protein folding chemistry Archives

MicroRNA-mediated denuclearization

April 21, 2018

by James Kohl with No Comment Adaptations biophotonics Diseases & Disorders Ecology microRNA editing Model Organisms RNA Directed RNA–Mediated Epigenetic Heredity Subatomic Variations What's in the News

Kim Says North Korea Is Stopping Nuclear and Missile Tests

Early today, he said the country was stopping nuclear and missile tests and shuttering its atomic test site, which has “done its job.” Those concessions were long demanded by the U.S., lifting hopes that next Friday’s planned summit between Kim and South Korean President Moon Jae-in will be conducted in good faith.

Added Perspective
Emergence of Human G2P[4] Rotaviruses in the Post-vaccination Era in South Korea: Footprints of Multiple Interspecies Re-assortment Events
Viruses do not emerge. They adapt in the context of proton gradients and microRNA-mediated changesin energy-dependent protein folding chemistry. The food energy-dependent fixation of RNA-mediated amino acid substitutions links interspecies re-assortment events to healthy longevity.
See for comparison: A Single Amino Acid at the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses
The ability of researchers in South Korea to create genetically modified viruses with increased pathogenicity links quantum physics from virus-driven energy theft to the degradation of messenger RNA and extinctions in many different populations of extinct organisms during the past 6,000 years.
See: Virus-mediated archaeal hecatomb in the deep seafloor

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

The population of North Korea could have been the next to be decimated by a genetically engineered virus if Kim Jong Un had not agreed to denuclearization.
See also: Reappraising the human mitochondrial DNA [mtDNA] recombination dogma

…studies dealing with human variation and evolution have assumed that human mtDNA does not recombine and should be considered as pathological or very infrequent. Using both direct and indirect approaches, we provide consistent evidence of mtDNA recombination in humans.

Food energy-dependent mtDNA recombination in humans appears to protect all organized genomes in all extant human populations. mtDNA recombination may be the best protection from extinction that any species already has. Given what is known to serious scientists about cell type differentiation, the link from light-activated endogenous substrates and the physiology of reproduction in all living genera causes many people to ridicule the assumptions still touted in the context of theories invented by neo-Darwinian theorists.
See also: Mechanisms of Recombination conference

Your indifference is killing you and others

August 16, 2017

by James Kohl with No Comment Adaptations biophotonics Cytosis Diseases & Disorders Ecology Human Pheromones Light Energy Model Organisms Nutrigenomics Physics RNA Directed RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression Variations

Summary: Coherence-inducing mechanisms is double-speak for mechanisms that are nutrient-dependent and pheromone-controlled.
Feedback loops link odor and pheromone signaling with reproduction has been presented in double-speak as Looplessness in networks is linked to trophic coherence

We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

Feedback loops link the sun’s anti-entropic virucidal energy from the food that organisms eat to the physiology of pheromone-controlled reproduction in all living genera. The virucidal effect of ultraviolet light biophysically constrains viral latency. Energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA are fixed in organized genomes via the physiology of reproduction and supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.
Coherence-inducing mechanisms is double-speak for nutrient-dependent and pheromone-controlled in the context of Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
Despite the validity of the model, it has not been accepted by neo-Darwinian theorists or “Big Bang” cosmologists. Ridiculous beliefs about emergence and evolution are pervasive and the pseudoscientific nonsense of their theories leads to claims about coherence-inducing mechanisms.
That is why I changed the FB page description at RNA-mediated after a series of posts (see below).

It took 20 years for others to realize that all life on Earth is food energy-dependent. Now, most people are indifferent to that fact. They refuse to learn anything about where the food energy comes from.

Differences in the energy of photons have been linked to quantized energy-dependent fixation of RNA-mediated amino acid substitutions. The substitutions biophysically constrain supercoiled DNA via the physiology of pheromone-controlled reproduction.

Virus-driven energy theft links the degradation of messenger RNA to mutations via amino acid substitutions in viruses. The substitutions in the viruses have been linked to all pathology via changes in the energy-dependent microRNA/messenger RNA balance.

For comparison, the pseudoscientific nonsense of neo-Darwinian theories links mutations from natural selection to the evolution of new species. In reality, light energy is quantized information. The information links physics, chemistry, and molecular epigenetics from the speed of light on contact with water and hydrogen-atom transfer in DNA base pairs in solution to learning, memory, and behavior via RNA-mediated events such as the energy-dependent creation of enzymes and the the de novo creation of G protein-coupled receptors such as olfactory receptor genes.

Top-down causation and de novo gene creation are exemplified by energy-dependent differences in the microRNA/messenger RNA balance that link natural selection for codon optimality to amino acid substitutions that link the physiology of reproduction to supercoiled DNA. Supercoiled DNA protects all organized genomes from virus-driven energy theft. That fact supports the beliefs of young earth creationists, which may be the only existing basis for discussion of quantum biology and refutations of neo-Darwinian theories that have linked olfaction to quantum souls. If there is another basis for the link from quantum physics to quantum souls, no one has detailed in in the context of top-down causation, which must include information about the creation of genes.

Most people seem unwilling to accept experimental evidence that attests to how genes are created or information that shows how virus-driven energy theft is linked to all pathology. Discussion of the energy-dependent paradigm shift would lead others away from pseudoscientific nonsense about emergence and/or beneficial mutations and evolution.

Only via discussion of facts about the paradigm shift will others learn what is currently known to serious scientists about the biophysically constrained nutrient energy-dependent chemistry of RNA-methylation and all biophysically constrained RNA-mediated protein folding chemistry. Simply put, the protein folding chemistry must be linked to all biodiversity by the physiology of energy-dependent pheromone-controlled reproduction in all living genera.

Your indifference to that fact is killing people.

See for comparison: Looplessness in networks is linked to trophic coherence (May 16, 2017)

Our theory correctly classifies a variety of networks-including those derived from genes, metabolites, species, neurons, words, computers, and trading nations-into two distinct regimes of high and low feedback and provides a null model to gauge the significance of related magnitudes. Because trophic coherence suppresses feedback, whereas an absence of feedback alone does not lead to coherence, our work suggests that the reasons for “looplessness” in nature should be sought in coherence-inducing mechanisms.

Reported August 14, 2017 as Trophic coherence explains why networks have few feedback loops and high stability

The researchers are also investigating whether negentropy – the opposite of entropy, and in which a physical, thermodynamic or biological process creates order – are affected by trophic coherence. “The modern concept of entropy,” Johnson points out, “comes from statistical physics and is a property of ensembles, as described above – that is, the entropy of an ensemble is simply a function of the number of elements it contains.” Moreover, he adds, graph ensemble entropy has proven to be a powerful tool for understanding various network properties. We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

See for comparison: Feedback loops link odor and pheromone signaling with reproduction

These studies also indicate that GnRH neurons are likely to influence numerous brain functions. They appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions (Badr and Pelletier, 1987; Jennes et al., 1988; Jennes et al., 1997). BL+ neurons likely to receive synaptic input from GnRH neurons were seen in areas associated with numerous different functions, including odor and pheromone processing, sexual behavior, appetite, defensive behavior, motor programs, and the relay of information to higher cortical areas. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

See my posts on Discovering Vismodegib in the Fight Against Skin Cancer: The First Approved Inhibitor of the Hedgehog Pathway
No one I know is likely to understand this link from the anti-entropic virucidal energy of sunlight to prevention of all pathology because they must first understand the fact that proteins do not create themselves. There is no need for this inhibitor of the Hedgehog pathway or inhibition of any other pathway if cancer is prevented. But most people are not willing to learn about prevention because they think they can rely on medical practitioners to effectively treat their diseases. Do you think that your physician knows anything about light scattering characterization of glycoproteins and their interactions with other proteins and antibodies?
Absolute Characterization of Glycoproteins and their Interactions with Proteins and Antibodies by Light Scattering
Light scattering can now be linked to the characterization of glycoproteins and their immune system interactions in all species on Earth. That suggests the speed of light on contact with water links energy as information to the de novo creation of the glycoproteins,
If so, the physiology of reproduction links pheromones to biophysical constraints on the creation of more glycoproteins in the context of morphological and behavioral differences in species from microbes to humans. That suggests the refutation of neo-Darwinism is complete, since the virus-driven degradation of messenger RNA has been linked to all pathology in bacteria that become archaea before virus-driven energy theft causes them to become L-forms.
Simply put, Carl Woese was wrong. There is only one domain of life and virus-driven energy theft is what destroys all life on Earth.

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 does that tell you about the late Carl Woese and/or Eugene Koonin?

Feng Zhang refutes theistic evolution

April 20, 2017

by James Kohl with One Comment Adaptations Alternative Splicings Diseases & Disorders Ecology Human Pheromones Model Organisms Neuronal Plasticity RNA Directed RNA methylation RNA-directed DNA methylation RNA-mediated gene silencing Variations

Nucleic acid detection with CRISPR-Cas13a/C2c2
My summary: Their ability to detect single base differences links differences in the energy of photons to the light-induced de novo creation of RNA and to RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all living genera. Any claims about mutations and evolution have already been replaced by what serious scientists have learned about natural selection for energy-dependent codon optimality and the pheromone-controlled physiology of reproduction, which biophysically constrains all biodiversity in the context of chromosomal inheritance. If Feng Zhang or anyone else tries to put nucleic acid detection back into the context of neo-Darwinian evolution, they will be asked “Where did the energy in a hydrogen atom come from?” Young earth creationists would then eat the theorists for lunch, if the theorists did not always leave such a bad taste in the mouths of serious scientists.
Reported as: A new transformative CRISPR test targets RNA (rather than DNA) as a rapid, inexpensive, highly sensitive diagnostic tool

In a study published today in Science, Broad institute members Feng Zhang, Jim Collins, Deb Hung, Aviv Regev, and Pardis Sabeti describe how this RNA-targeting CRISPR enzyme was harnessed as a highly sensitive detector – able to indicate the presence of as little as a single molecule of a target RNA or DNA molecule. Co-first authors Omar Abudayyeh and Jonathan Gootenberg, graduate students at MIT and Harvard, respectively, dubbed the new tool SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing); this technology could one day be used to respond to viral and bacterial outbreaks, monitor antibiotic resistance, and detect cancer.

The scientists demonstrate the method’s versatility on a range of applications, including:

Detecting the presence of Zika virus in patient blood or urine samples within hours;
Distinguishing between the genetic sequences of African and American strains of Zika virus;
Discriminating specific types of bacteria, such as E. coli;
Detecting antibiotic resistance genes;
Identifying cancerous mutations in simulated cell-free DNA fragments; and
Rapidly reading human genetic information, such as risk of heart disease, from a saliva sample.

CONCLUSIONS: Our data support the hypothesis that exosomal transfer of miR-181b from CDCs into MΦ reduces PKC δ transcript levels and underlies the cardioprotective effects of CDCs administered after reperfusion.

Exosomal transfer is nutrient energy-dependent. See also: Nutrition, microRNAs, and Human Health

miRs derived from diet and endogenous synthesis have been implicated in physiologic and pathologic conditions, including those linked with nutrition and metabolism.

It is generally assumed that genetic information passes faithfully from DNA to RNA to proteins. Proteome complexity, however, depends on a diverse set of post-transcriptional processes that modify and enrich genetic information beyond the genomic blueprint. RNA editing is one such process.

The trade-off is nutrient energy-dependent and controlled by the physiology of reproduction. Pheromones biophysically constrain the nutrient energy-dependent RNA-mediated editing of organized genomes. RNA editing is the only process that links the nutrient energy-dependent pheromone-controlled physiology of reproduction from the innate immune system of bacteria to all biophysically constrained biodiversity via CRISPR, which links the energy from protein folding chemistry to amino acid substitutions in supercoiled DNA. The supercoiled DNA protects all organized genomes from virus-driven energy theft, which links the degradation of messenger RNA from mutations to all pathology.
Attempts to obfuscate that fact, may help to clarify it. Any time anyone makes a statement link “It is generally assumed…” you can be reasonably sure that they are about to refute the assumptions of biologically uninformed theorists. In this case, starting from the detection of nucleic acids clearly starts with the energy-dependent creation of the nucleic acid, not with mutations. Links from RNA instead of DNA to cell type differences links the energy of creation to the physiology of reproduction via RNA-mediated amino acid substitutions.
See also: Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers

RNA editing, a widespread posttranscriptional mechanism, has emerged as a new player in cancer biology.

That’s a foolish statement. Facts about RNA editing did not emerge. The experimentally established facts linked the control of posttranscriptional mechanisms to nearly 60,000 articles that detail how energy-dependent changes in microRNAs effect cell type differentiation and healthy longevity. The same articles help to clearly link virus-driven energy theft from the degradation of messenger RNA to mutations and all pathology.
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. 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.

Filtering light through a prism to identify tissue type

Synthetic RNA-based switches

April 12, 2017

by James Kohl with No Comment Adaptations base editing Diseases & Disorders Ecology RNA Directed RNA editing

Synthetic RNA-based switches for mammalian gene expression control Current Opinion in Biotechnology, Volume 48, December 2017, Pages 54–60

If you wait until December, 2017 to see this article in print, you will probably be among the last of those to have missed a two decades-old paradigm shift.

The fact that these researchers created synthetic RNA-based switches attests to the fact that natural selection for energy-dependent codon optimality links what organisms eat to energy-dependent RNA-mediated amino acid substitutions. The substitutions help to ensure protein folding chemistry links the amino acids to the functional structure of supercoiled DNA in all organized genomes via the physiology of pheromone-controlled reproduction.

Minimally, what is known to all serious scientists about the biophysically constrained protein folding chemistry links Darwin’s “conditions of life” to the energy-dependent creation of all morphological and behavioral phenotypes.

For review, see: ‘Minimal’ cell raises stakes in race to harness synthetic life: Craig Venter’s creation comes as CRISPR gene-editing methods provide alternative ways to tinker with life’s building blocks.

“This old Richard Feynman quote, ‘what I cannot create, I do not understand’, this principle is now served,” says Martin Fussenegger, a synthetic biologist at the Swiss Federal Institute of Technology (ETH) in Zurich, Switzerland. “You can add in genes and see what happens.”

With nearly all of its nutrients supplied through growth media, syn3.0’s essential genes tend to be those involved in cellular chores such as making proteins, copying DNA and building cellular membranes. Astoundingly, Venter says that his team could not identify the function of 149 of the genes in syn3.0’s genome, many of which are found in other life forms, including humans. “We don’t know about a third of essential life, and we’re trying to sort that out now,” he says.

This has blown Fussenegger away. “We’ve sequenced everything on this planet, and we still don’t know 149 genes that are most essential for life!” he says. “This is the coolest thing I want to know.”

It should have long ago become obvious that the genes most essential to life are the genes that link the energy-dependent de novo creation of G protein-coupled receptors to ATP-dependent RNA synthesis.

The current issue of Discover Magazine features “Heroes of Science” without mention of any who helped to link the anti-entropic virucidal energy of ultraviolet light from endogenous RNA interference to all biodiversity via the physiology of reproduction.

If not for the mention of Rosalind Franklin, whose work with the tobacco mosaic virus caused her to doubt the ridiculous representation of the static DNA double helix, subscribers would never know that
1) Thomas Hunt Morgan,
2) Ernest Schrodinger,
3) Bruce McEwen,
and
4) Theodosius Dobzhansky
linked sunlight and ATP from the biosynthesis of RNA to the amino acid substitutions in supercoiled DNA that link chromosomal inheritance from the physiology of reproduction to all biophysically constrained biologically-based cause and effect in all living genera.
Overall, Discover Magazine’s “Heroes of Science” are biologically uninformed theorists who failed to link the epigenetic landscape to the physical landscape of supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy in the context of Darwin’s “conditions of life.”

In the same issue, an article on learning in plants links multipupose plant sensors to all biodiversity via RNA methylation and the physiology of reproduction in species from microbes to humans. See for instance: Multipurpose plant sensors startle scientists

Protein-protein interactions are energy-dependent and RNA-mediated.

Amino acid modification FA_Epigenetics_Table1

Thinking about energy is not radical re-thinking

March 19, 2017

by James Kohl with No Comment Adaptations biophotonics Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed 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 Variations

The brain: a radical rethink is needed to understand it

…Optogenetics, a technique that uses genetic modification of neurons so that their electrical activity can be controlled with light pulses – can help us to explore their specific contribution to brain function.

Optogenetics links the speed of light on contact with water to what is known about all energy-dependent cell type differentiation in all individuals of all living genera. Serious scientists, for example, have linked angstroms to ecosystems in all living genera because they know that brain function is experience-dependent and RNA-mediated.

Even in organisms that have no brain, cell type differentiation occurs in the context of biophysically constrained RNA-mediated protein folding chemistry. All chemistry is energy-dependent quantum chemistry and chemistry links quantum physics from the de novo creation of G protein-coupled receptors to the biological basis for all biodiversity on Earth.
For example, food odors link natural selection for energy-dependent codon optimality to the metabolism of food to pheromones. Biophysically constrained RNA-mediated feedback loops link the metabolism of food from the physiology of reproduction to supercoiled DNA, which protects all organized genomes from virus-driven entropy.
Simply put, quantum physics, quantum chemistry, and energy-dependent quantum biology prevent virus-driven entropy, which links everything known to serious scientists about niche construction to consciousness.
The Penrose Institute was established to link that fact to human consciousness in the context of everything known about cell type differentiation to everyone since the time that Lewis Thomas began making claims olfaction and smell.
A Fear of Pheromones (1971)
On Smell (1980)

The act of smelling is remarkably like the act of thinking itself.

Magnussen's "Faith fools" keep the faith

March 16, 2017

by James Kohl with No Comment Adaptations Diseases & Disorders Ecology Human Pheromones Model Organisms RNA Directed RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Variations

The biophysical constraints are linked across species via the need to ecologically adapt to virus-driven energy theft.
See: MicroRNAs in the Host Response to Viral Infections of Veterinary Importance
Nutrient stress and social stress effect pheromone production at the level of quantum physics, which is why most people cannot grasp the facts that serious scientists have linked across species to the need of individuals to eat and the need for species to reproduce in the context of their nutrient-dependent pheromone-controlled physiology of reproduction.
See for example this attempt at discussion about the ridiculous claims of Richard Dawkins.
Magnus S. Magnussen is a Dawkins supporter and also appears to be a Trump-hater. Our mutual friends on Facebook include Alice Andrews, Daniel Kruger, Mark Flinn, Graham Deeth, Russel Gardner, and Elizabeth Oberzaucher. I tagged them in a post to Magnussen in hopes that they will discuss their faith in neo-Darwinian theory — if they have not already lost it.
Highlights:

“If you base medicine on science you cure people.” — Richard Dawkins

The National Microbiome Initiative and Precision Medicine Initiative are based on what is known about energy-dependent changes in the potential of hydrogen, which is called pH. What do you think medicine should be based on?

Stat Profile Prime CCS Blood Gas Analyzer from Nova Biomedical

Measuring pH links nutritional epigenetics from the innate immune system to healthy longevity via everything known about virus-driven energy theft, which links stress from the replication of viruses to all pathology via critical care testing of other blood gas analytes such as pCO2, pO2, Sodium, Potassium, Chloride, Calcium, Glucose, Lactic Acid, and Hematocrit.

Magnus S. Magnusson If you don’t want to base medicine on science then on what? Could you provide an answer?
Magnus S. Magnusson So you are what they call a troll because nobody can be that incompetent and stupid. Good bye to you. I exclude faith-fools from my interactions.

“All about the base” came from the group that published this, because the “Structural Diversity of Supercoiled DNA” is energy-dependent and biophysically constrained by the physiology of reproduction.

Magnus S. Magnusson So you mean that medicine should be based on better science than is now available. That is not a contradiction relative to Dawkins position. BTW the video is the stupidest I have seen, only to be expected from faith-fools.

Faith fools?

See for comparison: Fossil or inorganic structure? Scientists dig into early life forms

By addition of just one other ubiquitous chemical—calcium or barium salt—this water produces tiny structures, such as tubes, helices, and worm-like objects that are reminiscent of the shapes of primitive organisms. The water also generates complex mineral structures that are similar to nacre—the shiny substance of sea shells.

The similarities between actual fossils and these inorganic structures go beyond appearance and extend to their chemical nature. This will make it even more complicated for scientists examining early evidence of life on Earth.

Experimental evidence from chemistry eliminated the pseudoscientific nonsense about billions of years of mutation-driven evolution, which theorists claimed was manifested in the biodiversity of bacteria via comparison to the Long-Term Evolution experiments of Richard Lenski’s group..
That means pseudoscientists must continue to avoid linking the weekend resurrection of the bacterial flagellum in Pseudomonas fluorescens from quorum sensing to biophysically constrained viral latency via the nutrient-dependent pheromone-controlled ecological adaptations manifested in the supercoiled DNA of all living genera. Supercoiled DNA links energy-dependent endogenous RNA interference from protein folding chemistry to all biodiversity on Earth via the physiology of reproduction.
When someone like Magnus S. Magnusson claims that Zechiedrich lab researchers who linked supercoiled DNA to all biodiversity are “faith fools,” his bias is clear. See also: Combating Evolution to Fight Disease.
Would Magnus S. Magnusson also claim that the researchers from the Rosenberg lab are faith fools?

Energy-dependent allelic imbalances, viruses, and pathology

February 28, 2017

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy Diseases & Disorders Ecology Human Pheromones Model Organisms RNA Directed RNA-directed DNA methylation RNA-mediated gene silencing Variations

Energy as information and constrained endogenous RNA interference poster presentation February 15, 2017

KRAS Allelic Imbalance Enhances Fitness and Modulates MAP Kinase Dependence in Cancer February 23, 2017

These studies demonstrate that serial genetic changes at the Kras/KRAS locus are frequent in cancer and modulate competitive fitness and MEK dependency.

Reported as: Genetic ‘balance’ may influence response to cancer treatment

Taylor developed mathematical algorithms and software to analyze relative dosage of mutant KRAS and normal KRAS in tumor cells from biopsy samples, which contain many normal cells as well as cancerous cells.

The energy-dependent balance of genes is RNA-mediated and controlled by supercoiled DNA, which links amino acid substitutions that stabilize all organized genomes from chirality to autophagy. In this study, they claim facts are “deeply understood” about the most common mutation in cancer and how oncogenic amino acid substitutions perturb activation of the molecular switch that enables protein folding chemistry.
Their understanding of biophysically constrained energy-dependent RNA-mediated protein folding chemistry fails to differentiate between virus-driven energy theft, which causes all mutations, and nutrient energy-dependent fixation of RNA-mediated amino acid substitutions in supercoiled DNA, which are linked from chromosomal inheritance to the transgenerational epigenetic inheritance of healthy longevity in all genera.
Simply put, the authors appear to be theorists using algorithms. There is no indication that they are serious scientists like those who have already linked energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of energy-dependent pheromone-controlled reproduction.
See also: Genome-wide identification of splicing QTLs in the human brain and their enrichment among schizophrenia-associated loci
Reported as: Changes in RNA splicing: a new mechanism for genetic risk in schizophrenia
Re: a “new” mechanism: See: From Fertilization to Adult Sexual Behavior

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

The authors who report on splicing QTLs in the human brain make it appear that the molecular mechanisms we detailed in our section on molecular epigenetics are something new. Only serious scientists know that why pseudoscientists continue to link energy-dependent changes in the microRNAs/messenger RNA balance to splicing QTLs. For example, pseudoscientists do not want more people to learn that energy-dependent alternative splicings of pre-mRNA (aka microRNAs) link

the sun’s anti-entropic virucidal effects from
changes in base pairs to the
single nucleotide polymorphisms that link
hydrogen-atom transfer in DNA base pairs in solution from
chirality to
autophagy
and all biophysically constrained RNA-mediated cell type differentiation in all living genera
via the physiology of reproduction.

This article, from the “Nature Publications Group” is another attempt to ignore the established facts about protein folding chemistry and place the facts back into the context of ridiculous theories about mutations and evolution.
See also: Alternative RNA Splicing in Evolution

…alternative splicing may be the critical source of evolutionary changes differentiating primates and humans from other creatures such as worms and flies with a similar number of genes.

Excerpt from my comment ~3 years ago:

The alternative splicings are nutrient-dependent and appear to be enabled by the experience-dependent de novo creation of olfactory receptor genes, which enable additional receptor-mediated nutrient uptake and the metabolism of nutrients to species-specific blends of pheromones that control reproduction in species from microbes to man.

See also: Microbes Conversations About Entering Brain Compartments
Energy-dependent allelic imbalances linked virus-driven energy theft from alternative RNA splicings to cancer and to schizophrenia in today’s science news. The conserved molecular mechanisms are consistently NOT linked to what is known about the nutrient-dependent pheromone-controlled physiology of reproduction and ecological adaptations in species from archaea to humans.

Theistic evolutionists fight back and lose (2)

February 27, 2017

by James Kohl with 2 Comments Adaptations Alternative Splicings biophotonics Diseases & Disorders Ecology Light Energy Model Organisms Physics RNA Directed RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Variations

For a historical perspective on the amount of ignorance theistic evolutionists and atheists have repeatedly displayed as they ignored everything known about the energy-dependent RNA-mediated de novo creation of genes, see:
The heat shock response is self-regulated at both the transcriptional and posttranscriptional levels (1982)
Thirty-five years later, there is another clear indication that theorists and atheists will never consider the fact that there must be an anti-entropic virucidal source of energy.
See for example: HSP90 Shapes the Consequences of Human Genetic Variation (2017)
Reported as: Researchers uncover a role for HSP90 in gene-environment interactions in humans

…uncovered a role for HSP90 in humans, not only as a modifier of the effects of mutations, but as a mediator of the impact of the environment on the function of mutant proteins. And these effects of HSP90 can alter the course of human diseases.

Serious scientists placed the effects of HSP90 and all other heat shock proteins into the context of thermodynamic cycles of microRNA-mediated protein biosynthesis and degradation. The fine-tuned cycles link virus-driven energy theft from the degradation of messenger RNA to all pathology via degrees of increasing genomic entropy in species from bacteria to Zika-virus infected humans.
Structural diversity of supercoiled DNA

Six decades after the elucidation of its double helical structure, DNA continues to surprise us by revealing new information. Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

The metabolic processes are energy-dependent. See also: Functional Metabolic Analysis in Live Cells

The role of metabolism in cellular and physiological processes is well established, with many diseases now linked to metabolic dysfunction or reprogramming.

Our work identifies a mechanism through which adhesion complexes regulate cellular behaviour and reveals their surprising association with the microprocessor.

Reported as Researchers find new code that makes reprogramming of cancer cells possible

with my comments, such as this one:

Oct 14, 2015

“By administering the affected miRNAs in cancer cells to restore their normal levels, we should be able to re-establish the brakes and restore normal cell function,” Dr. Anastasiadis says.
This suggests nutrient-dependent microRNAs can stop the progression of virus-proliferation that links viral microRNAs to cancer pathology.
The suggestion comes from experimental evidence of how biophysically constrained nutrient-dependent RNA-mediated cell type differentiation occurs in the absence of viral proliferation, which young earth creationists have linked to all pathology.
For comparison, evolutionary theorists would probably tell you that the progression of cancer is inevitable via ongoing processes that link accumulated mutations to pathology except when beneficial mutations are linked to the evolution of a new species.
But, I can’t really attest to what theorists might say, and don’t really care what they claim. They are biologically uninformed.

See also:

See for comparison: Dominant evolutionary theme emerges to better predict clinical outcomes for cancer (October 13, 2015)
The only thing that has emerged from any evolutionary theme is the failure to predict outcomes of treatments, which is due to the ignorance of theorists who refuse to consider experimental evidence of energy-dependent biophysically constrained biologically-based cause and effect.
See: Viral and cellular messenger RNA targets of viral microRNAs and Virus-mediated archaeal hecatomb in the deep seafloor

Theorists continue to ignore the fact that energy-dependent biophysically constrained protein-folding chemistry, which is manifested in endogenous RNA interference, is the link from sunlight to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
Sunlight, for example, is the source of anti-entropic virucidal ultraviolet (UV) light that clearly links the nutrient-dependent pheromone-controlled physiology of reproduction to the weekend resurrection of the bacterial flagellum in P. fluorescens.
See also: Energy as information and constrained endogenous RNA interference (2/15/2017)

See also: A third of Americans don’t believe in evolution (January 1, 2014)
My comment:

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

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.
That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.
See the claims of PZ Myers and his idiot minions for comparison: One crank dies, another rises to take his place

Bill Gates refutes theistic evolution (prequel)

February 23, 2017

by James Kohl with One Comment Adaptations Alternative Splicings biophotonics Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed 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 Variations What's in the News

On February 22, 2017, self-proclaimed fitness expert Amir Siddiqui, wrote: James Kohl you didn’t predict jack ____

See my predictions in the context of: Search Results for “”virus-driven energy theft””

…the world now has an emergency medical response team – which, astonishingly, it never had before.

Pardis Sabeti may still be part of the response team, and most of them still may not know how to link energy-dependent changes in SNPs from angstroms to ecosystems in all living genera via RNA-mediated hydrogen-atom energy transfer in DNA base pairs in solution.

Alternatively, the team members and others like them may be terrorists who seek to undermine the authority of the President of the United States. See: Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic

… EBOV is able to generate and fix nucleotide and amino acid variation within co-circulating viral lineages on the time-scale of individual outbreaks, including the presence of country-specific lineages, and which may ultimately produce variants with important fitness differences.

What about those fitness differences? What don’t fitness experts know about nutrient energy-dependent amino acid substitutions? Who is Amir Siddiqui, really? Is everyone who calls me a religious nut actually a terrorist, or are they simply too ignorant to learn how to link what people eat to their reproductive fitness via amino acid substitutions in supercoiled DNA?

See how this is done in species from microbes to humans: Measurements of translation initiation from all 64 codons in E. coli

Reported as: Start codons in DNA may be more numerous than previously thought
The measurements of energy-dependent translation initiation in E.coli must be linked from changes in the start codons to supercoiled DNA. That requires fixation of RNA-mediated amino acid substitutions in the context of the physiology of pheromone-controlled reproduction, which is linked to nutrient energy-dependent ecological adaptations in all living genera.
The fact that there are more energy-dependent start codons to be considered in the context of biophysically constrained protein folding chemistry became important to Bill Gates in the context of virus-driven energy theft and the forthcoming viral apocalypse.
See: Bill Gates refutes theistic evolution

Francis S. Collins refutes theistic evolution

February 15, 2017

by James Kohl with 2 Comments Adaptations Alternative Splicings Autophagy biophotonics Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed 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 Variations What's in the News

Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. — Andrew Jones, BA

Editor’s note

The 2013 review article by James Vaughn Kohl published in Socioaffective Neuroscience & Psychology and criticized in the above Letter to the Editor was subjected to standard peer review and the revised version was accepted by me after it had been accepted by both reviewers.

See for comparison: The Language of God: A Scientist Presents Evidence for Belief, by Francis S. Collins. The current director of the NIH also is a co-author of Genetic regulatory signatures underlying islet gene expression and type 2 diabetes

…T2D risk alleles that overlap with RFX footprints uniformly disrupt the RFX motifs at high-information content positions. Together, these results suggest that common regulatory variations have shaped islet TF footprints and the transcriptome and that a confluent RFX regulatory grammar plays a significant role in the genetic component of T2D predisposition.

No experimental evidence of biologically-based cause and effect suggest that any common regulatory variations has ever evolved. Let me make that fact perfectly clear in the words of the co-authors:

“Individuals who are heterozygous for a frameshift mutation in RFX6 have increased 2-h glucose levels (33). Importantly, rare autosomal recessive mutations that alter DNA-contacting amino acids in the DNA binding domain of RFX6 result in Mitchell–Riley syndrome, which is characterized by neonatal diabetes (29).

The frameshift mutation and rare autosomal recessive mutations occur outside the context of energy-dependent endogenous RNA interference (RNAi). For comparison RNA-directed DNA methylation (aka endogenous RNAi) typically links DNA-contacting amino acids to healthy longevity via the transgenerational epigenetic inheritance of morphological and behavioral phentoypes in species from microbes to humans. It is difficult to describe all the links, but it is clear that RNAi links RNA-directed DNA methylation from energy-dependent changes in chirallity to base pairs, single nucleotide polymorphisms (SNPs) and autophagy via the innate immune system.
Without any mention of how virus-driven energy theft links mutations from SNPs to pathology, Francis S. Collins and his co-authors link the rare autosomal recessive mutations to altered DNA-contacting amino acids. Apparently, they do not want to mention anything about the fact that natural selection for energy-dependent codon optimality is the link from RNA-mediated protein folding chemistry to all biophysically constrained healthy longevity. Instead, they seem willing to ignore the facts about energy-dependent fixation of RNA-mediated amino acid substitutions in cell types.
Indeed, they seem to put everything known to serious scientists into the context of the theistic evolution of pathology. Serious scientists know that nutrient energy-dependent pheromone-controlled cell type differentiation is the link from atoms to ecosystems in models of ecological adaptation.
Clearly, anyone who does not want to expose the pseudoscientific nonsense touted by neo-Darwinian theorists and theistic evolutionists should not mention “amino acid” and “mutation” in the same context. Using only the definitions of both terms in the same sentence (above) alerts all serious scientists to the fact that nutrient energy-dependent amino acid substitutions are not the same as mutations, which are caused by virus-driven energy theft.
Reported as: Diabetes in your DNA? Scientists zero in on the genetic signature of risk

…for now, it’s the first demonstration that many Type 2 diabetes-linked DNA changes have to do with the same DNA-reading molecule. Called Regulatory Factor X, or RFX, it’s a master regulator for a number of genes.

The regulation of genes is energy dependent.

“RFX is probably unable to read the misspelled words, and this disruption of regulatory grammar plays a significant role in the genetic risk of Type 2 diabetes.”

The concept of “misspelled words” is appropriate for use only in the context of pseudoscientific nonsense that fails to address facts about natural selection for energy-dependent codon optimality. Codon optimality links the speed of light on contact with water to biophysically constrained RNA-medidated cell type differentiation in all living genera.

They characterized differences not just in DNA sequences, but also in the way DNA was packaged and modified by epigenetic factors, and the levels of gene expression products that indicated how often the genes had been read and transcribed.

Epigenetically-effected reading and transcription is energy dependent and biophysically constrained via the speed of light and hydrogen-atom transfer in DNA base pairs in solution such as seawater and blood. Serious scientists noticed that pattern and linked virus-driven energy theft from pathology in bacteria to archaea and from the transgenerational epigenetic inheritance of Zika-virus damaged DNA in human infants. The craniofacial morphology and brain development of infected human infants clearly links energy-dependent fixation of amino acids to the morphological and behavioral phenotypes of all living genera.
See: Nothing in Biology Makes Any Sense Except in the Light of Evolution

E. Margoliash, W. M. Fitch, and others have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.

Facts about nutrient energy-dependent codon optimality also are known to be refutations of neo-Darwinian pseudoscientific nonsense because codon optimality links Darwin’s “conditions of life” to the physiology of reproduction in all living genera.
See: Codon optimality controls differential mRNA translation during amino acid starvation and Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See for comparison: Epigenetic Editing of Ascl1 Gene in Neural Stem Cells by Optogenetics

Each DNA change might alter this binding in a different way, leading to a slightly different effect on Type 2 diabetes risk or blood sugar regulation. But the common factor for many of these changes was its effect on the area where RFX is predicted to bind, in the cells of pancreatic islets.

So, says Parker, this shows how the genome – the actual sequence of DNA—can influence the epigenome, or the factors that influence gene expression.

The sequence of DNA cannot influence the epigenome before the energy-dependent sequence has been created via natural selection for codon optimality. That is why epigenetically-effected nutrient-dependent pheromone-controlled energy-dependent changes in supercoiled DNA were linked from the weekend resurrection of the bacterial flagellum in Pseudomonas fluorescens to all biodiversity in all living genera via the conserved molecular mechanisms that link light energy-induced changes in microRNAs to all biodiversity.
See also: Optokinetically encoded nanoprobe-based multiplexing strategy for microRNA profiling
Programmable artificial phototactic microswimmer

For active drug delivery, the nanomotor should be able to orient towards specific chemical signals, such as those demonstrated in chemotaxis21–25 and pH taxis26.

…assuming that it is possible to tune the preferred pH of bioactuators by genetic engineering, these biohybrid microsystems could potentially be applied to sense the pH gradient induced by cancerous cells in stagnant fluids inside human body and realize targeted drug delivery.

If naturally occurring chemotaxis could not readily be linked from pH-taxis and phototaxis to natural selection for codon optimaility and supercoiled DNA, light energy as information could not be linked to communication between the microscopic and the macroscopic world.
Light Could Propel Nanorobots on a “Fantastic Voyage” Through the Human Body

“Light is a more effective option to communicate between the microscopic world and the macroscopic world,” said Tang.

The fact that the energy-dependent virucidal effects of sunlight have been linked to the weekend resurrection of the bacterial flagellum in an organism that fluoresces on exposure to UV light was placed into the context of claims about two amino acid substitutions that were reported as if they were mutations.
Summary: Francis S. Collins, current NIH director, is a theistic evolutionist. He should not use his position to tout the pseudoscientific nonsense of evolution. He is supposed to link experimental evidence of biologically-based facts to healthy longevity or to pathology.
See also: United states health care reform: Progress to date and next steps

All of the individuals who assisted with the preparation of the manuscript are employed by the Executive Office of the President.

Former President Barrack Obama should not have used his position or his employees to mislead the voters in the United States of America. He correctly stated that “…partisanship and special interest opposition remain…,” which ensured that “…experience with the Affordable Care Act…” would demonstrate “…that positive change is achievable on some of the nation’s most complex challenges.” That claim was placed into the context of misrepresentations made by ~50% of people who are biologically uninformed theorists and/or those who are atheists. Clearly there is overlap among those groups of people. Hopefully, others will see why. They’ve been taught to believe in theistic evolution or nothing.
Experimental evidence of biologically-based cause and effect refutes theistic evolution by linking virus-driven energy theft to all pathology in all living genera. In the context of Genetic regulatory signatures underlying islet gene expression and type 2 diabetes, Francis S. Collins revealed either his ignorance or his treachery.
The article links the nutrient energy-dependent pheromone-controlled physiology of reproduction to the weekend resurrection of the bacterial flagellum in P. fluorescens via RNA synthesis, not mutations.
Virus-driven energy theft influences energy-dependent RNA-mediated gene expression, and the energy theft is clearly linked to mutations. See for example: 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.

Scent of Eros

Posts tagged: protein folding chemistry