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

Conceptual critique: Innateness vs the death gene (1)

Summary: The term innate is used in psychological explanations. The so-called explanations ignore facts about the light energy-dependent activation of endogenous substrates. The anti-entropic virucidal energy of sunlight links the endogenous substrates to biophysically constrained viral latency and healthy longevity via the physiology of reproduction in all living genera.

“Proximate mechanisms” and “evolution” are terms used by biologically uninformed theorists. That fact becomes perfectly clear in the context of  The conceptual critique of innateness (paywalled)

One proposal is that innateness can be defined in terms of the biological property of environmental canalization. On this view, a trait is innate to the extent that it is developmentally buffered against a range of different environments. Another proposal is that innateness serves as an explanatory primitive for cognitive science. This view holds that there exist a sharp boundary between psychological and biological explanations and that to identify a trait as innate means that it falls into the latter explanatory domain.

For comparison to the sharp boundary between psychological and biological explanations, we eliminated the concept of innateness and claims about evolution from our 1996 Hormones and Behavior review of experience-dependent epigenetically- effected RNA-mediated cell type differentiation: From Fertilization to Adult Sexual Behavior.

See how our section on molecular epigenetics was linked from effects on hormones to the affects of hormones on behavior via alternative splicings of pre-mRNAs.

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…

Also, in an award-winning 2001 review, other co-authors helped to link energy-dependent top-down causation to biophysically constrained cause and effect via the affects of hormones on behavior. Epigenetic effects on hormones and affects on behavior are studied and integrated in the context of human ethology. See: Human pheromones: integrating neuroendocrinology and ethology 

If you ignore the history of all published works on energy-dependent microRNA-mediated (aka pre-mRNA-mediated) top-down causation during the past two decades, you can continue to tout “evolution” as if it had any explanatory power. But it does not have any explanatory power whatsoever in the context of human ethology.

Simply put, “evolution” does not link epigenetic effects on hormones to the affect of hormones on behavior. Evolution, innate, and proximate mechanisms are terms used by biologically uninformed theorists whose ridicuous theories have no explanatory power.
See for comparison: Hormonal: The Hidden Intelligence of Hormones — How They Drive Desire, Shape Relationships, Influence Our Choices, and Make Us Wiser (Feb 13, 2018)
See for examples of explanatory power: pre mrna + alternative splicing and  microRNA 
Item: 1 of 69876 in today’s search at 9:23 AM Eastern Time A Genetic Network for Systemic RNA Silencing in Plants

Non-cell autonomous RNA silencing can spread from cell to cell and over long-distance in animals and plants.

That fact is commonly known among serious scientists. For comparison, pseudoscientists and other theorists also use the term “proximate mechanisms” outside the context of the links from the food energy-dependent non-cell autonomous RNA silencing and pheromone-controlled physiology of reproduction, which were obviously included in Darwin’s “conditions of life.” (Darwin’s “conditions of life” were bastardized by those who invented neo-Darwinian nonsense, and linked the nonsense to explanations of behavior in the context of human ethology.)

See for example: Jay R. Feierman is the antagonistic passive-aggressive moderator of the Human Ethology Yahoo Group.
After brief discussion of my claims in Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013), Jay R. Feierman reported this to the group:

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

and this:

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

See for comparison: Small RNA pathways responsible for non-cell-autonomous regulation of plant reproduction (reported in the context of my “Sokalian Hoax” series (1-10).
K.I. Nonomura and others have since published EAT1 transcription factor, a non-cell-autonomous regulator of pollen production, activates meiotic small RNA biogenesis in rice anther tapetum (February 12, 2018)

ETERNAL TAPETUM1 (EAT1) is a basic-helix-loop-helix (bHLH) transcription factor indispensable for induction of programmed cell death (PCD) in postmeiotic anther tapetum, the somatic nursery for pollen production.

It links what organisms “eat” (get it?)to the physiology of pheromone-controlled reproduction in species from microbes to humans via the honeybee model organism and everything known about biophysically constrained viral latency. Theorists and other pseudoscientists, like Jay R. Feierman, must continue to live in fear that their nonsense will be exposed in the context of what might otherwise have become a culture war.
Instead, this group of Japanese researchers appears to have an unparalleled, albeit somewhat biophysically constrained, sense of humor. Sarcasm, for example, is often a humorous way to force pseudoscientists to recognize the facts they have ignored. It is somewhat the same as a rabbinical debate that starts with “You Fool!”
For example, You fool! The link from ETERNAL TAPETUM1 (EAT1) and/or what you eat to a basic biophysically constrained helix-loop-helix (bHLH) transcription factor and/or cell death can be placed into the context of how the death gene is activated by stress in all living genera.
See: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene
The reduced expression is caused by the virus-driven theft of quantized energy, which links nutrient stress and/or social stress from  mutations to all pathology via the degradation of messenger RNA in species from archaea to humans.
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.

See for comparison: The extent of codon usage bias in human RNA viruses and its evolutionary origin (2003)

Revealing the determinants of codon usage bias is central to the understanding of factors governing viral evolution.

Molecular Clocks and the Puzzle of RNA Virus Origins (2003)

…in the case of the primate lentiviruses, amino acid residues that are highly variable in HIV are sometimes conserved in chimpanzee SIV (19), and this may have a significant effect on dating estimates.

A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder (2007)

The observation that irradiated combs from affected colonies can be repopulated with naive bees suggests that infection may contribute to CCD.

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.

Theorists have been repeatedly told told that there is no such thing as the emergence of the sun’s anti-entropic virucidal energy. They have also been repeatedly told there is no such thing as mutation-driven evolution. They have been warned that serious scientists have linked top-down causation to energy-dependent biophysically constrained viral latency. But, biologically uninformed theorists continue to ignore the facts about virus-driven pathology, and their ignorance will probably continue to cause the unnecessary suffering that leads to premature death, which may lead to the death of nearly everyone and everything on Earth.
Sudden emergence of human infections with H7N9 avian influenza A virus in Hubei province, central China (2018)

There have been five waves of H7N9 avian influenza virus (AIV) infection in humans since its initial emergence in China in 2013, posing a significant threat to public health. Hubei province was free local transmission during the first four waves of H7N9 AIV. However, multiple cases of human H7N9 infection were reported in Hubei during January 2017.

The emergence of influenza viruses has typically been constrained by ultraviolet light. This group of researchers recently presented their findings in that context.
Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases

This approach may help limit seasonal influenza epidemics, transmission of tuberculosis, as well as major pandemics.

See also: Conceptual critique: Innateness vs the death gene (2)
 

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

How to biophysically constrain the flu virus (1)

Excerpt: John E Walker (Factor-dependent archaeal transcription termination) will probably explain the molecular mechanism of how ATP is made, which may be important to know for those who have learned how important ATP is by playing “Cytosis.” The creation of ATP can be linked to the creation of RNA and the prevention of messenger RNA degradation in the context of the Virus-mediated archaeal hecatomb in the deep seafloor.
What the flu does to your body, and why it makes you feel awful

…when you have an influenza infection, you can rest assured that it is because your body is fighting hard. It’s combating the spread of the virus in your lungs and killing infected cells.

Why suffer needlessly or die prematurely. 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! (2 to 5 Players, Ages 10 & up, Plays in 50 to 75 mins)

Download the “Science Behind the Game” to learn how food energy-dependent alternative splicings of pre-mRNA protect all cell types, or see Alternative splicing and the evolution of phenotypic novelty.
Link the alternative splicings to species-specific behaviors via the physiology of reproduction in From Fertilization to Adult Sexual Behavior and anything else I have published or presented during the past two decades.
All behavior is energy-dependent. The energy comes from sunlight. Quantized energy as information from sunlight is linked to healthy longevity via its anti-entropic virucidal effect.
For example: Special UV light safely kills airborne flu virus, finds study

Scientists have known for decades that broad-spectrum UVC light, which has a wavelength of between 200 to 400 nanometers, or nm), is highly effective at killing bacteria and viruses by destroying the molecular bonds that hold their DNA together.

For comparison to vaccinations:
Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases

A key advantage of the UVC based approach, which is in clear contrast to vaccination approaches, is that UVC light is likely to be effective against all airborne microbes. For example, while there will almost certainly be variations in UVC inactivation efficiency as different influenza strains appear, they are unlikely to be large7,10. Likewise, as multi-drug-resistant variants of bacteria emerge, their UVC inactivation efficiencies are also unlikely to change greatly9.

In the context of vaccinations:
Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

Clearly, vaccinations may not protect you and prevention via use of UV light is desirable.
When you learn how UV light protects you at the level of particle physics, you will understand the horrors of neo-Darwinian theory and big bang cosmology .
See Subatomic
The link from quantum physics to quantum chemistry was reported last month. Modern diversification of the amino acid repertoire driven by oxygen.
Schrödinger at 75, The Future of Biology is scheduled for September 2018
John E Walker (Factor-dependent archaeal transcription termination) will probably explain the molecular mechanism of how ATP is made, which may be important to know for those who have learned how important ATP is by playing “Cytosis.” The creation of ATP can be linked to the creation of RNA and the prevention of messenger RNA degradation in the context of the Virus-mediated archaeal hecatomb in the deep seafloor.
People who have played “Cytosis” can predict what will happen at the Schrödinger at 75 conference. They will jump ahead of most academics if they play “Subatomic” and link particle physics to all biophysically constrained biodiversity.
The fun factor is important to most people. They don’t care about supercoiled DNA or the virus-driven degradation of messenger RNA. But other scientists are having fun watching the creator of the genious games teach facts to theorists. We are especially pleased about his help in teaching the facts about energy-dependent cell biology to anyone who wants to have fun, prevent or survive the flu, or to become a serious scientist.
Alternatively, play the Mutation-driven evolution game (available only as an outdated 2013 textbook).
But remember:  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
Simply put, you could be dead by the time pseudoscientists start to tell the truth. For example, this is the truth:

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

Lander just admitted that their assumptions may have made many serious scientists wrong about every aspect of energy-dependent life on Earth.
See also: Real Heroes Have the Guts to Admit They’re Wrong

…one reason we can’t admit we have the facts wrong is that it’s too painful to our self-conception as smart, right-thinking people—or to our political tribal identity.

In the past year alone, mathematicians have pulled papers when they’ve learned their proofs don’t hold and economists have retracted work after finding they’d misclassified their data. The Harvard stem-cell biologist Douglas Melton had a hit 2013 paper that got cited hundreds of times—but when colleagues couldn’t replicate the finding, he yanked it.

They discount the fact that any claims that have been placed into the context of neo-Darwinian theories have been invalidated first by Schrödinger in “What is Life? (1944) and since then by all serious scientists who have linked  the sun’s anti-entropic virucidal energy from the physiology of reproduction to biophysically constrained viral latency and all biodiversity.
See also: Windowed Granger causal inference strategy improves discovery of gene regulatory networks

Significance

Discovery of gene regulatory networks (GRNs) is crucial for gaining insights into biological processes involved in development or disease. Although time-resolved, high-throughput data are increasingly available, many algorithms do not account for temporal delays underlying regulatory systems—such as protein synthesis and posttranslational modifications—leading to inaccurate network inference. To overcome this challenge, we introduce Sliding Window Inference for Network Generation (SWING), which uniquely accounts for temporal information. We validate SWING in both in silico and in vitro experimental systems, highlighting improved performance in identifying time-delayed edges and illuminating network structure. SWING performance is robust to user-defined parameters, enabling identification of regulatory mechanisms from time-series gene expression data.

Reported as: New machine learning algorithm uncovers time-delayed interactions in cells

SWING puts together a more complete picture of the cause-and-effect interactions happening among genes by incorporating time delays and sliding windows. Rather than only looking at the individual perturbations and responses, SWING uses time-resolved, high-throughput data to integrate the time it takes for those responses to occur.

Researchers will continue to scramble in attempts to put their findings into the context of what has already been presented in: Olfaction Warps Visual Time Perception
and in:

 

 

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

Make no mistake, pseudoscientists have stolen the soul of science for more than 20 years, with their ridiculous claims about mutations and evolution.
For comparison, see:

“…considering that we have just 3 such round Nos ‘100’ ‘1000’ ‘10000’, its just three out of all realistic possibilities, no? Admit its looks cool just bec. we calc in Dec system. History books claims was invented by ancient societies; but I think its evolution: We have 10 fingers!”

My reply (SARCASM ALERT):

Thanks. The correlations are intriguing. Templeton funding might help you prove that the numbers game of evolution is true in the context of Cosmopsychism. With enough correlations, facts that link physics and chemistry to viral latency can be dismissed.

Thanks to the Ralser lab for bringing this to my attention with a claim about:
A reductive TCA cycle in a thermophile, which uses the same citrate synthase [enzyme] both for the oxidative and the reductive directionality.

“Every day it looks more likely that primoridial and modern metabolism look similar”

A link was provided to: A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile

…raises the possibility of a facultatively chemolithomixotrophic origin of life.

Has anyone else considered that possibility?
I tried to look at it from the perspective of chemoorganoheterotrophic metabolism and electron-eating microbes that enzymatically (not automagically) create uranium isotopes, but I got side-tracked by the claims about mutations and evolution. I could not link those claims from the physiology of reproduction in microbes to claims that link the metabolism of food energy to pheromones that biophysically constrain viral latency in species from microbes to humans.

Now, the physiology of pheromone-controlled reproduction in electron-eating microbes that create uranium isotopes suggests the same thing that the Ralser lab suggested: SARCASM ALERT: “It’s turtles all the way down” (the infinite regress problem in cosmology).Unless, like the folks at the Ralser Lab,  you are a serious scientist.

The problem for pseudoscientists, theorists, and many so-called science journalists may be familiar to those at the Ralser lab. McEwen et al., (1964) reported “The synthesis of RNA in isolated thymus nuclei is ATP dependent.” All serious scientists know “ATP controls the crowd.

These findings suggest an additional way for cells to use ATP to maintain proteostasis in the crowded cytoplasm and also fine-tune the material properties of nonmembrane-bound organelles and the cell interior in general.

Obviously, there are now several groups of serious scientists that can make fun of all the pseudoscientists and so-called science journalists who have failed to link physics and chemistry to biophysically constrained viral latency via energy-dependent changes in base pairs in species from thermophiles to those that create uranium isotopes. But Kudos to the first group, or one of the first, to do that:

12/10/14 All about that base and Structural diversity of supercoiled DNA 10/12/15

Sarcasm Alert: I hope that claims about the emergence of energy and mutation-driven evolution did not confuse others as much as they confused so-called science journalists such as John Hewitt, Philip C. Ball, Carl Zimmer, and many others.
When you see the facts reported by an intelligent science journalist, please tell others about the claims that link the creation of energy from the game “Subatomic” to biophysically constrained viral latency in “Cytosis.” Comparisons will be made. It will become clearer that pseudoscientists, theorists and many others have lost their games.
See for example: Attacked from All Sides: RNA Decay in Antiviral Defense

…RNA decay machinery plays important roles in antiviral defense. This can involve either direct effects on vRNA stability or indirect regulation of the intracellular milieu. Furthermore, an emerging theme suggests that many RNA binding proteins can be repurposed from their endogenous roles in the nucleus to antiviral roles in the cytoplasm. Future studies are necessary to further elucidate how these RNA binding…

…proteins recognize foreign RNAs and how they interface with the RNA decay machinery to restrict vRNA replication.”

Alternatively, everyone can simply accept the fact that food energy typically restricts the virus-driven degradation of messenger RNA, and tell all the pseudoscientists and so-called science journalists where to put their pseudoscientific nonsense (e.g., where the sun don’t shine).
For example: Is the Universe a conscious mind?

Cosmopsychism might seem crazy, but it provides a robust explanatory model for how the Universe became fine-tuned for life

For comparison: A Big Bang in spliceosome structural biology and Alternative splicing and the evolution of phenotypic novelty
But remember to link the claims about the evolution of phenotypic novelty to the missing claims about behavior, and see the claims made by Bruce McEwen and Martin Picard in:
Psychological Stress and Mitochondria: A Conceptual Framework (Part 1)

Mitochondria, a subcellular organelle with its own genome, produce the energy required for life and generate signals that enable stress adaptation. An emerging concept proposes that mitochondria sense, integrate, and transduce psychosocial and behavioral factors into cellular and molecular modifications. Mitochondrial signaling might in turn contribute to the biological embedding of psychological states.

Reported as: Cellular ‘powerhouses’ may explain health effects of stress
in the same context as Psychological Stress and Mitochondria: A Systematic Review (Part 2)

Evidence from metabolomic, proteomic, and transcriptomic studies also suggest additional layers of regulation by which stressful experiences may alter mitochondrial components among rodents. Although these metabolites, protein composition, and gene expression outcomes do not reflect the functionality of mitochondria, when assessed in parallel with functional outcomes, they will help explain and refine our understanding of the mechanisms by which stress influences mitochondrial function and health. In addition, whereas functional changes should be regarded as primary indicators of MAL (21), stress-induced molecular changes within mitochondria may also reflect compensatory mechanisms or recalibrations that contribute to long-term changes in mitochondrial function and to the accumulation of MAL. [mitochondrial allostatic load (MAL)]

Review: Subatomic
See also: Self-evident: Contrary to recent opinion, there is such a thing as the self, and it is empirically amenable to scientific investigation 
It has been investigated at every level of investigation that links quantum physics from quantum chemistry to quantum souls in the context of what is known to all serious scientists about biophysically constrained energy-dependent protein folding chemistry that protects supercoiled DNA from the virus-driven degradation of messenger RNA, which links mutations to all pathology.
Conclusion (from self-evident):

The multitudinous self mediates scientific explanations of the complexity of real people with and without mental disorders. It also provides resources for enhancing the moral agency that permits people to flourish. For me, flourishing is simply the development of a person’s psychological and social skills in engagement with herself and with others, in the face of the challenges triggered by her physical, social and psychological environment. If we know the characteristics of the self, we might be able to improve the lives of those whose self-experiences are not conducive to flourishing. The self is not an idle concept, either scientifically or ethically; it organises human experience and proliferates moral possibilities. So, yes, know thyself. Every single part.

See: From Fertilization to Adult Sexual Behavior

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

Make no more mistakes, pseudoscientists have stolen the soul of science for more than 20 years, with their ridiculous claims about mutations and evolution.

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)

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”