5th-6th Sept 2018 Dublin, Ireland

Part 3: Light-controlled cell biology (revisited)

Your cells are constantly being shed and replaced—so is your body ever completely refreshed? Does anything remain of the body that existed on Jan. 1, 2017? 2007? The day you were born? (video)

Out of Order: Undaunted 

…as I prepared for this issue’s Special Report on Microbiomics (starting on page 19), I am stunned by what I am only starting to understand. That our individual existence as humans may only be 10 percent of what we see in the mirror—and that perhaps only 1 percent of our personal ecological genome is a human genome…

When you understand the concept of biophysically constrained energy-dependent ecology (Frohlich, 1968), you may begin to understand the difference between ecological adaptation and evolution. Each cell type represents biophysically constrained viral latency, not mutation-driven evolution.

Outside the context of energy-dependent RNA-mediated DNA repair (aka autophagy), no cell types exist. Bacteria become archaea and archaea become L-forms and the L-forms become non-cells. The energy for cell type differentiation comes from sunlight or from food. It is biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans.

See also: This Compound Can Reverse Aging in Mice. Will It Work in People? and Mitotic progression, arrest, exit or death is determined by centromere integrity and independent of de novo transcription

Theorists used the term “de novo” in the context of de novo transcription and other aspects of energy-dependent cell type differentiation that they cannot explain with their ridiculous theories. For instance, David Sinclair has touted pseudoscientific nonsense until now.

He knows that the cell biology game, “Cytosis” for ages 10+ has exposed him to ridicule, and obviously won’t go away without a fight to maintain some scientific credibility.

See also: PhD title: Fibrillation of proteins involved in neurodegenerative diseases: influence of mRNA

State of art:
TDP-43 and FUS, two RNA-binding proteins (RBPs), have been recently the subject of increased attention due to their role in Amyotrophic Lateral Sclerosis (ALS) and FrontoTemporal Lobar Degeneration (FTLD). In non-pathological conditions, these proteins are mostly found in the nucleus where they participate to mRNA biogenesis and regulation of alternative splicing. However, TDP-43 and FUS are also present in the cytoplasm and they are able to shuttle from one compartment to another. TDP-43 and FUS notably participate in cytoplasmic functions such as mRNA transport and localized translation, which are of critical importance for neuron physiology. In neurons of ALS and FTLD patients, TDP-43 and FUS form insoluble cytoplasmic aggregates with fibrillar structure that can further spread the disease to other areas of the brain.

If this is the state of the art, was the information used to treat the late Stephen Hawking, or was he left to suffer unnecessarily until he died?

See also:

 More germane to DDNews, the most recent pattern I cannot seem to shake is discussion of the microbiome.

Neo-Darwinian theorists and Big Bang cosmologists seem to have no sense of pattern recognition in the context of Olfaction Warps Visual Time Perception

See for comparison: What Stephen Hawking’s Final Paper Says (And Doesn’t Say)

The claims in “Olfaction Warps Visual Time Perception” link the sense of smell in bacteria to our visual perception of energy and mass in the context of the space time continuum and biophysically constrained viral latency. Everything known to Hawking’s co-authors Roger Penrose and George FR Ellis has since been linked from what organisms eat to the physiology of reproduction via the creation of sunlight and biomolecules.

The difference between Hawking’s ridiculous theories and biologically-based facts will place the claims about his intelligence and insight into the historical context of how celebrity scientists have led to our unnecessary suffering and premature death. It’s ironic that Hawking could have been effectively treated with food energy-dependent microRNAs, but instead got stuck with a useless theoretical approach to life. I would not want that to happen to my children or grandchildren (if I had any). What are your children being taught to believe in: theories or experimentally established facts?.

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.

The MicroRNAome Strikes Back: A Sokalian hoax (2)

The problem with -omics has repeatedly been detailed in articles from social scientists and other theorists who fail to link what is known to serious scientists about the microRNAome to their theories. Pseudoscientists continue to create bricks that clutter the metaphorical physical landscape and prevent the epigenetic landscape from being linked from the physiology of nutrient energy-dependent pheromone-controlled reproduction to all cell type differentiation via energy-dependent changes in atoms to ecosystems in all living genera.
On 1/22/18, I discussed this with a plumber and his assistant, who is –like me– a veteran of the US Military. The plumber, prefaced the discussion with a comment about adaptations for comparison to evolution. The veteran provided supportive comments from his expertise in history, which he hopes will not repeat itself in the context of the 1918 Spanish flu, smallpox, or the bubonic plague.
I learned the value of social science because he believes that vultures put an end to the bubonic plague in the context of their unique ability to thermoregulate their organized genome by spreading their wings to create what most people would refer to as a virus-killing fever. I may not be so critical of other social scientists after meeting one that was not biologically uninformed.
There may be others, but I doubt it.
See: Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay

We identified and confirmed orthologous gene pairs with 3′-UTR SINEs that independently function in SMD control of myoblast metabolism. Expanding to other species, we demonstrated that SINE-directed SMD likely emerged in both primate and rodent lineages >20-25 million years ago. Our work reveals a mechanism for the convergent evolution of posttranscriptional gene regulatory networks in mammals by species-specific SINE transposition and SMD.

No mechanism for convergent evolution was revealed. All posttranscriptional gene regulatory networks require the energy-dependent creation of microRNAs that biophysically constrain viral latency. That fact was not mentioned.
See for comparison: microRNA  
For example: Genetic polymorphism in Hsp90AA1 gene is associated with the thermotolerance in Chinese Holstein cows

…one SNP in the promoter, three SNPs in the coding region, and one in 3′-UTR were novel and reported for the first time in this study.

[…]The expression of Hsp90AA1 in cow bearing mutant allele C was higher (4.18 +/- 0.928) than cows bearing wild-type allele G (1.008 +/- 0.0.129) in stress season. In summary, there was an association between genetic variations in the Hsp90AA1 and thermoresistance. This association could be used as a marker in genetic selection for heat tolerance in Chinese Holstein cattle breeds.

There is no such thing as genetic selection for heat tolerance. The limits of food energy-dependent thermotolerance are biophysically constrained in the context of food energy that biophysically constrains viral latency,which typically limits or prevents activation of the death gene.
Preventing activation of the death gene was reported as: Study finds convergent evolution of gene regulation in humans and mice January 18, 2018

Organisms that aren’t closely related may evolve similar traits as they adapt to similar challenges. It’s called convergent evolution, and familiar examples include the wings of birds, bats, and insects, and echolocation in bats and dolphins. Now, molecular biologists have found evidence of convergent evolution in an important mechanism of gene regulation in humans and mice.

Serious scientists do not call ecological adaptation convergent evolution, and serious scientists do not claim to discover important mechanisms of gene regulation. All the mechanisms are biophysically constrained by ecological variation in the availability of food and the physiology of pheromone-controlled reproduction in species from mice to humans (and from microbes to humans).
But see for comparison: A simple explanation of Born’s rule

…the agreement between quantum theory and experiments follows from a one-to-one correspondence between the logical possibilities and the physical possibilities and, in particular, implies that the outcomes of quantum measurements are not constrained by any physical reason.

Thanks to so-called science journalist Philip C. Ball for calling this to my attention. In my first blog post about Nonomura’s Sokalian hoax, I mentioned Frohlich (1968). Long-range coherence and energy storage in biological systems. I do not expect pseudoscientists or so-called science journalists to accept the facts about constrained energy storage. The facts are neo-Darwinian theory killers.  Once again, the theorists have a problem understanding how the creation of energy must be linked from energy storage to biophysically constrained viral latency and all biodiversity.
Nonomura’s hoax links the energy-dependent epigenetic silencing of transposable elements to the central events of germline transmission via the creation of sunlight, the creation of ATP, and the creation of microRNAs. The light energy-dependent creation of microRNAS must be linked to RNA-mediated DNA repair and to the relatively error-free genome of the next generation via the pheromone-controlled physiology of reproduction that biophysically constrains viral latency.
Unanswered questions about viral latency and transcriptional quiescence (aka gene silencing), which is a hallmark of the biophysically constrained germ cell lineage in many organisms, are the clear link to my claim that Nonomura has published a Sokalian hoax as Small RNA pathways responsible for non-cell-autonomous regulation of plant reproduction — as a peer-reviewed monograph.
The unanswered questions allow biologically uninformed peers to accept the claims of non-cell-autonomous regulation as if they could be part of an evolutionary approach to energy-dependent reproduction. For comparison, the first question a serious scientist would ask is about how non-cell-autonomous pathways compensate for ecological variation, which must be linked to energy-dependent ecological adaptation via the availability of some nutrients, materials and signals. Most serious scientists will realize that non-cell-autonomous pathways link sunlight to the activation of endogenous substrates (e.g., enzymes) that are created in the context of what happens when the speed of light hits water.
See: 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.
I noticed that this pinned post now appears first @rnomics:

Reconstructed ancient ocean reveals secrets about the origin of life (2014)

This was a report on Non‐enzymatic glycolysis and pentose phosphate pathway‐like reactions in a plausible Archean ocean
Fabrice Leclerc @rnomics seems to be ignoring the retractions of Jack Szostak’s works. See: Retraction Watch
Researchers who study the origins of life on Earth have hypothesized that RNA evolved before DNA or proteins. Szostak’s works seemed to suggest that RNA replicated itself without enzymes. Supposedly, a certain type of peptide — which may have existed in our early history — made it possible for RNA to copy itself. But where did the peptide come from?
Who cares? In subsequent experiments, no one reproduced the 2016 findings. Indeed, the peptide did not appear to provide an environment that fostered RNA replication. With two retraction of his groups works, claims about the microRNAome should have been placed into the context the energy-dependent creation microRNAs and enzymes.
The problem that serious scientists expect to be addressed is the one that links the nutrient-energy dependent source of the materials for developing germ cells to the development of differentiated cell typed in the context of metabolism and signaling. Again, we see how Nonomura helps to eliminate the magic of evolution without admitting to the hoax. Light energy is required, and he did not mention that fact.
For comparison, science journalist Philip Ball took the the magic several steps further. He placed the availability of the quantized energy as information, which is required for the creation of nutrients, into this context:

To turn quantum to classical, we don’t need a conscious mind to measure or look; we just need an environment full of stuff. With or without us, the Universe is always looking.

Nonomura claims that little is known about the mechanism that promotes the energy-dependent intercellular movement of small RNAs in plant reproductive organs. But, he also claims that the mechanism in humans is part of an energy-dependent exosome-mediated system, which was recently reported in the context of small RNA transfer in organ cross-talk. Philip C. Ball’s claims are based on the automagical creation of an environment full of stuff.
The link from the availability of nutrient-energy in pollen (i.e., Ball’s environment full of stuff) to energy-dependent foraging behavior and the pheromone-controlled physiology of reproduction in the honeybee model organism is missing. Nonomura’s conclusion is another example of Sokal-like wit. The cell membrane must automagically create itself before direct evidence for energy-dependent microRNA-mediated cell type differentiation can be linked to healthy longevity in all living genera via the physiology of reproduction in grasses like fescue.
The energy source for the transfer of materials or information between SCs [somatic cells] and the vegetative cell (VC) nucleus in not mentioned in Nonomura’s attack on the intelligence of theorists and science journalists who have failed to link the virus-driven theft of quantized energy from mutations to the transgenerational epigenetic inheritance of all pathology.
For comparison: My top tweet from this month was posted on January 5, 2018. So far it has accumulated 1484 impressions. In case you missed it:
A cartoon representation of “Long-range coherence and energy storage in biological systems” (1968) might help others establish facts about how the construction of the cell membrane protects against virus-driven genomic entropy.
A comic about the problems with the -omics, illustrated by Matteo Farinella
The problem with -omics, and especially with the ridiculous representation from 2014 as a pinned post @rnomics, has repeatedly been detailed in articles from social scientists and other theorists who fail to link what is known to serious scientists about the microRNAome to their theories. Pseudoscientists and biologically uninformed science journalists continue to create bricks that clutter the metaphorical physical landscape (an environment full of stuff) and human idiocy prevents the epigenetic landscape from being linked to all cell type differentiation via the nutrient energy-dependent pheromone-controlled links from atoms to ecosystems in all living genera.
The MicroRNAome Strikes Back: A Sokalian hoax (3)
See also: The Postmodernism Generator web page (generates a random postmodernist article each time loaded)
See also: Social science is pseudoscience
 

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.

The tipping point (revisited): 68,000 publications

MicroRNA  Items: 1 to 20 of 68011 (earlier today, on 12/21/17)

See for example: In Vitro Validation of miRNA-Mediated Gene Expression Linked to Drug Metabolism 12/20/17

The approaches described can be employed broadly for the validation of miRNA-mediated negative regulation of any gene. Determining miRNA-mediated regulation of enzymes and transporters affecting drug metabolism is a critical step in designing personalized therapy and for understanding the mechanisms responsible for variations in the responses to therapeutic agents.

The “…miRNA-mediated regulation of enzymes and transporters affecting drug metabolism…” links the National Microbiome Initiative to the Precision Medicine Initiative and to all healthy longevity or to all virus-driven pathology in all living genera via differences in energy as information.
For review, see: Energy as information and constrained endogenous RNA interference

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection. This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

For a historical perspective on what is known about energy-dependent RNA-mediated (aka microRNA-mediated) cell type differentiation, see:
The quantum / classical RNA-mediated ‘tipping point’ 3/26/15
The tipping point? 50, 000 publications 5/16/16
The tipping point? 50, 000 publications (2) 5/16/16
The tipping point? 50,000 publications (3) 5/17/16
The tipping point? 50,000 publications (4) 5/26/16
The tipping point? 50,000 publications (5) 7/27/16
The tipping point (revisited): 60,000 4/20/17
By May 16, 2016, the innate antiphage defense strategy was linked from quantum physics to classical physics by 50,000 publications that mentioned microRNAs. Nineteen months later, every aspect of the microRNA-mediated gene expression that had already been linked to drug metabolism attests to the fact that not all scientists have followed the extant literature.
Many scientists are still among the pseudoscientists who who failed to notice the most obvious links from the antiphage defense strategy to healthy longevity. Perhaps they were also too busy to notice the most obvious links from the virus-driven degradation of messenger RNA to the need for drug therapies.
If so, that may explain why the drug therapies have been largely ineffective. The drug therapies may be like vaccinations. They appear to link the virus-driven degradation of messenger RNA to more mutations, which clearly link the virus-driven theft of quantized energy to all pathology.
With more than 18,000 published works in the past 19 months, (8,000 in the past 8 months) it is time to again address the tipping point between quantum physics and classical physics in the context of food energy-dependent pheromone-controlled microRNA-mediated cell type differentiation via what is known about autophagy.
In the context of drug metabolism, the energy-dependent microRNA-mediated creation of enzymes was linked from the metabolism of food to all biodiversity on Earth via pheromone-controlled physiology of reproduction.
See for example page 19 of the sample report from Alpha Genomix that you can download as a pdf here. The food energy-dependent creation of the CYP enzymes protects our organized genome by biophysically constraining viral latency.

See for comparison: Our Top 17 in ’17: The Year in Science at PLOSBLOGS 

…the far-reaching war on science being conducted by the Trump administration, an assault on facts which, as several of our bloggers have noted, constitutes a removal of scientific evidence from the formation and discussion of public policy and an evisceration of funding and communication of vital research in medical research and regulation, public health, climate, energy, agriculture and education.

The only war on science that I know about, is the one in which serious scientists are Combating Evolution to Fight Disease. To place that claim into the context of what has happened during 2017, see the retraction of this article.
Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living [retracted]
It was retracted because the authors mentioned the creator of the hand. The creation of the hand occurs only in the context of biophysically constrained viral latency.

See for comparison: Retraction Watch

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.

Where else besides PLOS have you seen a retraction for the mention of a creator? Where did PLOS report on the retraction for misrepresentations in “Nature Chemistry?” Who still believes that microRNA and messenger RNAs created each other so that they could automagically constrain viral latency?
Who else besides PLOS is waging a far-reaching war on science?
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems 4/10/14

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. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

Obama Advisers Urge Action Against CRISPR Bioterror Threat 11/17/16

Scientific advisers to President Obama warn that the U.S. urgently needs a new biodefense strategy and should regularly brief President-elect Donald Trump on the dangers posed by new technologies like CRISPR, gene therapy, and synthetic DNA, which they say could be coöpted by terrorists.

See for comparison:  2017 Global Infectious Diseases Threats to the United States 12/22/16

Flu.  Influenza remains one of the greatest threats to the US population killing on average 3,000-49,000 Americans annually.  People at the greatest risk of severe flu and death are pregnant women, residents of long-term care facilities, the very old (adults over the age of 65), the very young (children less than 2), Native American populations, and those with underlying chronic conditions such as asthma, COPD, heart disease, obesity, and other conditions.  Timely vaccination remains the most proven and effective way to avoid serious injury from influenza.

The new Trump Administration will face a formidable array of global and indigenous infectious disease threats in 2017.  A Global Health Security Agenda will help provide a framework for tackling some of these tough issues, but enhanced efforts will be needed to prevent new epidemics, especially from vector-borne and zoonotic neglected tropical diseases, measles, and the ever-constant threats from AMR and flu.

The biggest threat that the Trump administration has faced in the first year is the fake news. The most recent example accused him of censorship at the CDC for his director’s efforts to biophysically constrain energy-dependent viral latency. The CDC director’s efforts to help others with budget concerns were linked to censorship, and the President of the United States was compared to Hitler. Wake up and “Remember the Alamo.”
SARCASM ALERT: No, that was a different war. Wake up and remember the Manhattan Project, which also linked censorship about energy to the winning of a war.

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

Cryo-EM from atoms to ecosystems

Summary: I’m not going to continue repeating myself indefinitely. See: Reduced protein synthesis in schizophrenia patient-derived olfactory cells
The reduced protein synthesis is a clear link from the virus-driven degradation of messenger RNA to all pathology.


October 5, 2017 Lactate Metabolism in Human Lung Tumors
Reported as: Study challenges long-standing concept in cancer metabolism

“We were completely shocked by our findings,” said Dr. Ralph DeBerardinis, Professor at CRI, Director of CRI’s Genetic and Metabolic Disease Program, and Chief of the Division of Pediatric Genetics and Metabolism at UT Southwestern. “The oldest observation in cancer metabolism, the Warburg effect, says that lactate is a waste product of the tumor. This concept has driven the vast amount of research in the field. Our finding is a fundamental change in how we think about tumor metabolism.”

The fact that these so-called experts know so little about metabolism and cancer can be viewed in the context of what is known about all the links from energy-dependent changes in atoms to ecosystems in all living genera.
See: Atomic structure reveals how cells translate environmental signals
The team identified an amino acid sequence in the leaflet that is conserved in parasites, suggesting structural insights that may assist in drug discovery for these devastating conditions.
See, for instance: The Supraspliceosome – A Multi-Task Machine for Regulated Pre-mRNA Processing in the Cell Nucleus
See also: Mitochondrial ribosome assembly in health and disease
There is an obvious need to link the conserved amino acid sequence in parasites to healthy longevity via mitochondrial ribosome assembly and from the virus-driven energy theft of quantized energy as information to all pathology via cryo-EM.See: Inching toward the 3D genome

Re: “…the nucleome structure changes as cells age, differentiate, and divide, and researchers want to understand how and why.”

Cell type differentiation is nutrient-dependent. RNA-directed DNA methylation links RNA-mediated amino acid substitutions to cell type differentiation via protein folding during life history transitions. Amino acid substitutions stabilize protein folding; mutations perturb it, during nutrient-dependent theromodynamic cycles of protein biosynthesis and degradation.

Life is physics and chemistry and communication — http://dx.doi.org/10.1111/nyas.12570

The metabolism of nutrients links metabolic networks to genetic networks via species-specific pheromones that control the physiology of reproduction. Simply put, pheromones link nutrient-dependent life via physics, chemistry, and the conserved molecular mechanisms of communication in species from microbes to man.

Until nutrient-dependent protein folding is linked via the conserved molecular mechanisms of amino acid substitutions and pheromone-controlled DNA stability in organized genomes, which links the epigenetic landscape to the physical landscape of DNA, researchers must take a piece-meal approach to integrating the requirements for life and successful life history transitions — despite the fact that life history transitions have been detailed in the context of the honeybee model organism. See: Honey bees as a model for understanding mechanisms of life history transitions http://www.ncbi.nlm.nih.gov/pubmed/15925525

I’m not going to continue repeating myself, indefinitely.
See: Reduced protein synthesis in schizophrenia patient-derived olfactory cells
The reduced protein synthesis is a clear link from the virus-driven degradation of messenger RNA to all pathology
For comparison see:
Re: Flaming by Glen Sizemore on the evolutionary-psychology group msg 89218
Jay R. Feierman: Being nasty and unkind is not a good strategy in an academic discussion or in human relations in general.”
Glen Sizemore: Yeah…but this isn’t a discussion. It is me ridiculing your hopelessly-moronic views.
Jay R. Feierman [NEW]: The problem is that your unkind and nasty remarks are not just directed at me. When you used to be on the human ethology group before you were removed they were directed at others as well. As moderator of the human-ethology group, I used to not post many of your comments for flaming related to many different people. On the evolutionary-psychology group, where Robert Karl Stonjek appears to have much more tolerance for flaming, your unkind and nasty comments are directed toward many other people, including Robert Karl Stonjek, the moderator. Life is too short to deal with people like you. I prefer to deal with nice people in my life and try to surround my self with nice and kind people. As a result, even though you often bring up interesting issues in your postings related to what I’ve posted, I am no longer going to respond to anything you write.
My response:89219
Please place your comments about me into the context of any “nasty” comment by others.
For example: 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.  https://groups.yahoo.com/neo/groups/human-ethology/conversations/topics/48182
My interpretation: You called me a biologically uniformed science idiot.
See also: Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.  https://groups.yahoo.com/neo/groups/human-ethology/conversations/topics/48229
My interpretation: You claimed that every professor of biology or genetics in any accredited university anywhere in the world knew more than me about my established area of expertise: RNA-mediated cell type differentiation.
The final solution???

Excerpt: Emerging evidence suggests that ecological heterogeneity across space can influence the genetic structure of populations, including that of long-distance dispersers such as large carnivores.
My comment: Indeed, the emerging evidence actually refutes all the neo-Darwinian nonsense of population genetics . . . etc., etc.
[MODERATOR NOTE: I’m not going to post more from Kohl until he answers the very direct and simple question posed to him by anon, which is whether he (Kohl) believes that RNA splicing can change DNA.] 10/6/17

Until today, I did not respond to Feierman’s hopelessly-moronic question about my beliefs.
 
He continued to edit or block any attempts to promote intelligent discussion in the Human Ethology Yahoo Group. And finally, after the 2017 Nobel Prize in Chemistry was awarded to the researchers who developed the cryo-EM tecnology, I can say this:
 

The fact that alternative splicings of pre-mRNA causes changes in DNA was central to the facts about cell type differentiation we placed into the context of the molecular epigenetics section of this 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html

Feierman did not post my reply to the question about alternative splicings of pre-mRNA.  Instead, he is continuing to ignore everything known to serious scientists about biologically based cause and effect, or to present it in a series of disparate attempts to obfuscate the facts about energy-dependent top-down causation and the pheromone-controlled physiology of reproduction, which helps to biophysically constrains the transgenerational epigenetic inheritance of all diseases.

Today he posted this link to the Human Ethology Yahoo Group

Smell or vision? The use of different sensory modalities in predator discrimination

The information animals obtain about potential predation risk may differ qualitatively depending on the sensory modality by which a cue is perceived.

Facts about multisensory integration were published as:

Global Sensory Impairment Predicts Morbidity and Mortality in Older U.S. Adults

and Olfaction Warps Visual Time Perception

Feierman also posted a link to: Local mating markets in humans and non-human animals

Biological market theory (BMT), which deals with cooperation among unrelated agents in general, is combined with sexual selection theory (SST), which deals with reproductive cooperation, to focus on an aspect that received little attention in the vast SST literature: adaptations that improve mating success when the market value of an individual varies considerably from one local mating market (LMM) to the next.

This, too: Divergence of developmental trajectories is triggered interactively by early social and ecological experience in a cooperative breeder

We found that individuals did specialize in distinct behavioral competences, which led to either delayed dispersal or early independent breeding. The divergence into different behavioral trajectories became apparent only by manipulating both early social and ecological experiences, highlighting the importance of multivariate influences on the development of social trajectories.

There are many different ways to claim that what organisms eat leads to the production of species-specific behaviors via ecological variation that must be linked to the pheromone-controlled physiology of reproduction. Feierman, and others like him, will continue to cite works that obfuscate the facts about cause and effect that have been known to all serious scientists since the time that McEwen et al., (1964) linked the creation of energy from the creation of ATP to the creation of RNA and all biophysically constrained biodiversity.

See: 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.

Feierman, and all other biologically uninformed science idiots are not going to admit that they were wrong about everything they ever claimed.

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.”

Alternative splicing of pre-mRNA

Host-derived creation of all pathology (1 of 2)

For more than 15 million years, human beings have co-evolved with thousands of microbial species…

Nothing known to serious scientists support ridiculous claims about 15 million years. See for comparison: Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees

See also: Nothing in Biology Makes Any Sense Except in the Light of Evolution

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

See also: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

Editor’s summary: Five antigenic sites in the virus surface hemagglutinin protein, which together comprise 131 amino acid positions, are thought to determine the full scope of antigenic drift of influenza A virus. Koel et al. (p. 976) show that major antigenic change can be caused by single amino acid substitutions.

The fact that one amino acid substitution alters antigenic changes in the influenza viruse and one amino acid substitution stabilizes the organized genomes of primates attests to what Richard Feynman referred to as human idiocy in this snippet about food energy from one of his lectures.

See: Food energy

See for comparison:

Your favorite phrase, “biologically uninformed science idiots” alienates you from people because it sounds insulting and egotistical. — Saibot Rodrigo

“Mutation-driven evolution” sounds insulting and egotistical to serious scientists. Only pseudoscientists use it to dismiss everything known about how quantum physics must be linked to the creation of quantum souls via food energy and the physiology of pheromone-controlled reproduction.

Here are two examples of how pseudoscientists alienate serious scientists. (Jay R. Feierman is a retired medical practitioner and former psychiatrist.)
 
For example: 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.
Jay R. Feierman:

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

See also: Past 5,000 years prolific for changes to human genome

Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report. 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years. More broadly, the results suggest that humans are carrying around larger numbers of deleterious mutations than they did a few thousand years ago. But this doesn’t mean that humans now are more susceptible to disease, says Akey. Rather, it suggests that most diseases are caused by more than one variant, and that diseases could operate through different genetic pathways and mechanisms in different people.

The claim that diseases could operate through different mechanisms in different people cannot be supported by experimental evidence of biologically-based cause and effect. Healthy longevity and virus-driven pathology have been linked from energy-dependent RNA-mediated cell type differentiation to all biophysically constrained biodiversity via the creation of the sun’s anti-entropic virucidal energy, which prevents the degradation of messenger RNA. The virus-driven degradation of messenger RNA has been linked from mutations to all pathology in all living genera via conserved molecular mechanisms.

Simply put, what organisms eat has been linked from the physiology of pheromone-controlled reproduction to all biophysically constrained biodiversity. What organisms eat links their species-specific nutrient-dependent pheromone-controlled physiology of reproduction to protection of all organized genomes from virus-driven entropy.

See: Herpesviruses shape tumour microenvironment through exosomal transfer of viral microRNAs (with my emphasis)

This flow of genetic information results in a metabolic shift toward aerobic glycolysis in the surrounding non-infected cells. Importantly, this exosome-mediated metabolic reprogramming of neighbouring cells supports the growth of infected cells, thereby contributing to viral fitness. Finally, our data show that this miRNA transfer-based regulation of cell metabolism is a general mechanism used by other herpesviruses, such as EBV, as well as for the transfer of non-viral onco-miRs. This exosome-based crosstalk provides viruses with a mechanism for non-infectious transfer of genetic material without production of new viral particles, which might expose them to the immune system. We suggest that viruses and cancer cells use this mechanism to shape a specific metabolic niche that will contribute to their fitness.

The flow of genetic information must link energy as information to all biologically based cause and effect via the physiology of pheromone-controlled reproduction in all living genera.

See also: RNA on the brain: emerging layers of post-transcriptional regulation in cerebral cortex development

New technological advances raise the potential for an increasingly sophisticated understanding of post-transcriptional control in the developing neocortex. Many RNA-binding factors are also implicated in neurodevelopmental diseases of the cortex. Therefore, elucidating how RBPs and miRs converge to influence mRNA expression in progenitors and neurons will give valuable insights into mechanisms of cortical development and disease.

The fact that food energy-dependent RNA-binding factors and the de novo creation of microRNAs in plants and animals prevent the virus-driven degradation of messenger RNA, which links mutations to all pathology has been established in the context of nearly 64,000 published works that are currently indexed on PubMed.

See: microRNA

See also: Chromogenic In Situ Hybridization Methods for microRNA Biomarker Monitoring of Drug Safety and Efficacy

Disease research and treatment development have turned to the impact and utility of microRNA. The dynamic and highly specific expression of these molecular regulators can be used to predict and monitor disease progression as well as therapeutic treatment efficacy and safety, thus aiding decisions in patient care. In situ hybridization (ISH) of biopsy material has become a routine clinical pathology procedure for monitoring gene structure, expression, and sample characterization. For ribonucleic acid (RNA), determining cell source and level of expression of these biomarkers gives insight into the cellular function and physiopathology. Identification and monitoring of microRNA biomarkers are made possible through locked nucleic acid (LNA)™-based detection probes.

My comment to the Exiqon FB page:

Energy-dependent changes in the microRNA/messenger RNA balance have now been linked to healthy longevity and all extant biodiversity via the physiology of pheromone-controlled reproduction in all living genera. “RNA on the brain: emerging layers of post-transcriptional regulation in cerebral cortex development.” https://www.ncbi.nlm.nih.gov/pubmed/28837264

The virus-driven degradation of messenger RNA has been linked from mutations to all pathology. See for example: “Herpesviruses shape tumour microenvironment through exosomal transfer of viral microRNAs.” https://www.ncbi.nlm.nih.gov/pubmed/28837697

Exiqon’s advances in detection of changes in the microRNA/messenger RNA balance has linked electrons to ecosystems via amino acid substitutions in all living genera. The company seems well-prepared to eliminate most, if not all theories, about the differences between healthy longevity and virus-driven pathology.

Most theorists have paid no attention whatsoever to the advances in technology. That fact attests to the difference between serious scientists and pseudoscientists. Pseudoscientists have been stuck with their theories.

For examples of those who have been stuck with their theories see: Host-derived creation of all pathology (2) in prep

 For a brief expose on the difference between mutations and amino acid substitutions, see also: “In order to make peptides, you start with amino acids obviously.” from:How Peptides Are Made

Cytosis

Your indifference is killing you and others (4)

Summary:
I suspect that Subatomic, like Cytosis, will help link atoms to ecosystems via my model of nutritional epigenetics and the pheromone-controlled visual perception of mass and energy, which has been linked from the sense of smell in bacteria across the space time continuum via olfaction.
From 7 years ago.
Published 7 years ago on 15 Aug 2010 by James V. Kohl of Pheromones.com, RNA-mediated.com, and Autophagy.pro
Kohl is the co-author of “The Scent of Eros” and he is the creator of: The Scent of Eros and The Mind’s Eyes human pheromone-enhanced products. This is an excerpt from his presentation at the 2010 Annual Gathering of Mensa (i.e., the “high IQ” society).

Pheromones have since been linked from suicide prevention to the prevention of all neurodegenerative diseases and the prevention of all other pathology, which includes cancer prevention.

See for examples:

 
 
 

Everything known to serious scientists about biophysically constrained energy-dependent RNA-mediated cell type differentiation and viral latency in the context of quantum physics and the space time continuum will soon be known to everyone older than 10 who plays the game “Cytosis” and the game “Subatomic.”

In less than 3 hours of play-time, it will become clear that the virus-driven theft of quantized energy causes the degradation of messenger RNA, which links mutations to all pathology.

Suzan Mazur: What is your definition of life?

Eviatar Nevo: Our understanding of origin of life is very slim. . . . [First] life didn’t fossilize. The best we can know about origin of life may be from viruses we are looking at. They could have been at the origin of life before they parasitized it, or became symbionts in prokaryotes and eukaryotes. . . .

Young earth creationist / scientists put the virus-driven parasitism of life into the perspective of perfect creation in: Viral Genome Junk Is Bunk

“The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6

The fact that viruses got their genes from their hosts became clear in the context of what is known about natural selection for energy-dependent codon optimality.

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

Revealing the determinants of codon usage bias is central to the understanding of factors governing viral evolution. Herein, we report the results of a survey of codon usage bias in a wide range of genetically and ecologically diverse human RNA viruses. This analysis showed that the overall extent of codon usage bias in RNA viruses is low and that there is little variation in bias between genes. Furthermore, the strong correlation between base and dinucleotide composition and codon usage bias suggested that mutation pressure rather than natural (translational) selection is the most important determinant of the codon bias observed. However, we also detected correlations between codon usage bias and some characteristics of viral genome structure and ecology, with increased bias in segmented and aerosol-transmitted viruses and decreased bias in vector-borne viruses. This suggests that translational selection may also have some influence in shaping codon usage bias.

Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

Synopsis

Embedded Image

In addition to spelling out protein sequence, mRNA codon triplets contain translation‐dependent regulatory information that influences transcript stability and contributes to controlled turnover of maternal mRNAs in frogs, mice, and flies.

  • Codon optimality forms a regulatory code within the genetic code that controls mRNA stability and translation efficiency.

  • Codon composition shapes maternal mRNA clearance during the maternal‐to‐zygotic transition in zebrafish, frog, mouse, and fly in a translation‐dependent manner.

  • Amino acid composition also influences mRNA stability in vertebrates.

  • Codon optimality correlates with codon bias, suggesting that codon optimality shapes steady‐state mRNA levels in homeostasis.

Excerpt:

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

Reported as: A code within a code: how codons influence mRNA stability

The sequence changes in the amino acid optimality code link energy-dependent changes in base pairs to fixation of amino acid substitutions in supercoiled DNA via the physiology of reproduction. The substitutions protect all organized genome from the virus driven degradation of messenger RNA that links mutations to all pathology.

See also: Kinetic Rain | Art + Com

The level of creativity required to link physics to chemistry and the conserved molecular mechanisms that link kinetic energy and food energy to RNA-mediated cell type differentiation via quantum mechanics and amino acid substitutions is exemplified in this moving sculpture and ignored by theorists who might unknowingly attribute all the interactions to mutations and evolution.

See also: The  Critical Thinking Cafe

The group has been archived. No more comments will be added by those who lack the critical thinking skills required to link what organisms eat to the physiology of pheromone-controlled reproduction and all biodiversity.

It should be even clearer that two games “Cytosis” and “Subatomic” will put an end to any theoretical nonsense about mutations and evolution.

I suspect that Subatomic, like Cytosis, will help link atoms to ecosystems via my model of nutritional epigenetics and the pheromone-controlled visual perception of mass and energy, which has been linked from the sense of smell in bacteria across the space time continuum via olfaction.
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

Alternative splicing of pre-mRNA

Irreconcilable differences: food energy vs de novo assembly

Developmental dynamics and contemporary evolutionary psychology: status quo or irreconcilable views? Reply to Bjorklund (2003), Krebs (2003), Buss and Reeve (2003), Crawford (2003), and Tooby et Al. (2003).

The authors argue that evolutionary psychology currently offers no coherent framework for how to integrate genetic, environmental, and experiential factors into a theory of behavioral or cognitive phenotypes.

An evolutionary perspective on the systems of adaptive immunity

We propose a revival of the concept of the ‘Big Bang’ of vertebrate immunity, arguing that its origin involved a ‘difficult’ (i.e. low-probability) evolutionary transition that might have occurred only once, in a common ancestor of all vertebrates. In contrast to the original concept, we argue that the limiting innovation was not the generation of somatic diversity, but the regulatory circuitry needed for the safe operation of amplifiable immune responses with somatically acquired targeting. Regulatory complexity increased abruptly by genomic duplications at the root of the vertebrate lineage, creating a rare opportunity to establish such circuitry. We discuss the selection forces that might have acted at the origin of the transition, and in the subsequent stepwise evolution leading to the modern immune systems of extant vertebrates.

All genomic duplications in vertebrates are food energy-dependent and RNA-mediated. None occur linearly. Natural selection for energy-dependent codon optimality links changes in base pairs to the fixation of amino acid substitutions, which have been linked to all morphological and behavioral diversity by biophysically constrained viral latency.
For example, a single amino acid substitution in the gonadotropin releasing hormone decapeptide links achiral glycine in position 6 to all vertebrate cell type differentiation.
See: Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity

We demonstrate here that a protochordate GnRH receptor does not distinguish GnRHs with achiral or chiral amino acids, whereas GnRH receptors of jawed vertebrates are highly selective for GnRHs with the central achiral glycine. The poor activity of the protochordate GnRH was increased >10-fold at vertebrate receptors by replacement of the chiral amino acid with glycine or a d-amino acid, which favor the type II′ β-turn.

lncRNAs in development and disease: from functions to mechanisms

This suggests that amplification of this lncRNA alone (even without MYC) can promote tumorigenesis in breast cancer by increasing MYC expression [44], which has been proposed to occur by protein stabilization. However, it is unlikely that this is the only mechanism of action for this lncRNA as this multi-exonic transcript encoding over 20 different isoforms is itself under the control of c-MYC and harbours multiple microRNAs within its locus [45].

Define isoform: any of two or more functionally similar proteins that have a similar but not an identical amino acid sequence.
The fact that a multi-exonic transcript encoding over 20 different proteins with similar but not identical amino acid sequences links the term isoforms from wordplay via multiple food energy-dependent microRNAs and RNA-mediated amino acid substitutions that control the virus-driven degradation of messenger RNA.
The phylogenetic utility and functional constraint of microRNA flanking sequences

…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 ridiculous claim about the slow evolution of energy-dependent RNA-mediated amino acid substitutions cannot be put back into any aspect of identification in de novo assemblies of genomes. The assembly of all organized genomes is energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction.

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/

 

Cytosis

God's shrinking role in salvation (3)

Summary: I believe there is a bipartisan trend that links conservative Republicans to survival of the species, but I don’t know for sure what will happen to the liberal Democrats. And, I can’t prove it!
 
Helicity and chirality https://www.facebook.com/ed.unverricht/videos/10155506720828729/

See also: God’s shrinking role in salvation (2)
A Theory of Reality as More Than the Sum of Its Parts

“Causal emergence is a way of claiming that your agent description is really real,” said Hoel, a postdoctoral researcher at Columbia University who first proposed the idea with Larissa Albantakis and Giulio Tononi of the University of Wisconsin, Madison. “If you just say something like, ‘Oh, my atoms made me do it’ — well, that might not be true. And it might be provably not true.”

For comparison, see also: How concepts of God have developed: God’s shrinking role. God’s survival. Conclusions.

The chances of a given person belonging to God’s “true” religious institution is rather small. Some people are willing to accept this conclusion. However, most are quite certain that their faith tradition is the one that is God’s. Sadly, many find it quite difficult to extend equal human rights to members of other religions. A few are quite capable of denying human rights to, and even killing, those that they consider to be infidels in order to further what they perceive to be their God’s wishes.

See also the historical perspective on the de novo creation of energy-dependent biophysically constrained cell type differentiation in species from microbes to humans. This must be manifested in the context of helicity, chirality, autophagy, and chromosomal inheritance.

From fertilization to adult sexual behavior (1996) and The zinc spark is an inorganic signature of human egg activation (2016)

The historical perspective links the creation of sunlight to injections of adenosine for repair of damaged DNA via a “minimal gene signature.”

See for example: Cross-species gene modules emerge from a systems biology approach to osteoarthritis

Consensus modules established between species

To establish concordance and divergence in the network organization across the two species, consensus modules, modules shared by both networks, were derived from each species network using the weighted average of the two correlation matrices. In all, there were six consensus modules (C1–C6), Figs. 1b and 2b and Supplementary Figs. 4b and 5b. Functional annotation of the consensus modules included: “muscle system process” (C1), “oxidative phosphorylation” (C2), “cell cycle” (C3), “system development” (C4), and “immune system process” (C5).

For comparison, most theorists have traditionally used inferences of top-down causation to establish a consensus, which they tout in simple-minded claims that “evolution is true.” Here is a fact about the pathology of osteoarthritis.

Reported as: Cross-species links identified for osteoarthritis

OA [osteroarthritis] is the destruction of the tissues of the joints and affects more than half of individuals over 65 years old; it is the leading cause of joint pain and disability in the UK.

Animal models are often used to replicate human disease; the relevance and similarity between animal models of joint disease and human osteoarthritis has not been fully evaluated.

Researchers from the University’s Institute of Ageing and Chronic Disease, led by Senior Lecturer in Orthopaedic Sciences Dr Simon Tew, examined molecular messages produced by cartilage cells in both humans and rats.

The molecular messages, which the researchers extended across species  also link the speed of light on contact with water to the energy-dependent de novo creation of all biodiversity on Earth.

See: New research explains hydrophobicity and A single ion impacts a million water molecules

See also: The interfacial structure of water droplets in a hydrophobic liquid, which was reported as: Water is surprisingly ordered on the nanoscale
Sunlight is also surprisingly ordered at the level of quantized energy. If it was not, serious scientists would not know how to link energy dependent changes from Ångströms to ecosystems in all living genera. Thank God, the information about water ordered on the nanoscale can now be linked from the color of the rainbow to all biodiversity on Earth via the physiology of reproduction.

Their surprising results have been published in Nature Communications. They pave the way to a better understanding of atmospheric, biological and geological processes.

Nanometric-sized water drops in the air as droplets or aerosols, in industrially produced medications,  within rocks and oil fields, and within supercoiled DNA interact with changes in temperature in their hydrophobic environment. Simply put, that is the concept of how theromodynamic cycles of protein biosynthesis and degradation are biophysically constrained by ecological adaptation to stress at different temperatures in different functional structures. At room temperature, water molecules at the surface of the droplets have stronger interactions than the water molecules in a normal water surface.

Does any of the above information surprise you? If so, see Water is surprisingly ordered on the nanoscale (discussion attempt)
Avishek Ghosh This is not at all surprising enough to be published in Nature!! There have been many publications by the Bakker group since 2003/2005. In fact my own publication in JACS, PRL discusses such a phenomena at lipid membrane interfaces back in 2007/8. Wonder what’s going on. And a fun fact, Sylvie and I were colleagues for a short while in AMOLF!!

James Kohl  The problem is hydrophobicity in supercoiled DNA. It’s energy-dependent and the anti-entropic energy comes from the sun. Add the fact that cryo-EM has linked hydrogen atom transfer in DNA base pairs in solution to all biophysically constrained biodiversity via the physiology of reproduction in species from microbes to humans. The Nature Publications Group must continue to tout pseudoscientific nonsense about emergence and evolution or rehash the ridiculous concepts until all neo-Darwinian nonsense is completely trashed. Help me. See RNA-mediated.com

James Kohl Non-radiative relaxation of photoexcited chlorophylls: theoretical and experimental study

Peer-review in the United States has prevented dissemination of facts like these, which link photosynthesis from the creation of ATP to the creation of microRNAs and all biodiversity or to the virus-driven degradation of messenger RNA, which links mutations to all pathology (e.g., not to evolution).

Radek Łoziński Maybe it was energized by some mighty magician!

How else could inorganic material be linked to the creation of all biodiversity via signal transfer in bacteria and the zink spark From Fertilization to Adult Sexual Behavior.


See also: Endogenous adenosine maintains cartilage homeostasis and exogenous adenosine inhibits osteoarthritis progression.

…adenosine, acting at A2AR, is an important homeostatic regulator of chondrocytes and cartilage and adenosine repletion may represent a novel approach to treating OA (Fig. 6).

Reported as: Rodents with trouble walking reveal potential treatment approach for most common joint disease

Important to the study’s implications, adenosine is derived from adenosine triphosphate (ATP), the molecule that stores the energy needed by the body’s cells until they break it up to use it. Scientists have known that both inflammation and aging lead to diminished ATP production (and so lower adenosine levels) in chondrocytes. Until now, they had not linked diminished adenosine levels to osteoarthritis, the commonplace, “wear-and-tear” form of arthritis.
The underlying gene regulatory mechanisms in osteoarthritis link injections of adenosine from A-to-I RNA editing via what is known about femtosecond blasts of UV light, which have been linked to the repair of DNA.  Simply put, the injecting adenosine is like an injection of virucidal ultraviolet light.

These consensus modules (in reverse order) support the link from the anti-entropic virucidal energy of sunlight to:

“muscle system process” (C1),

“oxidative phosphorylation” (C2),

“cell cycle” (C3),

“system development” (C4),

and

“immune system process” (C5).

The energy-dependent de novo creation of the innate immune system is the only way to link the other consensus models from angstroms to ecosystems in all living genera via the functional structure of supercoiled DNA.

Others have helped to establish the consensus models by starting with the obvious link from the innate immune system in E. coli, which is a model organism of nutrient-dependent pheromone-controlled ecological adaptation. This model organism also links the weekend resurrection of the bacterial flagellum in P. fluorescens to all biophysically constrained biodiversity on Earth via the sense of smell.

But, first see for comparison: Environment determines evolutionary trajectory in a constrained phenotypic space (2017)
reported as: Genetic mutation trade-offs lead to parallel evolution
In our 1996 Hormones and Behavior review of energy-dependent RNA-mediated cell type differentiation, we included a section on molecular epigenetics and stated this:

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

One generation (~21 years) later, other serious scientists linked energy-dependent changes from angstroms to ecosystems in all living genera via what is known about biophysically constrained physiology of reproduction.
This journal report on parallel evolution preceded, but the news report on the evolutionary trajectory of genetic mutations, followed the publication of  Mechanism of transmembrane signaling by sensor histidine kinases,  which as reported as: Scientists investigate how the sense of smell works in bacteria. That is how, after-the-fact, the sense of smell in bacteria was placed back into the context of mutation-driven evolution.
This excerpt removed mutation-driven evolution from any further consideration by serious scientists.

…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.

Serious scientists can compare the pseudoscientific nonsense about mutations and evolution to the accurate representation of how the sense of smell in bacteria links nutrient-dependent pheromone-controlled ecological adaptations from microbes to humans via signal transmission and an inorganic signature of human egg activation.
You can learn more about the energy-dependent spark that links the inorganic signature of gene activation in the human egg to adult sexual behavior in all living genera by learning more about cell biology,
You can learn more about the ignorance displayed by pseudoscientists who failed to learn anything about biophysically constrained energy-dependent RNA-mediated cell type differentiation by reading this article, which was co-authored by researchers I met during presentations at meetings of the Association for Chemoreception Sciences. Johan Lundström and
Mats Olsson are among the most biologically uninformed researchers I have encountered during those meetings. They demonstrate that fact by placing their recent study results into the context of neo-Darwinian nonsense.
See: Behavioral and neural correlates to multisensory detection of sick humans (subscription required)

A superadditive effect of olfactory–visual integration of sickness cues was found in the intraparietal sulcus, which was functionally connected to core areas of multisensory integration in the superior temporal sulcus and orbitofrontal cortex. Taken together, the results outline a disease-avoidance model in which neural mechanisms involved in the detection of disease cues and multisensory integration are vital parts.

If serious scientists attempt to tell people like this that God’s role in their salvation is clearly exemplified by the facts presented in Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants, the people would walk away as quickly as they have done when they passed by my poster sessions. Many other researchers have done that, and some professors have literally dragged their students away (lest they be unduly influenced by facts).
See for instance: Past 5,000 years prolific for changes to human genome

The findings confirm their earlier work suggesting that the majority of variants, including potentially harmful ones, were picked up during the past 5,000–10,000 years.

See also: Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over? (1995)

If substitutions at 10% of all nucleotide sites have selection coefficients within this range with the mean 10(-6), an average individual carries approximately 100 lethal equivalents. Some data suggest that a substantial fraction of nucleotides typical to a species may, indeed, be suboptimal. When selection acts on different mutations independently, this implies too high a mutation load. This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations. Several possible resolutions are considered, including soft selection and synergistic epistasis among very slightly deleterious mutations.

If natural selection for energy-dependent codon optimality did not link what organisms eat to the de novo creation of receptors that link the metabolism of food to the pheromones the biophysically constrain energy-dependent biodiversity via the physiology of reproduction and chromosomal inheritance, all life on Earth would have dies 100 times over.
See for example: 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!

Ultimately you must start with a link from the speed of light on contact with water and the: Hydrogen bonding ability of the amide group

See also: How Politics Is Changing Conversations Between Therapists And Patients

 
If substitutions at 10% of all nucleotide sites have selection coefficients within this range with the mean 10(-6), an average individual carries approximately 100 lethal equivalents. Some data suggest that a substantial fraction of nucleotides typical to a species may, indeed, be suboptimal. When selection acts on different mutations independently, this implies too high a mutation load. This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations. Several possible resolutions are considered, including soft selection and synergistic epistasis among very slightly deleterious mutations.
Natural selection for energy-dependent codon optimality fits into the context of Darwin’s “conditions of life,” and biophysically constrained viral latency via the pheromone-controlled physiology of reproduction. That suggests all neo-Darwinists are among the “walking dead” who may or may not be here after the forthcoming viral apocalypse. They are not prepared to meet their Maker because they believe energy emerged and then they evolved from nothing, which automagically became everything from the inorganic to the organic.
 
For comparison, I believe there is a bipartisan trend that links conservative Republicans to survival of the species, but I don’t know for sure what will happen to the liberal Democrats. And, I can’t prove it!
Cytosis

MicroRNAs light up life

Summary: Every aspect of cell type differentiation or mutation-driven pathology occurs downstream from the de novo creation of energy-dependent microRNAs. That fact should be considered in all aspects of top-down causation, which must link the sun’s energy to behavior via the physiology of reproduction and chromosomal inheritance.

On a relational theory of biological systems: a natural model for complex biological behavior (5/29/17)

In this paper, we develop a natural (empirical) relational theory for describing and modeling complex biological phenomena. We have as stepping stone the assertion: function implies structure. The theory is built upon a graph’s theory structure in which a diffusion model of information takes place, and where dynamics can be investigated in order to generate steady quantifiers. In this context, we improve a seminal work by adding a free context biological importance measure given by the Shannon’s Entropy. We also introduce the concept of biological loci. Such concept stands for closely related biological agents which plays a role as an agent by itself. Our results allow us to synthesize a natural model for complex biological behavior that takes into account: system’s update, irreducibility, and exploit of the dynamical behavior mounted over a diffusion model. The model deals in final terms to its natural capacity to model plasticity and environmental changes, which has an intrinsic relationship with Shannon’s Entropy and the sort of dynamics that biological systems can display.

It’s too late for any more of this pseudoscientific nonsense about entropy and increasing organismal complexity, which is energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction.

See also: Evolution Not Only About Natural Selection but Also Improvisation, Says Israeli Scientist

Evolution, he argues, is not limited to families of plants and animals, but also occurs inside individual living things – whether they are, say, cells, plants, horses or people.

It is too late for people like him to redefine “evolution” in the context of a theory of adaptive improvisation at the level of links from energy-dependent changes in angstroms to ecosystems. All biologically informed researchers have followed the lead of the late Eshel Ben-Jacob, who realized that natural selection for energy-dependent codon optimality links what organisms eat to the physiology of their pheromone-controlled reproduction. All serious scientists have known that for more than two decades.

To start from cell type differentiation in bacteria, see: Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information (2006)

…it is widely accepted that there is no need for some unknown laws of physics to explain cellular ontogenetic development. We take a different view and in Schrödinger’s foot steps suggest that yet unknown physics principles of self-organization in open systems are missing for understanding how to assemble the cell’s component into an information-based functioning “machine”.

If your ridiculous theory does not explain how the virus-driven degradation of messenger RNA is biophysically constrained by the physiology of nutrient-dependent pheromone-controlled reproduction in species from microbes to humans, you must start learning what serious scientists have learned during the past century.

Simply put, the last universal common ancestor had the ability to find food. That fact attests to the glory of all Creation, which starts with the Creation of sunlight. The claims of some creationists can be placed into the context of a light-activated endogenous substrate in all cell types that links energy as information to endogenous RNA-interference and all biophysically constrained biodiversity via the pheromone-controlled physiology of reproduction.

Theorists can continue to claim whatever they wish. But none of their claims make sense if they cannot link energy to healthy longevity via the physiology of reproduction and also link the virus-driven degradation of messenger RNA from mutations to all pathology.

Serious scientists have done that. See: 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.

Disease Awareness Months Work, Even If You Don’t Wear The Ribbon

For the people living with an illness that may lack effective treatments, much less a cure, even small increases in awareness are valuable. And that’s true whether or not anybody remembers what disease they’re supposed to be thinking about this month.

Think about this. Serious scientists have published more than 61,000 papers that link nutrient energy-dependent microRNAs to healthy longevity and virus-driven energy theft from the degradation of messenger RNA to mutations and all pathology. A PubMed search for “microRNA” and the name of the pathology you would like to cure will show you that the cure is always energy-dependent biophysically constrained viral latency.
autism
Myasthenia gravis
Congenital Cytomegalovirus

See for comparison: