Alternative splicing of pre-mRNA

Trashing the 2nd Law

Summary: Autophagy is the antiphage defense strategy. (December 8, 2016) Other definitions no longer apply.
See: Experiment shows that arrow of time is a relative concept, not an absolute one
Everything that theorists were taught to believe about entropy was probably based on the ridiculous assumption that “…there are no correlations between particles.”
Everything known to serious scientists about energy-dependent autophagy shows that the creation of energy must be linked from the biophysically constrained physiology of pheromone-controlled reproduction via feedback loops that protect life from the virus-driven degradation of messenger RNA, which links mutations to all pathology.
See:
1) Olfaction Warps Visual Time Perception
2) Molecular recognition in olfaction
3) QuEBS 2018: Workshop on Quantum Effects in Biological Systems
Research in the intersection of physics, chemistry and biology has been developed for more than 20 years based on what is known about the creation of quantized energy as information and details of the quantum effects in biological light-harvesting systems, which have been linked from the sense of smell in bacteria to our visual perception of energy and mass in the context of the space-time continuum.
See for comparison: Bamboo Specialists from Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbes
Reported on December 6, 2017 as: Separated Since the Dinosaurs, Bamboo-Eating Lemurs, Pandas Share Common Gut Microbes

“This really underscores the role that diet plays in determining what lives in our guts – and, in turn, how these microbial ecosystems can shape the way animals live,” McKenney says.

Microbial ecosystems are food energy-dependent and the pheromone-controlled physiology of reproduction biophysically constrains viral latency. Without the pheromone-controlled physiology of food energy-dependent reproduction, bacteriophages and the virus-driven theft of quantized energy would link mutations to loss of functional structures that protect organized genomes from the degradation of messenger RNA. Everything known about cell type differentiation in all living genera has been placed into the context of links from physics and chemistry to molecular epigenetics via what is known about supercoiled DNA.
For comparison, see this claim:

“The bamboo lemur’s evolutionary tree diverged from that of both panda species 83 million years ago – that’s 18 million years before dinosaurs went extinct,” says Erin McKenney, a postdoctoral researcher at North Carolina State University and lead author of a paper on the study. “These species are also separated by thousands of miles and the Indian Ocean. Red pandas and giant pandas aren’t closely related either, with their most recent ancestor coming 47.5 million years ago. Lemurs are primates, red pandas are related to raccoons, and pandas are related to bears.

“Yet all three species share these 48 gut microbes – more than 12 percent of the microbial types found in each species’ gut,” McKenney says. “The only common feature is their diet: all three species live almost exclusively on bamboo.”

The common feature was presented in this 2013 review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which is a refutation of all neo-Darwinian pseudoscientific nonsense, and also a refutation of the ridiculous misrepresentations of “Big Bang” cosmologists. Those misereqpresentations led to two retractions of works published by Jack Szostak’s group in which false claims were made about non-enzymatic RNA replication.
See for comparison to what is known about the links from food energy to the pheromone-controlled physioloy of reproduction in species from microbes to humans: Altered responses to social chemosignals in autism spectrum disorder
reported as: Study: Autism Linked with Different Reactions to Chemical Signals
Conclusion:

“we speculate that social dysosmia may underlie part of the impaired reading of emotional cues in ASD.”

See for comparison: Global Sensory Impairment Predicts Morbidity and Mortality in Older U.S. Adults
Reported as: Problems with senses may predict older adults’ overall health, ability to function

Until now, no studies have examined how losing multiple senses affects older adults. To learn more, a team of researchers from the University of Chicago [including Martha McClintock] designed a study to focus on just that. Their study was published in the Journal of the American Geriatrics Society.

Problems with the senses are tractable to differences in the energy-dependent changes in base pairs that link changes in the microRNA/messenger RNA balance from RNA editing to the pheromone-controlled fixation of amino acid substitutions that stabilize the organized genomes of all living genera by protecting the organized genomes from the virus-driven degradation of messenger RNA.
See: Structural diversity of supercoiled DNA
The complexity of the interactions was again recently placed into the context of quantum correlations — with new insights.

Reversing the thermodynamic arrow of time using quantum correlations 

…standard thermodynamics presupposes the absence of initial correlations between interacting systems. We here experimentally demonstrate the reversal of the arrow of time for two initially quantum correlated spins-1/2, prepared in local thermal states at different temperatures, employing a Nuclear Magnetic Resonance setup. We observe a spontaneous heat flow from the cold to the hot system. This process is enabled by a trade off between correlations and entropy that we quantify with information-theoretical quantities.

They linked the creation of the sun’s anti-entropic virucidal energy from the physiology of food energy-dependent pheromone-controlled reproduction to biophysically constrained viral latency in all living genera. Constrained viral latency exemplifies the constrained entropy that Schrodinger placed into the context of What is Life? (1944). The updated version of his work was reported as: Experiment shows that arrow of time is a relative concept, not an absolute one

The idea of entangled particles has been in the news a lot lately as researchers around the world attempt to use it for various purposes—but there is another lesser-known property of particles that is similar in nature, but slightly different. It is when particles become correlated, which means they become linked in ways that do not happen in the larger world. Like entanglement, correlated particles share information, though it is not as strong of a bond. In this new experiment, the researchers used this property to change the direction of the arrow of time.

Everything known to serious scientists about biophysically constrained energy-dependent RNA-mediated pheromone-controlled entropy (aka the “arrow of time”) is now referred to in the context of autophagy, which links the food energy-dependent fixation of amino acid substitutions to healthy longevity during species-specific developmental staging in species from microbes to humans.

See:Micro RNAs mir-184 and let-7 alter Drosophila metabolism and longevity

… adult-specific overexpression of let-7 in female nervous tissue increased median fly lifespan by ~22%. We provide evidence that this lifespan extension is not due to alterations in nutrient intake or to decreased insulin signaling.

That fact about biophysically constrained entropy (autophagy/the “arrow of time”)  replaces all theories about the emergence of life and evolution of biodiversity. Ridiculous theories were based on the 2nd Law of Thermodynamics, which assumes there are no correlations between subatomic particles. Darwin’s “conditions of life” and “Kohl’s Laws of Biology” show that the correlations are manifested at every level of examination.

See: Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels

The feedback controls energy-dependent differences in H2, which consists of two different hydrogens. Control begins at the level of subatomic particles. The controlled differences link the speed of light on contact with water (H20) to all biodiversity via the physiology of pheromone-controlled reproduction. That fact is exemplified in Drosophila and in the Amish population of Berne, Indiana. That modern human population manifests a nutrient energy-dependent pheromone-controlled 10-year increase in their  RNA-mediated lifespan.

The claim that “A null mutation in SERPINE1 protects against biological aging in humans” can be viewed in the context of what Richard Feynman claimed about human idiocy. Mathematical models of energy-dependent biophysically constrained entropy link autophagy to healthy longevity. They link the virus-driven degradation of messenger RNA from mutations to all pathology. Only biologically uninformed science idiots publish research that supports ideas about mutation-driven evolution.


Few intelligent people would argue against the fact that life is food energy-dependent. But see: 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.

My understanding is based on an understanding shared by many scientists and non-scientists, but no pseudoscientists.
Whether or not non-scientists know the facts about RNA-mediated cell type differentiation, they are not likely to believe that the selection of what to eat by the organisms that eat it is the most critical factor in species survival. That helps to explain why: A third of Americans don’t believe in evolution
My comment:

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

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

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

See also the attack on my scientific credibility by PZ Myers and his idiot minions: One crank dies, another rises to take his place (2014)

Is alternative splicing the only mechanism to create variants in cells? No, of course not. External signals cause changes in the phosphorylation state of proteins in the cytoplasm, for example, that can affect metabolic activity; no alternative splicing involved. Signals can also switch on and switch off specific genes, again, no alternative splicing needed.

Most of the serious scientists I know laugh at people like PZ Myers. Some of them use sarcasm to address the ignorance of pseudoscientists. For example, see: A not entirely serious future history of neuroscience (2017)
Sarcasm alert. Thanks to Luca Turin for calling attention to this.
Excerpt 1)

Author’s note: resting for a moment in a dark corner of the Society for Neuroscience conference’s poster hall, on the quiet solitude of the Wednesday afternoon in the History of Neuroscience aisle, a shambling figure, bent with age, appeared with a speed that belied his years. Suddenly lunging for me, he shoved a sheaf of papers into my hand, hissing in my ear “it gets worse — so much worse”. Startled, I glanced at the front page, and the date written at the top: 6th October 2106. “What is…” I began, but he’d already whirled away — “A warning!” he spat back over his shoulder. Then he stopped, growled “I hate this bit”, squeezed his conference badge — and vanished.
What follows is the text I have been able to reconstruct from those crumpled, torn, faded pages.

Excerpt 2)

2037: Janelia Farm announces its Drosophila model of schizophrenia. HHMI instructs it to diversify its range of species.

My addendum: Electron spin changes during general anesthesia in Drosophila (2014)

Back to the future: The insect-to-elephant model of pheromone-controlled biophysically constrained viral latency is abandoned, again. Insect pheromone in elephants

The insect-to-elephant model of the food energy-dependent pheromone-controlled physiology of reproduction links alternative splicing of pre-mRNA, which now are called microRNAs by all serious scientists, to survival of all individuals in all species. The virus-driven degradation of messenger RNA links mutations to all pathology.

When should you unfriend someone on Facebook?

What we need to remember is that the devil is in the details.

Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990)
See for comparison: An Evolving Approach: The Public Response to Darwinism at Abilene Christian University, 1935-1989 (Stone-Campbell Journal 20:2, 2017)
Only by ignoring everything that has been learned about energy-dependent RNA-mediated biophysically constrained viral latency can historians and other pseudoscientists  continue to tout their ridiculous theories.
 

Alternative splicing of pre-mRNA

MicroRNAs and the Cassandra syndrome (revisited)

Conclusion: Serious scientists can explain every aspect of energy-dependent biophysically constrained viral latency in the context of details about these pathways and everything that links changes from electrons to ecosystems in all living genera. Why are the serious scientists still challenged by “…the tendency of academia to reject any academic-like work from outside academia?” What aspect of the academic contribution that could lead to the cure for all pathology do biologically uninformed academics want to continue to reject and attack?
See: Creating genes and species

The “Cassandra syndrome” theme prevails throughout the history of all serious scientists. They are cursed with being able to predict the future because they are always disbelieved.

See for instance: Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice
The authors claim that differential effects of m6A may depend on interactions between microRNAs and cis-acting elements that are present on the RNA molecule.
Simply put, the interactions are energy-dependent and RNA-mediated. Pseudoscientists do not know where the energy came from that creates new cells and they do not know what kills the new cells.
But see: When You Learn, Your Brain Swells with New Cells — Then It Kills Them

In a new opinion paper, published online Nov. 14 in the journal Trends in Cognitive Sciences, researchers proposed that this swelling and shrinking of the brain is a Darwinian process.

The claim that this is a Darwinian process comes from: Expansion and Renormalization of Human Brain Structure During Skill Acquisition

MRIs use complex physics to peer through the walls of the skull into the brain.

Jaak Panksepp’s group won the 2002 award that my group won in 2001 for publication of Human pheromones: integrating neuroendocrinology and ethology. See for comparison:

If you don’t understand the foundational level, then you can do brain imaging until you’re blue in the face, but you still will not understand the process at a deep causal level. — Dr. Jaak Panksepp, Author of Affective Neuroscience: The Foundations of Human and Animal Emotions

The foundational level is food energy-dependent. See RNA-mediated.com or the FB group RNA mediated.
See the missing foundational level extended from a Darwinian process of swelling and shrinking of the brain to claims about human evolution.
From the Human Ethology Yahoo Group moderated by Jay Feierman.
Human evolution was uneven and punctuated, suggests new research

…this process was not a straightforward, smooth one – instead, it seems to have been punctuated, with different evolutionary patterns in different geographical regions.

More than 1300 hemoglobin variants attest to the obvious fact that evolutionary theorists cannot recognize any pattern that links food energy from what humans eat to the biophysically constrained pheromone-controlled physiology of reproduction. They ignore every aspect of food energy-dependent RNA-mediated amino acid substitutions, which protect all organized genomes from the virus-driven degradation of messenger RNA. The degradation of messenger RNA links mutations to all pathology.
See for examples of food energy-dependent pathology prevention: HbVar: A Database of Human Hemoglobin Variants and Thalassemias
To place food energy-dependent prevention of pathology into the perspective of difference in primates, see:

For example, 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).”

See also: Humans And Chimps Differ At Level Of Gene Splicing
The fact that gene splicing is linked to a single amino acid that differentiates the cell types of 2 primate species from the gorilla, led me to ask: What do other people do when they learn that everything they were taught to believe about evolution is a lie?
I placed the question to the Neuroscience FB group into this context: The Academic Ape: Instinctive aggression and boundary enforcing behaviour in academia

The Cassandra Effect describes the tendency of academia to reject any academic-like work from outside academia and that the more “academic” the contribution, the more strongly it is rejected and attacked.

This is the accurate representation of food energy-dependent pheromone-controlled learning and memory that has consistently been attacked or ignored since the time we published our 1996 Hormones and Behavior review. In our section on molecular epigenetics, we wrote:

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to….

Alternative splicing techniques of pre-mRNA have since been linked to every aspect of cell type differentiation in all individuals of all species. The pre-mRNAs are called microRNAs and detailed examples of how food energy-dependent changes in the microRNA/messenger RNA balance can be linked to what has been known about RNA-mediated cell type differentiation to serious scientists. For example, serious scientists know that all changes in the microRNA/messenger RNA balance are energy-dependent. No changes are random. All changes are biophysically constrained. The changes constrain viral latency. That fact has been established in more than 67,000 indexed published works.

See: microRNA Items: 1 to 20 of 67307

What do theorists do when they are repeatedly presented with overwhelming experimental evidence that links food energy-dependent microRNAs to refutation of all their ridiculous theories and all the pseudoscientific nonsense of neo-Darwinian evolution?

 

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.”

See for comparison: Food derived microRNAs
and

 
See also: Exploitation of microRNAs by Japanese Encephalitis Virus in human microglial cells

The microRNA gene targets, gene ontology, annotations and pathways were identified through various bioinformatics tools. Additionally, the pathways were mostly found common to “ubiquitin mediated proteolysis”, “cytokine signaling”, “maintenance of barrier function/cell junctions”, JAK/STAT pathway” “Toll-like receptor signaling”, “Wnt-signaling”, “adhesion molecules”, “apoptosis”, “endocytosis”, “vesicle mediated transport” etc.

Serious scientists can explain every aspect of energy-dependent biophysically constrained viral latency in the context of details about these pathways and everything that links changes from electrons to ecosystems in all living genera. Why are the serious scientists still challenged by “…the tendency of academia to reject any academic-like work from outside academia?” What aspect of the academic contribution that could lead to the cure for all pathology do biologically uninformed academics want to continue to reject and attack?

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

The next reformation: 500 years too late? (1)

Summary: The next reformation links the creation of the sense of smell to all biodiversity in the context of biophysically constrained viral latency.
The vibrational theory of olfaction for the win

Although there is nothing comparable to this kind of insight into the molecular world of scent within the shapist mentality, we should probably thank its supporters for making this battle of ideas so epic. There may yet be time for two more big events in the field, one a Nobel party [for Luca Turin], and the other, a funeral [for shape theory].

Shape theory has been touted in the context of the Watson and Crick model of the static DNA double helix. All serious scientists have since dismissed that ridiculous model. I admit, however, that in my review of the book, The Emperor of Scent, which was about Luca Turin, I was critical of his correct approach. But Wen Zhou’s group has since linked Turin’s claims from the creation of sunlight to the creation of ATP and the creation of RNA. The extension from the creation of RNA to the creation of olfactory receptors links the time-space continuum to the pheromone-controlled physiology of reproduction and all biodiversity via feedback loops.
That was expected by every serious scientist I know. The serious scientists know that gene activation is energy-dependent. They do not link sudden energy jumps from de Vries (1902) definition of mutation to all biodiversity. The next reformation links the creation of the sense of smell to all biodiversity in the context of biophysically constrained viral latency.
See: The next reformation: 500 years too late? (2)

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

The next reformation: 500 years too late? (2)

The problem for those who use definitions is that everything known about the links from food energy-dependent changes in electrons to ecosystems must now be ignored. Last week, publications in Nature and in Science linked energy-dependent changes in base editing to RNA editing, which means that all the ignorance of biologically uninformed theorists can be placed into the context of Feynman’s claims about “human idiocy.”
See also: RNA editing and alternative splicing: the importance of co-transcriptional coordination
Apparently, the theorists did not think the facts about energy-dependent RNA editing and alternative splicings of pre-mRNA would be detailed.
But see for comparison: James Kohl reviews: The Emperor of Scent: A Story of Perfume, Obsession and the Last Mystery of the Senses

More than a century ago, in 1900, Max Planck, one of the greatest physicists of all time, announced his revolutionary new scientific theory of an energy constant in quantum mechanics. Eighteen years later he was awarded a Nobel Prize.

As Luca Turin waits for his rewards/award, he and others may benefit from knowing more about Planck’s attitude: “…a new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”

See also the review by Avery Gilbert: a human pheromone-denier (per Leslie Vosshall). The link opens the .pdf
Gilbert, A.N. 2003. The emperor’s new theory. Review of “The emperor of scent: A story of perfume, obsession, and the last mystery of the senses”, by Chandler Burr. Nature Neuroscience 6:335.
Gilbert’s conclusion:

Against this reality, Emperor of Scent represents a triumphalist account of an unproven alternate theory. In ancient Rome, the honor of a triumph was reserved for an emperor who achieved a glorious victory. Should Turin’s conjecture prove correct, he will of course deserve one. But until then, this appears to be a case of premature adulation.

Gilbert’s claims about premature adulation can be compared to the claims of other pseudoscientists. Serious scientists have not been afraid to link claims of adulation from the creation of energy to the creation of all biodiversity via the physiology of reproduction. The serious scientists linked Turin’s theory to every aspect of energy-dependent biophysically constrained biodiversity via the feedback loops that link the sense of smell from the pheromone-controlled physiology of reproduction to viral latency.
See: Feedback loops link odor and pheromone signaling with reproduction
Even those who might not have believed that Luca Turin correctly represented energy-dependent top-down causation in the context of links from quantum physics to chemistry and all biologically-based diversity had little doubt that food odors and pheromones are the obvious link from olfaction to survival of all species.
The next reformation: 500 years too late? (3)

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

From base editing to RNA editing

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

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

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

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

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

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

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

Cryo-EM from atoms to ecosystems

Summary: I’m not going to continue repeating myself indefinitely. See: Reduced protein synthesis in schizophrenia patient-derived olfactory cells
The reduced protein synthesis is a clear link from the virus-driven degradation of messenger RNA to all pathology.


October 5, 2017 Lactate Metabolism in Human Lung Tumors
Reported as: Study challenges long-standing concept in cancer metabolism

“We were completely shocked by our findings,” said Dr. Ralph DeBerardinis, Professor at CRI, Director of CRI’s Genetic and Metabolic Disease Program, and Chief of the Division of Pediatric Genetics and Metabolism at UT Southwestern. “The oldest observation in cancer metabolism, the Warburg effect, says that lactate is a waste product of the tumor. This concept has driven the vast amount of research in the field. Our finding is a fundamental change in how we think about tumor metabolism.”

The fact that these so-called experts know so little about metabolism and cancer can be viewed in the context of what is known about all the links from energy-dependent changes in atoms to ecosystems in all living genera.
See: Atomic structure reveals how cells translate environmental signals
The team identified an amino acid sequence in the leaflet that is conserved in parasites, suggesting structural insights that may assist in drug discovery for these devastating conditions.
See, for instance: The Supraspliceosome – A Multi-Task Machine for Regulated Pre-mRNA Processing in the Cell Nucleus
See also: Mitochondrial ribosome assembly in health and disease
There is an obvious need to link the conserved amino acid sequence in parasites to healthy longevity via mitochondrial ribosome assembly and from the virus-driven energy theft of quantized energy as information to all pathology via cryo-EM.See: Inching toward the 3D genome

Re: “…the nucleome structure changes as cells age, differentiate, and divide, and researchers want to understand how and why.”

Cell type differentiation is nutrient-dependent. RNA-directed DNA methylation links RNA-mediated amino acid substitutions to cell type differentiation via protein folding during life history transitions. Amino acid substitutions stabilize protein folding; mutations perturb it, during nutrient-dependent theromodynamic cycles of protein biosynthesis and degradation.

Life is physics and chemistry and communication — http://dx.doi.org/10.1111/nyas.12570

The metabolism of nutrients links metabolic networks to genetic networks via species-specific pheromones that control the physiology of reproduction. Simply put, pheromones link nutrient-dependent life via physics, chemistry, and the conserved molecular mechanisms of communication in species from microbes to man.

Until nutrient-dependent protein folding is linked via the conserved molecular mechanisms of amino acid substitutions and pheromone-controlled DNA stability in organized genomes, which links the epigenetic landscape to the physical landscape of DNA, researchers must take a piece-meal approach to integrating the requirements for life and successful life history transitions — despite the fact that life history transitions have been detailed in the context of the honeybee model organism. See: Honey bees as a model for understanding mechanisms of life history transitions http://www.ncbi.nlm.nih.gov/pubmed/15925525

I’m not going to continue repeating myself, indefinitely.
See: Reduced protein synthesis in schizophrenia patient-derived olfactory cells
The reduced protein synthesis is a clear link from the virus-driven degradation of messenger RNA to all pathology
For comparison see:
Re: Flaming by Glen Sizemore on the evolutionary-psychology group msg 89218
Jay R. Feierman: Being nasty and unkind is not a good strategy in an academic discussion or in human relations in general.”
Glen Sizemore: Yeah…but this isn’t a discussion. It is me ridiculing your hopelessly-moronic views.
Jay R. Feierman [NEW]: The problem is that your unkind and nasty remarks are not just directed at me. When you used to be on the human ethology group before you were removed they were directed at others as well. As moderator of the human-ethology group, I used to not post many of your comments for flaming related to many different people. On the evolutionary-psychology group, where Robert Karl Stonjek appears to have much more tolerance for flaming, your unkind and nasty comments are directed toward many other people, including Robert Karl Stonjek, the moderator. Life is too short to deal with people like you. I prefer to deal with nice people in my life and try to surround my self with nice and kind people. As a result, even though you often bring up interesting issues in your postings related to what I’ve posted, I am no longer going to respond to anything you write.
My response:89219
Please place your comments about me into the context of any “nasty” comment by others.
For example: 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.  https://groups.yahoo.com/neo/groups/human-ethology/conversations/topics/48182
My interpretation: You called me a biologically uniformed science idiot.
See also: 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.  https://groups.yahoo.com/neo/groups/human-ethology/conversations/topics/48229
My interpretation: You claimed that every professor of biology or genetics in any accredited university anywhere in the world knew more than me about my established area of expertise: RNA-mediated cell type differentiation.
The final solution???

Excerpt: Emerging evidence suggests that ecological heterogeneity across space can influence the genetic structure of populations, including that of long-distance dispersers such as large carnivores.
My comment: Indeed, the emerging evidence actually refutes all the neo-Darwinian nonsense of population genetics . . . etc., etc.
[MODERATOR NOTE: I’m not going to post more from Kohl until he answers the very direct and simple question posed to him by anon, which is whether he (Kohl) believes that RNA splicing can change DNA.] 10/6/17

Until today, I did not respond to Feierman’s hopelessly-moronic question about my beliefs.
 
He continued to edit or block any attempts to promote intelligent discussion in the Human Ethology Yahoo Group. And finally, after the 2017 Nobel Prize in Chemistry was awarded to the researchers who developed the cryo-EM tecnology, I can say this:
 

The fact that alternative splicings of pre-mRNA causes changes in DNA was central to the facts about cell type differentiation we placed into the context of the molecular epigenetics section of this 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html

Feierman did not post my reply to the question about alternative splicings of pre-mRNA.  Instead, he is continuing to ignore everything known to serious scientists about biologically based cause and effect, or to present it in a series of disparate attempts to obfuscate the facts about energy-dependent top-down causation and the pheromone-controlled physiology of reproduction, which helps to biophysically constrains the transgenerational epigenetic inheritance of all diseases.

Today he posted this link to the Human Ethology Yahoo Group

Smell or vision? The use of different sensory modalities in predator discrimination

The information animals obtain about potential predation risk may differ qualitatively depending on the sensory modality by which a cue is perceived.

Facts about multisensory integration were published as:

Global Sensory Impairment Predicts Morbidity and Mortality in Older U.S. Adults

and Olfaction Warps Visual Time Perception

Feierman also posted a link to: Local mating markets in humans and non-human animals

Biological market theory (BMT), which deals with cooperation among unrelated agents in general, is combined with sexual selection theory (SST), which deals with reproductive cooperation, to focus on an aspect that received little attention in the vast SST literature: adaptations that improve mating success when the market value of an individual varies considerably from one local mating market (LMM) to the next.

This, too: Divergence of developmental trajectories is triggered interactively by early social and ecological experience in a cooperative breeder

We found that individuals did specialize in distinct behavioral competences, which led to either delayed dispersal or early independent breeding. The divergence into different behavioral trajectories became apparent only by manipulating both early social and ecological experiences, highlighting the importance of multivariate influences on the development of social trajectories.

There are many different ways to claim that what organisms eat leads to the production of species-specific behaviors via ecological variation that must be linked to the pheromone-controlled physiology of reproduction. Feierman, and others like him, will continue to cite works that obfuscate the facts about cause and effect that have been known to all serious scientists since the time that McEwen et al., (1964) linked the creation of energy from the creation of ATP to the creation of RNA and all biophysically constrained biodiversity.

See: 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.

Feierman, and all other biologically uninformed science idiots are not going to admit that they were wrong about everything they ever claimed.

A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”

Alternative splicing of pre-mRNA

Predicting who wins the 2017 Nobel Prizes (3)

Summary: The unique mechanism detailed in the context of “Roles of APOBEC3A and APOBEC3B in Human Papillomavirus Infection and Disease Progression” is obviously not a unique mechanism. The mechanism exemplifies the fact that RNA-directed DNA methylation is energy-dependent and the fact that virus-driven energy theft causes the degradation of messenger RNA, which serious scientists have linked to all pathology.
My failure to accurately predict who would win the 2017 Nobel Prize in Physiology or Medicine can now be placed into the context of more experimental evidence of biophysically constrained energy-dependent pheromone-controlled biologically-based cause and effect.
I mentioned the evidence published on 21 August 2017 as Roles of APOBEC3A and APOBEC3B in Human Papillomavirus Infection and Disease Progression in the context of my blog post about Viral infection linked to cancer via a “unique mechanism,” which was reported as: “Unique mechanism links viral infection by HPV with cancer through function of a single enzyme

The so-called unique mechanism is obviously the virus-driven degradation of messenger RNA, which has repeatedly been linked to all pathology, including the suicides of veterans who have served overseas.

See also experimental evidence of virus-driven degradation portrayed in the 2 October 2017 publication: Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability

Drosophila embryos with trr alleles encoding catalytic mutants manifest subtle developmental abnormalities when subjected to temperature stress or altered cohesin levels. Collectively, our findings suggest that animal development can occur in the context of Trr or mammalian COMPASS-like proteins deficient in H3K4 monomethylation activity and point to a possible role for H3K4me1 on cis-regulatory elements in specific settings to fine-tune transcriptional regulation in response to environmental stress.

The ability to fine-tune transcriptional regulation via energy-dependent changes in RNA-directed DNA methylation was reported as: Unexpected findings uncover new understanding of gene expression

“What is it about the whole body of the enzyme itself that functions in development and its mutations that can result in cancer? That’s what we need to figure out.”

Thanks for asking. The unique mechanism detailed in the context of Roles of APOBEC3A and APOBEC3B in Human Papillomavirus Infection and Disease Progression is obviously not a unique mechanism. The mechanism exemplifies the fact that RNA-directed DNA methylation is energy-dependent and the fact that virus-driven energy theft causes the degradation of messenger RNA, which serious scientists have linked to all pathology.
Clearly, the serious scientists are not asking questions about energy-dependent RNA-mediated cell type differentiation or attempting to place what is known back into the context of theories about the role of “enhancers.”
There are now more than 65,000 indexed published works that link pre-mRNAs, which are also called microRNAs, to biophysically constrained protein folding chemistry via the physiology of pheromone-controlled reproduction in species from microbes to humans. See for examples: microRNA or pre mrna.
Theorists and/or other biologically uninformed science idiots who use terms like enhancers, promoters, QTLs, et al., in their attempts to obfuscate what is known to serious scientists about the biophysically constrained energy of supercoiled DNA will be faced with the possibility of even more ridicule than was delivered in the context of this parody.

 
 
 

For God and Country

Life and death via chemical effects on photosynthesis

Summay: “…chemosignals are a promising approach both to modeling posttraumatic stress disorders in humans [36] and to searching for mehods of their treatment.”
Serious scientists linked the sense of smell in bacteria from the physiology of pheromone-controlled reproduction in all living genera to our visual perception of energy and mass in the context of the space time continuum.
The fact that food odors and pheromones biophysically constrain cell type differentiation in mammals was first placed into the context of [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] (1994)


For evidence of the link from the anti-entropic virucidal energy of sunlight to all biodiversity, see also: 1994 Effect of atrazine herbicide on growth, photosynthesis, protein synthesis, and fatty acid composition in the unicellular green alga Chlorella kessleri

Sublethal atrazine concentrations induced a general inhibition on growth, photosynthesis, and dark respiration in the green alga Chlorella kessleri….. Progressive reduction in protein synthesis was associated with increasing herbicide concentration at all experimental periods. The herbicide had preferential effect on the associated fatty acid composition of total and phospholipids. After 24 and 48 hr the herbicide stimulated fatty acids synthesis at concentrations where photosynthesis was inhibited. Meanwhile, stearic and miristic acids disappeared at 15 μM after 24 hr and the total polyunsaturated fatty acids were not affected after 48 hr. Fatty acid synthesis was sensitive to treatment at 72 hr by 5 and 10 μM atrazine, whereas the total saturated fatty acids were completely inhibited.

Sublethal effects of  chemicals on protein biosynthesis and degradation have been linked to all pathology via the virus-driven degradation of messenger RNA, which links changes in the microRNA/messenger RNA balance to mutations and all pathology. For example, this is what must happen to link the sun’s anti-entropic virucidal energy from electrons to ecosystems via the chemistry and physiology of pheromone-controlled reproduction in all living genera.

A dietary difference in nematodes links their chemistry of metabolism from what they eat to the pheromone-controlled physiology of reproduction in C. elegans and the ecological adaptations manifested in P. pacificus, a predatory nematode with teeth.
See other information on biophysically constrained biologically based cause and effect in Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

The epigenetic effects of nutrients on evolved differences in the diet and starch digestion of dogs and wolves (Axelsson et al., ) were detailed at the same time differences in the socialization of these subspecies were attributed to explorations involving only chemosensory input in 3 to 4-week-old wolf pups. For comparison, differences in starch digestion and exploration involving multisensory input in dogs begin a mere 2 weeks later (Lord, ). The differences in nutrient-dependent pheromone-controlled socialization, however, extend across a life-time of more aggressive behavior in wolves that have not been domesticated because less digested starch from their diet genetically predisposes infants to first respond to olfactory/pheromonal cues as they initially explore their postnatal environment.

See also: Dogs Recognize Themselves in Test Based on Smell, Not Sight

But, she said, her test and the mirror tests “all show that there’s this selective sensory investigation of something that comes from yourself, but is changed.”

The link from a light-induced change in an endogenous substrate — that comes from yourself — to the physiology of reproduction is changed by the pheromone-controlled physiology of reproduction, which is linked to all biodiversity.
That fact and facts about intelligence in different species started to become clear when Schrodinger (1944) wrote:

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

Perfect clarity was achieved among all intelligent serious scientists when McEwen et al, (1964) wrote; 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.

Nothing in life happens outside the context of the ATP-dependent creation of RNA.
Decades later, 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?” (Roger Penrose 8 August 1991)

See also: Olfaction Warps Visual Time Perception
The authors linked the sense of smell in bacteria from the physiology of pheromone-controlled reproduction in all living genera to our visual perception of energy and mass in the context of the space time continuum.
The fact that food odors and pheromones biophysically constrain cell type differentiation in mammals was first placed into the context of [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] (1994) in Russian
Abstract excerpt (in English)

The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

See also: [Cytogenetic effect of volatile components of urine of sexually mature animals on bone marrow cells of young female house mice Mus musculus L] (1996) in Russian

Effects of volatile components of the urine (VCU) of mature male and female CBA/LacStoRap mice on proliferating bone marrow cells in young females of the same line were analyzed.

In 2005,  a 2004 Nobel Laureate and her co-authors caught up to what researchers in Russia had already been claiming for 20 years. See: Feedback loops link odor and pheromone signaling with reproduction
See also: Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain (2014) with my emphasis

Humans also have various pheromone-induced physiological effects, especially those associated with reproduction [46, 47]. This suggests that the human olfactory system is still an effective pathway for influencing environmental factors on the human nervous system. Various psychoemotional states of the human nervous system can, in turn, disrupt the integrity of the chromosomal apparatus of target cells, for instance lymphocytes [41, 42]. Therefore, studies on the oppositely directional modulation of the mutagenic consequences of stress in rodents with the use of specific, volatile, and zoosocial important chemosignals are a promising approach both to modeling posttraumatic stress disorders in humans [36] and to searching for mehods of their treatment.

[46] is Kohl, J.V., Atzmueller, M., Fink, B., and Grammer, K., Human pheromones: integrating neuroendocrinology and ethology, Neuroendocrinol. Lett., 2001, vol. 22, pp. 309–321.
See also: Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems (2015)

Genetic monitoring of the environment is an important component in the analysis of the status of the biosystems. Its efficiency depends on the correct choice of (a) natural bioindicator species; (b) appropriate signs reflecting the state of the environment; and (c) appropriate statistical analysis. The assessment of genomes’ integrity plays the key role in the studies of mutagenicity in a polluted environment. We present a step-by-step recommendations for the analysis of the cytogenetic data and discuss the prospects of applying genetic tests for ecological monitoring, based on the example of analysis using crustacean species.

The nutrient energy-dependent pheromone-controlled ecological adaptations in all invertebrates and vertebrates were reviewed in the context of: Role of olfaction in Octopus vulgaris reproduction

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

See for comparison 1): Riding the Evolution Paradigm Shift With Eugene Koonin

“[T]he entire ideology of personalized medicine should be taken with many grains of salt. It’s not useless, it’s useful to sequence thousands of genomes. It’s useful to sequence everyone’s genome. It’s useful and desirable — yet, it’s wrong and to some degree dangerous to think that, by peering into the sequence of the A, G, T, and Cs in your genome, your family doctor is going to tell you how to treat all your conditions and what conditions you are going to develop, and which ones you are not going to develop, and so on.” — Eugene Koonin

See also for comparison 2): Riding the Evolution Paradigm Shift With Eugene Koonin

“The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…” — Eugene Koonin

The entire ideology of personalized medicine is based on what is known about how the anti-entropic virucidal energy of sunlight must be linked from endogenous RNA interference and foraging behavior to the physiology of biophysically constrained pheromone-controlled reproduction in species from microbes to humans. See this 7 minute representation from my Precision Medicine virtual conference presentation. Energy as information and constrained endogenous RNA interference (2017)
Do not be surprised if you cannot track the historical record of scientific advances in nutritional epigenetics from 1994 Effect of atrazine herbicide on growth, photosynthesis, protein synthesis, and fatty acid composition in the unicellular green alga Chlorella kessleri to the current representations of top-down causation and energy-dependent biophysically constrained biologically-based cause and effect. There are many pseudoscientists who will do everything possible to prevent you from learning that their ridiculous theories have never been supported by experimental evidence.
See for example: 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.”
See also: One crank dies, another rises to take his place by PZ Myers

I was asked to look at a string of comments left on a science article by a fellow going by the pseudonym JVK, and all the Davison traits were there. Pretentious phrasing. Repetition: if the audience didn’t get it the first time, just say the same thing again, twice. A kind of sneering anger that people don’t understand how smart he is. An obsession with one narrow idea, which is his, which explains all of evolution and proves that everyone else is wrong.
Behold James Vaughn Kohl.

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.
These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.
That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

Ecological adaptations are food energy-dependent and biophysically constrained in the context of biologically based chromosomal inheritance via the pheromone-controlled physiology of reproduction. There is only one model for that.
It’s my model:
Nutrient-dependent/pheromone-controlled adaptive evolution: a model
See for comparison: Interactome analysis reveals ZNF804A, a schizophrenia risk gene, as a novel component of protein translational machinery critical for embryonic neurodevelopment
Reported as: Gene associated with schizophrenia risk regulates neurodevelopment

A gene associated with the risk of schizophrenia regulates critical components of early brain development, according to a new study led by researchers from Penn State University. The gene is involved in the translation of proteins from RNA and in the proliferation and migration of neurons in the brain.

Gene regulation is energy-dependent and RNA-mediated. That fact is twisted into this misrepresentation: “The gene is involved in the translation of proteins from RNA and in the proliferation and migration of neurons in the brain.”

What they claim, in the most twisted way possible, is that the energy-dependent RNA-mediated translation of proteins must be linked to ecological adaptations via the proliferation and migration of neurons in the brain.

Alternative splicing of pre-mRNA

Pseudoscientists hate what science explains! (3)

See also: Pseudoscientists hate what science explains (2)
Summary: In addition to germline silencing via information transfer to the physical landscape of supercoiled DNA, multicopy transgene arrays are linked from changes in the microRNA/messenger RNA balance to variation in their somatic expression level. That fact helps to establish the difference between healthy longevity and pathology across generations.
Problems with DNA replication can cause epigenetic changes that may be inherited for several generations
My summary: The polycomb repressive complex 2, additional chromatin- and small RNA–related pathways carry quantized energy as information from the epigenetic landscape. The information causes changes in microRNAs that modify histones, which links the energy to the transgenerational epigenetic inheritance of morphological and behavioral phentypes in the nematode model organism.
In addition to germline silencing via information transfer to the physical landscape of supercoiled DNA, multicopy transgene arrays are linked from changes in the microRNA/messenger RNA balance to variation in their somatic expression level. That fact helps to establish the difference between healthy longevity and pathology across generations.
The difference is food energy-dependent, RNA-mediated, and biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera.
See for comparison: From Fertilization to Adult Sexual Behavior (1996)

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes…. Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans… That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

We propose that CNEs [conserved non-coding elements] represent the ‘hard-wired’ sequence traces of these core animal group-specific GRNs [gene regulatory networks]. The alternative core GRNs of different animal lineages are reflected in their having alternative CNEs. However, because of their co-evolution from a common metazoan ancestor, the core GRNs of different animal groups often utilize the same regulatory genes. As a result, distinct yet parallel sets of CNEs have become irreversibly associated with the same genes that coordinate core developmental networks in diverse animal groups. Indeed, this evolution of regulatory elements may underlie the astounding diversification of animal body plans that was seen during the Cambrian period approximately 550 million years ago.

No experimental evidence suggests that regulatory elements evolved.
Predicting phenotypic variation in yeast from individual genome sequences
No experimental evidence predicts a link from gain of function mutations to evolution
Differential DNA mismatch repair underlies mutation rate variation across the human genome
All experimental evidence links natural selection for energy-dependent codon optimality to mutation rate variation across species and to individual differences in the human genome via the pheromone-controlled physiology of reproduction.

3D structures of individual mammalian genomes studied by single-cell Hi-C

Reported as: Scientists have determined the 3D structures of intact mammalian genomes from individual cells, showing how the DNA from all the chromosomes intricately folds to fit together inside the cell nuclei. The research is published in Nature this week. http://go.nature.com/2n6psaw

My comments:

See also: 3D RNA and Functional Interactions from Evolutionary Couplings “…the ongoing explosion of available sequence data means that the outlook for elucidating functional interactions in mRNAs, lncRNAs, and viral genomes, as well as their protein-binding partners, is promising.” http://dx.doi.org/10.1016/j.cell.2016.03.030

Virus-driven energy theft causes the degradation of messenger RNA in all organized genomes. That fact threatens anyone who has ever reported results in the context of mutations, natural selection and evolution because natural selection occurs only for energy-dependent codon optimality.

It would be even more amazing if they told the truth about energy-dependent amino acid substitutions that stabilize supercoiled DNA, which links chromosomal rearrangement to all biodiversity via the physiology of reproduction in species from microbes to humans. See: http://science.sciencemag.org/content/355/6328/910

See other comments to this Nature Facebook page
Addendum: Say goodbye to mutation-driven evolution. Everything known to serious scientists about biophysically constrained endogenous RNA interference and the pheromone-controlled physiology of reproduction has been linked from the de novo creation of nucleic acids to energy-dependent amino acid substitutions that differentiate all cell types in all living genera via fixation in organized genomes.
See: Transgenerational transmission of environmental information in C. elegans
They link diet- and stress-induced changes in heterochromatin from repressed repetitive elements that escape epigenetic reprogramming to phenotypic variation in mammals. It is obvious that heterochromatin provides the link from the molecular mechanisms of biophysically constrained protein folding chemistry to the epigenetic transmission of information between generations. But they speculate that the transgenerational epigenetic inheritance of environmentally triggered changes in expression from repressed chromatin may be linked to ecological adaptations.
See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

 …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’.

Ben Lehner and his co-authors have consistently tried to sneak up from behind and link explanations of energy-dependent top-down causation from mutations to evolution.
Others are also ignoring the experimental evidence that links energy-dependent changes in microRNAs to healthy longevity or from virus-driven energy theft to all stress-linked pathology.
See: Stress-induced changes in miRNA biogenesis and functioning
See for comparison: I am not a story

Reported as: Life is not a neat narrative, it’s a patchwork of competing, even contradictory, forces. Sensations are too spurious and memory too fickle for the formation of reliable storylines. Reject the impulse to narrativise. Summer Reads from the Aeon archive: http://ow.ly/bLd430ekoJn

Re: Sensations are too spurious and memory too fickle for the formation of reliable storylines.

My comment: Too late for more of this nonsense. See: Olfaction Warps Visual Time Perception

 

The sense of smell in bacteria has been linked from the physiology of pheromone-controlled reproduction to our visual perception of mass and energy in the context of the space-time continuum via food energy.

See for comparison: Quantum common sense

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

My comment: No, it’s Santa Claus who sees you when your sleeping; He knows when you’re awake. And he knows if you’ve been bad or good, so be good for goodness sake.

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.