signal transduction Archives

MicroRNA-mediated denuclearization (2)

April 24, 2018

by James Kohl with No Comment Adaptations Autophagy base editing biophotonics Cytosis Diseases & Disorders Ecology microRNA editing Model Organisms Physics RNA Directed RNA editing RNA interference RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity

Summary:
The virus-driven theft of quantized energy creates a cellular environment that promotes the survival and self-proliferation of viruses by encoding viral miRNAs or miRNA-like molecules. The viral miRNAs or miRNA-like molecules target different types of host cells.
The sun’s anti-entropic virucidal energy biophysically constrains viral latency in the context of global control of human ES cell differentiation via circRNAs derived from lncRNAs. That fact refutes all neo-Darwinian gene-centric pseudoscientific nonsense. That fact also attests to the link from Chinese philosophy to scientific creationism in South Korea.
Scientific creationism appears to have defeated communism in the context of the electron cloud superimposed over the yin yang symbol of constrained energy.
For scientific support of the claims that appear to have defeated communism, see:
Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

Surprisingly, circRNAs derived from long non-coding RNAs (lncRNAs) were found to account for a significantly larger proportion of transcripts from their loci of origin than circRNAs from coding genes.

CONCLUSIONS:

Our results suggest that during human ES cell differentiation, changes in circRNA levels are primarily globally controlled.

Global control of human ES cell differentiation via circRNAs derived from lncRNAs refutes neo-Darwinian gene-centric pseudoscientific nonsense. The level of control comes as no surprise to serious scientists who start with the energy-dependent creation of microRNAs and link the energy to the RNA-mediated creation from genome assembly to the creation of all cell types.

The global control-based refutation is merely one more example of pattern recognition.

See: Three invariant Hi-C interaction patterns: applications to genome assembly

We suggest that simultaneously considering all three invariant patterns may lead to better Hi-C-based genome assembly methods.

Schrödinger suggested that genome assembly was energy-dependent in What is Life? (1944)

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.)

Examining virus-host cell interaction is important for elucidating mechanisms of virus proliferation in host cells. Viruses can create an environment that promotes their survival and self-proliferation by encoding miRNAs or miRNA-like molecules that target various host cell.

…fine-tuning of the base-pair stability at the cleavage site is essential for efficient processing of pri-miR156a at a low temperature and for reduced flowering sensitivity to ambient temperature changes.

…17-24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed. These results suggest that multiple interspecies re-assortment events might have contributed to the emergence of G2P[4] rotaviruses in the post-vaccination era in South Korea.

Several amino acid mutations were identified in PB2, PB1, PA, BM2, and/or NS1 protein coding regions, and one concurrent lysine (K)-to-arginine (R) mutation in PA residue 338 (PA K338R) was found in both maVc_BR60 and maYm_WI01 viruses. When analyzed using reverse-genetically rescued viruses, it was shown that PA K338R alone could increase the pathogenicity of both IBVs in mice and viral replication property in the respiratory tracts of ferrets.

The energy-dependent fine-tuning of the base-pair stability in plants prevents the emergence of rotaviruses via multiple interspecies re-assortment events linked to healthy longevity in post-vaccination era South Korea.

See for comparison: Engineered virus has artificial amino acid allowing it to serve as a vaccine

A team of researchers at Peking University has developed a new type of vaccine that they claim may allow for a new approach to generating live virus vaccines which could conceivably be adapted to any type of virus. In their paper published in the journal Science, the team outlines the means by which they modified an influenza virus causing it to incite an immune response without a risk of infection.

Scientific creationists in South Korea have showed that the Chinese cannot protect themselves from a viral apocalypse via vaccinations. The viruses adapt too quickly.

Knowing that also allows the scientific creationists to create a virus that damages the DNA of specific human populations who are less well-adapted to their food energy-dependent pheromone-controlled ecological, social, neurogenic, and socio-cognitive niches.

Would you threaten nuclear war after you learn that the population of your country could be decimated by a genetically engineered virus produced in a neighboring country. Or, would you denuclearize and de-escalate the tensions as soon as you learned that all niche construction is food energy-dependent and that the pheromone-controlled physiology of reproduction biophysically constrains viral latency.

That fact cannot be placed back into the context of atheism or communism. It is a neo-Darwinian theory killer and is the most likely reason for denuclearization in a reasonable world.

The facts about biophysically constrained viral latency and energy-dependent life will be discussed during Schrödinger at 75 – The Future of Biology – September 2018

See for comparison: Organ-specific metastases obtained by culturing colorectal cancer cells on tissue-specific decellularized scaffolds

…lung and liver decellularized scaffolds retained their tissue-specific tropism when injected in mice.

Reported as: Scientists create better laboratory tools to study cancer’s spread

The hypothesis is this is caused by both ‘seed and soil’ – that the cancer cells have something in them that drive them to a particular organ, and the soil has to be right for them to grow. Most of the focus has been on studying the cancer cell, or the seed, and not as closely looking at the soil, which is the organs that they go to. Our models will help us understand to better understand the conditions of the soil that help promote cancer metastasis.

The use of Schrödinger’s sunlight-to-soil metaphor of degraded organic matter and biophysically constrained viral latency is not likely to be a coincidence. It also appears in the context of the energy-dependent weekend resurrection of the bacterial flagellum and in the context of the weekend Resurrection of Christ.

Scientific creationism in South Korea supposedly began with the support of the US government in their attempt to fight against communism and atheism. Pseudoscientists have not linked energy-dependent RNA-mediated biophysically constrained viral latency to all healthy longevity in the context of Communism and atheism.

For comparison, all serious scientists who understand the role that the creation of energy plays in the creation of supercoiled DNA have won the war against communism by combating evolution to fight disease.

All disease has been linked to the virus-driven energy theft that causes the degradation of messenger RNA, which has been linked to all pathology.

The energy-dependent creation of microRNAs has been linked from the creation of the innate immune system to all biophysically constrained behaviors via what is known about how the physiology of pheromone-controlled reproduction must be linked from soil bacteria to the growth of seeds and all food energy-dependent life on Earth.

The Mind's Eyes (revisited)

June 12, 2016

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

Author’s copy: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences (2007)
Abstract:

The across-species genetic conservation of intercellular and extracellular chemical communication enables unicellular and multicellular organisms to functionally distinguish between self and non-self. Non-self olfactory/pheromonal input from the social environment elicits a vertebrate neuroendocrine response. The organization and activation of this neuroendocrine response modulates the concurrent maturation of the mammalian neuroendocrine system, the reproductive system, and the central nervous system during the development of sexual preferences that may be expressed in sexual behavior. Psychophysiological mechanisms for the development of these sexual preferences include focus on unconscious affects that are detailed in reciprocal cause and effect relationships. Olfactory/pheromonal conditioning elicits neuroendocrine effects accompanied by unconscious affects on the development of sexual preferences. Integrating these unconscious affects extends to humans a developmental model of behavior that includes the development of male sexual preferences for other males.

For comparison, see: How Can Physics Underlie the Mind? Top-Down Causation in the Human Context (2016)
by George Ellis

George Ellis, FRS, is one of the world’s leading researchers in general relativity theory and cosmology. He is Emeritus Distinguished Professor of Complex Systems in the Department of Mathematics and Applied Mathematics at the University of Cape Town in South Africa. He co-authored The Large Scale Structure of Space-Time with Cambridge physicist Stephen Hawking.

Book description:

Addresses one of science and philosophy’s biggest puzzles: how complex structures that emerge from atoms and molecules can become causative agent
Argues that the human mind and resultant social agency has a special status among complex systems
Is fully consistent with present day physics, but also takes into account key features of biology and how the brain functions
Will appeal to general and academic readers alike

Available 6/12/16 from Amazon books
Description:

Physics underlies all complexity, including our own existence: how is this possible? How can our own lives emerge from interactions of electrons, protons, and neutrons? This book considers the interaction of physical and non-physical causation in complex systems such as living beings, and in particular in the human brain, relating this to the emergence of higher levels of complexity with real causal powers. In particular it explores the idea of top-down causation, which is the key effect allowing the emergence of true complexity and also enables the causal efficacy of non-physical entities, including the value of money, social conventions, and ethical choices.

On pages 3 and 4 from my online version, look for:

In the influential book What Is Life, written in 1945, Erwin Schrödinger wrote [80, p. 81]: From all we have learnt about the structure of living matter, we must be prepared to find it
working in a manner that cannot be reduced to the ordinary laws of physics. And that not on the ground that there is any ‘new force’ or what not, directing the behaviour of the single atoms within a living organism, but because the construction is different from anything we have yet tested in a laboratory.

See for comparison:
What is Life? in the section on ORGANIZATION MAINTAINED BY EXTRACTING ‘ORDER’ FROM THE ENVIRONMENT
Excerpt:

…the awkward expression ‘negative entropy’ can be he replaced by a better one: entropy, taken with the negative sign, is itself a measure of order. Thus the device by which an organism maintains itself stationary at a fairly high level of the orderliness ( = fairly low level of entropy) really consists continually sucking orderliness from its environment. This conclusion is less paradoxical than it appears at first sight. Rather could it be blamed for triviality. Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight)

Look inside for information on the role of virus-driven energy theft. Search for viruses on page 172 in my online version
Excerpt:

Folding of Single-Stranded DNA Sequences Following Reverse Mutations. The selection of native nucleic acid folding (an irreducible higher level variable) is an epigenetic effect,with broad implications for the evolution of plants and their viruses. The folding structure (a higher level variable) corresponds to an equivalence class of lower level sequences, and is the biologically relevant variable determining the selection that occurs. How do we demonstrate this top-down causation? This has been shown in detail experimentally by Shepherd et al. [171].
Note: “…a three-nucleotide mutation adversely affected Rep nucleic acid folding…” and a “…single-nucleotide reversion [C(601)A] restored wild-type-like folding.”

My comment: This exemplifies the difference between virus-driven energy theft, which caused the mutation, and a nutrient energy-dependent change in a base pair, which was required to restore the energy-dependent biophysically constrained protein folding.
Look inside for information on the role of pheromones, on page 424 in my online version.
Excerpt:

Hartwell et al. express the last point in the following way [104]:

Much of twentieth-century biology has been an attempt to reduce biological phenomena to the behaviour of molecules […] Despite the enormous success of this approach, a discrete biological function can only rarely be attributed to an individual molecule, in the sense that the main purpose of haemoglobin is to transport gas molecules in the bloodstream. In contrast, most biological functions arise from interactions among many components. For example, in the signal transduction system in yeast that converts the detection of a pheromone into the act of mating, there is no single protein responsible for amplifying the input signal.

My comment: Sensing and signalling of differences in cell types is energy-dependent. No one who knows that would expect to find a single protein that was involved in two different biophysically constrained functions, which must link metabolic networks to genetic networks in yeasts and humans via the innate immune system, the physiology of reproduction, RNA methylation, and learning and memory which must be linked to supercoiled DNA and all biodiversity.
But wait, Ellis cites Schrödinger, and ignores what Roger Penrose claimed in the forward of the reprint.

How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?

It’s beginning to seem that George Ellis is going to tell only half of the story that he thinks explains how physics and the mind are connected, automagically. What about the energy source, George?

He is saved from ridicule only by the recognition that he may need to keep his faith in evolution despite the lack of experimental evidence of biologically-based cause and effect that could link neo-Darwinian theories to Darwin’s “conditions of life”. Clearly, he understands the need to establish the context in which his claims can be placed.

See page 141

4.1.4.2 Setting Values for Contextual Variables
Contextual variables set by the environment must lie in a suitable range. For example, the following are crucial to life as we know it:
• The environmental temperature must lie in a very narrow band.
• Oxygen and water must be available.
• A suitable energy source must be available (sunlight for a plant, food for an animal).
Without these contextual conditions being right,much life on Earth (animals, plants, and insects) would be in trouble. Other forms of life might have different sources of energy (e.g., thermal vents), but without some energy source, they will not survive.

My comment: Without a link from the contextual variables to the energy-dependent physiology of species-specific reproduction, the innate immune system could not be linked to all biodiversity. George Ellis knows that.

See also: Understanding and accounting for relational context is critical for social neuroscience
In the comments section, I wrote:
“New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.
Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”
— Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors Socioaffective Neuroscience & Psychology 2012; 2: 17338 – DOI: 10.3402/snp.v2i0.17338
George Ellis replied: This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: http://rsfs.royalsocietypublishing.org/content/2/1.toc
George Ellis also responded: Great links, thanks. I’m intrigued by your work on pheromones. It is just possible it might relate to the issue of primordial emotional systems, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3540967/
See also:

I added: It’s interesting to look at how our works fit, which they must do if our findings correctly represent biophysically constrained ecological adaptations manifested in morphological and behavioral phenotypes. Others are quickly eliminating any perceived incongruities. For example, see: Maternal nutrition at conception modulates DNA methylation of human metastable epialleles http://dx.doi.org/10.1038/ncomms4746. This takes physics and chemistry to the one-carbon metabolism level of DNA methylation, which links ecological variation to ecological adaptations via micronutrients and macronutrients.

Since you are familiar with Panksepp’s works, I will note that my group won the seminal award in 2001 that his group won in 2002 . See Human pheromones: integrating neuroendocrinology and ethology http://www.ncbi.nlm.nih.gov/pubmed/11600881 and Comparative approaches in evolutionary psychology: molecular neuroscience meets the mind http://www.ncbi.nlm.nih.gov/pubmed/12496741. Evolutionary theorists have since ignored or denied the role of nutrient-dependent species-specific pheromone production, which controls the physiology of reproduction, and continued to tout their ideas about mutations, natural selection and evolution.
Here we are more than a decade later and others are just now learning that the molecular mechanisms of signaling and sensing are conserved across species from yeasts to humans, which means the conserved molecular mechanisms must be the basis for emotional systems. At least one Nobel Laureate already has attested to that fact. See Feedback loops link odor and pheromone signaling with reproduction” http://www.ncbi.nlm.nih.gov/pubmed/16290036. “Indications that GnRH peptide plays an important role in the control of sexual behaviors suggest that pheromone effects on these behaviors might also involve GnRH neurons.” (p 683).
Start with yeasts: Signaling Crosstalk: Integrating Nutrient Availability and Sex http://stke.sciencemag.org/cgi/content/abstract/sigtrans;6/291/pe28 The nutrient-dependent production of the alpha mating pheromone exemplifies cell type differentiation at the advent of sexual reproduction, and when concentrated it elicits a luteinizing hormone (LH) response from the cultured pituitary cells of a mammal, the rat.
The mammalian GnRH-directed LH response has been the focus of my works for more than 2 decades since someone told me my mammalian model had to start with gene activation in hormone-secreting nerve cells of the brain. However, in 2010 , Richard Doty published a book an claimed that mammalian pheromones don’t exist. Simply put, they can’t — if you’re a social scientist. See: A Fear of Pheromones http://dx.doi.org/10.1056/NEJM197108122850708

When more experimental evidence became available, I added Timothy W. Bredy’s group has done it again. See: Long noncoding RNA-directed epigenetic regulation of gene expression is associated with anxiety-like behavior in mice. http://www.biologicalpsychiatryjournal.com/article/S0006-3223%2815%2900095-5/fulltext

Conclusion: Experience-dependent expression of lncRNAs plays an important role in the epigenetic regulation of adaptive behavior, and the perturbation of Gomafu may be related to anxiety and the development of neuropsychiatric disorders.

The most obvious correlation with what is now being discussed in the context of top-down causation and 4-D genome make-up that changes during life history transistions is: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults. http://dx.doi.org/10.1007/s00429-014-0895-5
It shows the difference that a single amino acid substitution can make during experience-dependent RNA-mediated life history transitions that link metabolic networks to genetic networks.

——————————————-

George Ellis left our brief discussion, perhaps to work on the misrepresentations of biologically-based cause and effect he just included in his book. In the book, he links information on the energy-dependent pheromone-controlled physiology of reproduction to the energy-dependent pheromone-controlled physiology of reproduction in primates via Dobzhansky’s claims from Nothing in Biology Makes Any Sense Except in the Light of Evolution.

Excerpt:

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).

My comment: Others have since shown that Feedback loops link odor and pheromone signaling with reproduction and that the energy-dependent changes linked from food odors to the pheromone-controlled physiology of reproduction are also linked to the Structural diversity of supercoiled DNA.

Many serious scientists have joined the ranks of others who are Combating Evolution to Fight Disease by linking everything known about physics and chemistry to the molecular mechanisms of energy-dependent brain development from the origin of the nervous system in nematodes to the glorious representations that have been placed into the context of the energy-dependent de novo creation of nucleic acids, cell type differentiation, and biodiversity in the context of our 1996 Hormones and Behavior review, From Fertilization to Adult Sexual Behavior, my book chapter in The Handbook of the Evolution of Human Sexuality, and this 2013 review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

George Ellis has set the stage for others to accept, deny, or ignore everything Schrödinger probably long-ago expected to be linked from the anti-entropic energy of sunlight to all biodiversity.

See for instance: Epigenetics and Genetics of Viral Latency
Excerpt:

…viral latency is responsible for life-long pathogenesis and mortality risk…

See also: Viral Nucleic Acids
Abstract excerpt:

…viral nucleic acids can be DNA or RNA, double-stranded or single-stranded, monopartite or multipartite, linear or circular, as short as 2 kb or up to 2500 kb long. The goal of a virus is to replicate itself. To do so, viruses have evolved various strategies to replicate their genomes…

1) Nucleic acid testing or nucleic acid amplification testing, often abbreviated as NAT or NAAT… has been associated with blood screening for some time. It was first introduced by the German Red Cross in 1997 for blood screening to reduce the risk of transfusion-transmitted viral infections due to the failure of serologic screening tests to detect recently infected donors in the pre-seroconversion “window” phase of infection.¹

2) NAT is extensively used to detect and identify organisms for proper diagnosis, prognosis, and treatment of diseases.

3) Nucleic acid testing helps to identify genetic variations and predicts predisposition to cancer, alters diagnostic categories, enhances treatment strategies, enables early detection and prevention, and improves outcomes for cancer patients. Nucleic acid testing has led to the emergence of precision and personalized medicine—that is, the tailoring of treatment based on the individual’s genetic make-up.

The emergence of nucleic acid testing led to the emergence of precision and personalized medicine. Persoalized medicine has since led to the emergence of attempts that will link Cracking the Olfactory Code from the National Microbiome Initiative to a series of successful attempts that led others to report on Cracking the epitranscriptome.

Excerpt:

…advances in recent years have dramatically expanded our toolkit for studying m6A and have begun to expose different levels at which RNA methylations are associated with phenotypic and molecular consequences.

George Ellis attempts to put everything known to physicists, chemists, and molecular biologists about the links from angstroms to ecosystems back into the context of the evolution of the human mind. But he waited to do that until after others cracked the epitranscriptome. That cracks me up. His sense of humor is as dry as Dobzhansky’s and hit wits are still sharp.

I’m almost certain the George Ellis is joking because he mentions Feynman’s works several times, but fails to put them into the context of Schrodinger’s anti-entropic force of sunlight; Dobzhansky’s “light of evolution;” or Roger Penrose’s question. “How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?“

For comparison, see:

Periodic Scarred States in Open Quantum Dots as Evidence of Quantum Darwinism

A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution.

If you’re not sure whether or not George Ellis is joking about the evidence of quantum Darwinism or the theory about docosahexanoic acid in energy-dependent cell type signaling that links the underlying physics from chemistry to the molecular epigenetics of brain development and the human mind, ask him a few questions. Does he know how my works on RNA-mediated amino acid substitutions linked the works of Luca Turin, Anna Di Cosmo, Eugene Daev, Bruce McEwen, the late Robert L. Moss, and Timothy W. Bredy to everything currently known about biophysically constrained energy-dependent RNA methylation and cell type differentiation in all living genera?

Filtering light through a prism to identify tissue type

Bacteria see the light and they adapt

February 10, 2016

by James Kohl with One Comment Adaptations Alternative Splicings biophotonics Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy Model Organisms Neuronal Plasticity Nutrigenomics Pharmacogenomics Physics RNA Directed RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations

Cyanobacteria use micro-optics to sense light direction

Excerpt:

From the observed dimensions of the spot of 488 nm light focused by Synechocystis cells (Figure 3c) we can estimate that Synechocystis “vision” has an angular resolution (FWHM) of about 21°, essentially limited by light wavelength and the area of the plasma membrane, which is tiny in comparison to an animal retina. However, this resolution is sufficient to incorporate quite complex spatial information into a 360° image of the cell’s surroundings, and our data in Figure 1e indicate that the cell can integrate information from distinct and spatially separated light sources. The directional motile responses of the cells (Figure 1c,d) show a distribution of displacement angles with FWHM ~30°. This is less accurate than the initial imaging of the light source, which suggests an unsurprising degree of spreading and noise during the signal transduction that comes between initial light perception and the response of the motility apparatus.

My comment: The spot of 488 nm light focused by Synechocystis cells links phototaxis and chemotaxis from photosynthesis to all nutrient-dependent RNA-mediated biodiversity. See for instance:

Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution

Introduction:

For over fifty years, the role of interstrand proton or hydrogen-atom transfer in double-helix DNA has been debated as a possible precursor for mutagenesis and carcinogenesis.[1] However, recent theoretical studies postulated that ultrafast interstrand electron-driven proton transfer (EDPT) instead contributes to the prevention of mutagenic photolesions in DNA excited by absorption of solar ultraviolet (UV) radiation. [2]

Excerpt:

At an excitation wavelength of 260 nm, about 80% of the photons are absorbed by G (see the Supporting Information, Figure S5).[5c,8a] Excitation at the red edge of the absorption spectrum at 290 nm promotes the same photochemistry, but the product bands observed in TEAS and TVAS are weaker because of the lower absorption by G at this wavelength. Excitation of C leads to monomer-like deactivation (see Section S12). Therefore, the discussion in this paper focuses on the results after 260 nm excitation.

My comment: The mechanism that emerges is not links UV light to everything currently know to serious scientists about biophotonics. The mechanism is not placed into the context of anything except a biophysically constrained epigenetic trap. The trap links the speed of light on contact with water from different wavelengths to differences in hydrogen-atom transfer in double-helix DNA. Hydrogen-atom transfer in DNA base pairs in solution links phototaxis and chemotaxis.
Chemotaxis links the nutrient-dependent physiology of reproduction to all biomass and all biodiversity. The mechanism that emerges can be compared to claims that evolutionary mechanisms link the emergence of life from mutations to increasing organismal complexity via natural selection in the context of ridiculous neo-Darwinian theories that ignored Darwin’s “conditions of life.”
For examples of that ignorance, see these reports on the article (with my emphasis): Cyanobacteria use micro-optics to sense light direction
Excerpt:

…findings are most likely an example of convergent evolution between bacteria and more complex multi-cellular organisms including animals and humans.

My comment: The findings link the speed of light on contact with water from hydrogen-atom transfer in DNA base pairs in solution to nutrient-dependent cell type differentiation via the biophysically constrained chemistry of RNA-mediated protein folding in all living genera.
Dobzhansky’s “light of evolution” can be placed into the context of the amino acid substitutions that differentiate the cell types of chimpanzees and modern humans from the cell types of gorillas.

Like all other serious scientists, Dobzhansky (1973) linked the anti-entropic energy of sunlight to all biodiversity via nutrient-dependent ecological adaptations and the physiology of reproduction.
Pseudoscientists hate the fact that they didn’t realize Dobzhansky was joking about mutations and evolution. They never learned the difference between mutations and amino acid substitutions, and Dobzhansky knew they would not. The jokes played on pseudoscientists by serious scientists may have started with Dobzhansky (1964).
Excerpt:

Cyanobacteria evolved around 2.7 billion years ago and the fact that they are able to produce oxygen and fix carbon dioxide using energy from the sun – photosynthesis – is thought to have caused mass extinctions and the oldest known ice age.

My comment: Phototaxis and chemotaxis are not linked from the sun’s biological energy to photosynthesis and EVOLUTION or EXTINCTION. Chemotaxis and phototaxis are linked from hydrogen-atom transfer in DNA base pairs in solution to nutrient energy-dependent RNA-mediated DNA repair and supercoiled DNA that protects the organized genomes of all living genera from virus-driven entropy.
For a reality check, see these reports on the article (with my emphasis): Cyanobacteria use micro-optics to sense light direction
Excerpt:

They get energy from photosynthesis, meaning they need plenty of light to perform the same chemical reaction as plants.

Previous studies have shown Synechocysti contain photosensors and that they are able to perceive the position of a light source and move towards it – a phenomenon called phototaxis. This study showed how this process works. Bacteria moving towards a light is pictured
Excerpt:

The ability of optical objects to distinguish fine detail is determined by “angular resolution”. In the human eye this is an impressive 0.02 degrees. The team estimate that in Synechocystis it is about 21 degrees.

My comment: Is anyone willing to place the change in the degrees of resolution into the context of beneficial mutations and evolution of human visual acuity and specificity?
Excerpt:

Within minutes, the bacteria grow tiny tentacle-like structures called pili that reach out towards the light source.

My comment: The light source is the energy source for growth of the pili, which occurs within minutes. The light source links metabolic networks from their energy source to genetic networks that control colony growth. Colony growth is biophysically constrained in bacteria via the systems complexity of nutrient-dependent quorum sensing, a function of pheromone-controlled morphological and behavioral phenotypes. The structure and function of the phenotypes extends to humans via biophysically constrained RNA-mediated amino acid substitutions in the context of protein folding chemistry.
Conclusion: The laws of physics and the chemistry of protein folding link the sun’s biological energy to RNA-mediated cell type differentiation via the physiology of nutrient-dependent reproduction, which is controlled by pheromones in species from microbes to humans.
See also: Researchers illuminate ‘dark side’ of the transcriptome

A new method to detect, quantify and visualize RNA splicing helps to shed light on the “dark side” of the transcriptome: complex splicing variations that have been known to exist but have not been well studied.

Credit: Illustration conceived by Matthew Gazzara in the Barash lab, Perelman School of Medicine, University of Pennsylvania

My comment: Credit for linking RNA splicing to cell type differentiation in species from microbes to humans should be given to Teresa Binstock, who co-authored our 1996 Hormones and Behavior review and was solely responsible for the section on molecular epigenetics.

See: From Fertilization to Adult Sexual Behavior
Excerpt:

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.
A potential ramification of epigenetic imprinting and alternative splicing may be occurring in Xq28, a chromosomal region implicated in homosexual orientation (Brook, 1993; Hu, Pattatucci, Patterson, Li, Fulker, Cherny, Kruglyak, and Hamer, 1995; Turner, 1995). Xq28 contains one of the X chromosome’s two pseudoautosomal regions (PARs), adjoins the telomere, and has various means of gene expression control (D’Esposito, Ciccodicola, Gianfrancesco, Esposito, Flagiello, Mazzarella, Schiessinger, and D’Urso (1996). Xq28, therefore, is a chromosomal region that has many of the heterochromatic and telomeric characteristics that participate in sexual determination and behavior in other species.

See also: The Light and Darkness of “Evolution 2.0”
Excerpt: The sun’s biological energy links its anti-entropic virucidal epigenetic effects to RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all living genera.”
See also: Sighted Microbes
Excerpt:

…the study offered an “elegant demonstration” of the mechanism for phototaxis in these bacteria. “Cyanobacteria are 2.7 billion years old…

My comment to “The Scientist”
Their results link phototaxis to chemotaxis. They also link microbial foraging behavior to human metabolic networks and genetic networks via hydrogen-atom transfer in DNA base pair in solutions like sea water and circulating blood.
Facts about light intensity and energy-dependent changes in base pairs link everything known to serious scientists about physics, chemistry, and the conserved molecular mechanisms of biologically-based RNA-mediated cause and effect. The insertion of the spurious claim that the “Cyanobacteria are 2.7 billion years old” should not be placed into the context of what is known to serious scientists about nutrient-dependent biophysically constrained cell type differentiation.
Theorists invite more ridicule when they make such claims and ignore facts like these:

…a family of microbes has persisted essentially unchanged for the past 2.3 billion years—half the age of Earth.

Bacteria that lack a vital protein for growing flagella—tail-like structures that enable the microbes to swim—can attain flagella in as little as four days given enough pressure to evolve…

The facts link energy-dependent base pair substitutions and RNA-mediated amino acid substitutions via the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to humans. Only neo-Darwinists and others who are equally biologically uninformed will continue to place what is known about hydrogen-atom transfer in DNA base pairs in solution into the context of evolution without explaining how “evolution” occurs in 4 days or does not occur in 2.3 billion years.

Conclusion:

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. It was a mistake to let such a sloppy review through to be published.

My comment: So far as I know, the criticisms of this biologically uninformed undergraduate have not been placed into the context of a model that links hydrogen-atom transfer in DNA base pairs in solution to RNA-mediated amino acid substitutions and cell type differentiation in all individuals of all living genera via the conserved molecular mechanisms I detailed.
The molecular mechanisms link information transfer in microbes to information transfer in the human brain via two epigenetic traps. Others have detailed aspects of the epigenetic trap that traps the anti-entropic virucidal energy of UV light. But, so far as I know, no one else has linked the first epigenetic trap to the de novo creation of odor receptor genes. The de novo creation of olfactory receptor genes in all vertebrates and invertebrates links the second epigenetic trap to supercoiled DNA during thermodynamic cycles of nutrient-dependent protein folding biosythesis and degradation. The supercoiled DNA protects organized genomes from virus-driven entropy.

That fact has now been placed into the context of RNA-mediated DNA repair, which typically occurs in the absence of nutrient stress and or social stress.
Stress alters pH via virus-driven energy theft. The proliferation of viruses prevents RNA-mediated DNA repair. For example, viruses would prevent repair of damage due to excess infrared light.

Scent of Eros

Posts tagged: signal transduction

MicroRNA-mediated denuclearization (2)

Bacteria see the light and they adapt

Cyanobacteria use micro-optics to sense light direction

Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution