Cytosis

Long-term adaptation replaces evolution (2)

The food energy-dependent “doubling up” on ‘junk DNA’ is biophysically constrained by the physiology of pheromone-controlled reproduction. The metabolism of food to species-specific pheromones links the conserved molecular mechanisms of RNA-mediated cell type differentiation in all individuals of all living genera to healthy longevity via what is known about amino acid substitutions in supercoiled DNA, which link energy-dependent changes in chirality to autophagy.

See: It’s all about that base

The virus-driven degradation of messenger RNA in bacteria links top-down causation to what happens to archaea and L-forms in the context of the viral hecatomb, which links the destruction of G protein-coupled receptors to all pathology because the de novo creation of G protein-coupled receptors links the creation of the sense of smell to all biodiversity.

Our ability to detect differences in amino acid substitutions in the blood has been linked to the ability of flies to find food and to reproduce via the physiology of food-energy-dependent pheromone-controlled reproduction.

See: A mammalian blood odor component serves as an approach-avoidance cue across phylum border – from flies to humans
See also:

Adaptive evolution by spontaneous domain fusion and protein relocalization

Phenotypic heterogeneity promotes adaptive evolution

My 2013 model of energy-dependent ecological adaptations: Nutrient-dependent/pheromone-controlled adaptive evolution: a model refuted neo-Darwinian pseudoscientific nonsense. That that model is being revisited each day that another publication is added to those that link the energy-dependent de novo creation of microRNAs to all biodiversity via hydrogen-atom transfer in DNA base pairs in solution. See: microRNA

For example:Recent advances in signal amplification strategy based on oligonucleotide and nanomaterials for microRNA detection-a review.

See also:

Overview of microRNA biology. Mohr AM et al. Semin Liver Dis. (2015)

MicroRNA Therapeutics: the Next Magic Bullet? Simonson B et al. Mini Rev Med Chem. (2015)

MicroRNAs in cancer: biomarkers, functions and therapy. Hayes J et al. Trends Mol Med. (2014)

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

Predicting who wins the 2017 Nobel Prizes (5)

Summary: If he was not still dead, the 1965 Nobel Laureate, Richard P. Feynman might claim that this year’s Physics Prize was awarded for “human idiocy.”
Nobel Prize in Physics Awarded to LIGO Black Hole Researchers

Einstein’s General Theory of Relativity, pronounced in 1916, suggested that matter and energy would warp the geometry of space-time the way a heavy sleeper sags a mattress, producing the effect we call gravity. His equations described a universe in which space and time were dynamic.
 

Other claims in this article appear to arise in the context of the emergence of energy from nothing with no mention of the biophysical constraints that link food energy from electrons to ecosystems via the pheromone-controlled physiology of reproduction in species from microbes to humans.

If he was not still dead, the 1965 Nobel Laureate, Richard P. Feynman might claim that this year’s Physics Prize was awarded for “human idiocy.”

See:

 
Facts about Einstein’s “General Theory” have since been validated with experimental evidence of biologically-based cause and effect. See: Olfaction Warps Visual Time Perception
 

The energy-dependent de novo creation of G protein-coupled receptors, such as odor receptors, links the sense of smell in bacteria to the physiology of pheromone-controlled reproduction, which links changes in chirality to autophagy. Autophagy links what organisms eat to cell type differentiation via amino acid substitutions that link our visual perception of energy and mass to the feedback loops that link what organisms eat to their behavior.

Experimental proof of concept might require the sacrifice of one mammal. If it can find a mass of energy that is biophysically constrained in a source of food, it must also eat the food and survive to reproduce. Foraging and reproduction occur in the context of facts presented in Feedback loops link odor and pheromone signaling with reproduction (co-authored by 2004 Nobel Laureate, Linda  Buck).

If an organism cannot find the food and eat it, entropy must clearly be linked to its death unless it is among the individuals of a species that mutated and evolved from a common ancestor. For comparison, theories about common ancestors can be linked to the billion dollar LIGO “black hole” project and to this year’s Nobel Laureates in Physics.

I encourage others who live on Earth to do that in the context of a money-saving effort to save all humanity from death that will be caused by the virus-driven entropy of organized genomes.

See for details: 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!

Cytosis

God vs host-derived creation of virus-driven pathology

Summary: The virus-driven theft of quantized energy forces cells to compete for nutrient energy-dependent RNA-mediated reprogramming in the context of the structure of photons, one-carbon metabolism, autophagy, and the physiology of reproduction, which links energy-dependent changes in chirality from base pairs to RNA-mediated amino acid substitutions.

Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton (with my emphasis)

Viruses often carry genes acquired from their host. In the present work, we show that a virus of a marine alga carries a gene encoding a transporter protein that mediates nutrient uptake. We confirm that the viral transporter protein is expressed during infection and show that the protein functions to take up sources of nitrogen. This is important because acquisition of nutrients often determines the ecological success of phytoplankton populations. This work demonstrates how a virus can amend host–viral dynamics by modulating acquisition of nutrients from the environment.

Reported as: Virus reprograms ocean plankton

The virus has stolen a gene from the phytoplankton, which has the surprising effect of making the infected plankton better at absorbing certain nutrients for a period – before the virus kills them.

Much of the planet’s carbon is stored in the sea by a process of algae dying and sinking to the ocean floor, and this research shows a new feature of that process.

“Availability of vitamins and nutrients determine how these phytoplankton function,” said Professor Thomas Richards, of the University of Exeter.

“We have shown that this virus reprogrammes how the phytoplankton obtain nutrients, which affects how they grow and is likely to affect how they absorb carbon dioxide.

“Cells that have the virus are more competitive in the short-term.

The virus-driven theft of quantized energy forces cells to compete for nutrient energy-dependent RNA-mediated reprogramming in the context of the structure of photons, quantum entanglement, one-carbon metabolism, autophagy, and the physiology of reproduction, which links energy-dependent changes in chirality from base pairs to RNA-mediated amino acid substitutions. The amino acid substitutions stabilize the organized genomes of all living genera. Virus-driven energy theft links amino acid substitutions to the stability of viruses at the expense of the stability of organized genomes in all living genera.
The significance of Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton can be viewed in the context of prescient predictions made by young earth creationists and other serious scientists. Unfortunately, most of them failed to link energy-dependent RNA-mediated cell type differentiation to all biophysically constrained biodiversity via viral latency.

Pseudoscientists did not mention the likelihood that viruses cause the mutations, which all serious scientists have linked to all pathology. That may be the most recognizable difference between a pseudoscientist and a serious scientist.
See for information reported by serious scientists: Who rules the waves? – Viruses might just be bit players in the drama of the seas. Then again, they could be major actors (1996)

Most consider viruses to be a legion of cripples, sterilised by ultraviolet radiation and rendered impotent by hosts that are largely immune to their threat. But a few researchers take the opposite view. And if they turn out to be right, viruses could radically alter the balance of life in the oceans, ripping away huge parts of the food web that supports whales, sea birds and the fisheries on which many people rely.

See also: 1999 Did God Make Pathogenic Viruses? (1999)
See also: Where do viruses come from? (2004)

“…when virus-infected bacterial cells burst, their energy-rich cell contents spill into the water for other bacteria to scavenge. ‘Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,’ says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.”

See also: Viral Genome Junk Is Bunk (2015)

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

See for comparison from 2017:
Overthrowing the Hegemony of the Culture of Margulis?
Asgard archaea illuminate the origin of eukaryotic cellular complexity
Mitochondria are not captive bacteria

Carl Woese failed to place his ideas about the three domains of life into the context of how biophysically constrained viral latency links the anti-entropic virucidal energy of sunlight from the physiology of pheromone controlled reproduction to all biodiversity. Woese was wrong about everything. There is one domain of life. In all living genera, the pheromone-controlled physiology of reproduction is energy-dependent and RNA-directed DNA methylation links amino acid substitutions in supercoiled DNA to all biodiversity.

See for comparison this example of human idiocy, On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

Only neo-Darwinian theorists insist on playing word games to link what they refer to as “enigmatic spacer repertoires” to biodiversity outside the context of energy-dependent changes in the microRNA/messenger RNA balance that link electrons to ecosystems via hydrogen-atom transfer in DNA base pairs in solution.

“Human idiocy” was the term used by Feynman before Roger Penrose reminded us that all organisms must eat. See: “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?” (1991)

For comparison see: Fink et al., (2017) Cross-Cultural Investigation of Male Gait Perception in Relation to Physical Strength and Speed Fink also is a co-author of the award-winning review: Human pheromones: integrating neuroendocrinology and ethology (2001)
See for comparison: A BRIEF ESSAY ON HOW COMPARATIVE PSYCHOLOGY BECAME AN ENDANGERED SPECIES (link opens pdf)

Rather than continue to link food energy from the pheromone-controlled physiology of reproduction to all biodiversity in all living genera, Fink joined the pseudoscientists. He appears to be following the lead of people like Jay R. Feierman. As moderator of the International Society for Human Ethology’s Yahoo Group, Feierman has inadvertently eliminated all works of human ethologists from any further consideration, and he admits it.

See: 8/21/17 [HUMAN ETHOLOGY MODERATOR NOTE: I could write a similar essay on why human ethology is an endangered species but the causes would be different.  I’m old enough to have seen many academic disciplines disappear and new ones take their place. It is rather easy to put this process into a cultural evolution model. Academic disciplines are like species, most of the ones who have ever lived are now extinct. New species are born and old species die…. jrf]

On July 25, 2013, Feierman [jrf] wrote: 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.
Four years later, the concept of “new species are born and old species die” is divorced from the claims Jay R. Feierman made.
See for comparison: Linking mental health and the gut microbiome

The main idea of our review is that there is strong communication between the gastrointestinal tract and the brain, and that changes to the microbiome-gut-brain axis could be associated with the etiology of different neuropsychiatric disorders such as depression…

Food energy-dependent changes in the microbiome-gut-brain axis link nutrient stress and social stress from the de novo creation of microRNAs in plants to changes in the microRNA/messenger RNA balance of animals via links from food odors to pheromone-controlled ecological adaptations in species from microbes to humans.
See: Feedback loops link odor and pheromone signaling with reproduction
See for comparison: “I Am I and My Bacterial Circumstances”: Linking Gut Microbiome, Neurodevelopment, and Depression

A better perception of the significance of the MGB axis in the etiology of depression will help us to obtain a better understanding about the pathophysiology of this syndrome. Also, it opens the possibility to offer better treatment strategies to our patients. This will be possible only if we accomplish to decipher the genetic, anatomical, functional, and behavioral characteristics of the human microbiota. The most important limitation in the area of the MGB axis’ research lies in the fact that there is very little knowledge about the gut microbiome.

The claim that there is very little knowledge about the gut microbiome can be compared to what is known about the link from the virus-driven degradation of messenger RNA in soil bacteria to all pathology in all living genera. Everything known to serious scientists was detailed in the context of this report: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression The changes in the microRNAome included the link to the transgenerational epigenetic inheritance of all pathology in all living genera. The links from the transgenerational epigenetic inheritance of cancer and the transgenerational epigenetic inheritance of behavioral disorders were place into the context of links from quantum physics to quantum souls.
See: Quantum Souls and Welcome to the official YouTube Channel of Quantum Souls.
Video interview about the death of Robin Williams
Superbugs, Bacteriophages and Phage Therapy: An Interview with James Kohl
Food Energy-Dependent Cell Type Differentiation Refutes Theory of Evolution
How to Treat Cancer as a Disorder of Energy Transfer
Charles Darwin Taught Conditions of Life, Not Mutations
Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 1
Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2
When you next see someone claim that “…there is very little knowledge about the gut microbiome” you may associate that claim with the ignorance touted by neo-Darwinian theorists and compare it to what anyone 10 years-old or older will learn when they play the cell biology game “Cystosis.”

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

Cytosis

Your indifference is killing you and others (3)

Summary: The speed of light on contact with water links the creation of microRNAs to Optical control of membrane tethering and interorganellar communication at nanoscales MicroRNA flanking sequences are linked to all biodiversity via hydrogen-atom transfer in DNA base pairs in solution. The physiology of reproduction links energy-dependent changes in the microRNA/messenger RNA balance to the fixation of amino acid substitutions in supercoiled DNA. Supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA.
See also: Combating Evolution to Fight Disease
See also: Biblical Genesis
…in the Garden of Eden but instructs them not to eat the fruit of the tree of knowledge of good and evil.

Tree of the knowledge of good and evil

…when God forbids the man to eat from that particular tree, he says that if he does so, he is “doomed to die”.
I am fascinated by the facts that link the Biblical metaphors from eating a virus-infected “fruit” to the death of everyone who will ever live and die.  That fact can be placed into this context: Past 5,000 years prolific for changes to human genome.

Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report. 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years.

See also: Chromogenic In Situ Hybridization Methods for microRNA Biomarker Monitoring of Drug Safety and Efficacy
Reported by Exiqon as: Robust one-day ISH protocol for disease microRNA biomarker development

ISH of biopsy material has become routine pathology procedure for monitoring gene expression and sample characterization. This could be of microRNAs which prove excellent as biomarkers for disease diagnosis, patient stratification and treatment efficacy.

A fast and robust microRNA ISH protocol well-suited for clinical biomarker studies has just been published in Methods Mol Biol using DIG or FAM double-labeled microRNA-specific LNA™-enhanced detection probes in formalin-fixed, paraffin-embedded (FFPE) tissue sections.

Monitoring gene expression and sample characterization via natrurally occuring microRNA biomarkers is the key to developing biomarkers for use in “…disease diagnosis, patient stratification and treatment efficacy.”
The microRNAs need only be linked from flanking sequences to all biodiversity via hydrogen-atom transfer in DNA base pairs in solution and the physiology of reproduction, which links energy-dependent changes in the microRNA/messenger RNA balance from the fixation of amino acid substitutions in supercoiled DNA to protection from the virus-driven degradation of messenger RNA.
See: Optical control of membrane tethering and interorganellar communication at nanoscales

All the observed interactions seem to require the presence of at least two consecutive positively charged residues (‘KK’ or ‘KR’). Replacement of a single lysine with alanine in such dyad motifs could lead to pronounced reduction in puncta formation; whereas KK-to-AA substitutions often abrogate the PB-lipid/PM associations (Fig. 4 and S4†). Further structural studies on the interaction between PB domains and PIs will likely provide a definitive answer by pinpointing the exact molecular determinants.

The temporal and spatial control that connects subcellular compartments to interorganellar communication, which links energy-dependent changes from angstroms to ecosystems in all living genera is RNA-mediated and biophysically constrained by the pheromone-controlled physiology of reproduction. The temporal and spacial control is linked to our visual perception of mass and energy via the sense of smell in bacteria and RNA-mediated amino acid substitutions in the organized genomes of all living genera.
See also: Mechanism of metabolic puncta formation and its functional significance

Many metabolic enzymes have recently been shown to assemble into multi-component puncta in cells, and this assembly is though to play some role in controlling metabolic flux. For example, substrate channeling within these structures could play an important role in metabolism, enabling intermediates to be directly fed from one enzyme to another without dilution. Therefore the assembly of enzymes into these puncta could be an important mechanism for cells to manipulate their metabolism in response to different signals. However, the mechanism of formation of these puncta is completely unknown.

If the energy-dependent formation of these puncta was not known to be linked from differences in the microRNA/messenger RNA balance to the pheromone-controlled physiology of reproduction in all living genera, I could not have found the obvious link from food energy to all biodiversity in this PubMed search.
puncta formation microRNA

For example, food energy is the obvious link from changes in chirality to autophagy. Autophagy protects all organized genomes from the virus-driven degradation of messenger RNA. Simply put, biophysically contrained energy-dependent autophagy protects all living genera from the mutations that serious scientists have linked to all pathology.
See also:
MicroRNA-141 Targets Sirt1 and Inhibits Autophagy to Reduce HBV Replication.
C. elegans Dicer interacts with the P-granule component GLH-1 and both regulate germline RNPs.

See also:  Bridging Length and Time Scales in Cell Organization

For comparison, see: “For the past century some people have regarded natural selection as “that secular God.” Now, that title belongs to CRISPR. “— Jay R. Feierman
Feierman has not learned that natural selection for energy-dependent codon optimality links a light-activated endogenous substrate from the innate immune system in bacteria: CRISPR, to the biophysically constrained physiology of pheromone-controlled reproduction in all living genera. That fact is proof of God’s energy-dependent Creation. The claim that the title of “secular God” belongs to CRISPR is as ridiculous as this claim.
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:  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.
CRISPR is the only obvious link from energy-dependent changes in chirality to autophagy, which protects all organized genomes from the theft of quantized information that links mutations to all pathology via the degradation of messenger RNA.
See also: Your indifference is killing you and others (4)

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

Evolutionary congruence (losers) vs ecological adaptation (winners)

This is the first DNA-sequence based phylogeographic assessment of Salvadora in the world. Sequence based phylogeographic assessment of tropical tree species is a relative rarity and in India, such investigations are almost non-existent.
 

Kalevi Kull: Censorship & Royal Society Evo Event

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.

In a rapidly changing world of post-censorship, the losers tout “DNA-sequence based phylogeographic assessment.” All serious scientists have linked energy-dependent RNA-mediated protein folding chemistry from changes in angstroms to ecosystems via supercoiled DNA, which protects all organized genomes from the virus-driven degradation of messenger RNA.

Each time you see a term like evolutionary congruence, ask for a definition that links it to what is currently known to all serious scientists about biophysically constrained energy-dependent RNA-mediated biologically based cause and effect.

You will learn There is no such thing as an evolutionary congruence. Molecular Phylogeography is not examined (e.g., by serious scientists) outside the context of the anti-entropic virucidal energy of the sun.

The virucidal energy links the creation of microRNAs in plants to the food energy-dependent creation of microRNAs in animals and all biophysically constrained biologically-based cause and effect on Earth via the physiology of pheromone-controlled reproduction in bacteria.
See: The phylogenetic utility and functional constraint of microRNA flanking sequences

See also: Cystosis

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

Food energy links the de novo creation of microRNA flanking sequences to the creation of enzymes, hormones and receptors that link ecological variation to ecological adaptation via the physiology of pheromone-controlled reproduction in species from microbes to humans. The pheromone-controlled physiology of reproduction biophysically constrains the transgenerational epigenetic inheritance of virus-driven energy theft, which has been linked from mutations to all pathology –except by Greg Bear, who linked biophysically constrained viral latency to the pheromone-controlled creation of a new human subspecies.

See: The Darwin Code by Greg Bear

Bacteriophages–phages for short–can either kill large numbers of host bacteria, reproducing rapidly, or lie dormant in the bacterial chromosome until the time is right for expression and release. Lytic phages almost invariably kill their hosts. But these latter types–known as lysogenic phages–can actually transport useful genes between hosts, and not just randomly, but in a targeted fashion.

See for comparison: A Crack in Creation review – Jennifer Doudna, Crispr and a great scientific breakthrough

Jennifer Doudna’s work began with organisms even further out on the Palin scale: bacteriophages, tiny viruses that prey on bacteria.

Conclusion: The difference between the works of science fiction novelist Greg Bear, and people like Jennifer Doudna, is clear. Greg Bear’s works (and the works of the late Eshel Ben-Jacob) predicted that, if viral latency was not biophysically constrained, the virus-driven degradation of messenger RNA would be linked to all pathology.
The works of biologically uninformed researchers tout the benefits of the virus-driven degradation of messenger RNA, which is used in their gene-editing technology, as if the concept of gene-editing exemplified a “Crack in Creation.” For comparison, natural selection for energy-dependent codon optimality links the pheromone-controlled physiology of reproduction from energy-dependent changes in chirality to autophagy, which protects all organized genomes from the virus-driven degradation of messenger RNA that Doudna and others have linked to all pathology.
See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes (Ikemura,
1982; Akashi, 1994; Akashi & Gojobori, 2002; Drummond & Wilke, 2008; Kudla et al, 2009; Novoa & Ribas de Pouplana, 2012). The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

See also:
The Origin of Information (3) If they do not know where the quantized energy in a hydrogen atom came from, they cannot discuss a Crack in Creation in the context of the virus-driven degradation of messenger RNA that is their key to gene editing.
See also: 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.

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

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
 

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 (9)

Summary: Energy determines genome compaction because activity in the nucleus is energy-dependent. Chromatin chains link energy-dependent changes in base pairs from single nucleotide polymorphisms to fixation of RNA-mediated amino acid substitutions in organized genomes via the physiology of pheromone-controlled reproduction. It’s all about the base.

Energy-dependent physical and biophysical constraints (8)

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells
Excerpt 1)

The chromatin structure of DNA determines genome compaction and activity in the nucleus.

My comment: Energy determines genome compaction because activity in the nucleus is energy-dependent.
Excerpt 2)

Chromatin chains have many different particle arrangements and bend at various lengths to achieve structural compaction and high packing densities.

My comment: Chromatin chains link energy-dependent changes in base pairs from single nucleotide polymorphisms to fixation of RNA-mediated amino acid substitutions in organized genomes via the physiology of pheromone-controlled reproduction.
Reported as: Scientists solve longstanding biological mystery of DNA organization

Besides potentially upending the textbook model of DNA organization, the team’s results suggest that controlling access to chromatin could be a useful approach to preventing, diagnosing and treating diseases such as cancer.

“We show that chromatin does not need to form discrete higher-order structures to fit in the nucleus,” adds O’Shea. “It’s the packing density that could change and limit the accessibility of chromatin, providing a local and global structural basis through which different combinations of DNA sequences, nucleosome variations and modifications could be integrated in the nucleus to exquisitely fine-tune the functional activity and accessibility of our genomes.”

The packing density of supercoiled DNA is energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera. Sunlight is the source of all biophysically constrained energy on Earth.The anti-entropic virucidal effect of sunlight biophysically constrains the degradation of messenger RNA.
Virus-driven energy theft causes negative supercoiling of supercoiled DNA. Without food energy-dependent RNA-mediated DNA repair (autophagy), viruses cause the degradation of messenger RNA that links mutations to all pathology. The sun’s anti-entropic virucidal energy links changes in chirality to autophagy and the de novo creation of enzymes, hormones and receptors that are needed to protect all organized genomes from viruses.
The textbook model of DNA organization was represented in Mutation-driven evolution for comparison to “Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which was published on the same day more than 4 years ago.
Masatoshi Nei used an ambiguous definition of mutation and linked any energy-dependent nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc, (any change in the structure of supercoiled DNA) from natural selection to an evolutionary process initiated by mutation.
In my review, I used examples of food energy-dependent changes in base pairs to link the honeybee model of nutrient-dependent pheromone-controlled biodiversity to a history of published works that began with The Scent of Eros: Mysteries of Odor in Human Sexuality (reviewed by Mark Sergeant)
The index from The Scent of Eros: Mysteries of Odor in Human Sexuality may help others to establish all the known links from the energy-dependent de novo creation of microRNAs to the creation of G protein-coupled receptors and gonadotropin releasing hormone (GnRH) secretion, which was linked to all biodiversity. See, for example, these entries from page 217:

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: Energy-dependent physical and biophysical constraints (10) in prep

Cytosis

God's shrinking role in salvation (3)

Summary: I believe there is a bipartisan trend that links conservative Republicans to survival of the species, but I don’t know for sure what will happen to the liberal Democrats. And, I can’t prove it!
 
Helicity and chirality https://www.facebook.com/ed.unverricht/videos/10155506720828729/

See also: God’s shrinking role in salvation (2)
A Theory of Reality as More Than the Sum of Its Parts

“Causal emergence is a way of claiming that your agent description is really real,” said Hoel, a postdoctoral researcher at Columbia University who first proposed the idea with Larissa Albantakis and Giulio Tononi of the University of Wisconsin, Madison. “If you just say something like, ‘Oh, my atoms made me do it’ — well, that might not be true. And it might be provably not true.”

For comparison, see also: How concepts of God have developed: God’s shrinking role. God’s survival. Conclusions.

The chances of a given person belonging to God’s “true” religious institution is rather small. Some people are willing to accept this conclusion. However, most are quite certain that their faith tradition is the one that is God’s. Sadly, many find it quite difficult to extend equal human rights to members of other religions. A few are quite capable of denying human rights to, and even killing, those that they consider to be infidels in order to further what they perceive to be their God’s wishes.

See also the historical perspective on the de novo creation of energy-dependent biophysically constrained cell type differentiation in species from microbes to humans. This must be manifested in the context of helicity, chirality, autophagy, and chromosomal inheritance.

From fertilization to adult sexual behavior (1996) and The zinc spark is an inorganic signature of human egg activation (2016)

The historical perspective links the creation of sunlight to injections of adenosine for repair of damaged DNA via a “minimal gene signature.”

See for example: Cross-species gene modules emerge from a systems biology approach to osteoarthritis

Consensus modules established between species

To establish concordance and divergence in the network organization across the two species, consensus modules, modules shared by both networks, were derived from each species network using the weighted average of the two correlation matrices. In all, there were six consensus modules (C1–C6), Figs. 1b and 2b and Supplementary Figs. 4b and 5b. Functional annotation of the consensus modules included: “muscle system process” (C1), “oxidative phosphorylation” (C2), “cell cycle” (C3), “system development” (C4), and “immune system process” (C5).

For comparison, most theorists have traditionally used inferences of top-down causation to establish a consensus, which they tout in simple-minded claims that “evolution is true.” Here is a fact about the pathology of osteoarthritis.

Reported as: Cross-species links identified for osteoarthritis

OA [osteroarthritis] is the destruction of the tissues of the joints and affects more than half of individuals over 65 years old; it is the leading cause of joint pain and disability in the UK.

Animal models are often used to replicate human disease; the relevance and similarity between animal models of joint disease and human osteoarthritis has not been fully evaluated.

Researchers from the University’s Institute of Ageing and Chronic Disease, led by Senior Lecturer in Orthopaedic Sciences Dr Simon Tew, examined molecular messages produced by cartilage cells in both humans and rats.

The molecular messages, which the researchers extended across species  also link the speed of light on contact with water to the energy-dependent de novo creation of all biodiversity on Earth.

See: New research explains hydrophobicity and A single ion impacts a million water molecules

See also: The interfacial structure of water droplets in a hydrophobic liquid, which was reported as: Water is surprisingly ordered on the nanoscale
Sunlight is also surprisingly ordered at the level of quantized energy. If it was not, serious scientists would not know how to link energy dependent changes from Ångströms to ecosystems in all living genera. Thank God, the information about water ordered on the nanoscale can now be linked from the color of the rainbow to all biodiversity on Earth via the physiology of reproduction.

Their surprising results have been published in Nature Communications. They pave the way to a better understanding of atmospheric, biological and geological processes.

Nanometric-sized water drops in the air as droplets or aerosols, in industrially produced medications,  within rocks and oil fields, and within supercoiled DNA interact with changes in temperature in their hydrophobic environment. Simply put, that is the concept of how theromodynamic cycles of protein biosynthesis and degradation are biophysically constrained by ecological adaptation to stress at different temperatures in different functional structures. At room temperature, water molecules at the surface of the droplets have stronger interactions than the water molecules in a normal water surface.

Does any of the above information surprise you? If so, see Water is surprisingly ordered on the nanoscale (discussion attempt)
Avishek Ghosh This is not at all surprising enough to be published in Nature!! There have been many publications by the Bakker group since 2003/2005. In fact my own publication in JACS, PRL discusses such a phenomena at lipid membrane interfaces back in 2007/8. Wonder what’s going on. And a fun fact, Sylvie and I were colleagues for a short while in AMOLF!!

James Kohl  The problem is hydrophobicity in supercoiled DNA. It’s energy-dependent and the anti-entropic energy comes from the sun. Add the fact that cryo-EM has linked hydrogen atom transfer in DNA base pairs in solution to all biophysically constrained biodiversity via the physiology of reproduction in species from microbes to humans. The Nature Publications Group must continue to tout pseudoscientific nonsense about emergence and evolution or rehash the ridiculous concepts until all neo-Darwinian nonsense is completely trashed. Help me. See RNA-mediated.com

James Kohl Non-radiative relaxation of photoexcited chlorophylls: theoretical and experimental study

Peer-review in the United States has prevented dissemination of facts like these, which link photosynthesis from the creation of ATP to the creation of microRNAs and all biodiversity or to the virus-driven degradation of messenger RNA, which links mutations to all pathology (e.g., not to evolution).

Radek Łoziński Maybe it was energized by some mighty magician!

How else could inorganic material be linked to the creation of all biodiversity via signal transfer in bacteria and the zink spark From Fertilization to Adult Sexual Behavior.


See also: Endogenous adenosine maintains cartilage homeostasis and exogenous adenosine inhibits osteoarthritis progression.

…adenosine, acting at A2AR, is an important homeostatic regulator of chondrocytes and cartilage and adenosine repletion may represent a novel approach to treating OA (Fig. 6).

Reported as: Rodents with trouble walking reveal potential treatment approach for most common joint disease

Important to the study’s implications, adenosine is derived from adenosine triphosphate (ATP), the molecule that stores the energy needed by the body’s cells until they break it up to use it. Scientists have known that both inflammation and aging lead to diminished ATP production (and so lower adenosine levels) in chondrocytes. Until now, they had not linked diminished adenosine levels to osteoarthritis, the commonplace, “wear-and-tear” form of arthritis.
The underlying gene regulatory mechanisms in osteoarthritis link injections of adenosine from A-to-I RNA editing via what is known about femtosecond blasts of UV light, which have been linked to the repair of DNA.  Simply put, the injecting adenosine is like an injection of virucidal ultraviolet light.

These consensus modules (in reverse order) support the link from the anti-entropic virucidal energy of sunlight to:

“muscle system process” (C1),

“oxidative phosphorylation” (C2),

“cell cycle” (C3),

“system development” (C4),

and

“immune system process” (C5).

The energy-dependent de novo creation of the innate immune system is the only way to link the other consensus models from angstroms to ecosystems in all living genera via the functional structure of supercoiled DNA.

Others have helped to establish the consensus models by starting with the obvious link from the innate immune system in E. coli, which is a model organism of nutrient-dependent pheromone-controlled ecological adaptation. This model organism also links the weekend resurrection of the bacterial flagellum in P. fluorescens to all biophysically constrained biodiversity on Earth via the sense of smell.

But, first see for comparison: Environment determines evolutionary trajectory in a constrained phenotypic space (2017)
reported as: Genetic mutation trade-offs lead to parallel evolution
In our 1996 Hormones and Behavior review of energy-dependent RNA-mediated cell type differentiation, we included a section on molecular epigenetics and stated this:

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.

One generation (~21 years) later, other serious scientists linked energy-dependent changes from angstroms to ecosystems in all living genera via what is known about biophysically constrained physiology of reproduction.
This journal report on parallel evolution preceded, but the news report on the evolutionary trajectory of genetic mutations, followed the publication of  Mechanism of transmembrane signaling by sensor histidine kinases,  which as reported as: Scientists investigate how the sense of smell works in bacteria. That is how, after-the-fact, the sense of smell in bacteria was placed back into the context of mutation-driven evolution.
This excerpt removed mutation-driven evolution from any further consideration by serious scientists.

…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.

Serious scientists can compare the pseudoscientific nonsense about mutations and evolution to the accurate representation of how the sense of smell in bacteria links nutrient-dependent pheromone-controlled ecological adaptations from microbes to humans via signal transmission and an inorganic signature of human egg activation.
You can learn more about the energy-dependent spark that links the inorganic signature of gene activation in the human egg to adult sexual behavior in all living genera by learning more about cell biology,
You can learn more about the ignorance displayed by pseudoscientists who failed to learn anything about biophysically constrained energy-dependent RNA-mediated cell type differentiation by reading this article, which was co-authored by researchers I met during presentations at meetings of the Association for Chemoreception Sciences. Johan Lundström and
Mats Olsson are among the most biologically uninformed researchers I have encountered during those meetings. They demonstrate that fact by placing their recent study results into the context of neo-Darwinian nonsense.
See: Behavioral and neural correlates to multisensory detection of sick humans (subscription required)

A superadditive effect of olfactory–visual integration of sickness cues was found in the intraparietal sulcus, which was functionally connected to core areas of multisensory integration in the superior temporal sulcus and orbitofrontal cortex. Taken together, the results outline a disease-avoidance model in which neural mechanisms involved in the detection of disease cues and multisensory integration are vital parts.

If serious scientists attempt to tell people like this that God’s role in their salvation is clearly exemplified by the facts presented in Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants, the people would walk away as quickly as they have done when they passed by my poster sessions. Many other researchers have done that, and some professors have literally dragged their students away (lest they be unduly influenced by facts).
See for instance: Past 5,000 years prolific for changes to human genome

The findings confirm their earlier work suggesting that the majority of variants, including potentially harmful ones, were picked up during the past 5,000–10,000 years.

See also: Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over? (1995)

If substitutions at 10% of all nucleotide sites have selection coefficients within this range with the mean 10(-6), an average individual carries approximately 100 lethal equivalents. Some data suggest that a substantial fraction of nucleotides typical to a species may, indeed, be suboptimal. When selection acts on different mutations independently, this implies too high a mutation load. This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations. Several possible resolutions are considered, including soft selection and synergistic epistasis among very slightly deleterious mutations.

If natural selection for energy-dependent codon optimality did not link what organisms eat to the de novo creation of receptors that link the metabolism of food to the pheromones the biophysically constrain energy-dependent biodiversity via the physiology of reproduction and chromosomal inheritance, all life on Earth would have dies 100 times over.
See for example: 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!

Ultimately you must start with a link from the speed of light on contact with water and the: Hydrogen bonding ability of the amide group

See also: How Politics Is Changing Conversations Between Therapists And Patients

 
If substitutions at 10% of all nucleotide sites have selection coefficients within this range with the mean 10(-6), an average individual carries approximately 100 lethal equivalents. Some data suggest that a substantial fraction of nucleotides typical to a species may, indeed, be suboptimal. When selection acts on different mutations independently, this implies too high a mutation load. This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations. Several possible resolutions are considered, including soft selection and synergistic epistasis among very slightly deleterious mutations.
Natural selection for energy-dependent codon optimality fits into the context of Darwin’s “conditions of life,” and biophysically constrained viral latency via the pheromone-controlled physiology of reproduction. That suggests all neo-Darwinists are among the “walking dead” who may or may not be here after the forthcoming viral apocalypse. They are not prepared to meet their Maker because they believe energy emerged and then they evolved from nothing, which automagically became everything from the inorganic to the organic.
 
For comparison, I believe there is a bipartisan trend that links conservative Republicans to survival of the species, but I don’t know for sure what will happen to the liberal Democrats. And, I can’t prove it!

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.