5th-6th Sept 2018 Dublin, Ireland

Abiogenesis vs microRNA biogenesis (3)

 

My comment to

Thank you for helping to show what has been missing from neo-Darwinian theories and other claims that were based on de Vries 1902 definition of mutation. Theorists may now want to learn more about the energy-dependent molecular mechanisms of recombination.

Most of them will not like the findings you have provided. The peer-review process is especially deadly to those who challenge the current dogma. But since you have made the quantum leap see also:

Mechanisms of Recombination conference  Start: Sunday, May 20, 9.00am Finish: Tuesday, May 22, 6.45pm

Natural selection for codon optimality link quantized energy-dependent RNA-mediated DNA repair from biophysically constrained viral latency to sympatric speciation and all biodiversity.

When people who you thought were your peers reject your findings, you need only wait until after “Schrödinger at 75 – The Future of Biology” – September 2018 to resubmit and publish in a top-tier journal (if you have not already done so).

Until then, see also: Systematic analysis of complex genetic interactions

Reported as: How Many Genes Do Cells Need? Maybe Almost All of Them
Theorists failed to note that the creation of genes in yeasts is quantized energy-dependent and biophysically constrained by the physiology of reproduction. Most of their ridiculous claims try to link abiogenesis to genome evolution.
See for example:  Genome evolution across 1,011 Saccharomyces cerevisiae isolates
The origin of the yeast species in China has been linked to all biophysically constrained sympatric speciation via the section on molecular epigenetics from this 1996 review of RNA-mediated cell type differentiation.
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…

From the Discussion:

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

See also: Correction of β-thalassemia mutant by base editor in human embryos
See for comparison: Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

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

Theorists must now face the facts about mitochondrial DNA that also attest to their ignorance. They will be forced to link the creation of anti-entropic virucidal energy to the creation of ATP synthase, the creation of ATP, and the creation of RNA, which links microRNA biogenesis from naturally occurring energy-dependent base editing and the origin of microbial yeasts in China to morphological and behavioral phenotypes in humans via biophysically constrained changes in the microRNA/messenger RNA balance.
After comparison to these “Levels of Biological Organization” (See slide # 6) and the examples from all species, anyone left touting ridiculous theories will be dismissed.

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

Is meat protein unhealthy? (2)

See also: Microbiome-Grade DNA Extraction Kits

…the thermal and chemical methods effectively lyse the gram-negative organisms and boost their population in the final profile, amplifying the bias.

This suggests that all links from food energy-dependent de novo creation of the pheromone-controlled biophysically constrained bull sperm microRNAome have been misinterpreted in the context of virus-driven fescue toxicosis.

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

…the miRNA profile of mature ejaculated sperm may in fact have downstream consequences upon embryonic development. The potential for sperm miRNA affecting zygote development has recently been reported in the literature [18] and has interesting implications for the use of sperm miRNA profiles as indicators of potential male fertility.

Fescue toxicosis links the virus-driven creation of enzymes to the degradation of messenger RNA in bull sperm and to the transgenerational epigenetic inheritance of mutations, which all serious scientists have linked from damage to supercoiled DNA to all pathology in humans and other species.

Eating the meat from other animals that have not ecologically adapted to the virus-driven theft of quantized energy has been linked from the viruses in their genomes to human pathology via the degradation of messenger RNA in bacteria that become archaea and L-forms.

See also: Dobzhansky (1973)

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

See also: The Breadth of Viruses in Human Semen

The presence of viruses in semen is probably more widespread than currently appreciated, and the absence of virus in genital secretions should not be assumed for traditionally non–sexually transmitted viruses. The investigation of virus detection and persistence in semen across a range of viruses is useful for clinical and public health reasons, in particular for viruses that lead to high mortality or morbidity rates or to epidemics.

No serious scientist has ever reported a link from the Virus-mediated archaeal hecatomb in the deep seafloor to the evolution of anything except pathology. All serious scientists have, for comparison, linked ecological variation to food energy-dependent  polycombic ecological adaptations via biophysically constrained viral latency in species from microbes to humans.

From Fertilization to Adult Sexual Behavior (1996)

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

See also: Cytosis: A Cell Biology Board Game for ages 10+

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

5th-6th Sept 2018 Dublin, Ireland

Is meat protein unhealthy? (1)

Patterns of plant and animal protein intake are strongly associated with cardiovascular mortality
Reported as: Meat protein is unhealthy, but protein from nuts and seeds is heart smart

In the context of everything known about how the creation of anti-entropic virucidal light must be linked to all biodiversity on Earth, watch this ridiculous misrepresentation of the honeybee model organism. Food energy-dependent microRNA-mediated pheromone-controlled biophysically constrained viral latency is portrayed as if visual input was most important.

Bee swarms work like giant brains

See instead:

RNA-mediated nutritional psychiatry

RNA-mediated nutritional psychiatry (2)

Psychophysical Laws of Biology: RNA-mediated nutritional psychiatry (3)

Learn how to prevent more school shootings via what is known about how the “Psychophysical Laws” of Biology are linked to food energy-dependent biophysically constrained behaviors via microRNA-mediated cell type differentiation and the fixation of RNA-mediated amino acid substitutions like COMT Val158Met during the transition from adolescence to adulthood.

Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults (Epub Oct 16 2014)

5th-6th Sept 2018 Dublin, Ireland

Complexity: Routes and Patterns (2)

Role of RNA modifications in brain and behavior

“Here, we summarize current knowledge of cellular consequences of RNA modifications, with a special emphasis on neuropsychiatric disorders. We present evidence for the existence of an “RNA code,” similar to the histone code, that fine‐tunes gene expression in the nervous system by using combinations of different RNA modifications.”

Different RNA modifications were referred to as alternative splicings of pre-mRNA in the molecular epigenetics section of this 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior

“Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species…”

The mechanism, alternative splicing techniques of pre-mRNA, has since been linked by all serious scientists to the functional structure of supercoiled DNA.
See: Structural diversity of supercoiled DNA (2015)
Serious scientists will continue to ridicule pseudoscientists in parodies such as this one from December 2014.
All About that Base (Meghan Trainor Parody) 12/10/14

 

5th-6th Sept 2018 Dublin, Ireland

Ecological adaptation: A new definition of heredity (1)

Excerpt: ” …long-standing presumptions led to the claims made by biologically uninformed theorists who failed to link biophysically constrained viral latency to the recent origin of most protein-coding variants via the physiology of pheromone-controlled reproduction in species from microbes to humans…”
She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity May 29, 2018 | 672 Pages
From the description of the book:

1) We need a new definition of what heredity is…

2) …Zimmer ultimately unpacks urgent bioethical quandaries arising from new biomedical technologies, but also long-standing presumptions about who we really are and what we can pass on to future generations.

The long-standing presumptions led to the claims made by biologically uninformed theorists who failed to link biophysically constrained viral latency to the recent origin of most protein-coding variants via the physiology of pheromone-controlled reproduction in species from microbes to humans. For comparison to the long-standing presumptions, see:
Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants May 11, 2012
Evolution and functional impact of rare coding variation from deep sequencing of human exomes May 17, 2012
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants
Reported as: Past 5,000 years prolific for changes to human genome November 28, 2012

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. More broadly, the results suggest that humans are carrying around larger numbers of deleterious mutations than they did a few thousand years ago. But this doesn’t mean that humans now are more susceptible to disease, says Akey. Rather, it suggests that most diseases are caused by more than one variant, and that diseases could operate through different genetic pathways and mechanisms in different people.

Akey dismissed everything known about the epigenetic effects of food energy and the metabolism of food to pheromones, which biophysically constrains viral latency in the context of the physiology of reproduction in species from microbes to humans.
See for comparison: A third of Americans don’t believe in evolution January 1, 2014
My comment:

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

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

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

When food energy-dependent pheromone-controlled autophagy (see: Autophagy.pro) fails to protect organized genomes from the virus-driven degradation of messenger RNA, organisms pass on mutations to future generations. Clear evidence of that fact was published in the context of this article: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants January, 2013.

Establishing the age of each mutation segregating in contemporary human populations is important to fully understand our evolutionary history1, 2 and will help to facilitate the development of new approaches for disease-gene discovery3.

The facts about the age of all mutations have since been placed into the context of:
Sperm epigenetics and influence of environmental factors February, 2018

… epigenetic variation may be genetically selected [41], which is in contradiction with the opposite model in which epigenetic variation is a cause of genetic variation. While both models can cooperate, more experimental evidence, other than computationally-based, should be provided to address the mutagenicity of regions subjected to environmentally-induced epigenetic variation and the evolutionary implications.

Conclusion:

Future research efforts may be able to identify a unified epigenetic remodeling response to lifestyle stress across species. Understanding the role of environmentally-driven epigenetic changes in gametes on the phenotype of the offspring constitutes not only a fascinating biological question on its own but also represents a moral obligation for the health of future generations.

See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression December, 2014

MicroRNA present in mature sperm… may actually serve important regulatory roles in fertilization and early developmental processes.

To see how much experimental evidence of biophysically constrained food energy-dependent pheromone-controlled biologically-based cause and effect has been ignored during the past two decades, see: From Fertilization to Adult Sexual Behavior December 1996

…we focus directly on molecular events themselves. Here the “environment” involved can be that within a DNA segment. We also expand the notion of “biologically based sex differences.” Although many, and perhaps most, important sex differences arise from gonadal and hormonal development, also important are sex differences which are neither gonadal nor hormonal. All these factors affect the internal workings of the individual and intervene in structuring how the social environment might or might not modify sexual behavior. This discourse calls attention to features that are central to the so-called nature-nurture discussion.

Our section on molecular epigenetics may have been the first to detail what is now being reported in the context of the cryo-EM technology, which links energy-dependent changes from electrons to ecosystems in all living genera via what is known about pre-mRNAs. Pre-mRNAs are now also referred to as microRNAs in more than 70,000 published works.
See: microRNA and/or pre-mRNA 
Clearly, what is known to all serious scientists about biophysically constrained viral latency and healthy longevity has forced Carl Zimmer to suggest that “We need a new definition of what heredity is…”
See also:
7/31/16 From hydrogen atom transfer in DNA base pairs to ecosystems
7/31/16 RNA-mediated physics, chemistry, and molecular epigenetics
7/30/16 What is life when it is not protected from virus driven entropy
7/29/16 RNA-mediated molecular epigenetics and virus-driven entropy
4/10/14 Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
8/8/13 Nutrient-dependent / pheromone-controlled adaptive evolution
3/8/13 Nutrient-dependent / Pheromone–controlled thermodynamics and thermoregulation
2/17/13 Nutrient-dependent / Pheromone-controlled Adaptive Evolution
Watch for Philip C. Ball’s newest book: Beyond Weird  March 22, 2018

Over the past decade or so, the enigma of quantum mechanics has come into sharper focus. We now realise that quantum mechanics is less about particles and waves, uncertainty and fuzziness, than a theory about information: about what can be known and how.

See: 5/8/17 Energy as information and constrained endogenous RNA interference May 8, 2017
See also: New Giant Viruses Further Blur the Definition of Life

“The gap between cellular organisms and viruses is starting to close,” Deeg said. “Which then brings us back to: What is a virus, and what is life?”

Has anyone else linked biophotonics to the energy-dependent proton motive force via the cryo-EM technology?
See for instance: Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase.
And preview, Schrödinger at 75 – The Future of Biology – September 2018
Nobel Laureates, Linda Buck, Ben Feringa, Michael Rosbash are among other Nobel Laureates who are scheduled to present.
See also: Are Humans “Smeller Underachievers?” Not So Fast…

…they will share their data and experience on the psychological influences on eating and behavior, the chemosensory properties of food and how we experience them, the role of food as medicine, and the history and evolution of flavor and flavor perception.

No experimental evidence of energy-dependent biophysically constrained top-down causation suggests that flavor perception “evolved.”  See: Feedback loops link odor and pheromone signaling with reproduction

Plenty of Room at the Bottom

Cryo-EM: Linking spatial and conformational constraints

On Darwin Day (2018) Carl Zimmer suggested use of the twitter hashtag #Istudyevolution to report whatever aspect of biology people were studying. For example, Richard Lenski reported that he studied adaptation in E. coli. When I told others that ecological adaptation is nutrient-dependent and pheromone-controlled in species from microbes to humans, he blocked me from seeing his comments. Evidently he did not want people to know that he had been studying ecological adaptation for more than 2 decades but reporting the adaptations in the context of neo-Darwinian theories about mutations and evolution. For further clarification of that fact see:
Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility

…the mechanisms responsible for increased transport activity are not well understood, largely owing to limited structural information. We used cryo-electron tomography (cryo-ET) to visualize the 3D structure of the MT-bound dynein–dynactin complex from Mus musculus and show that the dynactin–cargo adaptor complex binds two dimeric dyneins. This configuration imposes spatial and conformational constraints on both dynein dimers.

This spatial and conformational constraints were reported as: Microscopic chariots deliver molecules within our cells

This discovery was totally unexpected, and will change how this motor complex is represented in cell biology and biochemistry text books,” says Saikat Chowdhury, PhD, a TSRI research associate and co-first author of the study.

“There had been years of biophysical experiments and biochemical experiments, and it was always assumed that there was just one dynein molecule,” Lander adds.

Assuming there was just one dynein molecule is something that only a biologically uninformed theorist would do. An energy-dependent difference in two molecules is required for movement and for biophysical constraints on movement. For comparison, all discoveries that link energy-dependent changes from electrons to ecosystems were anticipated by Richard P. Feynman in his claims about Plenty of Room at the Bottom.He linked his claims about the size of letters in a code from atoms to ecosystems in the context of Food Energy and denigrated the works of all theorists in The key to science (Cornell, 1964)
See also McEwen et al., (1964) Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”
Everything known to serious scientists links cryo-ET and cryo-EM technology from ecological niche construction to socio-cognitive niche construction via food energy-dependent amino acid substitutions in the microtubules, which link differences in animal behavior to human consciousness.
See: Untangling Neurodegenerative Diseases using Cryo-Electron Microscopy
Everything known about prevention of all pathology starts with the creation of sunlight.
See: Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases

In conclusion, we have shown for the first time that very low doses of far-UVC light efficiently inactivate airborne viruses carried by aerosols. For example, a very low dose of 2 mJ/cm2 of 222-nm light inactivates >95% of airborne H1N1 virus. Our results indicate that far-UVC light is a powerful and inexpensive approach for prevention and reduction of airborne viral infections without the human health hazards inherent with conventional germicidal UVC lamps. If these results are confirmed in other scenarios, it follows that the use of overhead very low level far-UVC light in public locations may represent a safe and efficient methodology for limiting the transmission and spread of airborne-mediated microbial diseases. Public locations such as hospitals, doctors’ offices, schools, airports and airplanes might be considered here. This approach may help limit seasonal influenza epidemics, transmission of tuberculosis, as well as major pandemics.

Reported as: Special UV light safely kills airborne flu virus, finds study

In the study, aerosolized H1N1 virus—a common strain of flu virus—was released into a test chamber and exposed to very low doses of 222 nm far-UVC light. A control group of aerosolized virus was not exposed to the UVC light. The far-UVC light efficiently inactivated the flu viruses, with about the same efficiency as conventional germicidal UV light.

They confirmed the fact that UV light biophysically constrains the degradation of messenger RNA that links mutations to all pathology.
See also: Photon-Mediated Quantum Gate between Two Neutral Atoms in an Optical Cavity

Quantum logic gates are fundamental building blocks of quantum computers. Their integration into quantum networks requires strong qubit coupling to network channels, as can be realized with neutral atoms and optical photons in cavity quantum electrodynamics. Here we demonstrate that the long-range interaction mediated by a flying photon performs a gate between two stationary atoms inside an optical cavity from which the photon is reflected. This single step executes the gate in 2μs. We show an entangling operation between the two atoms by generating a Bell state with 76(2)% fidelity. The gate also operates as a cnot. We demonstrate 74.1(1.6)% overlap between the observed and the ideal gate output, limited by the state preparation fidelity of 80.2(0.8)%. As the atoms are efficiently connected to a photonic channel, our gate paves the way towards quantum networking with multiqubit nodes and the distribution of entanglement in repeater-based long-distance quantum networks.

Reported as: Light controls two-atom quantum computation

This interaction is the basis for performing characteristic gate operations between the atoms, for example the operation as a CNOT gate or the generation of entanglement. The new method offers a variety of advantages: for example, the gate operations take place within microseconds which is an asset for quantum information processing.

Quantized energy is the information that must be biophysically constrained and transferred from hydrogen-atoms in DNA base pairs in solution. That fact seems to have escaped the attention of biologically uninformed pseudoscientists and most so-called science journalists. The pseudoscientists and other theorists linked the emergence of the energy to the evolution of all biodiversity outside the context of the physiology of reproduction and autophagy, which biophysically constrains viral latency.
See for comparison to what serious scientist have done:Experimental Evidence of Radiation Reaction in the Collision of a High-Intensity Laser Pulse with a Laser-Wakefield Accelerated Electron Beam

The dynamics of energetic particles in strong electromagnetic fields can be heavily influenced by the energy loss arising from the emission of radiation during acceleration, known as radiation reaction. When interacting with a high-energy electron beam, today’s lasers are sufficiently intense to explore the transition between the classical and quantum radiation reaction regimes. We present evidence of radiation reaction in the collision of an ultrarelativistic electron beam generated by laser-wakefield acceleration (ϵ>500MeV) with an intense laser pulse (a0>10). We measure an energy loss in the postcollision electron spectrum that is correlated with the detected signal of hard photons (γ rays), consistent with a quantum description of radiation reaction. The generated γ rays have the highest energies yet reported from an all-optical inverse Compton scattering scheme, with critical energy ϵcrit>30MeV.

Reported as: Intense laser experiments provide first evidence that light can stop electrons

“One thing I always find so fascinating about this is that the electrons are stopped as effectively by this sheet of light, a fraction of a hair’s breadth thick, as by something like a millimetre of lead. That is extraordinary.”

The data from the experiment also agrees better with a theoretical model based on the principles of quantum electrodynamics, rather than Maxwell’s equations, potentially providing some of the first evidence of previously untested quantum models.

Effects of quantized energy as information cannot be defined in the context of equations, which is why physicists have traditionally been ridiculed for any attempt to explain energy-dependent top-down causation in the context of biophysically constrained healthy longevity.

All species on Earth exhibit an undefined, incalculable, innate ability to biophysically constrain energy-dependent viral latency. That ability is food energy-dependent and controlled by the physiology of reproduction. Food energy comes from sunlight, either directly or indirectly via plant grown and the creation of microRNAs in plants. Serious scientists know how to light the sun’s anti-entropic virucidal energy to DNA repair.
See: Watson–Crick Base Pairing Controls Excited-State Decay in Natural DNA (2014)
Reported as: Base-pairing protects DNA from UV damage

…the Watson-Crick base-pairing mechanism itself controls the dissipation of the absorbed UV energy. This contradicts the conventional wisdom, which holds that the base sequence within the same strand is responsible for the deactivation of excited states,” says Wolfgang Zinth.

See also:  Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution (2015)

Ultrafast deactivation pathways bestow photostability on nucleobases and hence preserve the structural integrity of DNA following absorption of ultraviolet (UV) radiation. One controversial recovery mechanism proposed to account for this photostability involves electron-driven proton transfer (EDPT) in Watson–Crick base pairs. The first direct observation is reported of the EDPT process after UV excitation of individual guanine–cytosine (G⋅C) Watson–Crick base pairs by ultrafast time-resolved UV/visible and mid-infrared spectroscopy. The formation of an intermediate biradical species (G[−H]⋅C[+H]) with a lifetime of 2.9 ps was tracked. The majority of these biradicals return to the original G⋅C Watson–Crick pairs, but up to 10 % of the initially excited molecules instead form a stable photoproduct G*⋅C* that has undergone double hydrogen-atom transfer. The observation of these sequential EDPT mechanisms across intermolecular hydrogen bonds confirms an important and long debated pathway for the deactivation of photoexcited base pairs, with possible implications for the UV photochemistry of DNA.

See also:  UV Irradiation Induces a Non-coding RNA that Functionally Opposes the Protein Encoded by the Same Gene (2017)
Reported as: Noncoding RNA Helps Cells Recover from DNA Damage
My comment to the Scientist:

There is clear evidence that femtosecond blasts of UV light repair DNA in the context of energy-dependent changes in the microRNA/messenger RNA balance and autophagy, which protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA.

The failure to integrate the Nobel Prize winning works of Ben Feringa (Chemisty 2016) and Yoshinori Ohsumi (Physiology or Medicine 2016) prevents theorists from linking what organisms eat to their pheromone-controlled physiology of reproduction in the context of Schrodinger’s claims in “What is Life?”(1944) and this claim by Roger Penrose in the reprint edition:

“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” (Roger Penrose 8 August 1991)

See also: From Fertilization to Adult Sexual Behavior In our section on molecular epigenetics, we wrote:

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…

The food energy that is linked from alternative splicing techniques of pre-mRNA to the chemistry of protein folding and the pheromone-controlled physiology of reproduction in all living genera seems to be largely ignored by those who are not Nobel Laureates.

It links the virus-driven theft of quantized energy from the degradation of messenger RNA to mutations and all pathology, and physicists cannot explain that fact with math and definitions. They tried with de Vries 1902 definition of mutations, and they have failed miserably ever since.

See: Amino acid–base interactions: a three-dimensional analysis of protein–DNA interactions at an atomic level (2001)

To assess whether there are universal rules that govern amino acid–base recognition, we investigate hydrogen bonds, van der Waals contacts and water-mediated bonds in 129 protein–DNA complex structures. DNA–backbone interactions are the most numerous, providing stability rather than specificity. For base interactions, there are significant base–amino acid type correlations, which can be rationalised by considering the stereochemistry of protein side chains and the base edges exposed in the DNA structure.

See also: Systematic prediction of DNA shape changes due to CpG methylation explains [quantized energy-dependent] epigenetic effects… (2018)
The effects of sunlight and quantum chemistry link energy-dependent fixation of RNA-mediated amino acid substitutions to the differentiation of all cell types in all living genera via the physiology of reproduction, which is controlled by pheromones in species from microbes to humans. Pheromones biophysically constrain viral latency in all animals that need to eat for their species to survive.

Cryo-EM technology predicts RNA-mediated DNA shape, which means the technology can be used to link the virus-driven degradation of messenger RNA from mutations to all pathology in the context of the games “Cytosis” and “Subatomic.”
When “Subatomic” is available, players will link what is known to all serious scientists who present during “Schrodinger at 75” to the overwhemling amount of pseudoscientific nonsense touted by theorists during the past 75 years.

Theorists failed to link subatomic particles to biophysically constrained viral latency via the “Virus Expansion” from “Cytosis.” That fact led to this admission of ignorance:

Microscopic chariots deliver molecules within our cells https://phys.org/news/2018-02-microscopic-chariots-molecules-cells.html

Excerpt: This discovery was totally unexpected, and will change how this motor complex is represented in cell biology and biochemistry text books,” says Saikat Chowdhury, PhD, a TSRI research associate and co-first author of the study.

“There had been years of biophysical experiments and biochemical experiments, and it was always assumed that there was just one dynein molecule,” Lander adds.

My comment: All the discoveries that have since linked energy-dependent changes from electrons to ecosystems were anticipated by Richard P. Feynman in his claims about “Plenty of Room at the Bottom.” Everything known to serious scientists links cryo-EM technology from ecological niche construction to socio-cognitive niche construction via food energy-dependent amino acid substitutions in the microtubules that link differences in animal behavior to human consciousness.

It will good to see “Subatomic” placed into the context of the admission that there are two dynein molecules. Others may begin to see the levels of complexity that must be represented in game play to prevent further assumptions based on ignorance of particle physics and energy transfer that biophysically constrains viral latency.

The fact that many people can readily learn more than most theoretical physicists have learned about subatomic particles and cell biology by playing games for fun is an exciting development for scientists and laypersons.

Magnus S. Magnusson wrote: James Kohl it [the Neil deGrasse Tyson meme] was not aimed at you, of course, understand that it is about the genera educational situation. BTW Einstein mostly missed biology and Hawking says the 21. century will be that of biology, which I also believe.”
The Icelandic atheist and hate monger, blocked me before I could comment further on Neil deGrasse Tyson’s overwhelming display of ignorance.
George FR Ellis, who co-authored with Stephen Hawking in the 60’s has already validated my model. See: Understanding and accounting for relational context is critical for social neuroscience

George F R Ellis This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics.

The Genius Games series from John Coveyou is the way forward. The games successfully link the creation of the sun’s anti-entropic virucidal energy from top-down causation to all biophysically constrained biodiversity via a model that links electrons to ecosystems.

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

An evolutionary theory killer

A reversible TCA cycle in a thermophile (3)

A pathway for mitotic chromosome formation

The combination of nested loops distributed around a helically twisted axis plus dense chromatin packing achieves the 10,000-fold compaction of chromatin into linearly organized chromosomes that is required for accurate chromosome segregation when cells divide.

The compaction of chromatin in the context of hydrophobicity is the topic of: Structural diversity of supercoiled DNA

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

Differential recognition of proteins clearly involves this link from natural selection for energy-dependent codon optimality to the physiology of reproduction via RNA-directed DNA methylation.
See for comparison: DNA-Methylation: Master or Slave of Neural Fate Decisions?

The involvement of splicing as effector of changes in DNA methylation is an exciting new angle to pursue with more precise epigenetic engineering tools. Distinguishing essential from specific, and causal from secondary marks will be essential for neuro-epigenetics. New approaches promise to answer long outstanding questions and will likely facilitate the discovery that DNA modifications might have new unexpected roles in the brain.

Splicing is not the effector of changes in DNA methylation, energy-dependent changes in the microRNA/messenger RNA balance must be given first consideration. But, this article is part of the Research Topic: Epigenetic Mechanisms of Neurogenesis in the Developing Neocortex

The topic is an example of human idiocy for comparison to this report on alternative splicing, which was linked to energy-dependent biophysically constrained viral latency in the context of:

 Alternative splicing and the evolution of phenotypic novelty and the cell biology game: Cytosis

This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.

The origins of morphological diversity cannot be evaluated outside the context of the origins of energy-dependent behavioral diversity, which requires that RNA-mediated DNA methylation be linked to differences in cell fate in all tissues of all individuals of all species on Earth. Typically, serious scientists do this by linking the creation of the sun’s anti-entropic viral latency from  subatomic particles to creation of atoms and ecosystems in the context of human brain development via mitotic chromosome formation.

See for instance: The Excitable Mitochondria and The vibrational theory of olfaction for the win by John Hewitt.
If he did not believe that “evolution did it” after the emergence of energy, he would not have placed his bets on ridiculous theories and criticized my life’s history of publications and presentations, which he claimed were BS.
See for comparison to his claims: Correcting for Differential Transcript Coverage Reveals a Strong Relationship between Alternative Splicing and Organism Complexity
We placed the facts about alternative splicing and increasing organismal complexity into the context of our section on molecular epigenetics in 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…

The sexual differentiation of all cell types in species from yeast to humans was presciently placed into the context of what was known about pre-mRNA mediated biophysically constrained viral latency in 1996. Food energy-dependent pre-mRNAs are now referred to as microRNAs (miRNAs). The creation of the miRNAs links the anti-entropic virucidal of the sun to all biodiversity via the physiology of reproduction,  and our details from 1996 have been extended across species via this recently published work:
Reproductive role of miRNA in the hypothalamic-pituitary axis

The hypothalamic-pituitary-gonadal (HPG) axis plays a critical role in regulating reproductive function. Gonadotropin-releasing hormone (GnRH), which is secreted by the hypothalamus, acts on pituitary gonadotrophs to stimulate luteinizing hormone (LH) and follicle-stimulating hormone (FSH) synthesis and secretion, ultimately affecting the animal’s fertility. MicroRNAs are small, non-coding RNAs that are widely expressed throughout the brain and can fine-tune gene expression post-transcriptionally. Recently, growing evidence has unveiled the central position of miRNAs within a key regulatory process involving GnRH secretion and subsequent activation in the pituitary. Although transcriptional regulation of reproduction has been well studied, the post-transcriptional processes are less well understood. In this review, we elaborate comprehensively on the critical role of miRNAs in the reproductive process, including both temporal and spatial aspects. A better understanding of how miRNAs impact the neuroendocrine system may improve our knowledge of reproduction and provide novel targets for therapeutic development.

For comparison, see: No Missing Link: Knowledge Predicts Acceptance of Evolution in the United States

Using a new demographically representative survey (N = 1100) that includes a detailed measure of evolution knowledge, we find that knowledge predicts level of acceptance, even after accounting for the effects of religion and politics. These results demonstrate that Americans’ views on evolution are significantly influenced by their knowledge about this theory and therefore might be amenable to change.

Reported as: Better knowledge of evolution leads to greater acceptance of the concept

…actual knowledge of the science seems to play a role, and we’ve documented that here for evolution for the first time in a representative population.”

If that claim was true, we would not see so many examples of people in other countries who have replaced the teaching of ridiculous evolutionary theories with facts that their students learn about ecological variation and ecological adaptations.
For example: Israeli Middle Schools School to Include Theory of Evolution (2014)

…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.

See also: Turkish schools to stop teaching evolution, official says (2017)
If you are willing to consider the facts about why many countries do not teach humans to believe in ridiculous theories, please see:
Subatomic: From thermophiles to humans (in prep)

 
 
 

5th-6th Sept 2018 Dublin, Ireland

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (4)

Summary: Antagonists such as John Hewitt have exhausted my patience. Now see this:

The authors invented the term “phosphate steering”  in an attempt to obfuscate what has been known to all serious scientists about oxidative phosphorylation for more than 50 years.

See: “oxidative phosphorylation” microRNA  (105 entries); “oxidative phosphorylation” (21955 entries) and “phosphate steering” (1 entry)

Compare the nonsense about phosphae steering to facts in the context of Modern diversification of the amino acid repertoire driven by oxygen (2017)
Reported on February 1, 2018 as: Quantum chemistry solves mystery why there are these 20 amino acids in the genetic code
Conclusion:

…we could characterize oxygen as the author adding the very final touch to the genetic code,” stated Moosmann.

Also reported on Feburary 2, 2018 as: Origin of Life: Quantum Chemistry Solves One of Genetics’ Biggest Mysteries Using Amino Acids From Space

Moosmann and his colleagues created a quantum chemistry model that compared amino acids on Earth to amino acids from space that had arrived via meteorites.

Conclusion:

The newer aminos’ reactivity still didn’t account for their presence in the genetic tool box to begin with. The researchers conducted additional experiments which verified their theoretical results. They found that at least three of the newer aminos—methionine, tryptophan and selenocysteine—were included in response to the rising levels of oxygen in our atmosphere. Since oxygen encourages the production of toxic-free radicals, we needed additional, nimbler amino acids to react to those free radicals and help our cells repair themselves.

Last month I advised John Hewitt against attemptng to link the creation of selenocysteine to biodiversity outside the context of the biophysical constraints on viral latency. Hewitt and many other biologically uninformed science journalists like the idea of neo-Darwinian evolution.
See why: On the unique function of selenocysteine — Insights from the evolution of selenoproteins

These evolutionary studies stem from the realization that patterns of amino acid conservation and substitution in proteins may provide important functional information.

The magic of evolutionary studies is easy compared to understanding the functional structure of supercoiled DNA in the context of the report from 2009. Hewitt likes that simple-minded ignorance compared to the difficulty of placing the structure and function of supercoiled DNA into the context of my model from 2013.

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

Conclusion:

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

But, I digress. My point is that no experimental evidence of biophysically constrained top-down causation suggests that amino acids from space arrived on Earth via transport in meteorites. The fact that the creation of the amino acids must be linked to biophysically constrained viral latency has repeatedly been reported at every level of examination by serious scientists.
See for instance: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
Reported as:Researchers may have solved origin-of-life conundrum

…the conditions that produce nucleic acid precursors also create the starting materials needed to make natural amino acids and lipids. That suggests a single set of [light activated] reactions could have given rise to most of life’s building blocks simultaneously.

John Hewitt’s claims can now be placed into the context of my model.
On February 3, 2018, John Hewitt tweeted:

“all the substitutions were figured out long ago by bacteria”

I replied:

Do you realize how ridiculous that sounds in the context of any other claims that you have accurately represented?

On February 4, 2018, John Hewitt wrote:

“slander me again James and you are blocked. those silly viruses were artificially engineered that way”

I’ve placed his comments about slander into the context of his past claims about viruses and energy.
1) MIT team genetically engineers a quantum virus for efficient energy transport (2015)

Although the virus has demonstrated the ability to capture and transfer light energy…

John Hewitt failed to put his reported fact about the capture of light energy into the proper context of my works. He has since been denigrating my model and peer-reviewed publications in a month-long escalation of “twitter” attacks.
Like others, he has resorted to attacks via social media, because that’s where the ignorance is. The ignorance of other theorists has typically been in his favor. But see two other news reports from John Hewitt.
2) The Excitable Mitochondria (2016) http://inference-review.com/article/the-excitable-mitochondria

By fine-tuning their fusion and fission rates, each cell maintains a large centralized mitochondrial syncytium that dispatches and recalls mitochondrial quanta to different parts of the cell.

John Hewitt joined the ranks of others who have claimed the fine-tuning is automagical. He removed consideration for the creation of  quantized energy and the virus-driven capture of quantized energy. That is how he bastardized everything known to serious scientists about energy-dependent biophysically constrained viral latency and healthy longevity in species from microbes to humans. But wait, he almost helped other serious scientists make progress.
3) The vibrational theory of olfaction for the win (2017)

In addition to these discoveries, Turin also just published a much more sweeping treatise on molecular recognition in olfaction in the journal Advances in Physics: X. In it, he and his co-authors delve into more of the specifics of olfactory receptors, including particular amino acid motifs, metal binding capacities, and disulphide bridge redox status. It turns out that amino acid side chains alone frequently pull off some rather interesting electron transfer effects without the need for fancy co-enzymes or prosthetic groups. Although there are only a few cases in which this has been proposed, we can take a brief anecdotal look at how this mechanism operates in other proteins.

John Hewitt likes Turin’s theory, but ignores my model, which links the creation of sunlight from the creation of quantized energy as information to the creation of ATP. Conserved molecular mechanisms in microbes link the creation of ATP to RNA-mediated cell type differentiation via the creation of amino-acid substitutions that stabilize the organized genomes of all living genera in the context of the physiology of reproduction.
See the the initial prescient support for the claims in my mode, which came from the first person who ever critiqued it:, Bruce McEwen.
Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

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

See also: Long-range coherence and energy storage in biological systems (1968) published in International Journal of Quantum Chemistry

The supplied [quantized] energy is thus not completely thermalized but stored in a highly ordered fashion.

Clearly, energy-dependent biophysical constraints on the well-ordered stability of organized genomes is required for the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes.
Quantum chemistry solves mystery why there are these 20 amino acids in the genetic code makes that fact perfectly clear.
But see also: Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment (2003)
and Learning from Bacteria about Natural Information Processing (2009)
and Stability of the hybrid epithelial/mesenchymal phenotype (2016)

…higher levels of these PSFs may be predictive of poor patient outcome. Finally, based on these specific examples, we deduce certain network motifs that can stabilize the hybrid E/M phenotype. Our results suggest that partial EMT, i.e. a hybrid E/M phenotype, need not be ‘metastable’, and strengthen the emerging notion that partial EMT, but not necessarily a complete EMT, is associated with aggressive tumor progression.

If you looked only at the works published by the late Eshel Ben-Jacob and his group, you would learn the difference between all serious scientists and all biologically uninformed theorists and their idiot minions: the biologically uninformed science journalists.
But for another 50-year-old historical perspective see: Non-singular general-relativistic collapse (1968) as cited in Absorption and Scattering Cross Section of Regular Black Holes Journal of Gravity (2014)
Reported as: What If the Big Bang Wasn’t the Beginning? New Study Proposes Alternative December 5, 2017

There is no empirical evidence for bouncing cosmologies today,” he said. “But there is no evidence for the initial singularity as well.

That’s two strikes against “Big Bang” cosmology before serious scientists start.
See for comparison: Non-singular quantum-inspired gravitational collapse (2013)
Biologically uninformed journalists continue to display their epic failure to understand any aspect of pattern recognition. For example, all patterns appear to be energy-dependent and the energy appears to be physically constrained in the context of gravity and and biophysically constrained in the context of all  biodiversity.
I placed that fact into the context of part three of this series.
Anti-entropic sunlight: Schrödinger’s Creationist Secret? (3)
The fact that two articles published in 1968 attest to the facts about the energy-dependent creation of ATP and RNA in McEwen et al., (1964) , links claims about human idiocy to science journalists — with John Hewitt as the best example of idiocy.
But, two days later, In an attempt to support the nonsense touted by John Hewitt, Nik Willmore added:

Replying to @jvkohl @jhewitt123

Stringing together walls of general science buzzword salad as an excuse to hurl quack insults makes you the poster boy for Pink Floyd’s album The Wall.

My response: See Andrew Jones unpublished thesis on abiogenesis and the editor’s comments on his criticisms: “…subjected to standard peer review and the revised version was accepted by me after it had been accepted by both reviewers.” Find your friends on The Dark Side of the Moon.
People like @nikwillmore and @jhewitt123 might claim that they want to see “Science” only after peer review. Most of them do not want to see anything published that refutes the pseudoscientific nonsense of their ridiculous theories. But see also: Universal Alternative Splicing of Noncoding Exons
Compare claims 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: our section on molecular epigenetics From Fertilization to Adult Sexual Behavior

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism…

We did not forget to mention the emergence of energy, abiogenesis, and evolution.
All serious scientists dismiss ridiculous claims. For comparison, all pseudoscientists and biologically uninformed science journalists dismiss the experimental evidence of energy-dependent biophysically constrained viral latency as if the experimental evidence was optional. See:  Combating Evolution to Fight Disease.
See also: The real reason behind The Big Bang Theory’s ratings drop

So how come Big Bang isn’t popping the way it used to?

It’s getting eclipsed by Young Sheldon

As Cheers begot Frasier and Buffy begot Angel, The Big Bang Theory has spawned Young Sheldon. It chronicles the oft-spoken of adventures of Sheldon when he was a socially oblivious, one-of-a-kind, once-in-a-generation genius growing up in a small town with a family that didn’t understand him. Enjoying a lead-in from The Big Bang Theory, Young Sheldon was a hit right out of the gate.

This appears to be proof that most people would rather be entertained to death rather than examine the facts about the creation of the sun’s anti-entropic virucidal energy and biophysically constrained viral latency.
See also: “You are blocked from following @jhewitt123 and viewing @jhewitt123’s Tweets. Learn more”
I do not need to learn more: See: A Few Good Man “You Can’t Handle the Truth”
See also: Energy as information and constrained endogenous RNA interference

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to… autophagy.

People like John Hewitt and Nik Willmore consistently test the patience of serious scientists until the ignorance of their ridiculous theories is exposed.
See also: Phosphate steering by Flap Endonuclease 1 promotes 5′-flap specificity and incision to prevent genome instability

Phosphate steering mutations could thus be the trans-modifiers of repeat expansions during either somatic, or intergenerational transmissions in human disease65. Moreover, as the basic residues implicated in phosphate steering are largely conserved in the 5′-nuclease superfamily, control over the +1 and −1 phosphates may be a superfamily-conserved mechanism.

The authors invented the term “phosphate steering”  in an attempt to obfuscate what has been known to all serious scientists about oxidative phosphorylation for more than 50 years.
See: “oxidative phosphorylation” microRNA  (105 entries)
“oxidative phosphorylation” (21955 entries) and “phosphate steering” (1 entry)
See for comparison: Gamma oscillations organize top-down signalling to hypothalamus and enable food seeking

Cortical cognitive processing9, 10 involves gamma oscillations11, 12, 13, 14, 15, which support memory16, 17, attention18, cognitive flexibility19 and sensory responses20. These functions contribute crucially to feeding behaviour by unknown neural mechanisms. Here we show that coordinated gamma (30–90 Hz) oscillations in the lateral hypothalamus and upstream brain regions organize food-seeking behaviour in mice.

Reported as: Gamma oscillations coordinate food seeking

“Preferential and selective control of feeding-related cells by rhythmic inputs to hypothalamus demonstrates a beautiful interaction of structure and function in the brain” says Alexey Ponomarenko. “Here we see how fast synchronization, combined with a precise information transfer between brain regions and cells types, drives behaviors crucial for survival.”

The behaviors linked to species survival can be viewed in the context of this report from 2005: Feedback loops link odor and pheromone signaling with reproduction
But first, serious scientists must start with the anti-entropic virucidal energy of sunlight, which is what Schrödinger did 75 years ago.

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)

For God and Country

The "walking fish" walks straight from quantum physics to quantum souls

Happy New Year! In 2018, serious scientists are prepared to help you prevent or effectively treat all pathology. We have nearly stopped the pseudoscientific nonsense touted by theorists — although some of them didn’t get the memo from 1968, which is when Frohlich published: Long-range coherence and energy storage in biological systems.
He linked certain processes in living systems from the creation of energy to hydrogen bonds in cell membranes and to dipolar oscillations that link the creation of the sense of smell in bacteria from the physiology of pheromone-controlled reproduction to all biodiversity via the creation of ATP; the creation of RNA, and fixation of energy-dependent RNA-mediated amino acid substitutions.
See: The vibrational theory of olfaction for the win
Historical perspective, based on Frohlich’s “speculation.”
From Fertilization to Adult Sexual Behavior (1996)

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation…

The sexual differentiation of cell types protects them from the virus-driven theft of quantized energy, which Frohlich linked to the degradation of the cell wall and what is now known about how unicellular bacteria become archaea before they become L-forms.
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!

Food energy-dependent pheromone-controlled biophysically constrained viral latency keeps egg cells fresh in the context of autophagy and sexual differentiation. Biophysical constraints prevent the transgenerational epigenetic inheritance of virus-driven pathology, which is caused by the virus-driven theft of quantized energy that links the degradation of messenger RNA to all pathology.
See for comparison: Keeping egg cells fresh with epigenetics (2017)
As soon as the Medical Xpress news source realized that they had destroyed neo-Darwinian pseudoscientific nonsense with their report on epigenetics, the post went missing.

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Sorry, the page you were looking for could not be found.

The page might have been removed, had its name changed, or become temporarily unavailable.

They cited: Courtney W. Hanna et al, MLL2 conveys transcription-independent H3K4 trimethylation in oocytes, Nature Structural & Molecular Biology (2017). DOI: 10.1038/s41594-017-0013-5
The cited work is not yet available at the DOI: I attempted to add this comment:
The speed of light on contact with water links food energy to the physiology of pheromone-controlled reproduction and all biophysically constrained biodiversity. Now, there is a mathematical model that refutes neo-Darwinism and “Big Bang” cosmology. Use it to make all biologically uninformed theorists recognize their foolishness. Quantum Vacuum Dynamics, Coherence, Superluminal Photons and Hypercomputation in Brain Microtubules
The human idiocy exposed by Courtney W. Hanna et al (2017?) was also exposed at least twice in September. See: Striking a balance: regulation of transposable elements by Zfp281 and Mll2 in mouse embryonic stem cells Published online 2017 Sep 25

Transposable elements pervading mammalian genomes mostly originate from retrotransposons, including long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and endogenous retroviruses (ERVs) (,). Retrotransposons shape host genome landscape and evolution through introducing, deleting or modifying cis-regulatory elements or genes (,). However, they can also induce detrimental genome instability and numerous human diseases (,).

The claim that retrotransposons shape host genome landscape and evolution is a ridiculous claim. Food energy links ecological variation to ecological adaptations via the pheromone-controlled physiology of reproduction in all living genera. Nothing links retrotransposons to evolution because viral latency must be biophysically constrained in the context of increasing organismal complexity.
See also: Genomic imprinting beyond DNA methylation: a role for maternal histones 2017 Sep 19

Sperm and oocytes exhibit different patterns of chromatin organisation: the sperm DNA is highly methylated and tightly packaged, with protamines replacing most canonical histones, while the oocyte genome has a bimodal methylation pattern, an extensively open chromatin conformation and atypical patterns of histone modifications [].Methylation and chromatin organization are food energy-dependent and biophysically constrained in the context of the physiology of pheromone-controlled reproduction and the space-time continuum.

See why Feynman was forced to comment on the facts about food energy, years before this information became generally known: Trinucleotide Repeats: Fragile X Syndrome

DNA (deoxyribonucleic acid)… contains a “code” of 3-letter words known as “codons” or “trinucleotides.” Many genes normally contain trinucleotide sequences that can be repetitive. These are called “trinucleotide repeats.” But when the number of trinucleotide repeats increases to a larger than normal number of copies, the DNA is changed. The gene may not function as it should, or may not work at all.

…extra trinucleotide repeats cause the DNA to become unstable, the repeats within that gene expand even more. The result is that the child has a gene that is not functioning properly (if at all), and the child is said to have the “full mutation.” An example of a trinucleotide repeat disorder is Fragile X syndrome.

See also: Researchers discover how cells remember infections decades later

On the surface and through the actions of their genes, they look like cells that have never been exposed to an infection, but on their DNA the researchers found a fingerprint, called a methylation pattern, that identifies them as having been through battle as an infection-fighting cell, which are called effector cells.

Thanks to passive-aggressive antagonist Jon Lieff for repeatedly bringing the difference between pseudoscientists and serious scientists to my attention. Pseudoscientists refer to “effector cells” so that the obvious link from food energy to autophagy to healthy longevity is obfuscated.
See for instance: Ancient Mutation may Help Explain Origin of Human Organs

1) Researchers have reported that a neutral mutation having no real purpose and occurring randomly over 700 million years ago may help to explain the origins of complex structures like organs in humans and other vertebrates.

The pseudoscientific nonsense reported by Labroots may have reached its peak.

2) The same gene can give rise to different proteins that can act in entirely different ways by editing those genes a little differently, in a phenomenon called alternative splicing…

A link to a video about alternative splicing is included; See: Alternative Splicing
Conclusion: 

“The new discovery confirms how versatile biological evolution is: the same foundation and gene tools can be used to build a wood cabin or a skyscraper,” concluded Garcia-Fernàndez.

There is no such thing as versatile biological evolution. It is long past time for serious scientists to stop the pseudoscientific nonsense touted by theorists.
For a reminder of how long serious scientists have known the facts about alternative splicing, see again:
From Fertilization to Adult Sexual Behavior (1996)

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation…

Alternative splicing is food energy-dependent and RNA-mediated in the context of the physiology of pheromone-controlled biophysically constrained viral latency.
All niche construction is food energy-dependent and controlled by the physiology of reproduction.
See: 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 organism exemplifies how ecological variation must be linked to ecological adaptation in species from microbes to humans. See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

Under strong selection for motility, these bacteria consistently regained flagella within 96 hours via a two-step evolutionary pathway. Step 1 mutations increase intracellular levels of phosphorylated NtrC, a distant homolog of FleQ, which begins to commandeer control of the fleQ regulon at the cost of disrupting nitrogen uptake and assimilation. Step 2 is a switch-of-function mutation that redirects NtrC away from nitrogen uptake and toward its novel function as a flagellar regulator. Our results demonstrate that natural selection can rapidly rewire regulatory networks in very few, repeatable mutational steps.

This was reported in the context of the classic phrase from the Jurrasic Park series of movies: Life finds a way (video)
The claim that life finds a way to resurrect the bacterial flagellum over the weekend via mutations can be compared in the context of this model organism. See: The Axolotl Limb Regeneration Model as a Discovery Tool for Engineering the Stem Cell Niche

…this model has identified a number of proregenerative signals, including growth factor signaling associated with nerves, and signals associated with the extracellular matrix (ECM) that induce pattern formation.

Educational video: Meet the creature that can regenerate its brain and resist cancer.
At the end of the video, the yin yang symbol from Chinese philosophy is superimposed over the electron cloud, which links the anti-entropic virucidal energy of sunlight to the physiology of pheromone-controlled reproduction and the viral latency that protects all organized genomes from the degradation of messenger RNA.
The virus-driven degradation of messenger RNA is clearly the link from mutations to all pathology, and all pathology can be examined in the context of the axolotyl model organism (aka: The “walking fish.”)
The portrayals of the “walking fish” as an example of neo-Darwinian evolution is a ridiculous example of what Feynman called human idiocy. Darwin place his “conditions of life” before natural selection because he knew that organisms must eat and reproduce. Neo-Darwinists assumed that the 2nd Law of Thermodynamics did not need to include any aspect of quantum entanglement.
Energy-dependent changes have since been linked from electrons to ecosystems by autophagy — the innate antiphage defense mechanism.
The defense mechanism protects the cell types of axolotyl and all other living genera from the virus-driven energy theft that links the destruction of the cell wall from bacteria to archaea and to L-forms, the last example on Earth of virus-driven energy theft and failed autophagy.

 
No automatic alt text available.

Energy-dependent base editing and correction of mutations (2)


On 12/10/17, a long-term business partner called to tell me he was ending his efforts to sell human pheromone-enhanced fragrance products to those who understand how the products help to biophysically constrain viral latency in all mammals.
QuEBS workshop has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. […] discussion of notable scientists and pioneers of Quantum Biology… established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.
Decades later, researchers reported on: Signatures of exciton condensation in a transition metal dichalcogenide. The mass media news representation is:  Physicists excited by discovery of new form of matter, excitonium.

…when an electron, seated at the edge of a crowded-with-electrons valence band in a semiconductor, gets excited and jumps over the energy gap to the otherwise empty conduction band, it leaves behind a “hole” in the valence band. That hole behaves as though it were a particle with positive charge, and it attracts the escaped electron. When the escaped electron with its negative charge, pairs up with the hole, the two remarkably form a composite particle, a boson—an exciton.

Wikipedia

“An exciton is a bound state of an electron and an electron hole which are attracted to each other by the electrostatic Coulomb force. It is an electrically neutral quasiparticle that exists in insulators, semiconductors and in some liquids.”

If excitons are found in water, the speed of light on contact with water could be linked to the quantized energy-dependent de novo creation of all biodiversity on Earth via the pheromone-controlled physiology of reproduction in all living genera. That fact led me to find information that links thermodynamic cycles of energy-dependent RNA-mediated protein folding chemistry to hydrophobicity in supercoiled DNA.

The Water-Food-Energy Nexus: Processes, Technologies, and Challenges

The book is organized into 4 sections on water, food, energy, and the future of sustainability, highlighting the interplay among these topics. The first section emphasizes water desalination, water management, and wastewater treatment. The second section discusses cereal processing, sustainable food security, bioenergy in food production, water and energy consumption in food processing, and mathematical modeling for food undergoing phase changes. The third section discusses fossil fuels, biofuels, synthetic fuels, renewable energy, and carbon capture. Finally, the book concludes with a discussion of the future of sustainability, including coverage of the role of molecular thermodynamics…

See for comparison. There is no coverage of the role of molecular thermodynamics in the symbols used to represent different religions. It’s as if the differences exist outside the context of what is known about the creation of the sun’s anti-entropic virucidal energy.

No automatic alt text available.

The role of molecular thermodynamics in energy-dependent RNA-mediated cell type differentiation was detailed in the context of: Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990)

Energy-dependent changes in base pairs have since been linked from changes in the microRNA/messenger RNA balance and RNA editing to fixation of RNA-mediated amino acid substitutions that differentiate the cell types of all living genera. However, there appears to be no mention of how the virus-driven degradation of messenger RNA has been linked from mutations to all pathology in Guidelines for Genome-Scale Analysis of Biological Rhythms (2017).

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding “big data” that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms.

Could ignoring this fact be a problem? See: Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

If the guidelines for linking the anti-entropic virucidal energy of sunlight to all biodiversity on earth via the physiology of pheromone-controlled reproduction in species from microbes to humans were applied, the guidelines could be extended to claims about the Molecular and cellular reorganization of neural circuits in the human lineage

…the dopaminergic interneurons found in the human neocortex were absent from the neocortex of nonhuman African apes. Such differences in neuronal transcriptional programs may underlie a variety of neurodevelopmental disorders.

Small but distinct differences among species mark evolution of human brain

Researchers found one gene, ZP2, was active in only human cerebellum — a surprise, said the researchers, because the same gene had been linked to sperm selection by human ova.

That claim can be placed into the context of what we detailed about energy-dependent RNA-mediated cell type differentiation in the molecular epigenetics section of our 1996 Hormones and Behavior review.
See: From Fertilization to Adult Sexual Behavior (1996)

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…

The alternative splicings of pre-mRNA have since been place into the context of energy-dependent changes in microRNAs (aka pre-mRNAs), which have been linked to differentiation of all cell types in all individuals of all living genera.
See: Human GW182 Paralogs Are the Central Organizers for RNA-Mediated Control of Transcription

In the cytoplasm, small RNAs can control mammalian translation by regulating the stability of mRNA. In the nucleus, small RNAs can also control transcription and splicing. The mechanisms for RNA-mediated nuclear regulation are not understood and remain controversial, hindering the effective application of nuclear RNAi and investigation of its natural regulatory roles.

The tractable changes in organized genomes can be viewed in the context of The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression (2014)
The link to sperm selection by human ova establishes the role of quantized energy as information in the context of the physiology of reproduction, which protects all species from the virus-driven degradation of messenger RNA. 
The link from the dopaminergic neuronal system to feedback loops that biophysically constrain behavior have been placed into the context of the transition from adolescence to adulthood.
Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
The authors fail to mention that Val158Met function is known to be affected by a functional single nucleotide polymorphism (SNP) in COMT (G-to-A base-pair substitution) leading to a methionine (Met) valine (Val) substitution at codons 108/158 (COMT Val158Met). Carriers of the Met allele have been found to display a fourfold decrease in enzymatic activity compared to Val allele carriers going along with an increase of prefrontal DA activity (Lachman et al. 1996; Lotta et al. 1995).
The degrading enzyme catechol-O-methyltransferase (COMT), determines dopamine availability in the prefrontal cortex. Thermostablility and exploratory behavior link the difference in the valine allele and the methionine allele to difference in primate brain development and behavior. That fact links the Second Law of Thermodynamics to one energy-dependent base pair change and the creation of one enzyme to changes in the microRNA/messenger RNA balance that link natural selection for energy-dependent codon optimality to one amino acid substitution that differentiates the cell types of the brain in different species of primates.
Dobzhansky (1973) presciently placed that fact into this context:

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

See also: Humans And Chimps Differ At Level Of Gene Splicing (2007)
See also: Tissue-specific alternative splicing remodels protein-protein interaction networks (2012)
Smocovitis (2006): Keeping up with Dobzhansky (link opens pdf):

The direction and speed of the evolution of any group of organisms at any given time is the resultant of the interaction of a series of reasonably well known factors and processes, both hereditary and environmental. The task of the evolutionist, therefore, is to seek out and evaluate all these factors and processes in respect to as many different organisms as possible, and from the specific information thus acquired construct such generalizations and hypotheses as he can. This requires the broadest possible knowledge of biology, which, if it cannot be acquired through direct contact with original research, must be built up vicariously through communication with biologists in different fields. — G. Ledyard Stebbins, Jr., ‘Preface’, Variation and Evolution in Plants, 1950.

Communication with biologists in different fields has revealed facts about the direction and speed of ecological adaptations linked to longevity.
See: The Secret to Long Life? It May Lurk in the DNA of the Oldest Among Us (2017)
The facts must be placed into the context of enzyme-dependent error-free DNA repair.
The secret to safe DNA repair (2015)

…if you don’t have this enzyme, then this error-free repair is stopped. You can’t do it. If you can’t do the error-free repair, among other things that happen is that you expect these cells to be cancer prone.

See for comparison: ”Definitely embarrassing:” Nobel Laureate retracts non-reproducible paper in Nature journal

In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments.

They touted their belief in the emergence and the evolution of all biodiversity on Earth.

As I was preparing this post, a long-term business partner called to tell me he was ending his efforts to sell human pheromone-enhanced fragrance products to those who understand how the products help to biophysically constrain viral latency in all mammals. Not enough people understand biologically-based cause and effect, which limits the market for anything that protects the organized genomes of people from the virus-driven degradation of messenger RNA.

See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)]

A study of the influence of pheromone stressor(s) on proliferating germ and somatic cells was performed on laboratory lines of house mouse in the context of the physiological hypothesis of mutation process, proposed by M.E. Lobashev in 1947. Data from experiments are presented, and results obtained during last 10-15 years are discussed. The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

My business partner and I discussed the obvious fact that most people do not want to learn anything about preventative medicine or effective treatments for all pathology, and that most are willing to accept what they are told by “pill-pushing” medical practitioners. The medical practitioners will not tell them that feedback loops link food odors and pheromones to the biophysically constrained pathways of healthy longevity. The medical practitioners will not tell people that vaccines and drug therapies alter the feedback loops. The vaccines and drug therapies act on the energy-dependent creation of the same enzymes linked from the creation of sunlight to all biodiversity on Earth.

In mammals, this is manifested in links from what offspring ingest to their food energy-dependent pheromone-controlled survival. See for example: MicroRNAs: Milk’s epigenetic regulators

The deficiency of exosomal miRNAs in infant formula and the persistent uptake of milk miRNAs after the nursing period via consumption of cow’s milk are two epigenetic aberrations that may induce adverse long-term effects on human health.

It has been more that two decades since publication of The Scent of Eros: Mysteries of Odor in Human Sexuality. We linked the pheromones from mother’s milk to the mother-infant bond and to adult behaviors. I am disappointed to admit that all experimental evidence of biologically-based cause and effect has been ignored by theorists who tout emergence and mutation-driven evolution.
Apparently, Nothing can stop them! They do not seem to realize that Dobzhansky’s “light of evolution” was sunlight and it linked ecological variation to ecological adaptation in all living genera via the pheromone-controlled physiology of reproduction.

Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

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

See for comparison: Cytosis – The Science Behind the Game (free pdf download)

This is the four page booklet that explains the science in Cytosis. It was written and edited collaboratively by 20 PhD’s and Doctors through the world.
 
Please take some time to learn what happens to biologically uninformed theorists when serious scientists collaborate.
 
The collaborators achieved their common goal. The link from the creation of the sun’s anti-entropic virucidal energy to ATP and the creation of RNA is clear to players 10y/o +. The link from the virus-driven degradation of messenger RNA to all pathology in species from microbes to humans is equally clear..
 
Simply put 1) What organisms eat links the pheromone-controlled physiology of reproduction to biophysically constrained viral latency.
 
Simply put 2) Food odors and species-specific pheromones biophysically constrain viral latency.
 
Simply put 3) Feedback loops typically prevent the hecatombic evolution of pathology that starts with viruses in seawater or the viruses in bacteria that eat electrons and produce uranium isotopes.
 

You may not believe that the sun was created and may not think that electrons were created to be eaten. Winners of this game will not care what losers believe. Losers can compare what they believe about the evolution of hydrogen and all biodiversity to the facts known to serious scientists who helped to create this game.

See also:

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