An evolutionary theory killer

MicroRNA-mediated denuclearization (6)

Summary: The EDAR V370A isoform links one quantized energy-dependent base pair change from changes in ultraviolet light (UV) exposure to fixation of one amino acid substitution. The substitution differentiates the cell types of mice and humans in the context of a mouse-to-human model of nutritional epigenetics and microRNA-mediated denuclearization in North Korea.

Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk

…a genetically isolated population living in this environment during the LGM ∼20,000 y ago experienced selection for polymorphisms in the FADS gene cluster and for EDAR V370A because of the advantage these genetic variants likely confer in transmitting nutrients from mother to infant through breast milk under conditions of extremely low UV.

Nina G. Jablonski (a co-author), is known for her research into the evolution of skin color in humans. Her neo-Darwinian pseudoscientific nonsense is refuted in this representation of natural selection for food energy-dependent codon optimality.
Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

The food energy-dependent pheromone-controlled amino acid optimality code has been linked to biophysically constrained viral latency in all living genera via the physiology of pheromone-controlled reproduction.
The EDAR V370A isoform links one quantized energy-dependent base pair change from changes in ultraviolet light (UV) exposure to fixation of one amino acid substitution. The substitution differentiates the cell types of mice and humans in the context of a mouse-to-human model of nutritional epigenetics and microRNA-mediated denuclearization in North Korea.

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

The scientific creationists in South Korea know how to protect organized genomes from the virus-driven degradation of messenger RNA. Atheistic communists believed vaccines would protect their supercoiled DNA in their organized genomes.
The communists and other atheists lost their battle to promote atheism and vaccines because serious scientists in South Korea liked the accurate representations of the creationists. The serious scientists proceeded to support scientific creationism and Americanism with experimental evidence of top-down causation and biophysical constraints.
Pseudoscientists still tout their nonsense about constraint-breaking mutations.  See: Mutation-Driven Evolution
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. — Kalevi Kull

The links from particle physics to biophysically constrained viral latency will be placed into the context of the game “Subatomic,” which should be available by the end of this year.

5th-6th Sept 2018 Dublin, Ireland

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

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

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

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

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

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

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

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

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

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

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

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

Mitochondria generate the cellular fuel ATP to sustain complex life. Production of ATP depends on the oxidation of energy-rich compounds to produce a chemical potential difference for hydrogen ions, the proton motive force (pmf), across the inner mitochondrial membrane (IMM). Disruption of the IMM, dissipation of the pmf, and cell death occur if the concentration of calcium ions inside mitochondria is sufficiently elevated to open a pore in the IMM. The identity of the pore is disputed. One proposal is that the pore is in the enzyme that makes ATP. Here, we show that proteins in the enzyme’s peripheral stalk are not involved in the formation or regulation of the pore.

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

Tagging activated neurons with light

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 

http://nnjournal.net/article/viewFile/2354/1850/10234

The MicroRNAome Strikes Back: A Sokalian hoax (5)

Premise: Sunlight is the quantized energy as information that is required to link endogenous RNA interference to healthy longevity (The energy-dependent creation of microRNAs links the physiology of reproduction from changes in electrons to ecosystems in all living genera via the creation of ATP, RNA, and supercoiled DNA in organized genomes.)
Counter claim:  The Quantum Thermodynamics Revolution: Information theory
Understanding entropy as a subjective measure allows the universe as a whole to evolve without ever losing information.
See, for comparison: On causal roles and selected effects: our genome is mostly junk 

The title is misleading, but this claim is not.

Selection is involved in such a story, but it is purifying selection against the loss of a component or activity (the chaperone), not positive selection for its presence.

Natural selection for food energy-dependent reproduction is purifying selection. I’ve already cited Frohlich (1968) in that regard. his proposals are no longer speculative. Purifying selection links the speed of light on contact with water to the creation of microRNAs that biophysically constrain the epigenetic effects of  food odors and pheromones via the creation of enzymes.

The epigenetic effects of food odor and pheromones on the creation of energy-dependent microRNAs and enzymes prevent the virus-driven degradation of messenger RNA in all living genera. The virus-driven theft of quantized energy degrades the enzymes linked to the degradation of messenger RNA and gene losses.

I am not the only one who knows that, but few others seem willing to admit that energy is required to create new genes. For example, here the authors make a claim about de novo assemblies of genomes.

See: The phylogenetic utility and functional constraint of microRNA flanking sequences

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

De novo assemblies of geneomes and inferred phylogeny are linked to the slow evolution of microRNAs and microRNA flanking sequences. If I thought the authors were not serious about that ridiculous claim, I would have reported their work in the context of another Sokalian hoax. They eliminated the need for the energy-dependent creation of the microRNAs and the biophysical constraints on viral latency, but I think they seriously considered the de novo assembly of genomes to be possible. Indeed, to some theorists, the creation of new genes is like the magic of evolution.

Instead, I wrote: My comment to Science published at 2:54 pm on 1/29/15 

The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made since the 2013 ecological epigenetics symposium. For example, since then authors claimed “…ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” 

Six months later, other authors traced signaling factors found in vertebrates to the origin of nerve cell centralization via the diffuse nerve net of animals like the sea anemone.  That fact suggests ecological variation is linked to ecological adaptations in morphological and behavioral phenotypes via signaling protein concentrations that differentiate various cell types in body axes and the central nervous system.

Links across species from the epigenetic landscape to the physical landscape of DNA in organized genomes appear to have their origins in the conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated protein folding. Two weeks after the publication that refuted ideas about independently evolved neural systems or muscle specification — and perhaps refuted the independent evolution of anything else, SICB presenters linked crustaceans to insects.

Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.

Why were they left with any questions about how crustaceans and insects could all be part of one big family? They linked RNA-mediated cell type differentiation to what we described in our section on molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior 

Instead of natural selection for the food energy-dependent protection of RNA and supercoiled DNA, this gene-centric pseudoscientific nonsense emerged on January 25, 2018, from the depths of theorist’s ignorance. (At times it seems that a conspiracy theory is linked from the insane ignorance of biologically uninformed theorists, to my insane obsession with disseminating facts.)

The new findings are in agreement with recent genetic studies that show changes in genes related to brain development in our lineage since the population split between Homo sapiens and Neandertals. They add to the accumulating archeological and paleoanthropological evidence demonstrating that Homo sapiens is an evolving species with deep African roots and long-lasting gradual changes in behavioral modernity, brain organization, and potentially brain function.

For comparison to experimentally established fact about selection for energy-dependent reproduction, archeological and paleoanthropological evidence suggests that genes emerged and that they automagically led to “…long-lasting gradual changes in behavioral modernity, brain organization, and potentially brain function.”

I have consistently failed to grasp the logic of  claims that fail to link what is known to serious scientists about the microRNAome to food energy-dependent “…long-lasting gradual changes in behavioral modernity, brain organization…” and biophysically constrained viral latency linked to brain function.

For instance, all organisms can find food without the energy-dependent creation of G protein-coupled photoreceptors. But the energy as information-dependent de novo creation of microRNAs, enzymes and  G protein-coupled receptors is required to linke for food odors and pheromones from pH-taxis to chemotaxis in all species that must forage to find food and reproduce.
All individuals of all species must also enzymatically metabolize the food to species-specific pheromones, which have consistently been linked, since the time of our 1996 review: From Fertilization to Adult Sexual Behavior, to epigenetically-effected sex differences in behavior in species from yeasts to mammals via the conserved molecular mechanisms of chromosomal rearrangements and the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes.
It is time to watch very closely for more Sokalian hoaxes as the Inter-kingdom communication mechanisms mediated by non-coding RNAs (e.g, pre-mRNAs or microRNAs) are placed back into the context of claims about what supposedly has not been known to all serious scientists for more than 25 years.

The Expressed MicroRNA—mRNA Interactions of Toxoplasma gondii 4 Jan 2018

MicroRNAs-Based Inter-Domain Communication between the Host and Members of the Gut Microbiome 27 Sep 2017

Microbiota-Derived Extracellular Vesicles as New Systemic Regulators 24 Aug 2017

HIV-1 Nef Signaling in Intestinal Mucosa Epithelium Suggests the Existence of an Active Inter-kingdom Crosstalk Mediated by Exosomes 08 June 2017

Viruses and miRNAs: More Friends than Foes 15 May 2017

In summary, we are far from fully understanding the molecular mechanisms underlying the complex crosstalks between miRNA pathways and viral infections.

New Insight into Inter-kingdom Communication: Horizontal Transfer of Mobile Small RNAs 01 May 2017

The Role of HCMV and HIV-1 MicroRNAs: Processing, and Mechanisms of Action during Viral Infection 21 April 2017

Gut Microbiota as a Trigger of Accelerated Directional Adaptive Evolution: Acquisition of Herbivory in the Context of Extracellular Vesicles, MicroRNAs and Inter-Kingdom Crosstalk 20 April 2017

Linking Diet to Colorectal Cancer: The Emerging Role of MicroRNA in the Communication between Plant and Animal Kingdoms 05 April 2017

Non-coding RNAs in Host–Pathogen Interactions: Subversion of Mammalian Cell Functions by Protozoan Parasites 21 March 2017

Small Luggage for a Long Journey: Transfer of Vesicle-Enclosed Small RNA in Interspecies Communication 16 March 2017

Exo-miRExplorer: A Comprehensive Resource for Exploring and Comparatively Analyzing Exogenous MicroRNAs 01 February 2017

The Development of Our Organ of Other Kinds—The Gut Microbiota 23 Dec 16

See for comparison: Big Strides in Cellular MicroRNA Expression

A lack of knowledge of the cellular origin of miRNAs has greatly confounded functional and biomarkers studies. Recently, three studies characterized miRNA expression patterns across >78 human cell types. These combined data expand our knowledge of miRNA expression localization and confirm that many miRNAs show cell type-specific expression patterns.

There is no lack of knowledge about the quantized energy-dependent creation of microRNAs, which are now used as biomarkers of healthy longevity for comparison the the number of viral microRNAs, which is linked to pathology in species from bacteria that become archaea and humans that become non-human primates in the context of one or more base pair changes and fixation, or not, of one RNA-mediated amino acid substitution.
Here’s the problem: 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. — Kalevi Kull
See for comparison: Energy as information and constrained endogenous RNA interference (4)
Watch what happens when so-called science journalists wake up and recognize the Sokalian hoax.

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!

diseases-disorders

Your indifference is killing you and others

Summary: Coherence-inducing mechanisms is double-speak for mechanisms that are nutrient-dependent and pheromone-controlled.
Feedback loops link odor and pheromone signaling with reproduction has been presented in double-speak as Looplessness in networks is linked to trophic coherence

We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

Feedback loops link the sun’s anti-entropic virucidal energy from the food that organisms eat to the physiology of pheromone-controlled reproduction in all living genera. The virucidal effect of ultraviolet light biophysically constrains viral latency. Energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA are fixed in organized genomes via the physiology of reproduction and supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.
Coherence-inducing mechanisms is double-speak for nutrient-dependent and pheromone-controlled in the context of Nutrient-dependent/pheromone-controlled adaptive evolution: a model. 
Despite the validity of the model, it has not been accepted by neo-Darwinian theorists or “Big Bang” cosmologists. Ridiculous beliefs about emergence and evolution are pervasive and the pseudoscientific nonsense of their theories leads to claims about coherence-inducing mechanisms.
That is why I changed the FB page description at RNA-mediated after a series of posts (see below).

It took 20 years for others to realize that all life on Earth is food energy-dependent. Now, most people are indifferent to that fact. They refuse to learn anything about where the food energy comes from.

Differences in the energy of photons have been linked to quantized energy-dependent fixation of RNA-mediated amino acid substitutions. The substitutions biophysically constrain supercoiled DNA via the physiology of pheromone-controlled reproduction.

Virus-driven energy theft links the degradation of messenger RNA to mutations via amino acid substitutions in viruses. The substitutions in the viruses have been linked to all pathology via changes in the energy-dependent microRNA/messenger RNA balance.

For comparison, the pseudoscientific nonsense of neo-Darwinian theories links mutations from natural selection to the evolution of new species. In reality, light energy is quantized information. The information links physics, chemistry, and molecular epigenetics from the speed of light on contact with water and hydrogen-atom transfer in DNA base pairs in solution to learning, memory, and behavior via RNA-mediated events such as the energy-dependent creation of enzymes and the the de novo creation of G protein-coupled receptors such as olfactory receptor genes.

Top-down causation and de novo gene creation are exemplified by energy-dependent differences in the microRNA/messenger RNA balance that link natural selection for codon optimality to amino acid substitutions that link the physiology of reproduction to supercoiled DNA. Supercoiled DNA protects all organized genomes from virus-driven energy theft. That fact supports the beliefs of young earth creationists, which may be the only existing basis for discussion of quantum biology and refutations of neo-Darwinian theories that have linked olfaction to quantum souls. If there is another basis for the link from quantum physics to quantum souls, no one has detailed in in the context of top-down causation, which must include information about the creation of genes.

Most people seem unwilling to accept experimental evidence that attests to how genes are created or information that shows how virus-driven energy theft is linked to all pathology. Discussion of the energy-dependent paradigm shift would lead others away from pseudoscientific nonsense about emergence and/or beneficial mutations and evolution.

Only via discussion of facts about the paradigm shift will others learn what is currently known to serious scientists about the biophysically constrained nutrient energy-dependent chemistry of RNA-methylation and all biophysically constrained RNA-mediated protein folding chemistry. Simply put, the protein folding chemistry must be linked to all biodiversity by the physiology of energy-dependent pheromone-controlled reproduction in all living genera.

Your indifference to that fact is killing people.

See for comparison: Looplessness in networks is linked to trophic coherence (May 16, 2017)

Our theory correctly classifies a variety of networks-including those derived from genes, metabolites, species, neurons, words, computers, and trading nations-into two distinct regimes of high and low feedback and provides a null model to gauge the significance of related magnitudes. Because trophic coherence suppresses feedback, whereas an absence of feedback alone does not lead to coherence, our work suggests that the reasons for “looplessness” in nature should be sought in coherence-inducing mechanisms.

Reported August 14, 2017 as Trophic coherence explains why networks have few feedback loops and high stability

The researchers are also investigating whether negentropy – the opposite of entropy, and in which a physical, thermodynamic or biological process creates order – are affected by trophic coherence. “The modern concept of entropy,” Johnson points out, “comes from statistical physics and is a property of ensembles, as described above – that is, the entropy of an ensemble is simply a function of the number of elements it contains.” Moreover, he adds, graph ensemble entropy has proven to be a powerful tool for understanding various network properties. We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

See for comparison: Feedback loops link odor and pheromone signaling with reproduction

These studies also indicate that GnRH neurons are likely to influence numerous brain functions. They 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 (Badr and Pelletier, 1987; Jennes et al., 1988; Jennes et al., 1997). BL+ neurons likely to receive synaptic input from GnRH neurons were seen in areas associated with numerous different functions, including odor and pheromone processing, sexual behavior, appetite, defensive behavior, motor programs, and the relay of information to higher cortical areas. 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 my posts on Discovering Vismodegib in the Fight Against Skin Cancer: The First Approved Inhibitor of the Hedgehog Pathway
No one I know is likely to understand this link from the anti-entropic virucidal energy of sunlight to prevention of all pathology because they must first understand the fact that proteins do not create themselves. There is no need for this inhibitor of the Hedgehog pathway or inhibition of any other pathway if cancer is prevented. But most people are not willing to learn about prevention because they think they can rely on medical practitioners to effectively treat their diseases. Do you think that your physician knows anything about light scattering characterization of glycoproteins and their interactions with other proteins and antibodies?
Absolute Characterization of Glycoproteins and their Interactions with Proteins and Antibodies by Light Scattering
Light scattering can now be linked to the characterization of glycoproteins and their immune system interactions in all species on Earth. That suggests the speed of light on contact with water links energy as information to the de novo creation of the glycoproteins,
If so, the physiology of reproduction links pheromones to biophysical constraints on the creation of more glycoproteins in the context of morphological and behavioral differences in species from microbes to humans. That suggests the refutation of neo-Darwinism is complete, since the virus-driven degradation of messenger RNA has been linked to all pathology in bacteria that become archaea before virus-driven energy theft causes them to become L-forms.
Simply put, Carl Woese was wrong. There is only one domain of life and virus-driven energy theft is what destroys all life on Earth.

 

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 (3)

See first: Energy-dependent physical and biophysical constraints (2)
Emily Balskus Pins Down the Chemistry and Metabolism of Human Microbiomes
Summary: The chemistry and metabolism of all microbiomes is food energy-dependent and pheromone-controlled via the physiology of reproduction.
See: Feedback loops link odor and pheromone signaling with reproduction

My comment to The Scientist:

…trans-4-hydroxy-L-proline (Hyp) dehydratase, a newly discovered member of an abundant family of proteins, produced by gut bacteria, known as the glycyl radical enzymes, helps in metabolizing trans-Hyp, an amino acid that is rare in bacteria but is common in eukaryotes.

The de novo creation of energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA protects the organized genomes of all living genera from the virus-driven degradation of messenger RNA, which has been linked from mutations to all pathology via the claims Schrodinger made in “What is Life?” (1944).

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

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

Natural selection for food energy-dependent codon optimality links the sense of smell in bacteria to the biophysically constrained viral latency that links ecological variation to ecological adaptations in species from microbes to humans via the conserved molecular mechanisms of RNA-mediated cell type differentiation.

Sunlight has since been placed into the context of quantized energy as information, which links our visual perception of mass and energy from the space-time continuum to the concept of the energy-dependent creation of quantum souls.
See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (2016) and From Fertilization to Adult Sexual Behavior (1996)
 

Cytosis

Energy-dependent physical and biophysical constraints (1)

Summary: The hitchhiking, the epistasis, and the dynamics of adapting populations are energy-dependent and biophysically constrained in the context of RNA-mediated protein folding chemistry. The virus-driven degradation of messenger RNA links mutations to all pathology in all living genera.

An upper limit on the functional fraction of the human genome

For the human population to maintain a constant size from generation to generation, an increase in fertility must compensate for the reduction in the mean fitness of the population caused, among others, by deleterious mutations. The required increase in fertility due to this mutational load depends on the number of sites in the genome that are functional, the mutation rate, and the fraction of deleterious mutations among all mutations in functional regions. These dependencies and the fact that there exists a maximum tolerable replacement level fertility can be used to put an upper limit on the fraction of the human genome that can be functional. Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 25%, and is probably considerably lower.

Reported as: Most of Human Genome Nonfunctional: Study

If only a small bit of the genome is functional, then the odds of a mutation taking out an important sequence are smaller, and therefore fertility rates can be lower.

That conclusion makes sense in the context of natural selection for food energy-dependent codon optimality, which biophysically constrains RNA-mediated protein folding chemistry.  Feedback loops link the physiology of pheromone-controlled reproduction to protection from the virus-driven degradation of messenger RNA.
Simply put, the structure of functional DNA is food energy-dependent because what organisms eat prevents virus-driven entropy of their organized genomes in the context of reproduction.

I would like to think that most knowledgeable biologists who properly appreciate evolutionary theory and genomic diversity are well aware of the many problems with ENCODE’s claim.

Anyone who is not aware of the problems should search PubMed for the term “microRNA” before release of the cell biology game “Cytosis” forces them to learn what anyone more than ten years old can learn from playing the game.
Energy-dependent viral latency is biophysically constrained in organized genomes. Nutrient stress and social stress break the constraints and the stress-linked degradation of messenger RNA links viruses to all pathology.
All life on Earth is energy-dependent, which means that the energy must be biophysically “trapped” at least twice.
See also: Gamma-ray telescopes reveal a high-energy trap in our galaxy’s center

…suggests the center of our Milky Way contains a “trap” that concentrates some of the highest-energy cosmic rays, among the fastest particles in the galaxy.

“Our results suggest that most of the cosmic rays populating the innermost region of our galaxy, and especially the most energetic ones, are produced in active regions beyond the galactic center and later slowed there through interactions with gas clouds…”

This appears to be another example of how ultraviolet light constrains the formation of new galaxies. Constraints on energy might be linked to quantum entanglement, which is something that theoretical physicists have not linked from quantum physics to quantum souls.
Should theoretical physicists be asked to include this new information in their theories so that their theories could be used to design experiments that link facts about sunlight as quantized energy to all energy dependent biodiversity on Earth via the physiology of reproduction?
Should theorists be asked about the facts included in these published works?
See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

See also: Universe’s ultraviolet background could provide clues about missing galaxies

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

See also: World’s brightest laser sparks new behavior in light

The claim of new behavior linked from the light of a billion suns begins to make more sense. Now, a high energy trap links the diffuse glow of gamma rays reaching nearly 50 trillion electron volts can be compared to gamma-ray energies and the energy of visible light, which ranges from about 2 to 3 electron volts.

I am happy that we already presciently linked the differences in constrained energy from “…a change in the electron, which abandoned its usual up-and-down motion in favor of a figure-8 flight pattern.”

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

See: Olfaction Warps Visual Time Perception and this two-part video interview:
Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 1
Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2

In the context of the solar analemma, Mobius strip, and the symbol for infinity, the report on the figure-8 “flight pattern” of electrons is consistent with representations of how the anti-entropic virucidal energy of sunlight is linked under ‘normal’ conditions to the collective energy of all scattered photons. That collective energy links energy as information to all biodiversity via the physiology of pheromone-controlled reproduction in the context of how quantum physics must be linked to quantum souls.

See also: Probabilistic epigenesis and A probabilistic classifier for olfactory receptor pseudogenes.

Everything known to serious scientists about the energy-dependent creation of receptors links the sense of smell in bacteria to our visual perception of mass and energy in the context of the space-time continuum via energy-dependent changes in the microRNA/messenger RNA balance

.For comparison see: Hitchhiking and epistasis give rise to cohort dynamics in adapting populations

Beneficial mutations are the driving force of adaptive evolution.

There is no such thing as a beneficial mutation. The virus-driven theft of quantized information is linked to increased virulence of viruses via a single amino acid substitution in the virus. The link from sunlight to food energy is the link to all ecological adaptations.

My comment: Reported on July 18, 2017 as Large-scale study of adaptation in yeast could help explain the evolution of cancer

See for comparison our 1996 Hormones and Behavior review of food energy-dependent RNA-mediated ecological adaptations that link sexual differentiation in yeasts to all biodiversity in all living genera in the context of our section on molecular epigenetics.
From Fertilization to Adult Sexual Behavior

The hitchhiking, the epistasis, and the dynamics of adapting populations are energy-dependent and biophysically constrained in the context of RNA-mediated protein folding chemistry. The virus-driven degradation of messenger RNA links mutations to all pathology in all living genera.

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

I used the term “adaptive evolution” instead of ecological adaptation to avoid problems with peer-review if the reviewers recognized that my review was a refutation of neo-Darwinian pseudoscientific nonsense.

Conclusion:

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

human-evolution

Food Energy-Dependent Cell Type Differentiation

A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution

Not since the atomic bomb has a technology so alarmed its inventors that they warned the world about its use.

Not since the time of his work on the Manhattan Project has a serious scientist like the late Richard Feynman presciently advised biologists on how to “get” theoretical physicists. Ask them who decided to use different terms for food energy and other source of the same quantized energy, which comes from sunlight.
Clearly, anyone who accepts the use of different terms for the same thing will accept the obfuscation of cause and effect that theorists must use to confuse intelligent people.
For example: “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 for comparison:

In her introduction to the interview, J.A. Parker mentions this news article:
Evolution Not Only About Natural Selection but Also Improvisation, Says Israeli Scientist

Prof. Yoav Soen sounds almost angry when he talks about the evolutionary concept of natural selection – or, more precisely, its total acceptance – suggesting it blinds people to thinking more broadly. Instead, they simply embrace the theory of evolution developed more than 150 years ago by Charles Darwin.

See also: Food Energy-Dependent Cell Type Differentiation (2) — in prep
I will start with a report on this conceptualization of the microbial metabolism of food energy to the biophysically constrained pheromone-controlled creation of at least one uranium isotope.
Figure 4: Conceptual model of uranium roll-front deposit formation.
Figure 4
Precursors and conditions favouring the formation of uraninite, biogenic uraninite and non-crystalline U(IV) are illustrated.

Alternative splicing of pre-mRNA

RNA-mediated adult learning, memory, and neurogenesis

Here is a way to assess the power of the media-industrial complex to suppress accurate representations of biophysically constrained biologically-based cause and effect.
Wait to see whether this experimental evidence is reported in the science news, or how it is reported.
Enriched Environment Increases PCNA and PARP1 Levels in Octopus vulgaris Central Nervous System: First Evidence of Adult Neurogenesis in Lophotrochozoa

The experimental data obtained by immunohistochemistry and western blot assay using proliferating cell nuclear antigen and poli (ADP-ribose) polymerase 1 as marker of cell proliferation and synaptogenesis, respectively, reviled cell proliferation in areas of brain involved in learning, memory, and sensory stimuli integration. Furthermore, we showed how enriched environmental conditions affect adult neurogenesis.

See also: Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice.

The link from energy-dependent RNA methylation and endogenous RNA interference to fixation of amino acid substitutions in supercoiled DNA has again become an important consideration to serious scientists who understand the facts about how viral latency is established.

In this report, the differential effects of m6A appear to depend on natural selection for energy-dependent codon optimality and distinct cis-acting elements such as microRNAs that link the energy-dependent stability of organized genomes from the physiology of pheromone-controlled reproduction in bacteria to invertebrates and all vertebrates via interactions among the RNA molecule, m6A, and microRNAs.

For comparison, see: Evolutionarily conserved serum microRNAs predict radiation-induced fatality in nonhuman primates

…the same seven transcription factors are predicted to regulate the radiation-responsive serum miRNAs in humans, macaques, and mice. However, these results need to be experimentally validated, and our ability to do so has been limited for the following reasons. First, we do not know the source (cell type) of the serum miRNAs…

Anyone who does not know that the energy-dependent creation of serum miRNAs is biophysically constrained by what organisms eat might be a member of a High IQ Society. Some of them are like other biologically uninformed science idiots and atheistic magicians.

Clearly, magicians, most Mensans, and all neo-Darwinian theorists are likely to share the claim that energy automagically emerged before energy-dependent changes in the microRNA/messenger RNA balance led to the evolution of all nutrient-dependent pheromone-controlled biodiversity.

See for instance: FROM THE DESK OF THE EXECUTIVE DIRECTOR of Mensa:

Finally, planning is under way for a great Annual Gathering and Colloquium in Hollywood, Fla. this July. The 5-star Diplomat Beach Resort has stunning waterfront views, and I can’t wait to see the Gala Dinner speaker, Penn Jillette of Penn & Teller fame.

See also: Famous Atheist Magician Penn Jillette Cites Bible as a Favorite Book

Penn Jillette, of the Penn and Teller comedy magic duo, named the Bible as one of his six favorite books in a column for “The Week.” Anyone who reads all of it will become an atheist, Jillette asserts.

Anyone who attends the 2017 Annual Gathering presentation and listens to this atheistic magician can compare his claims to those I made during my 2010 Annual Gathering presentation.
 

My claims are supported in their entirety by the claims in the Holy Bible that begin in Genesis with “Let there be light!” Light energy as information is the link to the Word of God in John 1:1.”In the beginning was the word.”

But, please keep in mind that Penn Jillette is a professional comedian, and I am not. I do not get paid to make fun of people and/or religions during presentations at Mensa Annual Gatherings.

I did include some humorous comments about those who have failed to link anything known about biologically-based cause and effect to their ridiculous behaviors, but no one seemed to be offended. I’ve already been too offended by the nonsense touted by other members of Mensa. Although I became a member in 1982, I will not renew this year. The insults of other Mensans are too much to bear, and now we see that the organization is promoting an atheistic agenda at the time when creationism is being linked to Americanism by the current President and his administration.
See for comparison: