genomic entropy Archives

Until death: Virus-driven failure of multisensory integration (1)

October 5, 2017

by James Kohl with No Comment Adaptations Cytosis Diseases & Disorders Ecology Human Pheromones Model Organisms RNA Directed RNA-directed DNA methylation Variations

Martha McClintock‘s works inspired my works. Publication of “The Scent of Eros: Mysteries of Odor Human Sexualty” (1995) led Denise Chen to study olfaction and pheromones. See for example: Encoding human sexual chemosensory cues in the orbitofrontal and fusiform cortices. Her student, Wen Zhou, returned to China and she is the senior author of Olfaction Warps Visual Time Perception.
Since 1995, all accurate representations of how foraging behavior links food odors and pheromones from feedback loops to sexual reproduction and the increasing complexity of all biophysically constrained biodiversity can be viewed in the context of what others have reported in examples like this.
See Mating Pheromone in Cryptococcus neoformans Is Regulated by a Transcriptional/Degradative “Futile” Cycle.
The fungus Cryptococcus neoformans is currently the fourth greatest cause of infectious death in regions of Africa and undergoes mating in phytonutrient-rich environments to create spores with infectious potential.
See also: Cryptococcosis Workup
My summary: The food energy-dependent pheromone-controlled physiology of reproduction of this organism is linked from protein biosynthesis and degradation to depressed concentration of glucose in cerebral spinal fluid (CSF), and to increased CSF protein concentrations. That fact is a clear indicator of how the virus-driven degradation of messenger RNA is linked to all pathology. The virus-driven changes in the level of glucose compared to protein concentration are prevented by supercoiled DNA. RNA-mediated amino acid substitutions in organized genomes link the energy-dependent creation of enzymes, hormones, and receptors to healthy longevity. Food odors and pheromones are linked to feedback loops and the supercoiled DNA that typically prevents the genomic entropy of organized genomes.
See: Feedback loops link odor and pheromone signaling with reproduction and Combating Evolution to Fight Disease
Every serious scientist knows there is no such thing as a “futile” cycle of food energy-dependent pheromone-controlled protein biosynthesis and degradation. Richard Feynman placed that fact into the context of the “human idiocy” exemplified by theoretical physicists. For comparison, serious scientists have linked the virus-driven degradation of messenger RNA to all pathology. If they had not already done this, the cell biology game “Cytosis” would not be delivered — as scheduled — during the month of October, 2017.

Cytosis Shipping Update

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

No one I know could have predicted that all pseudoscientists can now learn how to protect themselves from the virus-driven degradation of messenger RNA by playing: “A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!”
However, I recall the words of Martha McClintock after I supported her in a discussion among the biologically uninformed science idiots who attacked her representation of human pheromone-dependent biologically-based cause and effect (ovulatory synchrony).
See: Do human menstrual-cycle pheromones exist? (2006) and Women do not synchronize their menstrual cycles (2006)
After she reeducated the biologically uninformed members of J. Michael Baily’s “SexNet” listserver she wrote this to me:

Thanks for keeping the faith.

It will be interesting to see what happens with our antagonists who have continued to publish examples of human idiocy.
See for instance: Arousing Imaginations by David Puts

James Kohl authors the Handbook‘s final chapter, “The mind’s eyes: Human pheromones, neuroscience, and male sexual preferences.” Kohl posits innate sex differences in preferences for sexually dimorphic pheromones. These sex pheromones act as unconditioned stimuli that become associated with visual and tactile stimuli through classical conditioning. Consequently, men with innate preferences for women’s odors come to prefer the appearance and feel of women, for example. Homosexuality results from incomplete sexual differentiation of the olfactory system.

Kohl marshals supporting evidence, though it is often subject to alternative interpretation. For example, Kohl suggests that exposure to sex pheromones is “the most likely explanation for the recent finding that saliva [testosterone] levels in men increase with exposure to a young woman, but do not increase with exposure to a young man” (p. 327). Is it not likely that the young woman’s appearance raised men’s testosterone levels?

Multiple studies by independent researchers leave little doubt that odor affects human mate choice, but Kohl probably grossly overstates its importance. Why postulate that humans evolved only obligate olfactory/pheromonal preferences? Isn’t there likely to be useful information about mates that is better obtained through vision and touch than through smell? If so, selection would probably favor more reliable developmental patterns for visual and tactile preferences than classical conditioning to olfactory ones. Moreover, there is a trend among anthropoid primates, including humans, for reduced olfaction and increased reliance on vision for locating food and mates. This is witnessed in our tiny olfactory bulbs, which are relatively many times smaller than in rats; and our apparent lack of a functional vomeronasal organ, which is used by many mammals to detect pheromones.

Ironically, a seemingly fatal blow follows from a condition that Kohl presents in support of his hypothesis. Prior to treatment, people with Kallmann Syndrome (KS) lack both a sense of smell and much of a libido. Superficially, these facts appear to support Kohl’s hypothesis that olfaction is primary in sexual interest. However, the relation between olfaction and libido here is not causal. In most fetuses, some cells in the olfactory placode develop into olfactory cells while others migrate to the hypothalamus to become cells that trigger sex hormone secretion by the gonads. A mutation in one of three known genes can disrupt the development of these cells, so that a person not only lacks a sense of smell but also has gonads that do not produce sex hormones. It is the low sex hormone levels, rather than a lack of olfaction, that leads to reduced libido in adults with KS: Testosterone treatment at least partially restores libido in men with KS, but there is no known treatment for their anosmia.

For another alternative interpretation of everything published by serious scientists about food odors and pheromones, see:

Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. It was a mistake to let such a sloppy review through to be published.

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 also: Until death: Virus-driven failure of multisensory integration (2)

Viruses in pathogenic variants disrupt alternative splicings

April 17, 2017

by James Kohl with No Comment Adaptations Alternative Splicings Cytosis Diseases & Disorders Ecology 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 toxicity RNA–Mediated Epigenetic Heredity Variations

Pathogenic variants that alter protein code often disrupt splicing

Approximately 10% of exonic mutations altered splicing, mostly by disrupting multiple stages of spliceosome assembly. We present a large-scale characterization of exonic splicing mutations using a new technology that facilitates variant classification and keeps pace with variant discovery.

Assay of nearly 5,000 mutations reveals roots of genetic splicing errors

“Splicing errors can be very deleterious because instead of just changing one amino acid [the building block of a protein], it can take out a stretch of 40 or 50 amino acids,” he said.

All energy-dependent alternative splicing must be linked to the physiology of reproduction by amino acid substitutions in supercoiled DNA that protect all organized genomes from virus-driven energy theft and genomic entropy.
See for example: Difference in Plumage Color Used in Species Recognition between Incipient Species Is Linked to a Single Amino Acid Substitution in the Melanocortin-1 Receptor

Assuming that the signals used in species recognition are also used in mutual mate choice, our results indicate that a single amino acid substitution contributes to speciation.

Genome divergence and diversification within a geographic mosaic of coevolution

Our results further characterize a striking example of coevolution driving speciation within perhaps as little as 6000 years.

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.

The time has come for all theorists to choose between pseudoscientific nonsense about mutations and evolution during millions of years or natural selection for energy-dependent codon optimality, which is linked to all biodiversity by the physiology of reproduction and what is known about supercoiled DNA.
Supercoiled DNA prevents the virus-driven degradation of messenger RNA, which is linked to all pathology in all living genera.
Nature did not invent supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. Nature did not engineer anything.
See for contrast: Nanoscale-length control of the flagellar driveshaft requires hitting the tethered outer membrane

…bacteria have evolved elegant and robust regulatory mechanisms to ensure that flagellar morphogenesis follows a defined path, with each component self-assembling to predetermined dimensions.

Reported as: How nature engineered the original rotary motor

Because the flagellum is tied to a bacteria’s ability to move, an understanding of the controls on the flagellar system could help researchers learn how to immobilize harmful bacteria, and to hamper the flagellum-like systems that some bacteria use to infect host cells.

The claim that bacteria evolved a self-assembly mechanism does not fit into the context of any claim ever made by serious scientists who understand that the nutrient-dependent pheromone-controlled physiology of reproduction biophysically constrains any molecular mechanisms that link energy to controls on the flagellum. Researchers who make claims about self-assembly or the weekend resurrection of the bacterial flagellum in P. fluorescens reported in Science (Feb 2015) are not serious scientists. They are evolutionary theorists.

See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

Food for thought: Penrose v Ellis (3)

March 19, 2017

by James Kohl with No Comment Adaptations Diseases & Disorders Ecology Model Organisms RNA Directed RNA-directed DNA methylation Variations

Food for thought: Penrose v Ellis (2)
Thanks to Magnus S. Magnusson for calling my attention to this. He claimed it is an example of wonderful science. It is an example of pseudoscientific nonsense!
We Can Now Harness the Tardigrade’s Strangest Superpower – and Give It to Other Organisms

…tardigrades produce a special type of ‘bioglass’ that holds their essential proteins and molecules in a suspended state until they’re rehydrated back to life.

The nutrient energy-dependent de novo creation of the “bioglass” that holds essential proteins must sometimes be hydrophobic and sometimes be hydrophiic to link ecological variation to ecological adaptation via the physiology of reproduction. The nutrient-dependent pheromone-controlled physiology of reproduction biophysically constrains energy-dependent viral latency in the supercoiled DNA of all living genera.
Negative supercoiling associated with hydrophilic DNA permits virus-driven energy theft and proliferation of viruses that degrade messenger RNA. Obviously, the amount of food an water that is available to this model organism link it from the viral hecatomb to all pathology and from polycombic ecological adaptation to its healthy longevity in diverse environments.
When the viral load increases for other cell type, apoptosis provides needed food for the tardigrades and other organisms that eat DNA. Evidence of the switch from eating DNA to storing it while waiting for rehydration is the key to the pH balance that is the key to life.
pH links the epigenetic landscape to the physical landscape of DNA via biophysically constrained RNA-mediated protein folding chemistry. Inventing the term “bioglass” in the context of biophysically constrained protein folding chemistry leaves a missing piece out of the construction of proteins. Nutrient-dependent amino acids are the building blocks of proteins
The story-telling about bioglass is a lot like the “Just So” stories of all biologically uninformed theorists. In this case the authors start with the automagical creation of “bioglass” and link it to drug development. That’s how story-tellers get their funding.
Still, they must invent new words to get past the fact that viruses cause mutations and all pathology. No mutations are beneficial, which means the “bioglass” must be beneficial to the tardigrades. Truthfully, nutrient-dependent RNA-mediated amino acid substitutions are the source of all energy-dependent benefits linked to ecological adaptation via pH.
The problem with claims about intrinsically disordered proteins is that Boothby et al., (2015) showed that this model organism ecologically adapts by ingesting DNA. That fact links the de novo creation of nucleic acid precursors to all biodiversity on Earth.
See: A huge chunk of a tardigrade’s genome comes from foreign DNA
The foreign DNA is released when virus-driven energy theft causes the death by apoptosis of microbes that failed to adapt. Adaptation is nutrient-dependent, pheromone-controlled and biophysically constrained by RNA-mediated protein folding chemistry, which occurs in species that survive.

Boothby and other theorists refuse to deal with the facts about tardigrade protein-folding chemistry. It is nutrient-dependent because only nutrient energy can be linked from amino acid substitutions in supercoiled DNA, which protects all organized genomes from virus-driven energy theft.

We don’t know how the gene transfer occurs, but it almost certainly involves ingesting DNA in organic debris, which their environments are full of. Bdelloids will eat anything smaller than their heads!See also: Rival Scientists Cast Doubt Upon Recent Discovery About Invincible Animals

Debate about the number of genes that were created in tardigrades that ate the DNA of other species is largely irrelevant to the fact that there is no such thing as an intrinsically disordered protein. To Boothby’s credit, however, coining the term “bioglass” was a stroke of genius if his target audience consists of biologically uninformed theorists.

For example of more pseudoscientific nonsense touted by the biologically uninformed theorist, Jay R. Feierman, see:

Species are not much different from individuals within a species. As individuals, we’re expendable. We only live less than 100 years but our species has been around 200,000 years. So what if we as an individual die. So what if a particular species goes extinct. From the perspective of natural selection, which has no brain, it operates as though the unit it is preserving is life itself. Individuals as well as species are just disposable means to an end. Said slightly differently, natural selection does not select at the species level. It selects at the level of the breeding population, the individual, and the individual gene, with what is left when certain individuals died in past generations and certain species went extinct. Often, when whole species go extinct, it has nothing to do with natural selection, which only plays upon genetic variance among individuals. If individuals within a species can’t adapt to a changing environment, the individuals, as well as the species to which they belong, go extinct. Do you think that God is looking down and saying, “What a shame.” Does it really matter if Homo neanderthalensis went extinct 40,000 years ago? Does it really matter if Homo sapiens goes extinct? It is more likely than not that Homo sapiens, like 99% of all species that have ever lived, will also go extinct at some point.

His atheistic claim about our species being around for 200,000 years and claim that natural selection “…selects at the level of the breeding population…” can be compared to what happens when any organism in any species fails to find food. It dies because without food energy no organism survives to reproduce, which means no offspring contribute to survival of the species.

The same thing is true of nutrient stress and social stress Both cause the death of more organisms compared to those that survive via natural selection for energy-dependent codon optimality, which ensures the physiology of reproduction and links pheromones to biophysically constrained genomic entropy in the context of viral latency.

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.

Food for thought: Penrose v Ellis (1)

March 17, 2017

by James Kohl with One Comment Adaptations Ecology Model Organisms Physics RNA Directed RNA interference RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression

Food for thought.

The most popular ideas of atheists may still include hypothetical biogenic features that arrived from outer space. That’s how pseudoscientific nonsense appears to become a fact of life on Earth.

All experimental evidence of energy-dependent biologically-based cause and effect must be suppressed or ignored, and that’s what atheists prefer to do. See for instance: Hypothetical biogenic features in the context of the Alan Hills fossil. (Thanks to John Hewitt for reminding me of this.)

On August 6, 1996,^[3] ALH84001 became newsworthy when it was claimed that the meteorite may contain evidence of traces of life from Mars, as published in an article in Science by David S. McKay of NASA.^[14]

The electron microscope revealed chain structures in meteorite fragment ALH84001

Under the scanning electron microscope structures were revealed that some scientists interpreted as fossils of bacteria-like lifeforms.

See for comparison: NASA, Jesus & Templeton?

Religion has nothing to do with science and the NASA Astrobiology Program has squandered precious public funds — 5% of its annual budget — for an investigation into how the world’s religions might respond to the discovery of life on other planets. It has handed over $1.108M to a religious think tank, a nonprofit corporation with wealth management professionals on its board that already has in excess of $23M in assets. It is money that could be spent productively on authentic journalism to more effectively expose the politics that drives world disasters, including the use of group mind control, religious and otherwise.

My summary: They claim to provide new insight that links soil bacteria to plant growth in the context of the systems that simultaneously act to coordinate and maintain the assembly of the soil microbiome. The gut microbiome in humans, and the soil microbiome protect humans and plants from virus-driven energy theft. Simply put, the global microbiome protects all natural sources of food energy from genomic entropy.

Reported as: Researchers make discovery that could increase plant yield in wake of looming phosph

“We show precisely how a key ‘switch protein’,PHR1, controls the response to low levels of phosphate, a big stress for the plant, and also controls the plant immune system… “When the plant is stressed for this important nutrient, it turns down its immune system so it can focus on harvesting phosphate from the soil. Essentially, the plant sets its priorities on the cellular level.”

At the cellular level of plant life, the plant appears to automagically control light energy-dependent endogenous RNA interference in soil bacteria, which reproduce only in the context of nutrient-dependent pheromone-controlled quorum sensing.

Energy-dependent pheromone-controlled entropy (4)

March 14, 2017

by James Kohl with No Comment Adaptations biophotonics Diseases & Disorders Ecology Human Pheromones Light Energy Model Organisms 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 Epigenetic Heredity Variations

Solar-driven reforming of lignocellulose to H₂ with a CdS/CdO_x photocatalyst
Reported as: Scientists harness solar power to produce clean hydrogen from biomass
They claim that the rigid structure of nature’s equivalent to armored concrete evolved to protect plants and trees from degradation. They don’t make claims about what might cause the degradation.
They start with the likelihood that degradation automagically occurs. That led them to design a combination of catalyst and solution that mimics how the anti-entropic energy of sunlight is linked to the potential of hydrogen, which is referred to as pH. Their design allowed them to extract the potential of hydrogen in the context of naturally occurring hydrogen-atom transfer in DNA base pairs in solution. They placed their simple design into the context of the evolution of armored concrete.

Pieces of wood, paper and leaves were placed in test tubes and exposed to solar light.

Their sunlight-powered extraction technology reminds me Schrodinger’s (1944) inference. Schrodinger seemed to suggest that someone designed an anti-entropic force, when he attempted to support the answer to his question: “What is Life.”
Theosophically, the God of the Holy Bible and Schrodinger both seemed to be saying that God might have used “the force” as if it came from the “Star Wars” series of movies. The sun could be like other stars and brave souls used “the force” to protect other people from harm.
In the context of the movies series, God, Schrodinger, and all serious scientists have detailed every aspect of how the conserved molecular mechanisms of RNA-mediated protein folding chemistry protect all organized genomes from virus-driven energy theft and genomic entropy.
For comparison, their design enables the production of clean hydrogen from unprocessed biomass. They think they have created a viable alternative to high temperature gasification, which appears to be a renewable means of hydrogen production. It could be compared to God’s way of ensuring that food energy is linked to the physiology of reproduction via endogenous RNA interference and to all biodiversity via energy-dependent biophysically constrained supercoiled DNA. The supercoiled DNA is the linked to chromosomal rearrangements that protect organisms from evolving into something different than their ancestors.
However, their design runs in reverse. They are taking the hydrogen energy out instead of putting it into supercoiled DNA via what is known about quantum physics and how subatomic particles must be linked to the energy-dependent de novo creation of all biodiversity and/or the virus-driven energy theft that appears to be destroying it.

For comparison, this claim links the anti-entropic virucidal energy of sunlight on contact with water from the creation of nucleic acid precursors to all healthy longevity and biodiversity on Earth via the physiology of reproduction.
Virus decomposition provides an important contribution to benthic deep-sea ecosystem functioning

Viruses proliferate at the expense of their hosts. …approximately 25% of viruses released by lysed prokaryotic cells are decomposed at fast rates. We show that… virus decomposition provides a major source of labile organic compounds able to sustain the microbial food webs and nutrient cycling at a global scale.

If you are a theorist who still does not know where the anti-entropic force comes from that prevents virus-driven energy theft from destroying all life on earth, find out more about how the virucidal effect of sunlight feeds the world in the context of the nutrient energy-dependent pheromone controlled physiology of reproduction.
It may be too late for you to become a serious scientist, but at least you will not continue to be one of the pseudoscientists who had us outnumbered since the time neo-Darwinism was invented.
See for an example of a pseudoscientist:
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.

Proof: Sunlight is energy as information

March 13, 2017

by James Kohl with No Comment Adaptations Alternative Splicings biophotonics Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy Model Organisms Physics RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Variations

Hypothesis: Kallmann’s syndrome is proof that virus-driven energy theft causes all pathology in species from archaea to humans via the degradation of messenger RNA and the loss of one allele.

Thought experiment:

Step 1) The loss of one allele and the transgenerational epigenetic inheritance of Zika virus-damaged DNA can be compared to the degradation of messenger RNA in bacteria that is manifested in archaea and L-forms.

Step 2) The degradation of messenger RNA in primates differentiates healthy longevity from pathology via a single amino acid substitution in gorillas compared to chimpanzees and modern humans.

Discussion:

Unless someone shows how mutation-driven evolution leads to increasing organismal complexity in species from microbes to humans, the speed of light on contact with water clearly establishes the link from the de novo creation of microRNA flanking sequences to hydrogen-atom transfer in DNA base pairs in solution and all energy-dependent morphological and behavioral phenotypes.

Conclusion:

Unless there is another model for comparison to Kohl (2013), energy as information will be established as the link from endogenous RNA interference to all biodiversity. Until then, a natural law appears to link food odors and the pheromone-controlled physiology of reproduction from biophysically constrained RNA-mediated protein folding chemistry to feedback loops.

The feedback loops clearly link physics and chemistry to biodiversity from energy as information and food odors to pheromones that control the physiology of reproduction. Pheromones are the chemical signals that prevent virus-driven energy theft and genomic entropy in all living genera.

Light-induced-conformer-intercoversion-of-hydrogen-bond

Serious scientists refute theistic evolution again

February 20, 2017

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

See: Pseudoscientists fail to refute theistic evolution
Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes, and invertebrates
Reported as: Underwater grasslands can cut concentrations of harmful bacteria in half

…deadly coral diseases were 50% less prevalent in regions with seagrass meadows. The scientists aren’t entirely sure how the seagrass combats bacteria so effectively, but one possibility could be that it anchors the nutrient-rich sediment to the sea floor, effectively preventing harmful microbes from feeding on the nutrients.

They seem to be claiming that scientists do not know how to link virus-driven energy theft from the viral hecatomb to all pathology in species from marine bacteria to humans. How can serious scientists not be sure about this?
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.

That suggestion can be linked to the claim that bacteria living in ocean sediments had reportedly not changed in ~2 billion years. If the speed of light on contact with water limits the virus-archaea interactions, the anti-entropic virucidal effect of sunlight probably plays the most important role in global biogeochemical cycles. The stability of the global biogeochemical cycles can be placed into the context of claims about evolution.

Scientists discover organism that hasn’t evolved in more than 2 billion years

The greatest absence of evolution ever reported has been discovered by an international group of scientists: a type of deep-sea microorganism that appears not to have evolved over more than 2 billion years. But the researchers say that the organisms’ lack of evolution actually supports Charles Darwin’s theory of evolution.

Darwin clearly stated that “conditions of life” must be considered before natural selection. These researchers reported that the “conditions of life” did not change, which meant their was not reason for nutrient-dependent pheromone-controlled ecological adaptation to occur in the context of the physiology of reproduction in bacteria living in ocean sediments. The claims that they bacteria had lived there for more than 2 billion years have never been supported by experimental evidence. Instead, experimental evidence has repeatedly refuted those ridiculous claims,
See for example: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
From the Editor’s Summary
Losing and then regaining flagella

The ability to adapt to changes in the function of gene regulators, as opposed to structural genes, is a crucial aspect of evolutionary change. Taylor et al. mutated a central regulator for the formation of flagella in the bacterium Pseudomonas fluorescens. They then put the mutated flagella-free bacteria under strong selection pressure to regain mobility. The mutated bacteria regained the lost flagella, and motility, within 4 days.

The lost flagella could not have been regained outside the context of the nutrient energy-dependent biophysically constrained pheromone-controlled physiology of reproduction that links supercoiled DNA to protection of all organized genomes from virus-driven energy theft and genomic entropy. The supercoiled DNA also links the Virus-mediated archaeal hecatomb in the deep seafloor to the energy-dependent pheromone-controlled stability of the global biogeochemical cycles in the context of the physiology of reproduction via quorum sensing in bacteria and the energy-dependent pheromone-controlled physiology of reproduction in species from microbes to humans.

See also: Guide RNA
Guide RNAs (a.k.a. gRNA) are the RNAs that guide the insertion or deletion of uridine residues into mitochondrial mRNAs in kinetoplastid protists in a process known as RNA editing.
The facts about RNA editing link nutrient energy-dependent microRNA flanking sequences from hydrogen-atom transfer in DNA base pairs in solution to all biophysically constrained biodiversity via the physiology of reproduction in all living genera. For more evidence that virus-driven energy theft is linked to all pathology, see:
Upregulation of MicroRNA-15a Contributes to Pathogenesis of Abdominal Aortic Aneurysm (AAA) by Modulating the Expression of Cyclin-Dependent Kinase Inhibitor 2B (CDKN2B)

We also showed that miR-15a-5p could bind to the CDKN2B 3’UTR, resulting in a significant decrease in luciferase activity compared with the scramble control. Furthermore, we found that the cells isolated from AAA participants showed an over-expression of miR-15a-5p compared to the normal controls, while the CDKN2B mRNA and protein expression level of the AAA group were much lower than the normal control group. Additionally, the expression of CDKN2B mRNA and the protein of the cells transfected with miR-15a-5p mimics and CDKN2B siRNA was downregulated, while the cells showed upregulated expression subsequent to transfection with miR-15a-5p inhibitors compared to the scramble control.

Pseudoscientists fail to refute theistic evolution

February 17, 2017

by James Kohl with One Comment Adaptations Autophagy biophotonics Diseases & Disorders Ecology Human Pheromones Light Energy Model Organisms 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

Darwinism for the Genomic Age: Connecting Mutation to Diversification

…the chief cause of our natural unwillingness to admit that one species has given birth to other and distinct species, is that we are always slow in admitting any great change of which we do not see the intermediate steps. (Darwin, 1859)

Darwin put energy-dependent “conditions of life” before what is now known about natural selection for codon optimality. That is the chief cause for ignoring anything that neo-Darwinists claim about mutations and diversification.
Energy-dependent codon optimality links the epigenetic landscape to the physical landscape of supercoiled DNA in all living genera via endogenous RNA interference and fixation of amino acid substitutions. The energy-dependent fixation of amino acid substitutions differentiates all cell types in all living genera in the context of the pheromone-controlled physiology of reproduction and supercoiled DNA
For comparison: Virus-driven energy theft has been linked from mutations to all pathology.

…circulating plasma and exosomal miRNAs can be used as potential biomarkers specific for drug-induced liver, kidney or muscle injury.

The circulating microRNAs typically link nutrient energy-dependent changes in the microRNA/messenger RNA balance from endogenous RNA interference to supercoiled DNA via RNA-mediated DNA repair.

For comparison, see: DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification

Reported as: Study shows higher than expected sequencing errors in public databases

…the accuracy of public databases has been called into question by work done by the team at NEB, which in turn calls into question the accuracy of the cancer datasets.

The link to specimen processing to the number of errors helps to explain why only serious scientists have refuted theistic evolution. Pseudoscientists incorporated the specimen processing errors into their ridiculous mathematical models. Their mathematical models failed to link energy dependent changes in base pairs to single nucleotide polymorphisms and endogenous RNA interference. That fact destroyed any chance that natural selection for energy-dependent codon optimality would be linked from supercoiled DNA to protection from virus-driven energy theft and genomic entropy in all living genera.

See for example: 2007 Using genomic data to unravel the root of the placental mammal phylogeny

A revised molecular timescale based on these phylogenetic inferences suggests Afrotheria and Xenarthra diverged from other placental mammals ∼103 (95–114) million years ago.

Then this: 2013 Making the impossible possible: rooting the tree of placental mammals

…two groups of researchers have scrutinized the largest available genomic data sets bearing on the question and have come to opposite conclusions, as reported in this issue of Molecular Biology and Evolution.

Then this: 2016 Rooting the family tree of placental mammals

“The molecular clock analysis uses a combination of fossils and genomic data to estimate when these lineages diverged from each other,” said author Dr Mario Dos-Reis of Queen Mary London, UK. “The results show that the afrotherians and xenarthrens diverged from one another around 90 million years ago.”

“You don’t always need to overturn the status quo to make a big impact,” said Dr Tarver. “All of the competing hypotheses had some evidence to support them — that’s precisely why it was the source of such controversy. Proving the roots of the placental family tree with hard empirical evidence is a massive accomplishment.”

Nothing about the roots of any family tree has ever been proved in the context of the fossil record and genomic data. The organization of genomes is nutrient-dependent and pheromone-controlled in the context of energy-dependent links from chirality to autophagy and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy, which is clearly the only link to pathology that consistently shows up in the pathology of dead things.

It’s time to admit that many researchers do not know how RNA-mediated cell type differentiation is biophysically constrained in the context of energy-dependent endogenous RNA interference. The magnitude of the problem increases every day for students in the USA who are taught to believe in mutation-driven evolution.

See for comparison: Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans

Conclusion:

Our data presented here suggest the intriguing possibility that RNAi pathways may mediate distinct effects on gene expression in postdauer animals that experienced different environmental stresses. Since other animals, such as pea aphids, form polyphenisms due to crowding or starvation as well, we predict that this work may have broader implications for the RNAi-mediated regulation phenotypic plasticity.

My goodness, what an “intriguing possiblity.” It might be possible to link energy-dependent RNAi from chirality to autophagy and all biodiversity on Earth by starting from the anti-entropic virucidal energy of sunlight and linking it to the differences between bacteria and virus-infected archaea in the ocean via the physiology of their pheromone-controlled reproduction.

5. Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

Targeting viral elements with energy-dependent Cas+gRNA systems in microbes, plants, animals, or human cells links energy-dependent RNA-mediated amino acid substitutions to viral latency in all living genera. That fact links these three refutations of theist evolution to the examples of the refutations in this model. Nutrient-dependent/pheromone-controlled adaptive evolution: a model
One George Church refutes theistic evolution (3-part series)
Two Francis S. Collins refutes theistic evolution
Three Stuart Kauffman refutes theistic evolution
See also: Scientific Seeker Stuart Kauffman on Free Will, God, ESP and Other Mysteries

He proposed that our scientific understanding of reality is radically incomplete, and that some sort of anti-entropy, order-generating force remains to be discovered.

Let me make this perfectly clear:

The anti-entropic order-generating force is sunlight.

Energy as information and constrained endogenous RNA interference (3)

February 5, 2017

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy biophotonics Diseases & Disorders Ecology Light Energy Model Organisms Neuronal Plasticity 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 Scope (Febrary 4, 2017)

On World Cancer Day, we’re featuring some of the most exciting research developments of the past year. First up? Yoshinori Ohsumi, Nobel laureate, whose research could save your life.

2016 Nobel Prize Winner Yoshinori Ohsumi’s Discoveries Could Change How We Treat Disease

His initial work, first started in 1992, focused on the genes behind the autophagy process in yeast cells. Autophagy, however, has implications for several human diseases, including cancer, neurodegenerative diseases, infectious diseases and diabetes.

Autophagy is the energy-dependent link from chirality to endogenous RNA interference in species from bacteria to humans. Examples of how virus-driven energy theft is linked to all pathology can be found when bacteria become archaea or in the context of the transgenerational epigenetic inheritance of Zika virus-damaged DNA in human infants.

The molecular mechanisms of nutrient energy-dependent feedback loops that link quorum sensing to protection of supercoiled DNA from entropy do not vary across species. They are biophysically constrained by the physiology of reproduction. All serious scientists know that. Only pseudoscientists and other theorists have been stuck touting neo-Darwinian theories.

See for comparison, my FB group: RNA-mediated RNA-mediated currently has 815 members.

Description:

Light energy is quantized information. The information links physics, chemistry, and molecular epigenetics from…”

…the works of 2016 Nobel Laureate Ben Feringa to the works of 1933 Nobel Laureate Thomas Morgan Hunt, and the works of Schrodinger/Dirac who shared the 1933 Nobel Prize in Physics. Taken together, the refutation of neo-Darwinian nonsense about mutation-driven evolution has left theorists with no excuse.

Clearly, they should have examined the experimental evidence of biologically-based cause and effect sometime during the 20th century and stopped touting ridiculous theories based on their definitions and assumptions. If The Scope adds a report on the works of Ben Feringa, everyone could see that neo-Darwinian pseudoscientific nonsense has prevailed since 1933. The facts have been ignored and/or replaced with alternative facts.

See for comparison: Gamma oscillations organize top-down signalling to hypothalamus and enable food seeking

Reported as: Gamma oscillations coordinate food seeking

Gamma oscillations organize communication in hypothalamus

Optogenetics helped to shed light on neuronal mechanisms

Food seeking independent of food consumption

The section heads (above) confirm that energy as information must be linked from what organisms eat to their biophysically constrained physiology of reproduction by the metabolism of food to pheromones. However, there is no mention of the fact that pheromones control the physiology of reproduction in species from bacteria to humans.

See: Feedback loops link odor and pheromone signaling with reproduction

Anyone who takes biologically-based cause and effect outside the context of the feedback loops has also failed to link chirality from autophagy to biodiversity in the context of species-specific survival via the chemistry of protein folding.

See: Multipurpose Plant Sensors Startle Scientists

Scientists at Pacific Northwest National Laboratory built a catalyst that mimics nature’s hydrogen-splitting enzymes—working reversibly at room temperature and pressure without added energy. This was achieved by stabilizing the catalyst’s structure by attaching an amino acid…

This means they could also link the sun’s anti-entropic virucidal energy from the speed of light on contact with water to chirality and autophagy, which link the physiology of reproduction from supercoiled DNA to all biodiversity via hydrogen atom transfer in DNA base pairs in solution and endogenous RNA interference.

See for comparison: Coevolutionary dynamics of phenotypic diversity and contingent cooperation

How to understand the emergence and persistence of cooperation is a key problem in evolutionary biology [1–12], since individuals sticking to cooperation produce benefits to others at a cost to themselves.

Reported as: Study finds mutual reinforcement of phenotypic diversity and cooperation

A new model exploring how evolutionary dynamics work in natural selection has found that phenotypic diversity, or an organism’s observable traits, co-evolves with contingent cooperation when organisms with like traits work together to protect themselves from outsiders, according to a Dartmouth-led study published in PLOS Computational Biology. The study also finds that diversity helps prevent the collapse of cooperation.

What is known about natural selection for energy-dependent codon optimality makes their claims about evolutionary dynamics as useless as James Shapiro’s claims about “Natural Genetic Engineering.” He links whatever that is to evolutionary time outside the context of anything known to serious scientists about energy-dependent biophysically constrained protein folding chemistry, which links endogenous RNA interference to supercoiled DNA.

See: How Living Organisms Make Genetic Edits

In this lecture presented by the American Society for Microbiology, you can learn about how and why modifications to genomes happen in living organisms. It was thought that genomic changes primarily occurred because of errors. But cells are able to adapt; they can make alterations to meet demands brought on by their conditions.

Nutrient energy-dependent amino acid substitutions in supercoiled DNA protect all organized genomes from virus-driven energy theft and genomic entropy. The title of Shapiro’s lecture is appropriate for those who want to think in terms of how life emerged and everything automagically evolved to change itself, but the amount of pseudoscientific nonsense he include in 38 minutes may be difficult to bear.

It is a report on a published work from March 2016. Mitochondria operate as signaling platforms in yeast aging

Rarely do we see science journalists and pseudoscientists like Jame Shapiro collaborate in attempts to keep touting the pseudoscientific nonsense of neo-Darwinian theories. The yeast model of RNA-mediated cell type differentiation was in clouded in our 1996 review and linked to biologically based cause and effect in other model organisms. See: From Fertilization to Adult Sexual Behavior. Ignoring the claims we made in our section on molecular epigenetics has become increasingly annoying.

For comparison, read What is Life? and watch What is life when it is not protected from virus-driven entropy.

See also: Fake news, which includes ridiculous posts like this from Matti Pitkanen Why metabolism and what happens in bio-catalysis?