of RNA occurred. Instead, they link the virus-driven degradation of messenger RNA to all biodiversity via mutations and natural selection.

That, is foolish. See: Cytosis: A Cell Biology Board Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

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

Pattern recognition vs evolutionary processes (revisited)

Summary: Recent findings suggest that polyphenols display the ability to reverse adverse epigenetic regulation involved in pathological conditions, such as obesity, metabolic disorder, cardiovascular and neurodegenerative diseases, and various forms of cancer.
That suggests the ignorance of pseudoscientists who fail to link pattern recognition from the food that organisms eat to the pheromone-controlled physiology of reproduction via microRNAs is the cause of all pathology.

From egg to the air: 21 days of bee development condensed into one mesmerising minute

After just three weeks of development, worker bees emerge from their brood cells fully formed, flying out to begin supporting their hive. In a stunning high-definition time-lapse video, the US photographer Anand Varma follows the bee’s stages of development from egg to larvae to pupa to worker bee, with a sprightly score to match the insects’ rather startling journey into being.

From Fertilization to Adult Sexual Behavior links the 21 days of bee development to food energy-dependent pheromone-controlled RNA-mediated biodiversity in all living genera via the molecular mechanisms detailed in Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

This model details how chemical ecology drives adaptive evolution via: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction. This model exemplifies the epigenetic effects of olfactory/pheromonal conditioning, which alters genetically predisposed, nutrient-dependent, hormone-driven mammalian behavior and choices for pheromones that control reproduction…

The model is a refutation of neo-Darwinian pseudoscientific nonsense that linked atoms to ecosystems in Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems via food energy-dependent changes in microRNAs.

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

The energy-dependent innate ability to fend off attacking viruses links changes in chirality to autophagy and supercoiled DNA, which links the physiology of reproduction to the viral latency that protects all organisms from the virus-driven degradation of messenger RNA. The virus-driven degradation of messenger RNA is linked from mutations to all pathology by all serious scientists.
For example, see:Two new studies offer insights into gastrointestinal dysfunction in Parkinson’s patients

The GI distress has repeatedly been linked from the virus-driven degradation of messenger RNA in gut bacteria to all pathology via links from quantum physics to supercoiled DNA, which protects all organized genomes from virus-driven pathology. You need only look up “microRNA” in a search of the PubMed database to learn what theorists are not telling you about biologically-based cause and effect.

See also: Cell senescence is regulated by innate DNA sensing
The innate immune cells use a host of to sense and identify foreign parts of an invading pathogen, such as the DNA of a virus. DNA-sensing is accomplished through a two-receptor system comprising an enzyme called cGAS and an adaptor molecule called STING. Once activated, the cGAS-STING pathway triggers the production of inflammatory proteins that help fight off the pathogen.
The energy-dependent de novo creation of G protein-coupled receptors links the virus-driven degradation of messenger RNA to all pathology.  See: Olfaction Warps Visual Time Perception
For an example of someone who has failed to link pattern recognition to top-down causation and all biophysically-constrained biologically based-cause and effect, see: Discovering Hidden Temporal Patterns in Behavior and Interaction: T-Pattern Detection and Analysis with THEME™
Magnus S. Magnusson, who I sometimes describe as an atheistic hate-monger, claims that my model and all my comments to his FB page are:

“Ridiculously irrelevant. I may not be intelligent, but I give keynotes at international conferences in proteomics and mass spectroscopy and in a few weeks in nanotechnology. However, I have mostly worked on the biology of behavior and neuroscience especially regarding neuronal interactions in the brain with the University if Cambridge, UK.”

He won’t answer any questions about the role of energy-dependent receptor-mediated interactions that link the de novo creation of the receptors to all biologically-based cause and effect. He does not seem to grasp the fact that viruses steal the quantized energy that links the de novo creation of the receptors to healthy longevity, which may be why he cannot link virus-driven energy theft to all pathology.
See for comparison: Evolutionary processes shaping diversity across the Homo lineage

These results show that genetic drift, and, likely, small population sizes were important factors shaping the evolution of Homo and many of its novel traits, but that selection played an essential role in driving adaptation to new contexts.

When all else fails to convince any serious scientist, pseudoscientists will still have their “evolutionary processes.” For comparison, serious scientists will continue to link what organisms eat to the physiology of their pheromone-controlled biodiversity and use microRNA therapy to effectively treat or cure all pathology.
Study shows mango consumption has positive impact on inflammatory bowel disease
Facts about food consumption and ecological adaptations include links to the control of virus-driven messenger RNA degradation and control of inflammatory bowel disease. The facts make sense in the context of this model. Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

See also: Mango polyphenolics suppressed tumor growth in breast cancer xenografts in mice: role of the PI3K/AKT pathway and associated microRNAs
See also: Dietary polyphenols and chromatin remodeling
Recent findings suggest that polyphenols display the ability to reverse adverse epigenetic regulation involved in pathological conditions, such as obesity, metabolic disorder, cardiovascular and neurodegenerative diseases, and various forms of cancer.
See also: This brief exchange with Jay R. Feierman
James V. Kohl: “Evolution by natural selection cannot be the outcome if something is not first selected. Selection is always for nutrients. It is as simple as that.”
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
See for comparison: New Research Shocks Scientists: Human Emotion Physically Shapes Reality!
1)

In the presence of negative emotions the DNA tightened. In the presence of positive emotions the coils of the DNA relaxed.

The scientists concluded that “Human emotion produces effects which defy conventional laws of physics.”

2)

The DNA was placed in a different room in the same building. Both the donor and his DNA were monitored and as the donor exhibited emotional peaks or valleys (measured by electrical responses), the DNA exhibited the IDENTICAL RESPONSES AT THE EXACT SAME TIME.

3)

The third experiment proved something pretty shocking!

Scientists observed the effect of DNA on our physical world.

Light photons, which make up the world around us, were observed inside a vacuum. Their natural locations were completely random.

Human DNA was then inserted into the vacuum. Shockingly the photons were no longer acting random. They precisely followed the geometry of the DNA.

Scientists who were studying this, described the photons behaving “surprisingly and counter-intuitively”. They went on to say that “We are forced to accept the possibility of some new field of energy!”

They concluded that human DNA literally shape the behavior of light photons that make up the world around us!

Until you link quantum physics to quantum souls via olfaction, you may not understand any claim about light-induced energy-dependent changes in the endogenous substrate of all cell types that links the creation of RNA from top-down causation to every aspect of energy-dependent RNA-mediated cell type differentiation.
Human DNA does not shape the behavior of light photons. The speed of light on contact with water links the anti-entropic virucidal energy of sunlight to the de novo creation of amino acids and supercoiled DNA via feedback loops. The experiments linked the feedback loops from behavior to changes in DNA, and biologically uninformed science idiots claimed that DNA shapes the behavior of light photons.
The idiots (people who have no professional expertise in any scientific discipline) claim that “…we are connected to our DNA beyond space and time.”
See for comparison: Olfaction Warps Visual Time Perception
At this level of examination, the researchers link the sense of smell in bacteria from quorum-sensing to the physiology of pheromone-controlled reproduction in all living genera via the honeybee model organism and our visual perception of energy and mass in the context of the space-time continuum via feedback loops. Nothing happens to us that is outside our ability to unconsciously perceive energy and mass. No magic exists in the context of facts like this: Feedback loops link odor and pheromone signaling with reproduction
See also: Roger Penrose On Why Consciousness Does Not Compute

…I asked him if he thinks there’s any inherent meaning in the universe. His answer surprised me. “Somehow, our consciousness is the reason the universe is here.” So does he think there’s intelligent life—or consciousness—somewhere else in the cosmos? “Yes, but it may be extremely rare.” But if consciousness is the point of this whole shebang, wouldn’t you expect to find some evidence of it beyond Earth? “Well, I’m not so sure our own universe is that favorably disposed toward consciousness,” he said. “You could imagine a universe with a lot more consciousness that’s peppered all over the place. Why aren’t we in one of those rather than this one where it seems to be a rather uncommon activity?

“So, yes, we want to see the purpose of it. I don’t know. Maybe it’s attributing the wrong word. Purpose—what does that mean?” He chuckled.

Evolution–who thinks that the purpose of life can be placed into the context of ridiculous theories about evolutionary processes.
See for comparison: Structural diversity of supercoiled DNA (and this parody). See also: Chemists Know and m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs
 

Cytosis

New Testament Book Cover Refutes Theistic Evolution

Goats, bookworms, a monk’s kiss: Biologists reveal the hidden history of ancient gospels

Collins already had developed a method to identify ancient species by differences in the amino acid sequences of collagen and other proteins preserved in fossils.

See: Protein power by Robert F. Service

…methods to sequence amino acids lag behind DNA sequencing.

The report of 300 million year old proteins is based on ridiculous theories that failed to include what was known about food energy-dependent RNA-mediated fixation of amino acid substitutions.
Natural selection for energy-dependent codon optimality links the pheromone-controlled fixation of the substitutions to cell type differentiation in all individuals of all living genera.
Collins has since used the method he developed to recover amino acid sequences that reveal which animal skin was used for the leather cover for the Gospel of Luke.

Collins so-called revelation about the species-specificity of amino acid sequences was reported in Dobzhansky (1964) and again in 1973.

Pseudoscientists have ignored this fact:

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).” — Dobzhansky (1973)

The sequences of amino acids link what animals eat to the food energy-dependent pheromone-controlled morphological and behavioral biodiversity manifested in every species on Earth. See: Feedback loops link odor and pheromone signaling with reproduction

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

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.The species-specific link from food energy-dependent changes in base pairs to the fixation of amino acid substitutions in supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA.

See also:  Cytosis: A Cell Biology Board Game A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

See also: Olfaction Warps Visual Time Perception reported as: Odors Alter Subjective Time Experience 

The energy-dependent de novo creation of the sense of smell links food odors and natural selection for codon optimality to the physiology of reproduction. Feedback loops link the sense of smell in bacteria to all biodiversity via the pheromone-controlled physiology of reproduction.

Metaphorically, the sense of smell is like a time machine that links our experiences from the past to our behaviors throughout life. Experimental evidence of biologically-based cause and effect links the creation of the sense of smell to representations of food energy-dependent pheromone-controlled biodiversity in invertebrates to vertebrates. The fact that bookworms are invertebrates has aroused interest in the context of the Gospel of Luke.

Goats, bookworms, a monk’s kiss: Biologists reveal the hidden history of ancient gospels (revisited)

Others were more interested in the bookworms. Hedges announced that the wormholes he measured in the Gospel of Luke were 1.3 millimeters in diameter, suggesting that they were made by Anobium punctatum, a northern European beetle. That would confirm that the book was made in the United Kingdom or northern Europe, rather than in southern Europe. The DNA of bookworms “can provide clues as to when and where objects such as books originated and were transported,” Hedges says.

The energy-dependent creation of RNA-mediated amino acid substitutions in different species links experimental evidence of creation to the Dawn of Creation.

The New Testament Book Cover provides experimental evidence of how our visual perception of mass and energy is linked to the space-time continuum via olfaction and representations in Biblical Genesis that link energy as information at the “Dawn of Creation” for comparison to claims and theories about the emergence of energy and the evolution of all biodiversity.

See also: Researchers may have solved origin-of-life conundrum by Robert F. Service

… a pair of simple compounds, which would have been abundant on early Earth, can give rise to a network of simple reactions that produce the three major classes of biomolecules—nucleic acids, amino acids, and lipids—needed for the earliest form of life to get its start.

The origin of life is energy-dependent and RNA-mediated. Robert F. Service seems to be perfectly poised to prevent the dissemination of accurate information about how the virus-driven degradation of messenger RNA is linked from mutations to all pathology.
He has failed to link the energy-dependent creation of nucleic acids, amino acids, and lipids to the creation of the innate immune system and the pheromone-controlled physiology of reproduction in all living genera, which protects all organized genomes from the virus-driven energy theft that links mutations to all pathology.
Simply put, in the context of the Gospel of Luke, Robert F. Service has failed to link any aspect of biologically-based cause and effect from amino acid substitutions to biodiversity via supercoiled DNA.

That may explain why on 2/17/16, I received a message from Bob Grant who claimed to moderate reader comments on posts at www.the-scientist.com.

He claimed that many of my posts were off-topic and excessively long, and asked me to limit both the length and the focus of my comments in the future. He warned “If you continue to post long, rambling, or incoherent comments, I’ll be forced to bar you from our discussion board, something I do not want to do.”

I’ve been banned from many discussions, and consistently see why I am banned. Discussions of pseudoscientific nonsense prevails. For example, see:

First Support for a Physics Theory of Life Thanks to Oleksander Savsunenko for bringing this to my attention.

Take chemistry, add energy, get life. The first tests of Jeremy England’s provocative origin-of-life hypothesis are in, and they appear to show how order can arise from nothing.

My comment to Quanta Magazine

See for comparison: Olfaction Warps Visual Time Perception https://www.ncbi.nlm.nih.gov/pubmed/28334302

They link the energy-dependent creation of the sense of smell in bacteria to our visual perception of mass and energy in the context of the space-time continuum and everything known to serious scientists about RNA-mediated cell type differentiation via the physiology of reproduction.

Compared to the claims of Jeremy England, they start with Darwin’s food energy-dependent “conditions of life.”

Richard Feynman commented on the “conditions of life” and linked Jeremy England’s claims to examples of “human idiocy.” No one will complain that Jeremy England is an idiot (i.e., someone with no professional expertise), but everyone should remember that he has no professional expertise that can be linked to biologically-based top-down causation.

See: Food energy https://www.youtube.com/watch?v=roX2NXDUTsM
Richard Feynman, complains about all the different units that are used to measure the single concept of Energy.

Re: “Take chemistry, add energy, get life.” But do not tell a serious scientist about your theory.
And, do not expect those who moderate discussions to understand anything a serious scientist claims.
My follow-up to Bob Grant, who did not reply:

I am left with this impression.
I could respond to Roy Niles’ comment by linking virus-perturbed protein folding chemistry from loss of olfactory receptor genes to pathology in species from nematodes to humans. But, you might ban me.
The information comes from Cori Bargmann’s group, and she married Richard Axel, who shared the 2004 Nobel prize in Medicine with Linda Buck. Linda Buck extended our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation across species from microbes to man when she co-authored: Feedback loops link odor and pheromone signaling with reproduction
I know a few others who have since linked viruses to perturbed thermodynamic cycles of RNA-mediated protein folding chemistry via amino acid substitutions but you’re not likely to be hearing from them, either. Eugene Daev and Anna Di Cosmo are among those who people like Roy Niles are indirectly responsible for censoring. Simply put anyone who understood our claims in the section on molecular epigenetics from our 1996 review, has made progress akin to the progress of my mentor, Bruce McEwen, whose group just linked a single nutrient-dependent RNA-mediated amino acid substitution from stress to life history transitions in human behavior via the mouse model and BDNF Val66Met. Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity

From Fertilization to Adult Sexual Behavior

Most polymaths live in a world of their own because others don’t want to learn enough to catch up, and the polymaths are too far ahead to explain what they have known for several decades.
A 6-hour long conversation with Bruce McEwen in 1991 led to my breakfast conversation in 1995 with Gene Garfield, which is when he learned enough about cell type differentiation from me and his octogenarian friend “Bill” Turner, to comment on my book in the year it was published. Greg Bear linked the information from my works to his stories about the evolution of a new human sub-species. Evolution rising from the grave; Living with the Neanderthals
I’m not sure if “The Scientist” will help others continue to move forward if you think my comments are off topic — and ban me when I try to elaborate on the link to the topic of RNA-mediated cell type differentiation for comparison to the thoughts of others about mutation-driven evolution.  I lost any linear thinking skills I might have had before writing the book, and without the help of my co-author — it wouldn’t have made sense even to Gene.
Thanks for the opportunity to vent my frustrations,
James V. Kohl

Medical laboratory scientist (ASCP)
Independent researcher

http://rna-mediated.com/

 

Biology to a Physicist

Measuring energy vs human idiocy (social science)

Summary:
The “… universal applicability for determination of various targets such as metal ions, miRNAs, DNAs and proteins…” is the key to understanding the differences in the energy-dependent assembly of cell types with fixed amino acid substitutions that link natural selection for energy-dependent changes in base pairs from atoms to ecosystems in all living genera.

Richard Feynman complains about all the different units that are used to measure the single concept of Energy in this snippet  from one of his lectures in the series “The character of Physical Law.”

For an example of how the anti-entropic virucidal energy of sunlight can be measured and linked to the creation of microRNAs, see: Universal Ratiometric Photoelectrochemical Bioassay with Target-Nucleotide Transduction-Amplification and Electron-Transfer Tunneling Distance Regulation Strategies for Ultrasensitive Determination of microRNA in Cells

…using microRNA-141 (miRNA-141) as target model, the constructed biosensor demonstrated favorable accuracy and excellent sensitivity down to femtomolar level. Impressively, the proposed assay overcame the heavily dependence of target on photoactive materials in current ratiometric PEC assay, and demonstrated admirably universal applicability for determination of various targets such as metal ions, miRNAs, DNAs and proteins by merely two different photoactive materials

The “… universal applicability for determination of various targets such as metal ions, miRNAs, DNAs and proteins…” is the key to understanding the differences in the food energy-dependent assembly of cell types with fixed amino acid substitutions that link changes in base pairs from atoms to ecosystems in all living genera.
There is a model for that: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
See for comparison: A step-by-step microRNA guide to cancer development and metastasis

We propose that the balance between oncogenic versus tumor suppressive miRNAs acting within transcription factor-miRNA regulatory networks, influences both the multistage process of neoplastic transformation, whereby normal cells become cancerous, and their stress responses.

See for comparison: Feynman on social science
See also: Quantum common sense

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking

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

Energy-dependent physical and biophysical constraints (5)

Summary: Emmy Noethe’s theorems were developed in the early 1900’s. Richard Feynman inadvertently or purposefully alluded to them as examples of human idiocy.
Discover Magazine resurrected the examples of human idiocy in a 2017 article. For comparison, Choi et al., (2017) support the claims that intercellular and interkingdom communication is energy-dependent and controlled by the metabolism of food energy to pheromones.
It is obvious that pheromones biophysically constrain the virus-driven degradation of messenger RNA. That fact links everything currently known about RNA-mediated cell type differentiation to human love in the context of established links from quantum physics to quantum souls. It may surprise some people to know that the virus-driven evolution of love is the antithetical to the food energy-dependent physiology of pheromone-controlled reproduction in all living genera. Indeed, some people may realize that the virus-driven evolution of anything is based upon ridiculous theories that were invented by Emmy Noethe.
See: Energy-dependent physical and biophysical constraints (4)
Natural selection links odors and the food energy from what organisms eat to the de novo creation of microRNAs. The creation of microRNAs is linked to biophysically constrained energy-dependent codon optimality.
Odor and food energy-dependent changes in microRNAs link hydrogen-atom transfer in DNA base pairs in solution from the creation of amino acids to the ability to sense energy and mass in the context of the space-time continuum. The sense of smell in bacteria has been linked to our food energy-dependent visual perception of the space-time continuum.
Publication of Olfaction Warps Visual Time Perception precedes the September 2017 release of the cell biology game Cytosis. The cell biology game links virus-driven energy theft to all pathology.

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

Taken together, the facts about olfaction link the sense of smell in bacteria from quorum sensing to our visual perception of mass and energy in the context of the space-time continuum. It is no trouble for a serious scientist to consistently link quantum physics from food energy to the creation of quantum souls via changes in the microRNA/messenger RNA balance and the pheromone-controlled physiology of reproduction.
Richard Feynman inadvertently did that when he claimed that the different measures for units of energy used by other theoretical physicists were examples of human idiocy.

See for comparison: The Universe According to Emmy Noethe (Discover Magazine, 2017)

…energy may not be conserved “locally” — that is, in an arbitrarily small patch of space — but everything works out when the space is sufficiently large. That was one of two theorems she proved that year in Göttingen, Germany. The other theorem, which would ultimately have a far greater impact, uncovered an intimate link between conservation laws (such as the conservation of energy) and the symmetries of nature, a connection that physicists have exploited ever since. Today, our current grasp of the physical world, from subatomic particles to black holes, draws heavily upon this theorem, now known simply as Noether’s theorem.

Emmy Noethe’s so-called theorems, which she developed in the early 1900’s, attempted to explain how the concept of entropy might not appear to defy everything known to serious scientists about the biophysically constrained energy-dependent physiology of pheromone-controlled reproduction, which links feedback loops from odors and pheromones to the creation of all energy-dependent biodiversity on Earth.
Simply put, more than 100 years ago Emmy Noethe’s theorems suggested that all representations of energy-dependent biologically-based cause and effect are wrong. For a current representation of what is known, see: Feedback loops link odor and pheromone signaling with reproduction.
The physiology of pheromone-controlled reproduction links what organisms eat to all energy-dependent biodiversity via the de novo creation of genes and gene activation that is biophysically constrained by the metabolism of food to pheromones which control the physiology of reproduction in all living genera.
See also: AMP-enabled FLT3-ITD detection

Independent and bidirectional probes are specifically optimized to detect internal tandem duplications (ITDs) of all sizes. The reads originating from these probes are bioinformatically assembled by Archer Analysis using a de novo assembler to form longer consensus sequences that span the ITD. These longer sequences are then aligned to the reference genome to identify the presence of even very large ITDs (> 250bp).a
a Only available on Illumina® instruments

Use of a so-called “de novo assembler” eliminates any consideration of energy as information that must be used in the context of bioinformatics and the identify of reference genomes that are used to identify pathological gene variants that arise in the context of energy-dependent de novo gene creation.  The link from Emmy Noethe’s theorems to the pseudoscientific nonsense about the  “de novo assembler” may not be clear without examination of facts about the physiology of reproduction.
For example, see: Physiology is rocking the foundations of evolutionary biology

Perhaps the elegant mathematics and the extraordinary reputation of the scientists involved blinded us to what now seems obvious: the organism should never have been relegated to the role of mere carrier of its genes.

For information on Emmy Noethe’s reputation and her elegant mathematics, see:

The Mighty Mathematician You’ve Never Heard Of (2012)

She invented a theorem that united with magisterial concision two conceptual pillars of physics: symmetry in nature and the universal laws of conservation.

Noether’s brilliance was obvious to all who worked with her, and her male mentors repeatedly took up her cause…

A Fight for the Soul of Science (2015)

Silk accused these theorists of “moving the goalposts” of science and blurring the line between physics and pseudoscience. “The imprimatur of science should be awarded only to a theory that is testable,” Ellis and Silk wrote, thereby disqualifying most of the leading theories of the past 40 years. “Only then can we defend science from attack.”

See for comparison:

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems April by James V Kohl

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

From my publications alert: What’s new for ‘microRNA’ in PubMed on July 26, 2017
Tiny RNAs and their voyage via extracellular vesicles: Secretion of bacterial small RNA and eukaryotic microRNA

MicroRNAs are small non-coding RNAs that bind to the 3′-untranslated region of target mRNAs and have transcriptional or translational inhibitory function in eukaryotes. Before microRNAs were widely known, bacterial non-coding small RNAs around 50-200 nt in length were discovered whose mechanism of action resembled that of microRNAs. Recently, RNAs that are of similar size to or smaller than microRNAs have been discovered in bacteria and indeed, this class of small RNAs have been found throughout all domains of life. Moreover, recent findings suggest that these tiny RNAs can be released via extracellular vesicles (such as exosomes in eukaryotes and outer membrane vesicles in bacteria), which in turn heralds a new field of research, interkingdom communication. This review discusses two similar classes of small RNAs in evolutionarily distinct eukaryotes and bacteria. In addition to their biogenesis and regulation, we discuss small RNA vehicles and their secretion. Impact statement The possible endogenous functions of small RNAs such as regulatory small RNAs in bacteria and microRNAs in eukaryotes have been extensively studied since they were first discovered. However, their powerful functions should not be seen as limited to their cells of origin. Recently, several papers have demonstrated that small RNAs function as signaling molecules between cells. This is possible because small RNAs can be shuttled around after being incorporated into environmentally protective extracellular vesicles. It is now clearly plausible that secreted small RNAs can regulate other types of cells through biofluids. Given their “common molecule” status, the role of small RNAs in mediating bacteria-human crosstalk is an emerging and competitive area of genetic research. This review provides insight into the function of small RNAs in intercellular and even interkingdom communication.

See also:Impact statement

The possible endogenous functions of small RNAs such as regulatory small RNAs in bacteria and microRNAs in eukaryotes have been extensively studied since they were first discovered. However, their powerful functions should not be seen as limited to their cells of origin. Recently, several papers have demonstrated that small RNAs function as signaling molecules between cells. This is possible because small RNAs can be shuttled around after being incorporated into environmentally protective extracellular vesicles. It is now clearly plausible that secreted small RNAs can regulate other types of cells through biofluids. Given their “common molecule” status, the role of small RNAs in mediating bacteria-human crosstalk is an emerging and competitive area of genetic research. This review provides insight into the function of small RNAs in intercellular and even interkingdom communication.

As indicated in my 2014 invited review of nutritional epigenetics, which was returned without review, endogenous functions of regulatory RNAs such as small RNAs in bacteria and microRNAs in eukaryotes have been extensively detailed in the context of biophysically constrained biologically-based cause and effect. These authors attest to the fact that the structure and function of bacterial small RNAs and eukaryotic microRNAs are not limited to their food energy-dependent de novo creation in their cells of origin.
The fact that small RNA and micro-RNA-mediated cell type differentiation occurs in the context of hydrogen-atom transfer in DNA base pairs in solution links the information in this review to claims that small RNAs in seawater solutions and microRNAs in blood link “common molecule” status to “… the function of small RNAs in intercellular and even interkingdom communication.”  The fact that intercellular and interkingdom communication is energy-dependent and controlled by the metabolism of food energy to pheromones that biophysically constrain the virus-driven degradation of messenger RNA, links everything currently known about cell type differentiation from quantum physics to quantum souls via the food energy-dependent physiology of reproduction in all living genera.
See also: Choi JW[Author] microRNA
For example: MicroRNA profiling in the mouse hypothalamus reveals oxytocin-regulating microRNA
For comparison: @36:18 Larry Young explains the virus-driven evolution of love as if serious scientists had learned nothing about receptor-mediated behaviors.

Big Bang

Richard P. Feynman refuted theistic evolution

Summary: Among other delightful examples of his expertise in physics, Feynman presciently linked natural selection for energy-dependent codon optimality from food energy-dependent pheromone-controlled biophysically constrained chromosomal rearrangements to healthy longevity. He also linked the radiation-induced theft of quantized energy to mutations in phages via amino acids that increase the virulence of the viruses. Updated information is presented in the context of refutations by many others who might otherwise claim to believe in theistic evolution.
The miR-23a~27a~24-2 microRNA cluster buffers transcription and signaling pathways during hematopoiesis
This is an uncorrected proof.
They link food energy-dependent changes in the microRNA/messenger RNA balance from amino acid substitutions to cell type differentiation via the physiology of pheromone-controlled reproduction in species from microbes to humans in the context of this claim from Dobzhansky (1973) Nothing in Biology Makes Any Sense Except in the Light of Evolution.

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).

Cell type differentiation during hematopoiesis links the amino acid substitution that differentiates the alpha chains of hemoglobin to the differentiation of all other cell types in all other individuals of all vertebrate species via the conserved molecular mechanisms of energy-dependent pheromone-controlled cell type differentiation in all invertebrates.

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

This is my invited review of nutritional epigenetics that was returned without review by the guest editors of a special edition of the journal “Nutrients.”

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

See for comparison: Surely You’re Joking, Mr. Feynman! (Adventures of a Curious Character)

Chapter 10: A Map of the Cat?

My summary: Among other delightful examples of his expertise in physics, Feynman presciently linked natural selection for energy-dependent codon optimality from food energy-dependent pheromone-controlled biophysically constrained chromosomal rearrangements to healthy longevity. He also linked the radiation-induced theft of quantized energy to mutations in phages via amino acids that increase the virulence of the viruses.

The delayed dissemination of accurate information about biophysically constrained biologically-based cause and effect has already contributed to the unnecessary suffering and premature deaths of thousands to millions of people since the time that Richard Feynman reported on mutations in bacteriophages. He realized that the mutations link the theft of quantized energy from living organisms to the amino acid substitutions in viruses that cause the degradation of messenger RNA, which links mutations to all pathology. If not for his love of physics and the pseudoscientific nonsense of neo-Darwinian theorists, all serious scientists would have linked quantum physics to quantum souls.

See for example: 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: The Sense of Smell Impacts Metabolic Health and Obesity

A PubMed search for microRNA and the disease you wish to prevent or effectively treat will help you to eliminate the foolishness of theorists who have failed to link the de novo creation of microRNAs to all biodiversity via the physiology of reproduction and biophysically constrained viral latency.

For example: microRNA alzheimers

To place your searches into the proper context, see: Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition

Biologically uniformed theorists invented the term “enhancer” for ambiguous use in the context of energy-dependent changes in the microRNA/messenger RNA balance. They obfuscate facts about food energy and feedback loops that link pheromones to the biophysically constrained viral latency the enables ecological adaptations via use of “enhancer function.”

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

Natural selection for energy-dependent codon optimality links food energy-dependent changes in the microRNA/messenger RNA balance to protection from the virus-driven degradation of messenger RNA, which links mutations to all pathology unless terms such as enhancers and enhancer function are used to obfuscate facts about The phylogenetic utility and functional constraint of microRNA flanking sequences

Both miRNAs and their flanking sequences provide phylogenetic signals suitable for the inference of phylogeny with high levels of accuracy, when sufficient numbers of this type are concatenated. As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

There is no such thing as de novo assemblies of genomes. Food energy must be linked to the pheromone-controlled physiology of reproduction to link ecological variation to ecological adaptation via feedback loops.

See: Feedback loops link odor and pheromone signaling with reproduction

See for comparison:7/25/13

Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

7/26/13

Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.

See also: Researchers find new mechanism for genome regulation

Interestingly, this type of liquid-liquid phase separation is very sensitive to changes in temperature, protein concentration, and pH levels.

The sensitivity is food energy-dependent and RNA-mediated. Pseudosciedntists should stop their foolishness long enough to realize there is nothing new about the mechanisms of genome regulation. The mechanisms controlled by pheromones link the physiology of reproduction and chromosomal inheritance to healthy longevity unless they link virus-driven energy theft to all pathology via changes in the microRNA/messenger RNA balance.

See also: CSmiRTar: Condition-Specific microRNA targets database

…(Condition-Specific miRNA Targets). CSmiRTar collects computationally predicted targets of 2588 human miRNAs and 1945 mouse miRNAs from four most widely used miRNA target prediction databases (miRDB, TargetScan, microRNA.org and DIANA-microT) and implements functional filters which allows users to search (i) a miRNA’s targets expressed in a specific tissue or/and related to a specific disease…

See for comparison: Creationism support is at a new low. The reason should give us hope.

Stuart Kauffman refutes theistic evolution

MicroRNAs GnRH and the failure of sex research

Summary: “The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression” accurately represents what is known about food energy-dependent RNA-mediated cell type differentiation in species from soil microbes to humans. MicroRNAs are not new players in the hypothalamic control of fertility and the effects of food odors and pheromones on microRNAs link energy-dependent changes in hormones to behavior. That fact was detailed two decades ago in our Hormones and Behavior review.

Now see: [MicroRNAs: new players in the hypothalamic control of fertility]

MicroRNAs are small non-coding RNAs that modulate gene expression post-transcriptionally. Discovered more than 15 years ago, their functions start to be unraveled. Increasing evidence points to an important functional role of microRNAs in brain development. In particular, miRNAs have recently been established to play a vital role in the mechanisms underlying the infantile rise in gonadotropin-releasing hormone (GnRH) production by neurons in the hypothalamus, a phenomenon necessary for the onset of puberty in mammals.

The anti-entropic virucidal energy of ultraviolet light links the de novo creation of of microRNAs from flanking sequences that biophysically constrain all biodiversity by protecting the organized genomes of all living genera from the virus-driven degradation of messenger RNA, which links mutations to all pathology.

See: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

After scanning the article that accurately represents what is known about RNA-mediated cell type differentiation in species from soil microbes to humans, see this pseudoscientific nonsense for comparison:

Prenatal Influences on Human Sexual Orientation: Expectations versus Data. Breedlove SM. Arch Sex Behav. 2017 Feb 7. doi: 10.1007/s10508-016-0904-2.

Human Sexual Orientation: The Importance of Evidentiary Convergence. Balthazart J, Court L. Arch Sex Behav. 2017 May 12. doi: 10.1007/s10508-017-0997-2.

A Bird’s Eye View. Adkins-Regan E. Arch Sex Behav. 2017 May 10. doi: 10.1007/s10508-017-0998-1

Proceed with Caution: Interpreting Evidence for Prenatal Influences on Sexual Orientation. LeVay S. Arch Sex Behav. 2017 May 8. doi: 10.1007/s10508-017-0996-3

On Possible Hormonal Mechanisms Affecting Sexual Orientation. McFadden D. Arch Sex Behav. 2017 May 5. doi: 10.1007/s10508-017-0995-4

Reconsidering Prenatal Hormonal Influences on Human Sexual Orientation: Lessons from Animal Research. Baum MJ, Bakker J. Arch Sex Behav. 2017 May 4. doi: 10.1007/s10508-017-0994-5

Each published work represents the failure of the sex researchers to link energy-dependent RNA-mediated cell type differentiation from the pheromone-controlled physiology of reproduction to all biodiversity via the section on molecular epigenetics from our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior

In our section on molecular epigenetics, we linked the quantized energy-dependent de novo creation of microRNAs from fertilization to adult sexual behavior via this claim.

Small intranuclear proteins also participate in generating [quantized energy-dependent] 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.

The alternative splicing techniques of pre-mRNA are quantized energy-dependent and they link microRNA flanking sequences to all biodiversity via hydrogen-atom transfer in DNA base pairs in solution. The hydrogen-atom transfer was place into the context of the biophysically constrained physiology of reproduction and the role of microRNAs in this published work:

The phylogenetic utility and functional constraint of microRNA flanking sequences

Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

Genomes do not automagically assemble themselves. Placing the energy-dependent de novo creation of microRNAs into the context of the speed of evolution is a horrid error in logic that extends across all disciplines, which is the only way it can continue to be placed into the pseudoscientific claims of sexuality researchers.

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

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

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

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

If you take any time at all to review the published works of sex researchers, you will learn why Feynman referred to all social scientists as pseudoscientists.

See also:

Richard Feynman was a Nobel prize winning Theoretical Physicist who popularized physics with his entertaining lecture style. This snippet is taken from one of his lectures in the series “The character of Physical Law” where he complains about all the different units that are used to measure the single concept of Energy.

The human sexualilty researchers whose works were recently published in the Archives of Sexual Behavior represent the worst of pseudoscience. They skip past the facts about food energy and pheromones and link behavior to anything except the role that microRNAs (pre-mRNAs) play in energy-dependent RNA-mediated cell type differentiation, which links quantized energy from angstroms to ecosystems in all living genera via the sense of smell in bacteria.
Scientists investigate how the sense of smell works in bacteria

…the signaling and inactive states differ only very slightly at the nitrate-binding site – by 0.5-1 angstroms, which is approximately one fifth of the size of the ion itself (1 angstrom is 10-10 meters). However, when this ion binds to the sensor, it causes huge changes in the protein: The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.

See also this: Animation of a particle where the Helicity matches the Chirality.
This appears to be a match made in Heaven so far as young earth creationists are concerned. It links the creation of the sun’s anti-entropic energy to all biodiversity on Earth via the physiology of food energy-dependent pheromone-controlled reproduction in the context of what is known about autophagy (Yoshinhori Ohsumi) and chromosomal inheritance (Thomas Hunt Morgan).
But now, all the works of Nobel Laureates can be placed into the context of works by people like Lukin MD
See for example: Symmetry-protected collisions between strongly interacting photons and Lukin MD microRNA no entries found, for comparison
People like Lukin are not going to link microRNA-mediated cause and effect from the sun’s anti-entropic virucidal energy to all biodiversity on Earth via food energy and the pheromone-controlled the physiology of reproduction and transgenerational epigenetic inheritance. They are like the biologically uninformed sex researchers who have failed to make sense of anything known to serious scientists.
If symmetry protects collisions between strongly interacting photons, the virus-driven theft of quantized energy clearly can be linked to the assymetry manifested it in conditions where the degradation of messenger RNA can clearly be linked to all pathology via the sense of smell.
See Hormonal correlates of women’s mid-cycle preference for the scent of symmetry

When women are fertile in their cycles, in comparison with when they are in the luteal phase, they are more attracted to masculine facial features (Johnston, Hagel, Franklin, Fink, & Grammer, 2001; Penton-Voak & Perret, 2001; Penton-Voak et al., 1999), darker facial skin color (Frost, 1994), lower voice pitch (Feinberg et al., 2006; Puts, 2005), masculine body odor (Grammer, 1993), the scent of men who are socially dominant (Havlicek, Roberts, & Flegr, 2005), the scent of men displaying developmental stability/bilateral symmetry (Gangestad & Thornhill, 1998a; Rikowski & Grammer, 1999; Thornhill & Gangestad,1999; Thornhill et al. 2003), masculine (or dominant) behavioral displays (Gangestad, Garver-Apgar, Simpson, & Cousins, 2007; Gangestad, Simpson, Cousins, Garver-Apgar, & Christensen, 2004; Gangestad, Thornhill, & Garver-Apgar, 2008), masculine or muscular bodies (Gangestad et al., 2007; Little, Jones, & Burriss, 2007) and creative men (Haselton & Miller, 2006; see Thornhill & Gangestad, in press, for a critical review of these and other cycle effects). Substantial evidence indicates that these shifts are specific to women’s preferences for men evaluated as sex partners and not to their preferences for men as long-term, investing mates (e.g., Gangestad et al.,2004, 2007; Haselton & Miller, 2006; Penton-Voak et al., 1999; Puts, 2005).

All these preferences can be framed in the context of what is known about the sense of smell and the substitution of achiral glycine in position 6 of the GnRH decapeptide. One substitution stabilizes the organized genomes of all vertebrates by preventing nearly all the virus-driven degradation of messenger RNA, which has been linked to all pathology in all living genera.
See: Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

It is possible that GnRH has an early origin in life history as a regulator of reproduction, since yeast α mating factor has 80% amino acid homology with mammalian GnRH and stimulates gonadotropin release from the mammalian pituitary (Loumaye et al., 1982; King and Millar, 1995). There is a question whether the structure of the GnRHs and their receptors in invertebrates conserved their structure during evolution in a sufficient degree to support the homology with the structure of GnRHs and their receptors in vertebrates.

There is no longer any question about the conserved molecular mechanisms of biophysically constrained RNA-mediated cell type differentiation in all living genera. The mechanisms are light energy-dependent in the context of food energy and the pheromone-controlled physiology of reproduction.
When will all researchers learn to search PubMed for more information about the role of microRNAs before continuing to tout their pseudoscientific nonsense? What do serious scientists say, for comparison?
See: MicroRNA Items: 1 to 20 of 61842
For example: Computational identification of mutually homologous Zika virus miRNAs that target microcephaly genes.

Conclusions We suggest that following infection of fetal neurons ZIKV may modulate the action of various miRNAs, and miR-1304 in particular, resulting in microcephaly.

In reality, they suggest that all theorists are examples of human idiocy, which is the source of all virus-driven pathology.
 
 

rp_tumblr_ngykp0yfND1r5gzz6o1_500.jpg

Energy-dependent epigenetic translation to mRNA stability

Negative selection in humans and fruit flies involves synergistic epistasis

Negative selection against deleterious alleles produced by mutation influences within-population variation as the most pervasive form of natural selection.

Naturally occurring positive selection for energy-dependent codon optimality replaced every aspect of neo-Darwinian theories that linked natural selection from mutations to evolution of increasing organismal complexity. Positive selection for epigenetically-effected beneficial alleles links the epigenetic landscape to the physical landscape of supercoiled DNA via nutrient-dependent pheromone-controlled metabolic networks and genetic networks.
Everything from atoms to ecosystems was included in this invited review of nutritional epigenetics because all serious scientists know that organisms survive on food energy and that species exemplify the pheromone-controlled reproduction and chromosomal inheritance that ensures survival of all living genera.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction.

See also: Transcriptome-wide Discovery of microRNA Binding Sites in Human Brain

This interactome points to functional miRNA:target pairs across >3,000 genes and represents a valuable resource for accelerating our understanding of miRNA functions in brain. We demonstrate the utility of this map for exploring clinically relevant miRNA binding sites that may facilitate the translation of genetic studies of complex neuropsychiatric diseases into therapeutics.

See also: Connections Underlying Translation and mRNA Stability

…intimate connections between mRNA and the ribosome can drive biological regulation. In closing, we consider the likelihood that these connections between protein synthesis and mRNA stability are widespread or whether other modes of regulation dominate the mRNA stability landscape in higher organisms.

No experimental evidence of evolution includes biophysically constrained biologically-based cause and effect, which integrates the required link from ecological variation to the physics, chemistry, and molecular epigenetics of what Darwin presciently linked from his “conditions of life” to ecological adaption via energy-dependent changes in messenger RNA (mRNA).
See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (with my emphasis)

…the ribosome interprets two codes within the mRNA: the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.

Natural selection for energy-dependent codon optimality conserves the amino acid substitutions in the context of the stability of supercoiled DNA. That stability protects all organized genomes from virus-driven energy theft and genomic entropy. Protection from viruses occurs via the pheromone-controlled biophysically constrained physiology of reproduction in all living genera. Experimental evidence of that fact was included in our section on molecular epigenetics from this 1996 Hormones and Behavior review.
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).

See for comparison: Tracing the Enterococci from Paleozoic Origins to the Hospital

Host energy-dependent speciation

Graphical abstract from “Tracing the Enterococci from Paleozoic Origins to the Hospital”

Reported as: Enterococci may have evolved antimicrobial resistance millions of years ago

…researchers have traced evidence of the bacteria’s evolutionary history back 425 million years and theorize that the same traits that allow the bacteria to thrive in hospitals likely emerged when they were carried onto land in the guts of the world’s first terrestrial animals. The study was funded in part by the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health.

The physiology of reproduction in bacteria and all other living genera is nutrient-dependent and pheromone-controlled. Researchers who think they have traced evidence back to the bacteria’s evolutionary history across 425 million years have not considered the weekend resurrection of the bacterial flagellum to be proof of their pseudoscientific nonsense. Instead, they report “Speciation: Host energy source driven” in their graphical abstract.
Where did the energy come from?
See: Evolutionary Rewiring
The nutrient-dependent pheromone-controlled physiology of reproduction in P. fliuorescens was linked to the weekend evolution of the bacterial flagellum.
See also for an invertebrate example of nutrient energy-dependent pheromone-controlled top-down causation: Inhibition of miR-274-3p increases BmCPV replication by regulating the expression of BmCPV NS5 gene in Bombyx mori  From: Virus Genes. 2017 May 10. doi: 10.1007/s11262-017-1466-7
See also: Two fatty acyl reductases involved in moth pheromone biosynthesis

Studies over the last two decades have pinpointed that the epigenetic effect of pheromone-driven adaptive evolution is one of the major factors driving the successful diversification of Lepidopteran insects10. In moths, a few substitutions in critical amino acids in the key pheromone biosynthetic enzymes are sufficient to create a novel pheromone component11,12.

Facts about pheromones in species from microbes to humans have now been placed into their proper context.
Poor human olfaction is a 19th-century myth, which was reported as: “The human sense of smell: It’s stronger than we think” May 11, 2017
See for comparison: Human pheromones: integrating neuroendocrinology and ethology

The ‘affective primacy hypothesis’ [5] asserts that positive and negative affective reactions can be evoked with minimal stimulus input and virtually no cognitive processing. Olfactory signals seem to induce emotional reactions whether or not a chemical stimulus is consciously perceived. We theorize that the importance of human non-verbal signals is based upon information processing, which occurs in the limbic system, and without any cognitive (cortical) assessment. Affect thus does not require conscious interpretation of signal content. Underlying this fact is that affect dominates social interaction and it is the major currency in social interactions [6]. Affective reactions can occur without extensive perceptual and cognitive encoding. They are made with greater confidence than cognitive judgments, and can be made sooner [5, 7]. Olfactory input from the social environment is well adapted to fit such assertions. For example, chemical cues allow humans to select for, and to mate for, traits of reproductive fitness that cannot be assessed simply from visual cues.

See also: The RNA Age: A Primer
What is currently known about energy-dependent biophysically constrained RNA-mediated cell type differentiation refutes every aspect of neo-Darwinian evolution by placing natural selection for codon optimality and the pheromone-controlled physiology of reproduction first.
All published works and reviews of RNA-mediated events must be placed into the context of the paradigm shift that led to the development of this game.
Cytosis: A Cell Biology Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

Some researches may continue to ignore details about energy-dependent RNA-mediated protection from virus-driven energy theft; the degradation of messenger RNA; and the pathology that is linked from mutations to the loss of enzymes, hormones and receptors in all living genera.
Others will obfuscate what is known to serious scientists.
See for comparison: Ontological Systems In Cognition

There is investigated the possibility of cognition of everything that somehow and other is able to influence to the cognizer – its Existing, which exists for him and may be cognized by him. It is proved that all parts of the Existing are interconnected, it is closed and is the only one for all cognizers in it, and everything differed from the Existing is indistinguishable for the cognizer from non-Existing and cannot be cognized by him. It is shown that the surrounding world of the cognizer, understood as a collection of objects and interconnections identified by him, corresponds to the cognizer’s `nature’ – its ontology and are only a part of the Existing. Objects and interconnections of different ontology differ from each other on level of notions, so are uncertain, inconsistent and paradoxical in relation to each other, and corresponding systems of representations with definite ontology cannot be unified in frames of one system, so are irredundant with each other. There are found the correlations of physical objects of quantum theories, also as cosmological dark matter and dark energy with objects with different ontology. There are analyzed the methods of mathematical description of objects with different ontology, the so-called `correlation principle’ of physical theories in irredundant systems of representations, the `principle of freedom’ for formation of the universe understood as the surrounding world of the cognizer. There are considered the philosophical aspects of the existence of irredundant representations, the physical picture of the world, which this concept leads to. The surrounding worlds corresponding to irredundant representation systems, being parts of the one Existing, are closely interconnected, mutually complemented and form each other, without mixing and being different `by nature’, and contradictions between them stand as moving forces of their evolution.

All aspects of anything that has ever been linked to the “moving forces” of evolution have clearly been linked from food energy and movement to biodiversity and from stress-related virus-driven energy theft to mutations that link the lack of movement at the molecular level to all pathology.
See for instance: Valerie Horsley Gets Under Skin

The Yale University cell and molecular biologist is probing the deep mysteries of epidermal cells.

My comment:
See also: Brain on stress: How the social environment gets under the skin

The authors note that on page 17184, right column, first paragraph, line 4, “effect” should instead appear as “affect.”

The failure to provide a neurobiological framework for understanding natural selection for energy-dependent codon optimality, which is the basis for the biological embedding of epigenetically-effected positive health, positive affect, self-efficacy and self-esteem via effects on reactive alleles in the genome, continues to link all pathology from the virus-driven degradation of messenger RNA to the negative supercoiling of DNA.
No one asked me to establish that framework for healthy longevity or pathology, but I did it anyway after I was told to start with gene activation in GnRH neuroscrectory neurons by Bruce McEwen.
See also: Genome Digest

What researchers are learning as they sequence, map, and decode species’ genomes

The researchers found that genes involved in key survival functions, such as the removal of cellular toxins, the stabilization of proteins, and the activity of the innate immune system, were expanded in deep-sea mussels.

Anna Di Cosmo’s group presciently placed these finding into the context of General and Comparative Endocrinology in Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000). — p. 61

The fact that the energy-dependent stability of RNA-mediated protein folding chemistry links physics from autophagy to biophysically constrained viral latency went missing during the past 4 years, but is not likely to continue to be ignored.
See why: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Conclusion:

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

There is still no other model for comparison, despite the publication of Mutation-Driven Evolution on the same day my 2013 review was published.

(1) Mutation is the source of all genetic variation on which any form of evolution is dependent. 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.

That claim differentiates ridiculous theories from my model of biophysically constrained biologically-based cause and effect. The differences were noted in 1991 when Roger Penrose wrote:

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? – From What is Life? (reprint edition)

See also: The Latest Discovery In Quantum Physics Shows Reality Is Not What It Seems

New experiments and studies conducted in laboratories such as CERN seem to suggest that everything is actually composed of energy rather than material particles, including human beings.
rp_PO9583119-frontl.png

Epigenetically-effected nucleosome repositioning sheds Dobzhansky's light on evolution

Crystal structure of the overlapping dinucleosome composed of hexasome and octasome

My summary: Nucleosomes are dynamic entities that are repositioned by energy-dependent links from sunlight to ATP and RNA biosynthesis that act on DNA during the chromatin remodeling, which is biophysically constrained by the pheromone-controlled physiology of reproduction during the transgenerational epigenetic inheritance of all morphological and behavioral phentoypes. processes.

Reported as: Unveiling how nucleosome repositioning occurs to shed light on genetic diseases

…an incomplete formation of overlapping dinucleosome may trigger abnormalities in the genetic switch, turning normal cells into tumor cells. Accordingly, understanding the atomic structure of the overlapping dinucleosome may provide valuable information for understanding how the abnormal dynamics of chromatin are related to cancer…

The atomic structure of the dinucleosome is energy-dependent. The atomic structure links the sun’s anti-entropic virucidal energy to all healthy longevity via endogenous RNA interference (RNAi). RNAi is is the nutrient energy-dependent link from atoms to ecosystems via what is known to all serious scientists about supercoiled DNA. Virus-driven energy theft causes the incomplete formation of the overlapping dinucleosome and all pathology in all living genera.
See for comparison my invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

See also: Structural diversity of supercoiled DNA and the parody from the Zechiedrich lab.

Nothing in Biology Makes Any Sense Except in the Light of Evolution

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

Combating Evolution to Fight Disease

It’s time for biophysicists to tell theorists and pathologists how to differentiate between theories about the genesis of different cell types and the biological facts about the nutrient-dependent pheromone-controlled ecological adaptations that enable the genesis of different cell types in individuals of different species. Simply put, it’s time to stop trying to explain ecological adaptations in the context of mutations and evolution.

Feedback loops link odor and pheromone signaling with reproduction
Roles of differential expression of microRNA-21-3p and microRNA-433 in FSH regulation in rat anterior pituitary cells

Taken together, our results show that both miR-21-3p and miR-433 down-regulate FSHb expression and cause FSH secretion decreased. These findings provide insights into the effects of the regulatory mechanisms of miRNAs on the reproductive functions of the pituitary.

FSH secretion links the nutrient energy-dependent pheromone-controlled epigenetic effects on endogenous RNA interference to healthy longevity and biodiversity in all vertebrates via the substitution of achiral glycine in position 6 of the gonadotropin releasing hormone decapeptide.
See also: Gonadotropin releasing hormone and human sexual behavior (1991)

Targeting Gut Bacteria May Be The Key To Preventing Alzheimer’s   (2/21/17)

…mice with Alzheimer’s have a different gut bacterial profile than those that do not have the disease.


 

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.