Lethal virus kills 5 billion people?

Until death: Virus-driven failure of multisensory integration (3)

What Your Nose Knows: Sense of Smell and Your Health August 2016

What the Nose Knows May Affect Your Brain Health October 2017

Doty’s research found a strong connection between low scores on a 40-item smell test and damage to this area of the brain. His recent article in The Lancet outlines possible ways that sense of smell and overall brain health could be linked and “may be the genesis of many neurodegenerative diseases.

See: ”Olfactory dysfunction in neurodegenerative diseases: is there a common pathological substrate?

…a large body of literature suggests that viruses do play a role in Parkinson’s disease and some other neurodegenerative diseases.82 Thus, antibodies or other evidence of viral infection have been found to be higher in the autopsied brains of people with neurodegenerative diseases with the most smell loss (figure 2), relative to the brains of healthy controls. Whether a close relationship exists between smell dysfunction and antibodies or other indicators of viral involvement is unknown. Included are cytomegalovirus in vascular dementia83 and Alzheimer’s disease,84 HSV-6 in Alzheimer’s disease,84 HSV-1 in Alzheimer’s disease,84 and hepatitis C in vascular parkinsonism.85 Additionally, NWS and WSN strains of neurotropic influenza Ao virus have been detected in post-encephalitic parkinsonism.86 A meta-analysis87 found that brains from patients with Alzheimer’s disease were five times more likely to be infected with Chlamydophila pneumoniae than brains from those without Alzheimer’s disease.

Richard L. Doty and others like him fell ~20 years behind the experimental evidence. In 1994, it began to show that pheromones biophysically constrain food energy-dependent viral latency.
See: Daev (1994) [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)]
Doty (2010) The Great Pheromone Myth

The Great Pheromone Myth directly challenges ideas about the role chemicals play in mammalian behavior and reproductive processes. It is a must-have reference for biologists, psychologists, neuroscientists, and readers interested in animal behavior, ecology, and evolution.

Daev et al., (2010) The role of social factors in the regulation of stability of the cell genetic machinery in animals
Daev et al., (2014) Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain  (cites Kohl et al., 2001 Human pheromones: integrating neuroendocrinology and ethology)
So far as I know, Richard L. Doty has never cited any of my published works. After Robert T. Francoeur and I published “The Scent of Eros: Mysteries of Odor in Human Sexuality (1995), Doty told me and others who were attending the same conferences that he was writing a book about human pheromones. He became the laughing stock of the Association for Chemoreception Sciences when he published and claimed “…that — in contrast to insects — pheromones in mammals do not exist.”
For contrast, see also: Daev et al., (2015) Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems
The development of the cryo-EM technology that led to the 2017 Nobel Prize in Chemistry for the developers now links the life’s works of Eugene Daev and others to refutation of the life’s works by Richard L. Doty and others.Doty  (2017) concludes:

Research is needed to understand how damage to cholinergic and other neurotransmitter circuits occurs in the first place, reflecting issues related to neurogenic precursors, environmental toxins, genetics, epigenetics, and the breakdown of the blood–brain barrier.

Search strategy and selection criteria

I searched PubMed, ISI Web of Science, and Google Scholar for papers published between Jan 1, 1990, and Feb 11, 2017. Multiple search terms were used, including “olfaction”, “neurotransmitters”, “neuromodulators”, “acetylcholine”, “serotonin”, “neurepinephrine”, “dopamine”, “GABA”, “viruses”, “nanoparticles”, “xenobiotics”, “herbicides”, “pesticides”, “interactions”, and the names of all of the diseases outlined in figure 2. I also searched for references within reviews, including reviews that I have authored.

Conclusions based on search strategies like his will continue to prevent others from learning what has been known to all serious scientists about the virus-driven degradation of messenger RNA and how virus-driven energy theft links changes in the microRNA/messenger RNA balance from mutations to all pathology via the sense of smell.
See for comparison:  Cytoplasmic chromatin triggers inflammation in senescence and cancer
Breast tissue, oral and urinary microbiomes in breast cancer

Reported as: Breast cancer: Bacterial deficiency linked with onset

Previous studies have also examined the link between gut microbiota and the development of breast cancer. These studies have suggested that the microbes in the gut may regulate estrogen levels, leading to estrogen-receptor positive breast cancer.

But less attention has been paid to the microbiome residing in the breast tissue of breast cancer patients. Now, researchers break new ground by uncovering the bacterial composition in the breast tissue of cancer patients.

The study found that breast cancer patients had considerably lower levels of a bacterial genus called Methylobacterium.

Methylobacterium is a facultative methylotroph, (meaning it has the ability to grow by reducing carbon compounds with one or more carbon atoms but no carbon-carbon bonds (Chistoserdova et al.2003)), that grows on methylamine, methanol, and C2, C3, and C4 compounds, including the methanol emitted by the stomata of plants.
The virus-driven theft of quantized energy occurs at the level of one-carbon metabolism in the context of Hard Two-Photon Contribution to Elastic Lepton-Proton Scattering Determined by the OLYMPUS Experiment
There is no excuse for Doty’s ignorance or for the ignorance of others who have failed to link olfaction from food odors and what organisms eat to energy-dependent changes in electrons to ecosystems via the physiology of pheromone-controlled reproduction. With the advent of game play “Cytosis” and “Subatomic,” anyone age 10 and over can learn more about biophysically constrained viral latency than Doty and other like him learned during the entirety of their academic careers.
 

Amino acid modification FA_Epigenetics_Table1

Predicting who wins the 2017 Nobel Prizes (6)

I failed to correctly predict who would win this year’s Nobel Prize in Chemistry, but there is still hope for my prediction of who will win the Nobel Peace Prize. I thought Lynn Zechiedrich would win for linking cryo-EM to the Structural diversity of supercoiled DNA

Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. 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.

“Electron cryo-tomography (ECT, also called cryo-electron tomography, cryo-ET or CET) is an imaging technique used to produce high-resolution (~4 nm) three-dimensional views of samples, typically biological macromolecules and cells.[1] ECT is a specialized application of transmission electron microscopy (TEM) in which samples are imaged as they are tilted, resulting in a series of 2D images that can be combined to produce a 3D reconstruction, similar to a CT scan of the human body. In contrast to other electron tomography techniques, samples are immobilized in non-crystalline (“vitreous”) ice and imaged under cryogenic conditions (< −150 °C), allowing them to be imaged without dehydration or chemical fixation, which could otherwise disrupt or distort biological structures.[2]
See for comparison: Cryo-electron microscopy (cryo-EM), or electron cryomicroscopy, is a form of transmission electron microscopy (TEM) where the sample is studied at cryogenic temperatures (generally liquid-nitrogen temperatures).[1] Cryo-EM is gaining popularity in structural biology.[2]
The Zechiedrich group used cryo-ET to link the energy-dependent transfer of hydrogen atoms in DNA base pairs in solution from quantum physics to chemistry and the functional structure of DNA via RNA-directed DNA methylation. For example, fixation of amino acid substitutions differentiates all cell types in all living genera in the context of their pheromone-controlled physiology of reproduction.
I apologize for being wrong about this award. Obviously,  I do not know the diffference between cryo-EM and cryo-ET Instead, see:  Scientists Who Developed Cryo-Electron Microscopy Win Nobel Prize

The Nobel Prize in Chemistry was awarded this morning (October 4) to three scientists who developed cryo-electron microscopy, a method that allows scientists to freeze biomolecules and view them at atomic resolution. Using this technique, researchers have been able to study the structure of a variety of biological molecules, from proteins involved in circadian rhythms to the Zika virus.

This is the first of the three Prizes awarded to researchers this year who have linked quantum physics from chemistry to biology via the claims of Richard Feynman about food energy, which can now be placed into the context of links from cryo-EM and possibly also from cryo-ET to all biodiversity — especially if there are unremarkable differences between cryo-ET and cryo-EM.
In any case, Feynman knew that observation at the level of atomic resolution would be required to link food energy-dependent changes in electrons to ecosystems in all living genera (via hydrogen-atom transfer in DNA base pairs in solution) and the physiology of reproduction. Bruce McEwen also knew at the time he co-authored: 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.

Those who have failed to link quantized energy as information to ATP dependent life and all biodiversity via the synthesis of RNA have also failed to link the virus-driven degradation of messenger RNA from mutations to all pathology. For comparison, see: All About that Base (Meghan Trainor Parody).
Perhaps the Nobel Prize Committee does not value the use of parodies to ridicule pseudoscientists who have failed to link energy-dependent changes from the epigenetic landscape to the physical landscape of supercoiled DNA via RNA-mediated amino acid substitutions and the biophysically constrained physiology of pheromone-controlled reproduction in species form microbes to humans.
For comparison, this parody is about what “Chemists Know” about how to link energy-dependent changes in electrons to ecosystems.
See also: Celebrate Your Inner Virus 10/3/17

Viruses are amazingly complex and beautiful machines. They exhibit all the hallmarks of being designed, though we often fail to recognize them as such. Therefore, we seek to highlight the strengths of what makes a virus on this Virus Appreciation Day.1 The design in viruses is highlighted in many different ways, from being essential during normal developmental processes to being used as novel therapy for treating brain cancer. It is important that we understand the design present in viruses because God made them. All creatures of our God demonstrate his handiwork, and viruses are no different.

I was shocked to see the claim that God created viruses come from “…an apologetics ministry, dedicated to helping Christians defend their faith and proclaim the gospel of Jesus Christ.” The claims that viruses are like “All creatures of our God…” is even more amazing given the publication history of “Answers in Genesis.”
This was also reported in the same publication:  Did God Make Pathogenic Viruses? 4/1/1999

…viruses are not living, and in order to reproduce and to make ATP, they require all of the complex cellular machinery present in bacterial cells. Other scientists speculate that a reverse symbiosis occurred, and that viruses arose out of cell parts such as bacterial plasmids and other organelles, and eventually evolved into separate forms of life.18

See also: Research is showing that viruses are a critical part of life. Holmes has noted:

‘For sheer numbers, no other ocean beings can match viruses. Thousands, sometimes even millions of these molecular parasites inhabit every drop of surface seawater, outnumbering even bacteria by 10 to 1 … evidence that suggests that viruses are a powerful force in the sea, and one that determines how many plankton and ultimately how many fish, and even humans, an ocean ecosystem can support … viruses must have a profound influence on the entire oceanic ecosystem. When protozoans eat bacteria, energy passes along the food chain leading from protozoa to other zooplankton to larger predators, including fish. But when virus-infected bacterial cells burst, their energy-rich cell contents spill into the water for other bacteria to scavenge. “Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,” says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.’62

Eugene Koonin admitted that  The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…
Kalevi Kull wrote: 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.
It has become obvious that the virus-driven energy theft of quantized energy as information causes the mutations that all serious scientists have linked to all pathology in species from microbes to humans. In a twist of fate, an apologetics ministry appear to support claims linked to the Modern Synthesis. At the same time, the cutting edge research of all serious scientists and the cell biology game “Cytosis” have linked the creation of the sun’s anti-entropic virucidal energy to the creation of ATP and the creation of RNA. Energy-dependent RNA-mediated DNA repair has been linked to all biophysically constrained biodiversity via the physiology of pheromone-controlled reproduction.
Thank God, as we wait for more information to come from apologetics ministries and from biologically uninformed neo-Darwinian theorists, some of us can begin to learn how to protect ourselves from viruses, just in case that is what God intended us to be able to do.

Cytosis Shipping Update  

The fulfillment centers in the UK and Australia started shipping Cytosis out to backers last week, and the fulfillment centers in the US and Germany are planning to start shipping packages out this week (Let’s keep our fingers crossed). Shipments to Canada will be 3-4 days behind US shipments since those games got delivered to the US and then split off to Canada

 
 

Cytosis

God vs host-derived creation of virus-driven pathology

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

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

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

Reported as: Virus reprograms ocean plankton

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

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

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

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

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

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

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

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

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

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

See also: Viral Genome Junk Is Bunk (2015)

So, where do viruses come from that essentially share the same sequences as those found in their host genomes? Perhaps the evolutionists have placed the cart before the horse on this issue, as proposed by several creationist scientists.4,6 In fact, in an ironic twist, the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6

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

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

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

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

“Human idiocy” was the term used by Feynman before Roger Penrose reminded us that all organisms must eat. See: “How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” (1991)

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

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

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

On July 25, 2013, Feierman [jrf] wrote: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.
Four years later, the concept of “new species are born and old species die” is divorced from the claims Jay R. Feierman made.
See for comparison: Linking mental health and the gut microbiome

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

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

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

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

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

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

Your indifference is killing you and others (2)

Two family members and two close friends are among those who have unfriended me on Facebook. Like the late Carl Woese and Eugene Koonin, they are not willing to examine any of the facts about energy-dependent RNA-mediated cell type differentiation.

I have never asked anyone to do that until after they have claimed or inferred that my facts are wrong or that the facts do not prove anything. At that point, their indifference is what causes more unnecessary suffering and premature death.

The indifference of family members, friends, and others will lead to the virus-driven degradation of messenger RNA until it leads to the death of us all.

See for instance: Cytosis: A Cell Biology Board Game

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

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

Do not pretend you were not given a chance to save yourself from the attacking viruses

Building Bridges within the Cell—Using Light How a new technique allows researchers to tune communication between organelles on the scale of nanometers
A process called membrane tethering is responsible for bridging the gap between organelles at a specialized subcellular zone called membrane contact sites and, now, researchers have a way to manipulate this tethering.

For the first time, we’re able to build bridges of different lengths in living cells to connect subcellular compartments with great temporal and spatial control…

That fact was predicted by experimental evidence presented in Olfaction Warps Visual Time Perception
The energy-dependent temporal and spatial control were linked from the sense of smell in bacteria to our visual perception of mass and energy in the context of the space time continuum via the physiology of pheromone-controlled reproduction in all living genera.
See also: Comparative approaches in evolutionary psychology: molecular neuroscience meets the mind
The late Jaak Panksepp’s group argued for the a relatively novel scientific approach that tethered hypotheses regarding the human mind to the discipline referred to as neuroevolutionary psychobiology. In a 2001 review, we dismissed that discipline by publishing Human pheromones: integrating neuroendocrinology and ethology. Both papers won the same award. Both advocated the use of animal models to link what was known about molecular biology to the biological substrates that have since been linked by all serious scientists from quantum physics to quantum souls.
We claimed:

The functional assessment of such a positive-negative mood-inducing signal requires consideration of a set of evolutionary hypotheses.

However, that was a misrepresentation made by my co-authors who appeared to believe in neo-Darwinian nonsense.
We also claimed:

According to this theory, it is adaptive for females and males to develop and use cognition in mate selection, which takes into account biological constraints. Thus, mate selection is a task of information processing, and evolution would favor individuals who were able to quickly and reliably process information that allowed them to make appropriate mating decisions. Adaptive cognition could be expected to lead to optimal decision-making under a wide spectrum of socio-economic constraints. The existence of ubiquitarian sex specific differences in mate selection criteria [72] attests that male and female cognition is adapted to the biological constraints of mate selection.

We actually showed that only the facts about quantized energy as information needed to be considered to link what organisms eat from their physiology of pheromone-controlled reproduction to all biophysically constrained biodiversity on Earth. When my co-authors realized what they had helped me do, they divorced themselves from the concept. Although they had already declared their intent to publish another review with me and to link pheromones to sexual orientation, they published this without me: Homosexual Orientation in Males: Evolutionary and Ethological Aspects.
They acknowledged my help:

The authors wish to thank James V. Kohl for reading earlier drafts of this paper and for his helpful suggestions.

But, they failed to cite our award-winning 2001 review, which would have linked their claims from ecological variation to ecological adaptation via animal models.
Thank God, I have not needed to exhibit that type of despicable behavior. It led to 16 more years of confusion about how the energy-dependent RNA-mediated pheromone-controlled sexual differentiation of cell types occurs. See for example: Bacterial membrane vesicles transport their DNA cargo into host cells 
Nutrient energy-dependent pheromone-controlled protection from the virus-driven degradation of messenger RNA linked chromosomal rearrangements in prokaryotes to sex differences in the chromosomes of all eukaryotes as predicted in this 1996 Hormones and Behavior review. 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).

For comparison, ask yourself: Is this science? 

In the effort to understand the underlying nature of reality, theoretical physics has run into challenges that are so abstract that the scientists are no longer able to provide concrete, testable predictions about the world. They describe conditions that we may never be able to replicate on this planet.

But first, be prepared for the attacks on your credibility and the personal attacks from friends and family members who were taught to believe that Darwin’s conditions of energy-dependent life might someday be linked by serious scientists from from the virus-driven degradation of messenger RNA to mutations and all biodiversity.
Then see the perspective offered by others who are fighting for the soul of science.
A Fight for the Soul of Science
Einstein’s theory of general relativity, which cast the force of gravity as curves in space and time, made risky predictions — ones that, if they hadn’t succeeded so brilliantly, would have failed miserably, falsifying the theory. But Freudian psychoanalysis was slippery: Any fault of your mother’s could be worked into your diagnosis. The theory wasn’t falsifiable, and so, Popper decided, it wasn’t science.
See also: Your indifference is killing you and others (3)

Cytosis

New Testament Book Cover Refutes Theistic Evolution

Goats, bookworms, a monk’s kiss: Biologists reveal the hidden history of ancient gospels

Collins already had developed a method to identify ancient species by differences in the amino acid sequences of collagen and other proteins preserved in fossils.

See: Protein power by Robert F. Service

…methods to sequence amino acids lag behind DNA sequencing.

The report of 300 million year old proteins is based on ridiculous theories that failed to include what was known about food energy-dependent RNA-mediated fixation of amino acid substitutions.
Natural selection for energy-dependent codon optimality links the pheromone-controlled fixation of the substitutions to cell type differentiation in all individuals of all living genera.
Collins has since used the method he developed to recover amino acid sequences that reveal which animal skin was used for the leather cover for the Gospel of Luke.

Collins so-called revelation about the species-specificity of amino acid sequences was reported in Dobzhansky (1964) and again in 1973.

Pseudoscientists have ignored this fact:

…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).” — Dobzhansky (1973)

The sequences of amino acids link what animals eat to the food energy-dependent pheromone-controlled morphological and behavioral biodiversity manifested in every species on Earth. See: Feedback loops link odor and pheromone signaling with reproduction

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

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.The species-specific link from food energy-dependent changes in base pairs to the fixation of amino acid substitutions in supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA.

See also:  Cytosis: A Cell Biology Board Game A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

See also: Olfaction Warps Visual Time Perception reported as: Odors Alter Subjective Time Experience 

The energy-dependent de novo creation of the sense of smell links food odors and natural selection for codon optimality to the physiology of reproduction. Feedback loops link the sense of smell in bacteria to all biodiversity via the pheromone-controlled physiology of reproduction.

Metaphorically, the sense of smell is like a time machine that links our experiences from the past to our behaviors throughout life. Experimental evidence of biologically-based cause and effect links the creation of the sense of smell to representations of food energy-dependent pheromone-controlled biodiversity in invertebrates to vertebrates. The fact that bookworms are invertebrates has aroused interest in the context of the Gospel of Luke.

Goats, bookworms, a monk’s kiss: Biologists reveal the hidden history of ancient gospels (revisited)

Others were more interested in the bookworms. Hedges announced that the wormholes he measured in the Gospel of Luke were 1.3 millimeters in diameter, suggesting that they were made by Anobium punctatum, a northern European beetle. That would confirm that the book was made in the United Kingdom or northern Europe, rather than in southern Europe. The DNA of bookworms “can provide clues as to when and where objects such as books originated and were transported,” Hedges says.

The energy-dependent creation of RNA-mediated amino acid substitutions in different species links experimental evidence of creation to the Dawn of Creation.

The New Testament Book Cover provides experimental evidence of how our visual perception of mass and energy is linked to the space-time continuum via olfaction and representations in Biblical Genesis that link energy as information at the “Dawn of Creation” for comparison to claims and theories about the emergence of energy and the evolution of all biodiversity.

See also: Researchers may have solved origin-of-life conundrum by Robert F. Service

… a pair of simple compounds, which would have been abundant on early Earth, can give rise to a network of simple reactions that produce the three major classes of biomolecules—nucleic acids, amino acids, and lipids—needed for the earliest form of life to get its start.

The origin of life is energy-dependent and RNA-mediated. Robert F. Service seems to be perfectly poised to prevent the dissemination of accurate information about how the virus-driven degradation of messenger RNA is linked from mutations to all pathology.
He has failed to link the energy-dependent creation of nucleic acids, amino acids, and lipids to the creation of the innate immune system and the pheromone-controlled physiology of reproduction in all living genera, which protects all organized genomes from the virus-driven energy theft that links mutations to all pathology.
Simply put, in the context of the Gospel of Luke, Robert F. Service has failed to link any aspect of biologically-based cause and effect from amino acid substitutions to biodiversity via supercoiled DNA.

That may explain why on 2/17/16, I received a message from Bob Grant who claimed to moderate reader comments on posts at www.the-scientist.com.

He claimed that many of my posts were off-topic and excessively long, and asked me to limit both the length and the focus of my comments in the future. He warned “If you continue to post long, rambling, or incoherent comments, I’ll be forced to bar you from our discussion board, something I do not want to do.”

I’ve been banned from many discussions, and consistently see why I am banned. Discussions of pseudoscientific nonsense prevails. For example, see:

First Support for a Physics Theory of Life Thanks to Oleksander Savsunenko for bringing this to my attention.

Take chemistry, add energy, get life. The first tests of Jeremy England’s provocative origin-of-life hypothesis are in, and they appear to show how order can arise from nothing.

My comment to Quanta Magazine

See for comparison: Olfaction Warps Visual Time Perception https://www.ncbi.nlm.nih.gov/pubmed/28334302

They link the energy-dependent creation of the sense of smell in bacteria to our visual perception of mass and energy in the context of the space-time continuum and everything known to serious scientists about RNA-mediated cell type differentiation via the physiology of reproduction.

Compared to the claims of Jeremy England, they start with Darwin’s food energy-dependent “conditions of life.”

Richard Feynman commented on the “conditions of life” and linked Jeremy England’s claims to examples of “human idiocy.” No one will complain that Jeremy England is an idiot (i.e., someone with no professional expertise), but everyone should remember that he has no professional expertise that can be linked to biologically-based top-down causation.

See: Food energy https://www.youtube.com/watch?v=roX2NXDUTsM
Richard Feynman, complains about all the different units that are used to measure the single concept of Energy.

Re: “Take chemistry, add energy, get life.” But do not tell a serious scientist about your theory.
And, do not expect those who moderate discussions to understand anything a serious scientist claims.
My follow-up to Bob Grant, who did not reply:

I am left with this impression.
I could respond to Roy Niles’ comment by linking virus-perturbed protein folding chemistry from loss of olfactory receptor genes to pathology in species from nematodes to humans. But, you might ban me.
The information comes from Cori Bargmann’s group, and she married Richard Axel, who shared the 2004 Nobel prize in Medicine with Linda Buck. Linda Buck extended our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation across species from microbes to man when she co-authored: Feedback loops link odor and pheromone signaling with reproduction
I know a few others who have since linked viruses to perturbed thermodynamic cycles of RNA-mediated protein folding chemistry via amino acid substitutions but you’re not likely to be hearing from them, either. Eugene Daev and Anna Di Cosmo are among those who people like Roy Niles are indirectly responsible for censoring. Simply put anyone who understood our claims in the section on molecular epigenetics from our 1996 review, has made progress akin to the progress of my mentor, Bruce McEwen, whose group just linked a single nutrient-dependent RNA-mediated amino acid substitution from stress to life history transitions in human behavior via the mouse model and BDNF Val66Met. Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity

From Fertilization to Adult Sexual Behavior

Most polymaths live in a world of their own because others don’t want to learn enough to catch up, and the polymaths are too far ahead to explain what they have known for several decades.
A 6-hour long conversation with Bruce McEwen in 1991 led to my breakfast conversation in 1995 with Gene Garfield, which is when he learned enough about cell type differentiation from me and his octogenarian friend “Bill” Turner, to comment on my book in the year it was published. Greg Bear linked the information from my works to his stories about the evolution of a new human sub-species. Evolution rising from the grave; Living with the Neanderthals
I’m not sure if “The Scientist” will help others continue to move forward if you think my comments are off topic — and ban me when I try to elaborate on the link to the topic of RNA-mediated cell type differentiation for comparison to the thoughts of others about mutation-driven evolution.  I lost any linear thinking skills I might have had before writing the book, and without the help of my co-author — it wouldn’t have made sense even to Gene.
Thanks for the opportunity to vent my frustrations,
James V. Kohl

Medical laboratory scientist (ASCP)
Independent researcher

http://rna-mediated.com/

 

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

Energy-dependent physical and biophysical constraints (10)

Summary: The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…— Eugene Koonin
My comment: Viruses are not life forms. They steal the quantized energy that links sunlight to viral latency in the context of everything known to all serious scientists about the fact that Feedback loops link odor and pheromone signaling with reproduction
See for comparison: Olfaction Warps Visual Time Perception Energy as information links the sense of smell in bacteria to our visual perception of energy and mass in the context of the space-time continuum and food odors that link the physiology of reproduction in bacteria to the pheromone-controlled physiology of reproduction and biophysically constrained viral latency in all living genera.
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Energy-dependent physical and biophysical constraints (9)

2010 A single amino acid substitution confers enhanced methylation activity of mammalian Dnmt3b on chromatin DNA

…the I662N substitution in mammalian Dnmt3b conferred enhanced chromatin DNA methylation activity and contributed to functional adaptation in the epigenetic system.

Energy-dependent amino acid substitutions link what organisms eat to their pheromone-controlled physiology of reproduction and chromosomal rearrangements that have been linked to all biodiversity via the sense of smell in bacteria and quorum sensing.
2013 Nutrient-dependent/pheromone-controlled adaptive evolution: a model

CONCLUSION:

An environmental drive evolved from that of nutrient ingestion in unicellular organisms to that of pheromone-controlled socialization in insects. In mammals, food odors and pheromones cause changes in hormones such as LH, which has developmental affects on pheromone-controlled sexual behavior in nutrient-dependent reproductively fit individuals across species of vertebrates.

2013 The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
2017 Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention

There are at least four sources of R mutations in normal cells: quantum effects on base pairing (30), mistakes made by polymerases (31), hydrolytic deamination of bases (32), and damage by endogenously produced reactive oxygen species or other metabolites (33).

2015 Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes

…their covalently bonded 13C/15N nuclei were assigned using heteronuclear single/multiple quantum coherence correlation experiments (HSQC or HMQC).

2017 Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer

…/the observed extremely fast decoherence should be viewed as general, bringing to question any significant quantum coherent transport contributions to photosynthesis.

2017 Recent progress on the effects of microRNAs and natural products on tumor epithelial-mesenchymal transition
My summary: Two researches in NATURE denied the role that microRNAs play epithelial-mesenchymal transition in tumors and their denial of everything known about food energy-dependent biophysically constrained pheromone-contolled biodiversity is discussed in this review. See for comparison the section on Regulation of miRNA on EMT in tumors
The role of miRNA/ZEB in head and neck squamous cell carcinoma, in breast cancer, in lung cancer, in pancreatic cancer and in bladder cancer was anticipated in reports by serious scientists such as the late Eshel Ben-Jacob. See: MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination, which was reported as:

They found that there is a molecular “on” and “off” switch that cancer cells use to determine their fate. Evidently, there is an on or off state for metastasis (migration), but also a third possibility, according to this recently-discovered molecular data.

The researchers discovered that there was an intermediate function, which is termed a “ternary,” or three-way switch. This function relates to the fact that ZEB has the ability to turn itself on due to a positive feedback system. This allows a cell to keep intermediate levels of all four proteins required for the switch. Ben-Jacob notes that the hybrid, or partially on-off state, also supports cancer metastasis by enabling collective cell migration and by imparting stem-cell properties that help migrating cancer cells evade the immune system and anticancer therapies.

See also: Stability of the hybrid epithelial/mesenchymal 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.

The food energy-dependent stability of the hybrid epithelial/mesenchymal phenotype has been linked from photosynthesis to the creation of energy-dependent microRNAs in plants and in animals via what has been known to all serious scientists about the physiology of pheromone-controlled reproduction in bacteria.
See:
2003 Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment
2006 Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information
2009 Learning from Bacteria about Natural Information Processing with my emphasis

Focusing on the energy, matter, and thermodynamic imbalances provided by the environment, Schrodinger proposed that life required the consumption of negative entropy, that is, the use of thermodynamic imbalances in the environment. From the perspective of thermodynamics, each bacterium can be viewed as a complex system that is composed of an “engine” that uses imbalances in the environment to do work, and a “machine” that uses this energy (to act against the natural course of entropy increase) for the synthesis of organic substances.13 A third information-processing system is also needed for the coordination and synchronization of the functioning of the engine and the machine. Namely, a living cell is analogous to a complex man-made cybernetic system, or a “chimera,” composed of information processing systems and of at least two thermodynamic elements. In addition, using the outer membrane, cells sense the environment.

We proposed that, besides “negative entropy,” organisms sense the environment to extract latent embedded information.13 By latent information we refer to data embedded in the environment that, once processed cognitively, initiates change in the organism’s function or behavior. Information induces changes; hence it can be used to generate an internal condensed description (model or usable information) of the environment, which guides the organism’s functioning.

Conclusion: Olfaction Warps Visual Time Perception Energy as information links the sense of smell in bacteria to our visual perception of energy and mass in the context of the space-time continuum and food odors that link the physiology of reproduction in bacteria to the pheromone-controlled physiology of reproduction in all living genera.
See for comparison (Koonin is a co-author): On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires
…another cause of the lack of detectable protospacers is likely to be the existence of a virtually untapped pool of mobile genetic elements that, at any given time, are not represented in a given environment (10). This paucity of spacer matches is conceivably explained by the vastness and diversity of viromes…
Biologically uninformed evolutionary theorists have failed to link the anti-entropic virucidal energy of the sun to all biodiversity and failed to link the virus-driven degradation of messenger RNA to all pathology via changes in the microRNA/messenger RNA balance. The release of the game “Cytosis” in September (2017) will make all theorists appear to be among the biologically uninformed science idiots who invented ridiculous theories in attempts to explain away Darwin’s “conditions of life.”
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!
See also the comments on: Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention
For example:  2017 Jul 28 06:45 a.m. (research profile) challenges the “bad luck” theory of cancer.

Cancer etiology: assumptions lead to erroneous conclusion

The authors claim that cancer is caused and driven by mutations, and that two-thirds of the mutations required for cancer are caused by unavoidable errors arising during DNA replication. The first claim is based on the somatic mutation theory. The second claim is based on a highly positive correlation between the lifetime number of stem cell divisions in a tissue and the risk of cancer in that tissue, and on their method for estimating the proportion of mutations that result from heredity (H mutations), environmental factors (E mutations) and unavoidable errors arising during DNA replication (R mutations). These claims raise several questions:

1. Sequencing studies have found zero mutations in the genes of a variable proportion of different cancer types (see, e.g., https://dx.doi.org/10.1093/jnci/dju405 and references therein). If cancer is caused by mutations in driver genes, could the authors explain what causes these cancers with zero mutations? Could the authors use their method for estimating the proportion of cancer risk that is preventable and unpreventable in people with tumors lacking driver gene mutations?

2. Environmental factors are known to affect stem cell division rates. According to IARC, drinking very hot beverages probably causes esophageal cancer (Group 2A). If you drink something hot enough to severely damage the cells lining the esophagus, the stem cells located in deeper layers have to divide to produce new cells to replace the damaged cells. These stem cell divisions, triggered by an environmental factor, will lead to mutations arising during DNA replication. However, these mutations are avoidable if you do not drink very hot beverages. Should these mutations be counted as environmental mutations (H mutations) or as unavoidable mutations arising during DNA replication (R mutations)?

3. The authors’ work is based on the somatic mutation theory. This theory is primarily supported by the idea that cancer incidence increases exponentially with age. Since our cells are known to accumulate mutations throughout life, the accumulation of driver gene mutations in our cells would perfectly explain why the risk of cancer increases until death. However, it is now well established that cancer incidence does not increase exponentially with age for some cancers (acute lymphoblastic leukemia, testicular cancer, cervical cancer, Hodgkin lymphoma, thyroid cancer, bone cancer, etc). It is also well known that cancer incidence decreases late in life for many cancer types (lung cancer, breast cancer, prostate cancer, etc). For example, according to SEER cancer statistics review, 1975-2014, men in their 80s have approximately half the risk of developing prostate cancer than men in their 70s. The somatic mutation theory, which is the basis for this article, does not explain why the lifetime accumulation of driver gene mutations in the cells of many tissues is not translated into an increase in cancer incidence throughout life. Are the authors’ conclusions applicable to all cancers or only to those few cancers in which incidence increases exponentially with age until death?

4. The authors estimate that 23% of the mutations required for the development of pancreatic cancer are associated with environmental and hereditary factors; the rest (77%) are mutations arising during DNA replication. However, Notta et al. recently found that 65.4% of pancreatic tumors develop catastrophic mitotic events that lead to mutations associated with massive genomic rearrangements (https://doi.org/10.1038/nature19823). In other words, Notta et al. demonstrate that cell division not only leads to mutations arising during DNA replication, but also to mutations arising during mitosis. For this cancer type, the authors could introduce a fourth source of mutations, and estimate the proportion of mutations arising during mitosis (M mutations) and re-estimate those arising during DNA replication (R mutations). Alternatively, they could reanalyze their raw data without assuming that the parameters “stem cell divisions” and ”DNA replication mutations” are interchangeable. Cell division, process by which a cell copies and separates its cellular components to finally split into two cells, can lead to mutations occurring during DNA replication, but also to other cancer-promoting errors, such as chromosome aberrations arising during mitosis, errors in the distribution of cell-fate determinants between the daughter cells, and failures to restore physical interactions with other tissue components. Would the authors’ conclusions stand without assuming that the parameters “stem cell divisions” and ”DNA replication mutations” are interchangeable?

5. The authors report a striking correlation between the number of stem cell divisions in a tissue and the risk of cancer in that tissue. They do not report any correlation between the number of mutations in a tissue and the risk of cancer in that tissue; in fact, these parameters are not correlated (see. e.g., https://doi.org/10.1038/nature19768). In addition, the authors discuss that most of the mutations required for cancer are a consequence, not a cause, of the division of stem cells. So, why do the authors use their correlation to say that cancer is caused by the accumulation of mutations in driver genes instead of saying that cancer is caused by the accumulation of cell divisions in stem cells?

For references and additional information see: Comment on ‘Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention’ DOI: 10.13140/RG.2.2.28889.21602 https://www.researchgate.net/publication/318744904; also https://www.preprints.org/manuscript/201707.0074/v1/download

See also: Miguel Lopez-Lazaro
My comment: Like him, others from a new generation of researchers, will no longer tolerate the pseudoscienitfic nonsense touted by evolutionary theorists and “Big Bang” cosmologists who know nothing about natural selection for energy-dependent codon optimality, which links the physiology of reproduction to biophysically constrained viral latency.

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

Energy-dependent physical and biophysical constraints (6)

Conclusion: Like Richard Dawkins, Magnus S. Magnusson is a pseudoscientist.

A light-induced change in an endogenous substrate found in all cell types of all living genera links femtosecond blasts of UV light from the de novo creation of the innate immune system to RNA-mediated DNA repair in species from microbes to humans. The theft of quantized energy by viruses has been linked to all pathology.

The speed at which quantum decoherence occurs makes it difficult for virus-driven energy theft to be carried from one generation to the next via chromosomal inheritance, which is the only way that nutrient-dependent pheromone-controlled transgenerational epigenetic inheritance occurs — if it does not occur automagically in the small minds of theorists.

See first: Energy-dependent physical and biophysical constraints (5)
See next: Design of a synthetic yeast genome
They use what occurs in the context of natural selection for quantized energy-dependent changes in base pairs and link RNA-mediated amino acid substitutions from changes in enzymes and feedback loops. The feedback loops link the pheromone-controlled de novo creation of more receptors via the physiology of reproduction, which biophysically constrains viral latency in all organized genomes.
Their work was reported today, July 26, 2017 in the context of Scientists build DNA from scratch to alter life’s blueprint with my emphasis

Boeke, a researcher at New York University, directs an international team of 11 labs on four continents working to “rewrite” the yeast genome, following a detailed plan they published in March.

The research may reveal basic, hidden rules that govern the structure and functioning of genomes.

All serious scientists known that the structure and function of all organized genomes is energy-dependent and RNA-mediated. For example, in all animals the functional structure of supercoiled DNA is controlled by food odors and pheromones in the context of the physiology of energy-dependent reproduction that links food energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity. Alternatively, virus-driven energy theft links the degradation of messenger RNA from mutations to all pathology.

See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

The question arises: Does Boeke or anyone like him know that the organized genome of yeast is rewritten only in the context of the food energy-dependent pheromone-controlled biophysical constraints on viral latency? I ask because he may be hiding something. Anyone who does not know how chirality and autophagy biophysically constrain viral latency is not likely to have written a book chapter like this, which was co-authored by J.D. Boeke in 1988.

See: Yeast Ty Elements as Retroviruses in  Viruses of Fungi and Simple Eukaryotes

The title of J.D. Boeke’s latest effort: Design of a synthetic yeast genome, would make any young earth creationist proud of his Boeke’s accomplishment. It attests to facts about “design” that atheistic hate mongers like Richard Dawkins and other pseudoscientists have linked from mutations and natural selection to evolution.

See: Mutation-Driven Evolution

See also for example: Magnus S. Magnusson’s comments on Richard Dawkins event cancelled over his ‘abusive speech against Islam’ Magunsson started removing my responses a few hours ago.

I attempted to discuss the fact that Boeke and others use base substitutions within ORFs to introduce or remove enzyme recognition sites. That is how they facilitate the energy-dependent assembly of synthetic chromosomes.

But there’s more! Boeke’s history of publications links nearly 30 years of pseudoscientific nonsense to an impressive refutation of neo-Darwinian theory. The design of the synthetic yeast genome via the energy-dependent assembly of synthetic chromosomes attests to the fact that natural selection for energy-dependent codon optimality is the link to the design of all biophysically constrained biodiversity.

See for instance: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

Some people might think that pseudoscientists can recover from refutation linked to the stability of messenger RNA (mRNA), but the recovery time ended two decades ago with publication of From Fertilization to Adult Sexual Behavior

See our section on molecular epigenetics.

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…

The proteins do not automagically create themselves. Energy-dependent changes in chirality must be linked from autophagy to biophysically constrained viral latency. In that context, this report is another clear refutation of mutation-driven evolution.

See: Lipophilic siRNA targets albumin in situ and promotes bioavailability, tumor penetration, and carrier-free gene silencing

These data reveal the immense promise of in situ albumin targeting for development of translational, carrier-free RNAi-based cancer therapies.

The increased amount of information on naturally occurring energy-dependent RNA interference (RNAi) linked to cancer treatment was reported as: Molecular hitchhiker on human protein signals tumors to self-destruct

“What fascinates and excites me most about this approach, in addition to improved tumor penetration, is lack of toxicity at a relatively high dose,” she said. “We could potentially use our siRNA delivery system to target several genes simultaneously or sequentially. Most cancers are driven by multiple abnormal genes, so targeting one often leads to activation of others as the tumor adapts.”

Tumors do not adapt. Viruses quickly adapt via energy theft and the substitutions of amino acids in their genomes. The amino acid substitutions in the tumors cause the tumors to adapt to the lack of energy-dependent microRNAs carried by albumin. That is how virus-driven energy theft is linked to the proliferation of undifferentiated cell types in all tissues of all organisms.

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

As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

The energy-dependent microRNA flanking sequences do not evolve and genes do not assemble themselves.  Quantized energy as information biophysically constrains virus-driven energy theft, which would otherwise link mutations to all pathology.

Young earth creationists recently placed the virus-driven theft of quantized energy into the context of Cancer Research Confirms the Curse.

…the cancer-suppressing molecule NAD+ diminishes with age appeared in the same Science issue.3Harvard Medical School News summarized the findings. As NAD+ lessens, “DNA breaks go unrepaired and, as these breaks accumulate over time, precipitate cell damage, cell mutations, cell death and loss of organ function.”4 It seems the only way to cure cancer would be to somehow reach into and constantly correct every cell’s mutations.

Carrier-free gene silencing links femtosecond blasts of UV light from the anti-entropic virucidal effects of sunlight on contact with water to everything serious scientists know about food energy-dependent top-down causation and changes in the microRNA/messenger RNA balance, which have been linked to all biophysically constrained biodiversity via what organisms eat and the physiology of their pheromone-controlled reproduction.

See: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

The sequences have been selected according special charge distributions and lifetimes of excimer states previously characterized by femtosecond infrared spectroscopy.(3a, 3c, 3d) With these selected sequences we demonstrate that repair occurs when the intrastrand charge transfer leads to a suitably charged nucleotide adjacent to the lesion.

A femtosecond is the SI unit of time equal to 10−15 or 1/1,000,000,000,000,000 of a second; that is, one quadrillionth, or one millionth of one billionth, of a second.[1] For context, a femtosecond is to a second as a second is to about 31.71 million years; a ray of light travels approximately 0.3 µm (micrometers) in 1 femtosecond, a distance comparable to the diameter of a virus.[2]

For comparison: One picosecond is equal to 1000 femtoseconds (fs). Theoretical physicists who thought they knew something about the nature of quantum coherence based their theories on measurements of timescales up to 1.5 picoseconds (ps), but they have since learned that decoherence occurs within 60 fs. The transfer of energy in the context of photosynthesis clearly links the anti-entropic virucidal energy of UV light to RNA-mediated DNA repair in much less time than theorists realized.

See: Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer

Given the relatively well-defined structure of the FMO protein, and comparative couplings between chlorophylls to other photosynthetic systems, the observed extremely fast decoherence should be viewed as general, bringing to question any significant quantum coherent transport contributions to photosynthesis.

See also: OLYMPUS experiment sheds light on structure of protons

…unlike the theoretical predictions, analysis of the OLYMPUS measurements suggests that, most of the time, only one of the photons has high energy, while the other must carry very little energy indeed…

The differences in the energy of photons and the amount of time it takes for energy-dependent RNA-mediated DNA repair link displays of ignorance by Magnus S. Magnusson and other atheistic hate-mongers that can be compared to any display by anyone who has ever been involved in linking pattern recognition to biophysically constrained life on Earth.

For comparison, that is what young earth creationists have done with the information about energy as information from Biblical Genesis.

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

The light’s coming off at different angles, with different colors, depending on how bright it is.

That phenomenon stemmed partly from a change in the electron, which abandoned its usual up-and-down motion in favor of a figure-8 flight pattern. As it would under normal conditions, the electron also ejected its own photon, which was jarred loose by the energy of the incoming photons. But the researchers found that the ejected photon absorbed the collective energy of all the scattered photons, granting it the energy and wavelength of an X-ray.

See: The Reality of Color Is Perception

Color is one of the longstanding puzzles in philosophy, raising doubts about the truthfulness of our sensory grasp on things, and provoking concerns as to the metaphysical compatibility of scientific, perceptual, and common sense representations of the world. Most philosophers have argued that colors are either real or not real, physical or psychological. The greater challenge is to theorize the subtle way that color stands between our understanding of the physical and the psychological.

See for comparison: Olfaction Warps Visual Time Perception

The fact that olfaction warps visual time perception links the speed of light on contact with water from the visual appeal of a rainbow to the integration of all sensory input and our appreciation of how energy and mass are linked across the time-space continuum via what is known about the sense of smell in bacteria and the food energy-dependent pheromone-controlled physiology of reproduction in all living genera.

For comparison, Magnus S. Magnusson co-authored “Complex spike patterns in olfactory bulb neuronal networks”  He and his colleagues failed to link fast decoherence from the anti-entropic virucidal energy of sunlight to all biodiversity via the physiology of reproduction and RNA-mediated DNA repair.

In the world of those who have consistently linked olfaction to our visual perception of energy and mass in the context of the space-time continuum, Magnusson can be referred to as a biologically uninformed science idiot — if only because he has no expertise in any scientific discipline.

Conclusion: Like Richard Dawkins, Magnus S. Magnusson is a pseudoscientist.

A light-induced change in an endogenous substrate found in all cell types of all living genera links femtosecond blasts of UV light from the de novo creation of the innate immune system to RNA-mediated DNA repair in species from microbes to humans. The theft of quantized energy by viruses has been linked to all pathology via the difference between “Nature” and God’s perfect “Creation.”

The speed at which quantum decoherence occurs makes it difficult for virus-driven energy theft to be carried from one generation to the next via chromosomal inheritance, which is the only way that nutrient-dependent pheromone-controlled transgenerational epigenetic inheritance occurs — if it does not occur automagically in the small minds of theorists.

Although that fact has been repeatedly revealed in the extant scientific literature, which includes texts like the Holy Bible, atheistic hate-mongers refuse to read anything that challenges their beliefs at the same time they either claim to believe in nothing or attack the beliefs of intelligent scientists.

See for examples of what pseudoscientists are likely to believe.

This New Equation Could Unite The Two Biggest Theories in Physics

Quantum entanglement… describes the way that two particles can interact in such a way that they become inexorably linked, and essentially ‘share’ an existence.

The Universe According to Emmy Noethe

…energy may not be conserved “locally” — that is, in an arbitrarily small patch of space — but everything works out when the space is sufficiently large.

That claim forced others to make their ridiculous theories fit into the context of “…the idea that the Universe expanded just like a balloon shortly after the Big Bang.”

Stephen Hawking And 32 Top Physicists Just Signed a Heated Letter on The Universe’s Origin

…three physicists heavily criticised inflation theory – the idea that the Universe expanded just like a balloon shortly after the Big Bang. The article went as far as claiming that the model “cannot be evaluated using the scientific method” – the academic equivalent of saying it isn’t even real science.

Cytosis

Epigenetic effects of stress by Bruce McEwen (2)

Summary:

…rapid mRNA turnover starts with the energy-dependent de novo creation of microRNAs and ends with the virus-driven degradation of messenger RNA, which links mutations to all pathology.
 
This was reported in the following context: “RNA molecules live short lives” July 12, 2017

See also: Epigenetic effects of stress by Bruce McEwen (1)

Summary:

In the early 1990’s, Bruce McEwen inspired my life’s works, which link the epigenetic effects of nutrient-stress and/or social stress to the fact that RNA biosynthesis is ATP-dependent. That fact helped all serious scientists link the virus-driven energy theft of quantized energy to the degradation of messenger RNA, which links mutations to all pathology.

Pseudoscientists refuse to accept that fact.

New research uncovers the secrets of photosynthesis that could help develop computer technology

Energy and charge transfer is what drives photosynthesis and any solar-to-chemical or electrical-to-chemical energy conversion.

That fact links the anti-entropic virucidal energy of sunlight from the de novo creation of microRNAs to all biodiversity. Bruce McEwen published on the role that microRNAs play in: Characterization of the vulnerability to repeated stress in Fischer 344 rats: possible involvement of microRNA-mediated down-regulation of the glucocorticoid receptor (2008)

We also identified that microRNA (miR)-18a inhibited translation of GR mRNA in cultured neuronal cells and that increased expression of miR-18a in the PVN was observed in F344 rats compared with SD rats. These strain differences in GR protein levels were not found in the hippocampus and prefrontal cortex, and the expression of miR-18a was much lower in these brain regions than in the PVN. Our results suggest that F344 rats could be a useful animal model for studying vulnerability to repeated stress, and that miR-18a-mediated down-regulation of GR translation may be an important factor to be considered in susceptibility to stress-related disorders.

See also: Early Life Stress Enhances Behavioral Vulnerability to Stress through the Activation of REST4-Mediated Gene Transcription in the Medial Prefrontal Cortex of Rodents (2010)

Figure 3.

Expression analyses of mRNAs of RE-1-containing genes and brain-enriched pre-microRNAs in the mPFC of the maternally separated rats. A, B, The expression of mRNAs (A) and pre-microRNAs (B) of a variety of RE-1-containing genes in the mPFC of AFR, HMS15, and HMS180 rats at P14 were quantified by Q-PCR (n = 6 for all groups). C, D, The expression of mature microRNAs in the mPFC of AFR, HMS15, and HMS180 rats at P14 were quantified by Northern blotting analysis (n = 5–6 for each group). E, The mRNA and pre-microRNA expression of RE-1-containing genes in the mPFC of adult AFR, HMS15, and HMS180 rats were quantified by Q-PCR (n = 6 for all groups). *p < 0.05.

Bruce McEwen subsequently linked what is known about energy-dependent changes in single nucleotide polymorphisms to effects of hormones on behavior in mice and humans via a food energy-dependent biophysically constrained amino acid substitution.

See: Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity (2015)

Excitatory amino acids play a key role in both adaptive and deleterious effects of stressors on the brain, and dysregulated glutamate homeostasis has been associated with psychiatric and neurological disorders. Here, we elucidate mechanisms of epigenetic plasticity…  In WT mice after CRS and in unstressed mice with a BDNF loss-of-function allele (BDNF Val66Met), we show that the epigenetic activator of histone acetylation, P300, plays a pivotal role in the dynamic up- and down-regulation of mGlu2 in hippocampus via histone-3-lysine-27-acetylation (H3K27Ac) when acute stressors are applied. These hippocampal responses reveal a window of epigenetic plasticity that may be useful for treatment of disorders in which glutamatergic transmission is dysregulated.

See also: Multiplexed gene control reveals rapid mRNA turnover (open access)

The rapid mRNA turnover starts with the energy-dependent de novo creation of microRNAs and ends with the virus-driven degradation of messenger RNA, which links mutations to all pathology.
 
This was reported in the following context: “RNA molecules live short lives” July 12, 2017
“Sometimes it is hard to believe that scientists could have unknowingly worked with methods that produce inconsistent results for almost 30 years”, says Becskei.
 
Becskei adds insult to the injury, unnecessary suffering, and the premature death caused by misrepresentations of biologically-based cause and effect. An accurate representation was reported in 1964 as: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” 
 

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

The fact that some researchers still do not know that the synthesis of RNA is energy-dependent makes it impossible for them to link virus-driven energy theft from the degradation of messenger RNA to mutations and all pathology in all living genera.

It will soon become “child’s play” for anyone over 10 years old. 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!

fruit-dove

Food energy-dependent epigenetic adaptation (3)

Food energy-dependent epigenetic adaptation (2)

On 5/24/17 I attempted to post this to the ISHE’s human ethology group in response to the post on How concepts of God have developed: God’s shrinking role. God’s survival. Conclusions.

For comparison, see the expanding role of anti-entropic virucidal energy that theorists claim automagically emerged to sustain all evolved biodiversity.

I included a link to:


I also included a link to:

The moderator of the group responded quickly: Jay R. Feierman wrote:

What you are posting has nothing to do with the thread article.

See also: 7/25/13
Jay R. Feierman:

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

My summary of past interactions with Jay R. Feierman:

He refuses to accept the fact that conditions of life are energy-dependent. He refuses to accept the fact that other biologically uninformed science idiots and many anonymous fools have consistently removed Darwin’s ‘conditions of life’ and replaced them with ridiculous theories about mutations and evolution.

At a conference we both attended in 1995, Jay R. Feierman was the first to challenge the entirety of the model I presented with the question “What about birds?”

He has continued to prevent dissemination of accurate representations of energy-dependent biologically-based cause and effect since then. He exemplifies the impact that one biologically uninformed science idiot can have across an entire generation of unsuspecting anonymous fools who are likely to believe that the creation of energy has nothing to do with the claims in: How concepts of God have developed: God’s shrinking role. God’s survival. Conclusions.

See also: The general form of Hamilton’s rule makes no predictions and cannot be tested empirically

Hamilton’s rule asserts that a trait is favored by natural selection if the benefit to others, B, multiplied by relatedness, R, exceeds the cost to self, C. Specifically, Hamilton’s rule states that the change in average trait value in a population is proportional to BR−C. This rule is commonly believed to be a natural law making important predictions in biology, and its influence has spread from evolutionary biology to other fields including the social sciences. Whereas many feel that Hamilton’s rule provides valuable intuition, there is disagreement even among experts as to how the quantities B, R, and C should be defined for a given system. Here, we investigate a widely endorsed formulation of Hamilton’s rule, which is said to be as general as natural selection itself. We show that, in this formulation, Hamilton’s rule does not make predictions and cannot be tested empirically. It turns out that the parameters B and C depend on the change in average trait value and therefore cannot predict that change. In this formulation, which has been called “exact and general” by its proponents, Hamilton’s rule can “predict” only the data that have already been given.

Simply put, the authors attest to the fact that every aspect that has ever been included in mathematical models of natural selection cannot link natural selection to anything that could not be predicted by what is known about how food energy must be linked from ecological variation to ecological adaptation by the sense of smell in all living genera. The sense of smell predictably links what is known about natural selection for energy-dependent codon optimality to biophysically constrained viral latency via publication in 2005 of Feedback loops link odor and pheromone signaling with reproduction.

There has never been any experimental evidence of biologically based cause and effect that link anything but olfaction, food odor, and pheromones directly to the survival of all species. Yet Feierman’s claim continues to be echoed in the claims of all others who are biologically uninformed:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. — Jay R. Feierman

See for comparison: Scientists investigate how the sense of smell works in bacteria

…the signaling and inactive states differ only very slightly at the nitrate-binding site – by 0.5-1 angstroms, which is approximately one fifth of the size of the ion itself (1 angstrom is 10-10 meters). However, when this ion binds to the sensor, it causes huge changes in the protein: The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.

 

Alternative splicing of pre-mRNA

Food energy-dependent epigenetic adaptation (2)

Due to the overwhelming support for my model of top-down causation and all energy-dependent biophysically constrained biodiversity on Earth, I will replace
Food energy-dependent epigenetic adaptation (2)
with the more appropriately titled
God’s shrinking role in your salvation
See: Food energy-dependent epigenetic adaptation
and God’s shrinking role in your salvation (in prep)
before proceeding to the rest of this series on epigenetic adaptation.