olfaction Archives - Scent of Eros

A reversible TCA cycle in a thermophile (2)

February 9, 2018

by James Kohl with No Comment Adaptations biophotonics Cytosis Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy microRNA editing Model Organisms Neuronal Plasticity Nutrigenomics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation

Summary: The energy-dependent creation of ATP has been linked from the energy-dependent creation of RNA to feedback loops that link the pheromone-controlled physiology of reproduction to biodiversity in species from microbes to humans via olfaction and pheromones. Anyone who continues to try to place the facts into the context of brain stimulation by visual input and ignore the facts about how the creation of microRNAs must be linked from creation of the sense of smell to all biophysically constrained viral latency and all biodiversity is playing a fool’s game.
See first: A reversible TCA cycle in a thermophile
See also: Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990)
Thermodynamic cycles of ATP-dependent protein biosynthesis and/or the virus-driven degradation of messenger RNA have since been linked to healthy longevity or from circadian disruption to diseases of the brain and body, such as depression, Crohn’s disease, IBD, heart disease or cancer.
See: Timing is everything, to our genes

This will have huge impact on understanding the mechanisms or optimizing cures for at least 150 diseases.”

If that was true, the work in the 1990’s that led to Rosbash sharing the 2017 Nobel Prize for Physiology or Medicine would already have been placed into the context of this published work.Olfactory Receptor Patterning in a Higher Primate (2014).
See also, Feedback loops link odor and pheromone signaling with reproduction another work by LInda Buck, who shared the 2004 Nobel Prize for Physiology or Medicine and who coauthored both articles.
Instead of linking the energy-dependent pheromone-controlled feedback loops from the physiology of reproduction in thermophiles to the physiology of food energy-dependent pheromone-controlled feedback loops in humans, we have been left the examples of human idiocy in the context of Richard Feynman’s claims and the claims of all other serious scientists.
See:

See also: Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex Published online: 11 December 2017

Activity-dependent transcriptional responses shape cortical function.

Reported as: Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex on December 13, 2017

…these results reveal the dynamic landscape of the stimulus-dependent transcriptional changes occurring across cell types in the visual cortex; these changes are probably critical for cortical function and may be sites of deregulation in developmental brain disorders.

Reported on and on February 8, 2018 Single-cell analysis reveals diverse landscape of genetic changes in the brain after a sensory experience

Experience and environmental stimuli appear to almost constantly affect gene expression and function throughout the brain. This may help us to understand how processes such as learning and memory formation, which require long-term changes in the brain, arise from the short bursts of electrical activity through which neurons signal to each other,” Greenberg said.

One especially interesting area of inquiry, according to Greenberg, includes the regulatory elements that control the expression of genes in response to sensory experience. In a paper published earlier this year in Molecular Cell, he and his team explored the activity of the FOS/JUN protein complex, which is expressed across many different cell types in the brain but appears to regulate unique programs in each different cell type.

The energy-dependent creation of ATP has been linked from the energy-dependent creation of RNA to feedback loops that link the pheromone-controlled physiology of reproduction to biodiversity in species from microbes to humans via olfaction and pheromones. Anyone who continues to try to place the facts into the context of brain stimulation by visual input and ignore the facts about how the creation of microRNAs must be linked from creation of the sense of smell to all biophysically constrained viral latency and all biodiversity is playing a fool’s game. They should stop doing that long enough to play the cell biology game “Cytosis” and wait to link particle physics to from quantum chemistry to all biodiversity by what is known to serious scientists about energy-dependent top-down causation is biophysically constrained by the physiology of reproduction.

Enzyme-constrained interethnic diversity (8)

January 16, 2018

by James Kohl with No Comment Adaptations Diseases & Disorders Ecology Human Brain Human Pheromones RNA Directed

I am intrigued by the fact that I detailed the energy-dependent links to interethnic diversity in this blog post on the same day that the so-called science journalist Ed Yong placed everything known to serious scientists back into the context of neo-Darwinian evolution.
See for comparison to Ed Yong’s nonsense: “Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!”
Yong’s addendum:

*This article has been corrected to reflect the fact that Arc genes were co-opted by animals from a group of genes that also gave rise to retroviruses, and are not directly descended from retroviruses, as originally stated. We regret the error.

Retractions by Szostak reflect a similar theme.

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

The food energy-dependent creation of Arc genes links the virus-driven theft of quantized energy to the creation of retroviruses, which are biophysically constrained by RNA-mediated amino acid substitutions in the context of the pheromone-controlled physiology of reproduction.
Something has gone horribly wrong in the context of respected scientist’s retractions and the addendums by science journalists who have failed to link ridiculous theories from top-down causation to biophysically constrained viral latency during the past two decades.
See for comparison: The vibrational theory of olfaction for the win
John Hewitt will almost undoubtedly be the first science journalist to link the energy-dependent creation of enzymes from the sense of smell in bacteria to our visual perception of mass and energy.
Olfaction Warps Visual Time Perception will then be linked to “The Darwin Code: Intelligent Design without God” and interethnic biodiversity via food energy-dependent pheromone-controlled RNA-mediated amino acid substitutions.

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

December 31, 2017

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy biophotonics Cytosis Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy microRNA editing Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Subatomic What's in the News

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

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

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

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

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

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

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

Transposable elements pervading mammalian genomes mostly originate from retrotransposons, including long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and endogenous retroviruses (ERVs) (2,3). Retrotransposons shape host genome landscape and evolution through introducing, deleting or modifying cis-regulatory elements or genes (4,5). However, they can also induce detrimental genome instability and numerous human diseases (3,6).

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

Sperm and oocytes exhibit different patterns of chromatin organisation: the sperm DNA is highly methylated and tightly packaged, with protamines replacing most canonical histones, while the oocyte genome has a bimodal methylation pattern, an extensively open chromatin conformation and atypical patterns of histone modifications [4–6].Methylation and chromatin organization are food energy-dependent and biophysically constrained in the context of the physiology of pheromone-controlled reproduction and the space-time continuum.

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

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

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

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

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

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

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

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

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

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

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

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

Alternative splicing is food energy-dependent and RNA-mediated in the context of the physiology of pheromone-controlled biophysically constrained viral latency.
All niche construction is food energy-dependent and controlled by the physiology of reproduction.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

This model details how chemical ecology drives adaptive evolution via: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction.

This model organism exemplifies how ecological variation must be linked to ecological adaptation in species from microbes to humans. See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

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

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

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

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

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.

Darwinian adaptation: a clear evolutionary trail?

December 22, 2017

by James Kohl with No Comment Adaptations Autophagy biophotonics Cytosis Diseases & Disorders Ecology Light Energy microRNA editing Model Organisms Nutrigenomics Pharmacogenomics Physics RNA editing RNA interference RNA-directed DNA methylation Subatomic

Summary: The light harvesting occurs in the ocean and on land. It links the creation of sunlight from food energy to the physiology of pheromone-controlled viral latency in all living genera, and all serious scientists know that.

Origins of photosynthesis in plants dated to 1.25 billion years ago

The world’s oldest algae fossils are a billion years old, according to a new analysis by earth scientists. Based on this finding, the researchers also estimate that the basis for photosynthesis in today’s plants was set in place 1.25 billion years ago.

A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

See for comparison: Energy as information and constrained endogenous RNA interference (video)
For contrast, Philip Ball separates the origin of photosynthesis in plants from the origin of bioluminescence in bacteria in the ocean.
See: Water is an active matrix of life for cell and molecular biology

1) Water is a complex fluid in its own right (4, 5), and Darwinian adaptation to a complex milieu might be expected to generate much the same kind of enmeshing and interplay of the biological and environmental at the molecular scale that we find at higher levels of life’s organizational hierarchy.

Higher levels of organization are no different than other levels of organization. Organization is organization. But Philip Ball is a deceptive journalist. Neo-Darwinian evolution becomes Darwinian adaptation, which links the sun’s anti-entropic virucidal energy from feedback loops and the physiology of pheromone-controlled reproduction to microRNA-mediated autophagy and biophysically constrained viral latency in species from microbes to human. That causes the biologically uniformed journalist to claim:

2) All of this touches on the astrobiological question mentioned at the outset: should we, like Henderson (88) in 1913, regard water as uniquely “biophilic” and “fit” to act as life’s matrix?

There is no astrobiological question. See the comments section on 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. This is explored here: http://rsfs.royalsocietypublishing.org/content/2/1.toc 25 Apr 2014 at 07:49am
I wrote: Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).
Philip Ball has since changed the clear evolutionary trail that links the sense of smell to ecological adaptation. Ecological variation links the creation of enzymes that metabolize food and drugs to his claim about Darwinian adaptation.
See also for a recent representation of his word-play: Quantum common sense

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking

There are stark difference in his claims about a Universe that is always looking that can be compared via claims about the creation of a universe in which viral latency is biophysically constrained by feedback loops. The feedback loops link food odors and pheromones from the physiology of reproduction in all living genera to all biodiversity via autophagy and the microRNA-mediated creation of supercoiled DNA.
In the spirit of the Christmas season and an attempt to stop the pseudoscientific nonsense touted by biologically uniformed theorists and journalists like Philip Ball, see: Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2 (video excerpt <2 minutes long)
Remember, Santa Claus (or someone like him) is coming soon. Philip Ball may not be prepared for that. He has been a very bad boy. At the same time that President Trump, who tries his best to be good, has been accused of censorship and compared to Hitler. I do not think that President Trump would try to change neo-Darwinian evolution to Darwinian adaptation without mentioning how the speed of light on contact with water changes everything.
Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
Reported as: … 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.
All the theories can be linked via facts to creationist science that has been supported with experimental evidence of biophysically constrained viral latency as presciently foretold by
1) Schrodinger,
2) Feynman,
3) Dobzhansky
4) McEwen,
and by
5) Eshel Ben-Jacob, who wrote: Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment
Note his use of the term adaptability. It may have led Philip Ball to change Darwinian evolution to Darwinian adaptation.
See also: Learning from Bacteria about Natural Information Processing

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.

See also: QuEBS 2018: Workshop on Quantum Effects in Biological Systems has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has… established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.
The light harvesting occurs in the ocean and on land. It links the creation of sunlight from food energy to the physiology of pheromone-controlled viral latency in all living genera, and all serious scientists know that. If Philip Ball just realized that, he knows he has a long-standing problem with misrepresentations of top-down causation. In any case, it is important to know that he has forced all theorists and journalists to acknowledge the likelihood that Santa Claus is not just a figment of a child-like imagination, and that the creation of sunlight must be linked from its contact with water to the physiology of pheromone-controlled reproduction and biophysically constrained viral latency in all living genera.

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

Reporting new scientific truths is not allowed in the USA (2)

November 29, 2017

by James Kohl with No Comment Adaptations Alternative Splicings base editing biophotonics Cytosis Diseases & Disorders Ecology Human Brain Human Pheromones microRNA editing Model Organisms Physics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation

Summary: Genetic mutations do not drive evolution. Energy-dependent RNA-mediated fixation of amino acid substitutions links the physiology of reproduction to biophysically constrained viral latency.
With minimal effort, you can peruse the science news each day to see how many pseudoscientists report their findings outside the context of food energy-dependent pheromone-controlled biophysically constrained RNA-mediated cell type differentiation.
See for example:
Type 2 diabetes has hepatic origins

The researchers are now working on identifying the endogenous ligand produced by the body, or on developing molecules that could mimic its function.

Clearly, they are aware of the fact that they must link food energy to the endogenous substrate without claiming that gene activation and the creation of the protein automagically occur.
Diabetes, obesity behind 800,000 cancers worldwide: study

“Our study shows that diabetes—either on its own or combined with being overweight—is responsible for hundreds of thousands of cancer cases each year across the world.”

Who did not know that?
New study finds mycobacteria can sense presence of proteins that cause disease

The transcription factor regulates the levels of the protein cargo transported by the machinery. When the bacteria sense the machinery is absent, the levels of the protein substrates are reduced.

Fat distribution in women and men provides clues to heart attack risk

“We hypothesized that there are gender-based differences in body composition and ectopic fat depots and that these could be associated with gender-specific risk profiles for diseases like diabetes, heart disease and stroke,” said lead author Miriam A. Bredella, M.D., radiologist at Massachusetts General Hospital and associate professor of radiology at Harvard Medical School in Boston.

Sex-differences in cell types link the food energy-dependent pheromone-controlled physiology of reproduction to RNA-mediated cell type stability in all living genera.
Women may be more vulnerable to concussions because of ‘leaner’ nerve fibers

The paper shows us that there is a fundamental, anatomical difference between male and female axons,” Smith said. “In the male axon, there are a great number of microtubules, which make the entire structure stronger, whereas in female axons, it’s more of a leaner type of architecture, so it’s not as strong.

This representation of energy-dependent RNA-mediated cell type differentiation is sexist. If researchers claimed there were racial differences in biophysically constrained cell type differentiation, the claim would be racist.

That’s the problem that all pseudoscientists have with cryo-EM. It makes everything that will be reported in the context of energy-dependent links from electrons to ecosystems appear to be racist in the context of A Civic Biology: Presented in Problems (New York, 1914)

Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity

Exploratory whole-exome analysis revealed higher expression of humanin-like 8 (MTRNR2L8, or HN8) in both suicide and depression (Figure 1, Supplementary Table 2). MTRNR2L8 is an isoform of the humanin gene (HN) (43), a newly discovered mitochondrial-derived 24 amino acid peptide (44), which is coded by nuclear DNA.

A null mutation and healthy longevity?

November 17, 2017

by James Kohl with No Comment Adaptations Alternative Splicings base editing biophotonics Cytosis Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy Model Organisms Neuronal Plasticity Nutrigenomics Pharmacogenomics Physics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity

Summary: Food odors and pheromones biophysically constrain all pathology in species from microbes to humans. What kind of biologically uninformed science idiot leaves out everything known to serious scientists about the virus-driven degradation of messenger RNA and tells others they must falsify the neutral null theory that led to claims about a biophysically constrained beneficial “null mutation” in the Amish population of Berne, Indiana?
Glutamylation Regulates Transport, Specializes Function, and Sculpts the Structure of Cilia
Reported as: How to Control Traffic on Cellular Highways

Intracellular and extracellular traffic control

Reported in: How to control traffic on cellular highways http://neurosciencenews.com/enzyme-transportation-7915/

See for comparison: A null mutation in SERPINE1 protects against biological aging in humans
Reported as: Amish gene can make them live 10 years longer and avoid diabetes

A gene variant that arose decades ago in an Amish group…

All gene variants are quantized energy-dependent and the pheromone-controlled physiology of reproduction protects all organized genomes from the virus-driven degradation of messenger RNA. The degradation of messenger RNA links mutations to all pathology. Any claim that “a gene variant arose” is a claim made by a biologically uninformed science idiot. Gene variants in humans are biophysically constrained by the availability of food energy. Other humans may not know that.
Watch and listen to Richard P. Feynman presciently claim that the “null mutation” theory of healthy longevity is an example of “human idiocy.”

Help others to find any experimental evidence that suggests a “null mutation” can be beneficial and/or protect them from biological aging. See for alternative representations of biologically-based facts: Best matches for “null mutation“: and others.
If you cannot find experimental evidence of a beneficial “null mutation” see: Consciousness in the universe: A review of the ‘Orch OR’ theory They inadvertently linked quantum physics from consciousness to quantum souls.
Reported as: Anesthesia Points to Deeper Level ‘Quantum Channels’ as Origins of Consciousness subtitle “Electron resonance pervades the brain”

“Using molecular modeling, the US-Canadian team of Travis Craddock, Stuart Hameroff and Jack Tuszynski had previously shown anesthetic binding in ‘quantum channels’, non-polar arrays of amino acid pi resonance clouds, winding through microtubules.”

The same kinds of amino acid substitutions that control the separations and interactions of side chains in fluorescent proteins also play an essential role in tuning the proposed mechanism for vibration detection—inelastic electron tunneling. Life literally runs on electron tunneling through the respiratory chain complexes in mitochondria.

For comparison, see the conclusion to: Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2
Beneficial “null mutations” can now be placed into the context of the creation of a universe that — with or without us — is always watching, like Santa Claus.
For a historical perspective on that pseudoscientific nonsense, see:
Splendor and misery of adaptation, or the importance of neutral null for understanding evolution

To claim adaptation, the neutral null has to be falsified.

A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

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
What kind of biologically uninformed science idiot leaves out everything known to serious scientists about the virus-driven degradation of messenger RNA and tells others they must falsify the neutral null theory that led to claims about a biophysically constrained beneficial “null mutation” in the Amish population of Berne, Indiana?
Food odors and pheromones biophysically constrain all pathology in species from microbes to humans.
See for comparison: Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain

…specific, volatile, and zoosocial important chemosignals are a promising approach both to modeling posttraumatic stress disorders in humans [36] and to searching for mehods of their treatment.

Humans also have various pheromone-induced physiological effects, especially those associated with reproduction [46, 47]. This suggests that the human olfactory system is still an effective pathway for influencing environmental factors on the human nervous
system.

[46] is Kohl, J.V., Atzmueller, M., Fink, B., and Grammer, K., Human pheromones: integrating neuroendocrinology and ethology, Neuroendocrinol. Lett., 2001, vol. 22, pp. 309–321.
See also: Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems

The assessment of genomes’ integrity plays the key role in the studies of mutagenicity in a polluted environment. We present a step-by-step recommendations for the analysis of the cytogenetic data and discuss the prospects of applying genetic tests for ecological monitoring, based on the example of analysis using crustacean species.

I suspect that the manufacturer of my human pheromone-enhanced fragrance products asked to speak with me next week due to the all-to-obvious link from human pheromones to biophysically constrained viral latency and the prevention of all pathology, which was detailed in the context of the creation of sunlight, which was subsequently linked from the creation of ATP to the creation of RNA.
Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
The last time I spoke with him, he asked how to monetize the facts. Bergdhal’s pathology may have prompted renewed interest. Attempts to discuss that fact with other veterans have failed. I think that some of them would rather see him crucified rather than link the energy-dependent weekend resurrection of the bacterial flagellum in P. fluorescens to the the energy-dependent Resurrection of Christ.
Bergdhal’s pathology can also be placed into the context of the problematic transitions from adolescence to adulthood that are altered by fixation of one energy-dependent RNA-mediated amino acid substitution.
See: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
The A or Met allele is associated with lower enzymatic activity and the polymorphism is associated with many different personality traits. The USAF is leading the way forward towards effective treatment of mental disorders in veterans, which is something the psychiatrists who evaluated Bergdhal know about. See for instance: US Air Force Studying Impact of Exome Sequencing in Routine Care

"Evolution of Man. - Undoubtedly there once lived upon the earth races of men who were much lower in their mental organization than the present inhabitants.

Natural selection for racism and all pathology

November 5, 2017

by James Kohl with No Comment Adaptations Alternative Splicings base editing Cytosis Diseases & Disorders Ecology Nutrigenomics Physics RNA Directed RNA editing RNA-directed DNA methylation Variations

Why is natural selection hard to grasp? It is not what you think….

…human cognitive tendencies interfere more with deep understanding of how natural selection works.

Simply put, our intelligence and teleological reasoning interferes with the teaching of pseudoscientific nonsense. The nonsense does not place Darwin’s “conditions of life” before natural selection for reproductive fitness. Natural selection is food energy-dependent and pheromone-controlled in the context of biophysically constrained viral latency.
See for comparison: The vibrational theory of olfaction for the win

Darwin’s energy-dependent conditions of life link biophysically constrained viral latency to healthy longevity. Luca Turin’s works are among those that exposed the fraudulent claims of neo-Darwinian theorists.

See for example: Molecular recognition in olfaction

For physicists, maybe the single most important development that can be envisaged is the production of a high quality X-ray structure of a one or more olfactory receptors. This would open the door to large scale computer simulations that would help shed light on both the mechanical and electrical responses of olfactory receptors.

The X-ray structure of the virus that destroys olfactory receptors is more important. It can be viewed in the context of everything know to serious scientists who have linked quantum physics to quantum souls.
For example, see: Rosalind Franklin: The Hero Denied Her Due

Franklin was also a brilliant chemist and a master of X-ray crystallography, an imaging technique that reveals the molecular structure of matter based on the pattern of scattered X-ray beams. Her early research into the microstructures of carbon and graphite are still cited, but her work with DNA was the most significant — and it may have won three men a Nobel.
Franklin left King’s in 1953 in a long-planned move to join J.D. Bernal’s lab at Birkbeck College, where she discovered the structure of the tobacco mosaic virus. But in 1956, in the prime of her career, she developed ovarian cancer — perhaps due to her extensive X-ray work. Franklin continued working in the lab until her death in 1958 at age 37.
“As a scientist, Miss Franklin was distinguished by extreme clarity and perfection in everything she undertook,” Bernal wrote in her obituary, published in Nature. Though it’s her achievements that close colleagues admired, most remember Franklin for how she was forgotten. — C.E.

For comparison, these authors take the ball that Nesse and other theorists put into play, and these theorists run with it. They even pretend to be “biologically informed,” in response to my oft repeated claim that people like them are biologically uninformed science idiots.
The Future of Secularism: a Biologically Informed Theory Supplemented with Cross-Cultural Evidence

…earlier trends toward secularization (due to science education surrounding advancements in science) are currently being counter-balanced by genetic and reproductive forces. The authors also propose that the inverse association between intelligence and religiosity, and the inverse correlation between intelligence and fertility lead to predictions of a decline in secularism in the foreseeable future.

The agenda of at least two co-authors: Nyborg and Ellis, is clear. See: Race and Sex Differences in Intelligence and Personality: A Tribute to Richard Lynn at Eighty

Nyborg and Lee Ellis promote the works of J. Phillipe Rushton who was reported to be among the top racists of the 20th century.

See: Do pigmentation and the melanocortin system modulate aggression and sexuality in humans as they do in other animals?

Pigmentation of the hair, skin, cuticle, feather and eye is one of the most salient and variable attributes of vertebrates. In many species, melanin-based coloration is found to be pleiotropically linked to behavior. We review animal studies that have found darker pigmented individuals average higher amounts of aggression and sexual activity than lighter pigmented individuals. We hypothesize that similar relationships between pigmentation, aggression, and sexuality occur in humans. We first review the literature on non-human animals and then review some of the correlates of melanin in people, including aggression and sexual activity. Both within human populations (e.g., siblings), and between populations (e.g., races, nations, states), studies find that darker pigmented people average higher levels of aggression and sexual activity (and also lower IQ). We conceptualize skin color as a multigenerational adaptation to differences in climate over the last 70,000 years as a result of “cold winters theory” and the “Out-of-Africa” model of human origins. We propose life history theory to explain the covariation found between human (and non-human) pigmentation and variables such as birth rate, infant mortality, longevity, rate of HIV/AIDS, and violent crime.

Pigmentation is food energy-dependent and RNA-directed DNA methylation links food odors to pheromones and the physiology of reproduction in all living genera. It would be interesting to hear what Jay R. Feierman thinks about this since I met him at a 1995 conference that Lee Ellis organized and J. Phillipe Rushton also attended (by invitation only).

All (~90) attendees should be familiar with works that extended the social science theories to “hate-mongering.” I have tried to stop the hate-mongering, but history may repeat itself with Feierman’s help, of course.
See for comparison: 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.

Natural selection for energy-dependent codon optimality has been linked via olfaction from quantum physics to all biologically based RNA-mediated cell type differentiation via amino acid substitutions in organized genomes. But Nesse and others like him want to keep their teaching positions and that requires them to deny everything known to serious scientists about physics, chemistry, and molecular epigenetics.
See for comparison: A Civic Biology: Presented in Problems (New York, 1914): pp. 193-196, 253-254, 261-263.
Social scientists ignored Darwin’s “conditions of life.” Most of them don’t seem to understand why I claim that their ignorance has caused the deaths of millions.
See for comparison: 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…
Will history repeat itself? Will most of us return to the racism of Hunter (1914)?

In the review The Future of Secularism: a Biologically Informed Theory Supplemented with Cross-Cultural Evidence, they obfuscate the claim that Muslims are less intelligent and more fertile than Jews or Buddhists. What will happen when their claim is linked to this claim from Hunter: “A Civic Biology: Presented in Problems” pp. 195-196

Evolution of Man. – Undoubtedly there once lived upon the earth races of men who were much lower in their mental organization than the present inhabitants. If we follow the early history of man upon the earth, we find that at first he must have been little better than one of the lower animals.

Any and all links from intelligence to fertility are claims that attempt to support the pseudoscientific nonsense touted by neo-Darwinian theorists. Their ridiculous theories are the cause of all pathology.

The Root Cause Of Cancer and Why it Has Been Kept a Secret!

…the root cause of cancer is too much acidity in the body, meaning that the pH in the body is below the normal level of 7.365, which constitutes an “acidic” state. Warburg investigated the metabolism of tumors and the respiration of cells and discovered that cancer cells maintain and thrive in a lower pH, as low as 6.0, due to lactic acid production and elevated CO2. He firmly believed that there was a direct relationship between pH and oxygen.

Anyone who ever performed a blood gas analysis could have helped to establish the fact that the virus-driven degradation of messenger RNA is the cause of all pathology. See for instance: 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.

That fact made it obvious to all serious scientists that energy-dependent RNA mediated DNA repair was required for healthy longevity. The anti-entropic virucidal energy of the sun was linked to the creation of ATP by Schrodinger (1944) in “What is Life?” The food energy-dependent pheromone-controlled physiology of reproduction in species from microbes to humans now links the creation of RNA to all biodiversity, and that links pheromones to biophysically constrained transgenerational epigenetic inheritance of healthy longevity via viral latency.

Nothing has been hidden. There was no reason to hide the facts after theorists made it possible to teach their pseudoscientific nonsense to students in high school via the Scopes Trial in Dayton, TN (1925). Sinclair Lewis published “Arrowsmith” in 1925 and since then, ATP-dependent biophysically constrained viral latency has been detailed in the context of the cell biology game “Cytosis” with its “Virus Expansion.”

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!

The next reformation: 500 years too late? (1)

October 31, 2017

by James Kohl with No Comment Adaptations Alternative Splicings base editing Cytosis Diseases & Disorders Ecology Light Energy Model Organisms RNA Directed RNA editing RNA-directed DNA methylation Variations What's in the News

Summary: The next reformation links the creation of the sense of smell to all biodiversity in the context of biophysically constrained viral latency.
The vibrational theory of olfaction for the win

Although there is nothing comparable to this kind of insight into the molecular world of scent within the shapist mentality, we should probably thank its supporters for making this battle of ideas so epic. There may yet be time for two more big events in the field, one a Nobel party [for Luca Turin], and the other, a funeral [for shape theory].

Shape theory has been touted in the context of the Watson and Crick model of the static DNA double helix. All serious scientists have since dismissed that ridiculous model. I admit, however, that in my review of the book, The Emperor of Scent, which was about Luca Turin, I was critical of his correct approach. But Wen Zhou’s group has since linked Turin’s claims from the creation of sunlight to the creation of ATP and the creation of RNA. The extension from the creation of RNA to the creation of olfactory receptors links the time-space continuum to the pheromone-controlled physiology of reproduction and all biodiversity via feedback loops.
That was expected by every serious scientist I know. The serious scientists know that gene activation is energy-dependent. They do not link sudden energy jumps from de Vries (1902) definition of mutation to all biodiversity. The next reformation links the creation of the sense of smell to all biodiversity in the context of biophysically constrained viral latency.
See: The next reformation: 500 years too late? (2)

The next reformation: 500 years too late? (2)

October 31, 2017

by James Kohl with One Comment Adaptations base editing Ecology RNA Directed RNA editing

The problem for those who use definitions is that everything known about the links from food energy-dependent changes in electrons to ecosystems must now be ignored. Last week, publications in Nature and in Science linked energy-dependent changes in base editing to RNA editing, which means that all the ignorance of biologically uninformed theorists can be placed into the context of Feynman’s claims about “human idiocy.”
See also: RNA editing and alternative splicing: the importance of co-transcriptional coordination
Apparently, the theorists did not think the facts about energy-dependent RNA editing and alternative splicings of pre-mRNA would be detailed.
But see for comparison: James Kohl reviews: The Emperor of Scent: A Story of Perfume, Obsession and the Last Mystery of the Senses

More than a century ago, in 1900, Max Planck, one of the greatest physicists of all time, announced his revolutionary new scientific theory of an energy constant in quantum mechanics. Eighteen years later he was awarded a Nobel Prize.

As Luca Turin waits for his rewards/award, he and others may benefit from knowing more about Planck’s attitude: “…a new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”

See also the review by Avery Gilbert: a human pheromone-denier (per Leslie Vosshall). The link opens the .pdf
Gilbert, A.N. 2003. The emperor’s new theory. Review of “The emperor of scent: A story of perfume, obsession, and the last mystery of the senses”, by Chandler Burr. Nature Neuroscience 6:335.
Gilbert’s conclusion:

Against this reality, Emperor of Scent represents a triumphalist account of an unproven alternate theory. In ancient Rome, the honor of a triumph was reserved for an emperor who achieved a glorious victory. Should Turin’s conjecture prove correct, he will of course deserve one. But until then, this appears to be a case of premature adulation.

Gilbert’s claims about premature adulation can be compared to the claims of other pseudoscientists. Serious scientists have not been afraid to link claims of adulation from the creation of energy to the creation of all biodiversity via the physiology of reproduction. The serious scientists linked Turin’s theory to every aspect of energy-dependent biophysically constrained biodiversity via the feedback loops that link the sense of smell from the pheromone-controlled physiology of reproduction to viral latency.
See: Feedback loops link odor and pheromone signaling with reproduction
Even those who might not have believed that Luca Turin correctly represented energy-dependent top-down causation in the context of links from quantum physics to chemistry and all biologically-based diversity had little doubt that food odors and pheromones are the obvious link from olfaction to survival of all species.
The next reformation: 500 years too late? (3)

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

October 13, 2017

by James Kohl with No Comment Adaptations biophotonics Cytosis Diseases & Disorders Ecology Human Brain Human Pheromones Model Organisms Neuronal Plasticity Physics RNA Directed RNA–Mediated Epigenetic Heredity Subatomic Variations What's in the News

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.