Sal Giardina: apologetics revisited

March 27, 2017

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy 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

March 26, 2017 Sal Giardina wrote:

“James, I appreciate your responding to my posts but I would prefer that your input would be related to the content of the post.”

My reply: If you do not want people to learn how my claims are linked to yours, please tell me that you intend to continue with apologetics rather the concept of energy as information.

Apologetics:

… the religious discipline of defending or proving the truth of religious doctrines through systematic argumentation and discourse.^[1]^[2]^[3] Early Christian writers (c. 120–220) who defended their beliefs against critics and recommended their faith to outsiders were called Christian apologists.^[4] In 21st century usage, ‘apologetics’ is often identified with debates over religion and theology.

In the context of debates over religion and theology, Sal Giardina opened discussion of physics, chemistry, and the conserved molecular epigenetics of RNA-mediated cell type differentiation. Secular humanists are scared by the ghosts of their biologically uninformed past and their ongoing ignorance. Fortunately for them, Sal Giardina and others like him cannot prove anything via the use of apologetics. So far as I know, the apologeticists have never convinced anyone to believe in any of their claims.
See for example: What does DNA have to do with the Origin of Life ?
Unfortunately, you must join this “false flag” group go find this post: https://www.facebook.com/groups/231023426993207/permalink/1119981528097388/?comment_id=1120290524733155&reply_comment_id=1120913471337527&notif_t=group_comment&notif_id=1477870268849582 I’ve been banned from the group twice, but just submitted a request to re-join.
My comments: Secular humanists seem willing to believe that the origin of life could somehow lead to consciousness as a side effect.
See for example: Consciousness could be a side effect of ‘entropy’, say researchers
My comment: Serious scientists do not make such ridiculous claims. These researchers are theorists who tout meaningless pseudoscientific nonsense. Their ridiculous claims makes news when biologically uninformed journalists, like Fiona Macdonald pass the unsupported claims on to others who do not know that the theorists are touting meaningless pseudoscientific nonsense.
See also: Virus evolution and this special issue on Orgasms: Introductory editorial to ‘Orgasm: Neurophysiological, Psychological, and Evolutionary Perspectives’
My comment: Who are the people trying to convince others that virus evolution links prairie vole monogamy to the evolution of human love via organsm? One of them is James Pfaus.
Excerpt:

In ‘The Role of Orgasm in the Development and Shaping of Partner Preferences’, Coria-Avila, Herrera-Covarrubias, Ismail, and Pfaus (2016) explore the relationship between orgasm and sexual preference-formation in animals. Of particular significance with respect to human orgasm, Coria-Avila et al. describe the pre- and post-ejaculatory factors contributing to male rats forming conditioned sexual preferences.

See this article by Rachel Feltman, who placed the ridiculous claims of Pfaus before my detailed model of nutrient-dependent pheromone-controlled biologically-based cause and effect.
What Do We Actually Know About Pheromones?
Excerpt:

But Kohl’s products, which he likens to food spices (“They give you an extra kick!”), make some researchers roll their eyes. Dr. Jim Pfaus, professor of psychology at Concordia University in Montreal, is one of them.

See for comparison: Ecologically relevant neurobehavioral assessment of the development of threat learning
Summary: “Informed Conditioning” is linked to the differences between wolves and dogs and biophysically constrained cell type differentiation in all living genera.
See for example: A Comparison of the Sensory Development of Wolves (Canis lupus lupus) and Dogs (Canis lupus familiaris)
See also (link opens pdf): Early life experiences: enduring behavioral, neurological and endocrinological consequences

…no study has yet shown an effect of manipulating the expression of a particular microRNA on a behavioral or brain sex difference. In other words, we are still awaiting the demonstration that microRNAs contribute to sexual differentiation of the brain.

Olfaction is important to humans as well, but visual stimuli are far more potent and the arousal potential of same-sex versus opposite-sex images depends on the partner preference of the observer (see for review Baum, 2006).

Michael Baum and others still make ridiculous claims about visual input compared to the epigenetic effect of food odors and pheromones on energy-dependent microRNA-mediated cell type differentiation in species from microbes to humans. That fact supports my claim that people like him are biologically uninformed.

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

Pioneering experiments by Allfrey and Mirsky >50 years ago identified methylation and acetylation of histones by isotope incorporation and showed that histone modification can influence whether RNA synthesis of genes is switched on or off [3].

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

If you knew nothing about the energy-dependent de novo creation of nucleic acid precursors, you still could start from the energy-dependent creation of RNA and link RNA-directed DNA methylation to all biophysically constrained biologically-based cause and effect in all living genera to their physiology of pheromone-controlled reproduction in the context of learning and memory at the cellular level of intracellular and extracellular communications.

See also: Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice
My comment: The conserved molecular mechanisms of experience-dependent learning and memory have been linked from energy-dependent RNA-mediated cell type differentiation to all biodiversity via quantised energy and all subsequent levels of examination the must begin with the origins of information, the sun’s anti-entropic virucidal energy.

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

My comment: Femtosecond blasts of UV light link the sun’s virucidal energy to RNA-mediated DNA repair in all living genera. People who do not know that should simply admit that they biologically uninformed. Most of them are theorists who know nothing about anything that must be linked from angstroms to ecosystems. They should not antagonize those who are biologically informed serious scientists. Serious scientists publish experimental evidence in reports such as this one.

UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

Excerpt:

The sequences have been selected according special charge distributions and lifetimes of excimer states previously characterized by femtosecond infrared spectroscopy.(3a, 3c, 3d) With these selected sequences we demonstrate that repair occurs when the intrastrand charge transfer leads to a suitably charged nucleotide adjacent to the lesion.

My comment: The sequences cannot be selected outside the context of natural selection for energy-dependent codon optimality, which is the basis for the control of hydrogen-atom transfer in DNA base pairs in solution. Control is manifested in the measurement of pH.

See: Control of pH responsive peptide self-association during endocytosis is required for effective gene transfer

Excerpt:

Coulombic interactions between the histidine residues modulate protonation and subsequent conformational transitions required for peptide mediated gene transfer activity and are an important factor to consider in future peptide design.

My comment: Coulomb barrier:The Coulomb repulsion which tends to keep positively charged bombarding particles out of the nucleus. Specifically, the Coulomb potential associated with this force.

Energy-dependent Coulombic interactions link autophagy to polycombic ecological adaptations for comparison to what happens when virus-driven energy theft is linked to the hecatombic evolution of all pathology.

See for comparison: Jonas Edward Salk (October 28, 1914 – June 23, 1995) was an American medical researcher and virologist. He discovered and developed one of the first successful polio vaccines.

My comment: The fact that Jonas Edward Salk died in the same year that information about Coulombic interactions was published exemplifies the fact that we still need people like Salk to lead the way towards more scientific progress.

Is everyone who could do that already dead? Have people like Sal Giardina and other apologeticists replaced them. Will any of the works from the early 1990s to 1964 be resurrected before all of humanity is irreversibly impacted?

See for example: Biology, molecular and organismic (1964)

The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.

Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.

Links from the creation of nucleic acid precursors to entropy and mutation-driven evolution are still being addressed by apologeticists who know nothing about physics, chemistry, or molecular epigenetics.
See also: Biblical Creation / Entropy

See for comparison: What is life when it is not protected from virus driven entropy (6 minutes)
I think most people can understand the concept of Creation by God of all biophysically constrained life on Earth. If not, they should be told about the examples, since all examples show that all organisms must eat or die. If they die, they do not reproduce, which means they never became an extant species. Instead, the individuals and/or species became part of the fossil record or they became nothing recognizable to serious scientists as anything more than dirt.
See also: godordirt.org
See also: Virus Documentary | Discovering & Understanding Viruses || How Viruses Work ? (60 minutes)

My comment: Terra Firma is the battlefield mentioned in the video (a village in central Brazil). Stephen Morse, virologist at Rockefeller is fighting on the side of virus-driven entropy, which he attributes to emergence and evolution. For example, His book, Emerging Viruses (Oxford University Press) was selected by “American Scientist” for its list of “100 Top Science Books of the 20th Century”.

My comment: According to the book, our innate immune system emerged and evolved to become the source of all pathology. If the innate immune system is referred to as our “immune system” the word innate changes to evolved, and mutations are linked to evolution in the context of ridiculous neo-Darwinian theories. That is how emerging viruses are automagically linked to all healthy longevity via polycombic ecocological adaptation and to all pathology via hecatombic evolution.
We have come full circle back to the definitions that are used and discussed in Polycombic ecological adaptation as a science, not a theory (2):
See also: The Human Virome

For comparison, see: Mutation-Driven Evolution

Excerpt:

Mutation… includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc.

My comment: The definition above links mutations to any change in any genome. It does not link virus-driven energy theft toi mutations and all pathology.

See for comparison: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

Excerpt:

Single nucleotide substitutions or indels [insertions/deletions] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects [mutations] in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.

My comment: The facts about nutrient energy-dependent single nucleotide substitutions and RNA-mediated amino acid substitutions link hemoglobin variants to healthy longevity and the facts link molecular defects to the pathology of α-, β- or δ-thalassemia, respectively.

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

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

If we wanted to compare the diversity of two forests, we would want to look at climate, elevation, drainage, available nutrients, proximity to human disturbance, soils, etc. Diversity can be impacted by a slew of factors. While this is a fun and rather ridiculous example of how species counts and diversity works, the leap to how this can inform ecology, management, and conservation is clear.

My comment: The fact that nothing known about virus-driven energy theft is included in their comparisons makes the most important of all comparisons irrelevant to their claims about how climate, elevation, drainage, available nutrients, proximity to human disturbance, soils, etc. link ecological variation to polycombic ecological adaptation via the physiology of reproduction in all living genera.
See for comparison: An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells

G540A supports virus replication in mammalian cells while retaining replication ability in avian cells. Host splicing regulator, SF2, interacts with this ESE to regulate splicing of NEP/NS1 mRNA and G540A substitution affects SF2–ESE interaction. The NS1 protein directly interacts with SF2 in the nucleus and modulates splicing of NS mRNAs during virus replication.

Reported as: Single nucleotide change responsible for allowing H7N9 flu to jump from birds to humans found
The identification of the G540A links the single nucleotide polymorphism (SNP) from a biomarker in fowl infected with a flu variant to what was reported as mutation.
Researchers assumed that “…the mutation played a role in allowing the virus to spread between humans once it made the leap from an avian source.”
As usual, they found no evidence to support that ridiculous claim. That ridiculous claim is among many others that theorists thought could be used to link mutations to evolution via mathematical models instead of facts about nutrient energy-dependent pheromone-controlled biophysically constrained RNA-mediated cell type differentiation.

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?

Polycombic ecological adaptation as a science, not a theory (2)

November 1, 2016

by James Kohl with 3 Comments Adaptations Alternative Splicings Autophagy 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

Evolutionary Constraints in the β-Globin Cluster: The Signature of Purifying Selection at the δ-Globin (HBD) Locus and Its Role in Developmental Gene Regulation

Conclusion:

… the results here presented indicate that purifying selection is driving not only HBD evolution but also its neighbor pseudogene, HBBP1. In the light of recent advances in the characterization of the β-globin cluster, we propose that the complex patterns of diversity observed in this genomic region arose from distinct functional constraints related with the intricate process of chromatin and protein interactions coordinating the differential expression of genes at the β-globin cluster during development.

My comment: No experimental evidence of biologically-based cause and effect suggests that any locus of genes or any pseudogene has ever evolved. Purifying selection cannot drive evolution. Only energy-dependent variations can can be linked to polycombic ecological adaptation, and only virus-driven energy theft has been linked to the creation of pseudogenes in the context of biophysical constraints on viral latency.

See for comparison: microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection

Excerpt:

miRNA function is generally limited to cytokine levels in response to RNA viruses

Reported as: Mount Sinai Researchers Use Cellular miRNA-Elimination Tool to Study Viral Infection Dynamics

Excerpt:

…while the loss of miRNAs had a negligible impact on the cell’s immediate reaction to a virus or the short-term biology of the cell, sustained depletion had dramatic results on gene expression that was coupled to a burst of cytokines. The researchers concluded in the paper that miRNA function is limited to modulating the biology of the cell over long periods of time.

My comment: In my model, energy-dependent changes in the microRNA/messenger RNA balance link nutrient energy-dependent changes to all healthy longevity and virus-driven energy theft is linked to all pathology. Over long periods of time, autophagy is the link to polycombic ecological adaptation or virus-driven hecatombic evolution of pathology via energy-dependent biophysically constrained RNA-mediated protein folding chemistry. For example, fixation of amino acid substitutions differentiates all cell types in all individuals of all living genera in the context of the physiology of reproduction. For comparison, virus-driven hecatombic pathology is linked from mutations to all pathology.

Simply put, in my model of polycombic ecological adaptation, differential gene expression is nutrient-dependent and controlled by the physiology of reproduction.

See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Conclusion:

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

My comment: Claims about RNA-mediated polycombic ecological adaptation were first placed into the context epigenetic imprinting in our 1996 review.

See: From Fertilization to Adult Sexual Behavior

Excerpt:

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). 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.

My comment: Polycombic ecological adaptation appears to link energy-dependent epigenetic effects on hormones (i.e., proteins) to chromatin structure in telomeric regions, which links the effect on transcription and silencing of various genes to hormone-organized and hormone-activated affects on behavior. The hormone-organized and hormone-activated behaviors link the epigenetic landscape of yeasts to the physical landscape of supercoiled DNA in species from bacteria to invertebrates and all vertebrates via the de novo creation of G protein-coupled receptors, which link chemotaxis and phototaxis to all biodiversity.

For comparison, see: Mutation-Driven Evolution

Excerpt:

Mutation… includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc.

My comment: The definition above links mutations to any change in any genome.

See for comparison: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

Excerpt:

Single nucleotide substitutions or indels [insertions/deletions] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects [mutations] in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.

My comment: The facts about nutrient energy-dependent amino acid substitutions link hemoglobin variants from ecological adaptation to healthy longevity and the facts also link molecular defects from mutations to the pathology of α-, β- or δ-thalassemia, respectively. It would be difficult to include facts about biophysically constrained energy dependent cell type differentiation in the context of any other model that links amino acid substitutions to healthy longevity and links mutations to all pathology in all living genera.

See for example: Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

Excerpt:

…James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research.

My comment: The claims of a biologically uninformed undergraduate student reviewer were placed into the context of modern evolutionary theory, which involves Masatoshi Nei’s simple-minded revision of neo-Darwinian pseudoscientific nonsense. Nei does not compare his theory of mutations to the facts about nutrient energy-dependent fixation of amino acid substitutions in supercoiled DNA. The problem appears to be the use of the term “mutation” in the textbook published on the same day as my 2013 review was published.

I linked the energy-dependent fixation of amino acid substitutions to all healthy longevity. Nei’s textbook misrepresentations did not link anything to healthy longevity, but linked mutations to what I claimed are nutrient-dependent pheromone-controlled polycombic ecological adaptations.

I failed to include what is known about energy-dependent codon optimality in the context of polycombic ecological adaptations because there was no experimental evidence of biologically-based cause and effect to support those claims at the time of our 1996 review or my 2013 review. For comparison, there has never been any experimental evidence of biologically-based cause and effect to support claims about mutation-driven evolution. Simply put, nothing known to serious scientists about cell type differentiation suggest that mutation-driven evolution can occur.

For comparison, see: New analysis of big data sheds light on cell functions
Excerpt:

With today’s technology, scientists are able to generate data about a cell’s or organism’s complete set of genes, proteins, RNA profiles, metabolites and much more—known as omic data. Using omic data, scientists can model complex biological interactions and gain a more holistic view of different cellular processes.

See also: Research Topic Multi-omic Data Integration

Excerpt:

Stable, predictive biomarkers and interpretable disease signatures are seen as a significant step towards personalized medicine. In this perspective, integration of multi-omic data coming from genomics, transcriptomics, glycomics, proteomics, metabolomics is a powerful strategy to reconstruct and analyse complex multi-dimensional interactions, enabling deeper mechanistic and medical insight.

My comment: Glycomics, transcriptomics, proteomics, metabolomics and genomics have established fact about the biological basis of complex multi-dimensional interactions that link the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria from quorum sensing to the molecular mechanisms that enable deeper mechanistic and medical insight in the context of the National Microbiome Initiative and Precision Medicine Initiative.

See for example: ‘Oming in on RNA–protein interactions

Excerpt:

…the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities without the need to create additional genes and without affecting existing proteins [4-6].

See for comparison: 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…. That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

My comment: Detailed examples of how the interactions between pre-mRNA and alternative splicings create new genes in the fine-tuned energy-dependent functional structure of supercoiled DNA explain how all cell types of all individuals of all living genera are protected from virus-driven energy theft. Energy-dependent RNA-mediated amino acid substitutions are fixed in organized genomes via the physiology of reproduction, which helps to prevent the transgenerational epigenetic inheritance of nearly all pathology by linking innate immune system to supercoiled DNA.

For comparison, viruses steal the energy that is required for cell type differentiation, which is how mutations are linked to all pathology. All differences between healthy longevity and virus-driven human pathology can be explained in the context of how nutrient energy-dependent microRNAs. The nutrient energy-dependent microRNAs are carried by erythrocytes in species with circulating blood.

See: Pitfalls of analysis of circulating miRNA: role of hematocrit

MicroRNAs are are delivered to the cell types on an as needed basis. When too few nutrient energy-dependent microRNAs are available, viruses use the existing energy they steal from cells to replicate. Eventually, the replication of the viruses causes the mutations, which are linked to all pathology. That’s why it is important to revisit the facts presented in the context of this article, which was published on 10/26/16

See: Multi-omic data integration enables discovery of hidden biological regularities
I reported this here as: Polycombic ecological adaptation as a science, not a theory for comparison to Biological evolution as a philosophy, not a science.
Despite several attempts to discuss the difference between science and philosophy, no progress was made.
See for example: Evolutionary assumptions (revisited)
See also the impasse that was reached in this attempt to discuss the anti-entropic virucidal energy of the sun.
It is worth joining The Battlefield FB group to see that others would rather hold on to their theories and opinions despite the overwhelming amount of experimental evidence that I have used to support my claims. For me, it is time to move forward and focus on the rediscovery of hidden biological regularities.
Finally, others have discovered that small intranuclear proteins generate alternative splicing techniques of pre-mRNA, which is how microRNAs link hydrogen-atom transfer in DNA base pairs in solution to the conserved molecular mechanisms of energy-dependent cell type differentiation, and to all cell type differences in all individuals of all living genera.
For comparison, this is an example of how virus-driven energy theft is linked viral replication and to virulence:
Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

For an example of how nutrient energy-dependent RNA-mediated amino acid substitutions are linked to healthy longevity via the physiology of reproduction, see:

…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: The facts stated above have forced theorists to invent evolutionary cell biology.
See Evolutionary cell biology: Two origins, one objective
Reported as: Why some junk DNA is selfish, but selfish genes are junk
Excerpt:

“A commonly held but incorrect stance is that essentially all of evolution is a simple consequence of natural selection.” They point out, for example, that many pathways to greater complexity of both genomes and cells don’t confer any selective fitness.

My comment: Greater complexity requires a link from ecological variation to polycombic ecological adaptation, which links supercoiled DNA to protection from the virus-driven hecatombic evolution of all pathology.
My comment: New theories are worthless if they do not include information on the role of energy in cell type differentiation or the role of virus-driven energy theft in all pathology.
See for comparison the facts about: Detection of hemoglobinopathies and thalassemias using automated separation systems
See also: In vivo correction of anaemia in β-thalassemic mice by γPNA-mediated gene editing with nanoparticle delivery
Excerpt:

The combination of nanoparticle delivery, next generation γPNAs and SCF treatment may offer a minimally invasive treatment for genetic disorders of the blood that can be achieved safely and simply by intravenous administration.

My comment: That fact suggests all suffering and death caused by hemoglobin variants is caused by neo-Darwinian theorists who do not know how the variants link ecological variation to polycombic ecological adaptation.

Reported as: Scientists edit gene mutations in inherited form of anemia
Excerpt:

The researchers found that the technique corrected the mutation to such a degree that the mice no longer had symptoms of thalassemia. After 140 days, they tested hemoglobin levels in the animals and found them to be normal.
“The fundamental result here is that with nanoparticles containing PNAs, along with template DNA, and simple IV infusion of molecules, we achieved enough gene editing to effectively cure the anemia in mice that had thalassemia,” Glazer said.

My comment: The ability to correct the mutation requires a link from energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solutions such as blood. That’s how their IV therapy works. It changes the microRNA/messenger RNA balance and that forces the innate immune system to repair the damaged DNA.
See also: Two novel loci, COBL and SLC10A2, for Alzheimer’s disease in African Americans
Excerpt:

Two SNPs at novel loci, rs112404845 (P = 3.8 × 10−8), upstream of COBL, and rs16961023 (P = 4.6 × 10−8), downstream of SLC10A2, obtained genome-wide significant evidence of association with the posterior liability.

Reported as: Study Identifies Two New Genes Responsible for Alzheimer’s in African Americans
Excerpt:

In 2013, a genome-wide association study of AD in more than 5,500 African Americans identified two genetic risk factors for AD. This study looked at genetic variants across subjects’ entire genome and compared their frequency in cases versus controls.
By doing so they were able to identify two new genes (COBL and SLC10A2) associated with risk of AD in African Americans.

My comment: The author’s study results link hydrogen-atom transfer in DNA base pairs in solution to energy-dependent changes in the microRNA/messenger RNA balance. The neuroscience news report claims they identified two new genes. The neuroscience news report then links the genes — instead of the energy-dependent changes — to the disease in a human population. Many African Americans are examples of how ecological variation has been linked to polycombic ecological adaptation via hemoglobin variants. The adaptations include amino acid substitutions linked to the stability of organized genomes in populations where malaria is endemic. Failed adaptations are included in examples of virus-driven energy theft linked to mutations and the pathology of Alzheimer’s disease.

My comment: The ability to edit out gene mutations clearly links RNA-mediated amino acid substitutions to supercoiled DNA and all biodiversity.
See also: Inventing neo-Darwinism
See also: Pioneering Geneticist Explains Ambitious Plan to “Write” the Human Genome

Many Edits, All at Once

Excerpt:

…he notes that with an editing tool like CRISPR, one base out of many can be altered, but with a synthesis approach, a hundred edits could be made. This sort of change, he tells JAMA, could make a cell resistant to multiple viruses.

My comments: All the changes in base pairs may already have been linked from natural selection for codon optimality and energy-dependent changes in RNA-mediated cell type differentiation to supercoiled DNA, which links the physiology of reproduction from the innate immune system to fixation of the amino acid substitutions that differentiate the cell types of all living genera. If so, what might happen to an organized genome when a hundred edits are made?

Will anyone be able to stop the hecatombic evolution of pathology via the polycombic ecological adaptation, which links autophagy to healthy longevity via protection of organized genomes from virus-driven entropy?

See also: Yale scientists edit gene mutations in inherited form of anemia Genetics & Genomics

A new gene therapy is being tested for its ability to treat thalassemia, a form of anemia caused by genetic mutations. So far, scientists have successfully corrected gene mutations causing the disease in mice, and now researchers are interested in seeing if the same approach will work effectively in humans.
“The fundamental result here is that with nanoparticles containing PNAs, along with template DNA, and simple IV infusion of molecules, we achieved enough gene editing to effectively cure the anemia in mice that had thalassemia. We demonstrated we have extremely low off-target effects.”

See for comparison:

Product Development Pipeline

Excerpt:

Each microRNA mimic in our pipeline is designed to replicate the activity of a single tumor suppressor miRNA and regulate the expression of key oncogenes across multiple oncogenic pathways which can prevent proliferation and induce apoptosis in cancer cells.

See also: VACRC Projects

Excerpt: Future Projects

The Influence of Carbon Dioxide Enhancement on Plant Growth

Thermoregulation in Honey Bees

Biochemistry and Taxonomy in Pine Trees

The Formation of Multiple Tree Rings in Bristlecone Pine Trees

The VACRC suddenly seems willing to take everything I have claimed about RNA-mediated cell type differentiation during the past twenty years and begin to investigate the claims. This would have been a desirable outcome 20 years ago, but now it might prevent progress via use of my model. The model links energy-dependent changes from angstroms to ecosystems in all living genera, it and links virus-driven energy theft to all pathology.

The Pacific Yew Tree and production of taxol is an example of how the physi0logy of reproduction in soil bacteria can be linked from plant growth to the honeybee model organism of thermoregulation and behavior, which must be linked to the biochemistry and taxonomy of all species. That becomes meaningful via the explanatory power of a model that links RNA-mediated amino acid substitutions to all energy-dependent biodiversity via the conserved molecular mechanisms of polycombic ecological adaptation we detailed in our 1996 review.

However, when others wait too long to accept a model that may already have led to a paradigm shift, they may also realize it. That fact was addressed by Kaveli Kull in the context of next week’s meeting of the Royal Society.

See: Kalevi Kull: Censorship & Royal Society Evo Event

Excerpt:

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.

My comment: Some work by young earth creationists has been at the cutting edge since 1996, as indicated here: Where do viruses come from?

Excerpt:

‘Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,’ says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.”9

My comment: 9 is Holmes, B. (1996) Who Rules the Waves? New Scientist 152(2054):8-9, supp I have not read it in its entirety but the claim fits into the context of everything else I have learned about physics, chemistry, and conserved molecular mechanisms of RNA-mediated cell type differentiation, which appears to be biophysically constrained in all living genera via their nutrient-dependent pheromone-controlled physiology of energy-dependent reproduction.

Filtering light through a prism to identify tissue type

Hydrogen-atom energy in DNA base pairs

September 19, 2016

by James Kohl with One Comment Adaptations biophotonics Diseases & Disorders Ecology Light Energy Model Organisms Neuronal Plasticity Physics RNA Directed RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity Variations

Hydrogen atom transfer (HAT) reactions are ubiquitous and play a crucial role in chemistries occurring in the atmosphere, biology, and industry.

My comment: The link from physics to chemistry and the conserved molecular mechanisms of biologically-based RNA-mediated cell type differentiation has been the focus my works for more than 20 years, even before I knew what I would need to explain about the energy-dependent links from angstroms to ecosystems via hydrogen-atom energy in all living genera.
See also: For first time, researchers see individual atoms keep away from each other or bunch up as pairs
Excerpt:

Different configurations of electrons give rise to specific elements, making carbon atoms, for instance, distinct from hydrogen atoms.

My comment: Without the different configurations of electrons, energy-dependent changes in angstroms could not be linked from hydrogen-atom transfer (HAT) in DNA base pairs in solution to all biodiversity in all ecosystems. Simply put, the sun’s biological energy must be linked from atmospheric chemistry to biophysically constrained protein folding chemistry on Earth.
When these interactions are seen for the first time the experimental evidence must confirm theories. Otherwise physicists will try to come up with new untestable theories to stall scientific progress. Serious scientists make progress when experimental evidence is accepted. Chemists typically know what to accept. So do molecular biologists.
What do evolutionary theorists or other social scientists know about physics, chemistry, or molecular epigenetics? How do pseudoscientists known what to accept when they already have accepted only theories?
For comparison, serious scientists know that angstroms measure distance, and every angstrom is dynamic in the context of energy-dependent RNA-mediated cell type differentiation. How can any serious scientist understand the claims of theorists made in the context of articles like this:
Humans and Neanderthals had sex. But was it for love? An investigation
Excerpt:

We know for sure humans and Neanderthals had sex because of a Swedish scientist named Svante Pääbo, who “more or less invented the field of paleogenetics,” Elizabeth Kolbert wrote in a terrific New Yorker article in 2011.

My comment: Elizabeth Kolbert lied and used Svante Pääbo’s works to support her ridiculous claim:

We know for sure humans and Neanderthals had sex…

Serious scientists know that Svante Pääbo is the senior author of two articles. The two articles linked Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees and Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates.
Natural selection for the de novo creation of olfactory receptor genes and the loss of genes is not an indicator that humans and Neanderthals had sex. It is an indicator that natural selection for energy-dependent codon optimality occurred in the context of the physiology of reproduction in all primates. For contrast, all serious scientists know that members of two different species do not have sex. Chromatin remodeling and chromosomal rearrangements limit fertility among species via their nutrient-dependent pheromone-controlled physiology of reproduction and their behavior. The behavior is linked to energy-dependent codon optimality via the physiology of reproduction, not by sex between consenting humans and Neanderthals.
Is is silly to ask questions about sex for love without consideration of fertility, since the sexual interactions must be linked to survival of the species via biophysically constrained RNA-mediated protein folding chemistry in the context of the physiology of reproduction. The biophysical constraints are energy-dependent, but the theorists’ and journalists’ preference for fiction is clear.
Excerpt:

Robert Sawyer is a science fiction author who won the Hugo Award — one of sci-fi’s highest honors — for his 2002 book Hominids, a story that imagines a parallel world where Neanderthals survived and we didn’t. In the book (which spawned a trilogy), a Neanderthal physicist opens up a rift between the worlds and falls in love with a human.

For comparison, see this presentation text about Greg Bear’s novels in which he detailed for his non-technical audience how the nutrient energy-dependent pheromone-controlled physiology of reproduction is linked from RNA-amino acid substitutions to all cell type differentiation in all individuals of all species. The Darwin Code
See also: Structural and Functional MRI Differences in Master Sommeliers: A Pilot Study on Expertise in the Brain
Excerpt:

This study identified enhanced structural and functional patterns in the olfactory network of sommeliers. These findings are consistent with the learning they undergo in achieving the status of Master Sommelier. Furthermore, the volume of a region of the brain involved in olfactory memory was associated with experience, suggesting that the continued training results in morphological changes of the brain. These results speak to the plasticity of the adult brain in response to sensory expertise.

Reported as: Smelling Lots Of Wine Makes Your Brain Alzheimer’s Resistant

Overall, these differences suggest that specialized expertise and training might result in enhancements in the brain well into adulthood,” the study states. “This is particularly important given the regions involved, which are the first to be impacted by many neurodegenerative diseases.

See also: What Sensory Receptors Do Outside of Sense Organs
My comment to the Scientist (I have posted: 361 comments so far)

20 years ago, we published: From Fertilization to Adult Sexual Behavior, which was a review of RNA-mediated cell type differentiation. We included a section on molecular epigenetic in the Hormones and Behavior review.

Unfortunately, few people realize that natural selection for energy-dependent codon optimality links the de novo creation of genes from the creation of G protein-coupled receptors to chemotaxis and to phototaxis before biophysically constrained energy-dependent biodiversity via RNA-mediated protein folding biochemistry can be linked to all biodiversity by amino acid substitutions.
When others report that mutations are linked to pathology, they seem to miss the fact that virus-driven energy theft causes the mutations. Nutrient-energy dependent viral latency has gone missing from explanations that would otherwise link what is known about biologically-based cause and effect from physics to chemistry and everything known about molecular epigenetics.
See also: Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization
My comment: Pseudoscientists could challenge representations like this if they had experimental evidence for comparison. They don’t. They have only their ridiculous theories, which they report in the story about sex between modern humans and Neanderthals. It is unadulterated pseudoscientific nonsense and nothing more than an unsubstantiated fictional account. It is not science fiction. The theorists claims are not scientifically based.
See for comparison: Role of olfaction in Octopus vulgaris reproduction and Two fatty acyl reductases involved in moth pheromone biosynthesis
Both articles cite Kohl (2013) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
See also: The Ancient Origins of Consciousness: How the Brain Created Experience
Excerpt:

12. Plotnick, Dornbos, and Chen (2010). Others who advocate smell-first are Lucia Jacobs (Jacobs, 2012), who says the building of smell maps of environmental space came first and James Kohl (Kohl, 2013), whose model says chemical ecology is the main driver of adaptive evolution. — p. 263

My comment: Chemical ecology is the main driver of energy-dependent ecological adaptations. It is not not the driver of mutation-driven evolution, and so far there is no other model for comparison to my model of chemical ecology. I deliberately used the term adaptive evolution to see if someone would take the bait and offer another model for comparison. No one did.
See also: How Psychiatrist Jon Lieff Turned an Interest in Cellular Intelligence into Award-Winning Blogging!
My comment: Lieff still presents cellular intelligence in the context of evolution. He ignores what is known about hydrogen-atom energy in DNA base pairs in solution. That shows how successful a blogger can be if they simply fail to address what is known about biophysically constrained RNA-mediated cell type differentiation. His focus is on evolution! That means he does not need to explain anything about how evolution occurs, or explain what he thinks cellular intelligence is or where it came from!
See for comparison: Direct interrogation of the role of H3K9 in metazoan heterochromatin function
Reported as: Tight DNA packaging protects against ‘jumping genes,’ potential cellular destruction
Tight DNA is supercoiled DNA and it protects the orgnaized genomes of all living genera from virus-driven energy theft and genomic entropy. Simply put, supercoiled DNA biophysically constrains virus-driven energy theft, which is the only way to establish a link from ecological variation to ecological adaptation without inventing another ridiculous theory.

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

Nutrient energy-dependent microRNAs are the obvious link from olfaction to biophysically constrained RNA-mediated protein folding chemistry, plasticity, and prevention of all pathology.
See for example: Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization

Supercoiled DNA is the link to viral latency, which is the link to healthy longevity.

See also, from the Neuroscience FB group “As simple as random can be”
See also: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
My comment: There is no experimental evidence of biologically-based cause and effect that links anything except energy or energy theft to the species-specific COMT Val158Met amino acid substitution during life history transitions and the development of morphological and behavioral phenotypes.

COMT val158met polymorphism and molecular alterations in the human dorsolateral prefrontal cortex: Differences in controls and in schizophrenia
Excerpt:

…the COMT val158met polymorphism is not found in species other than humans (Palmatier et al., 1999).

My comment: That fact makes the COMT val158met polymorphism a “smoking gun” in the context of energy-dependent de novo gene creation and virus-driven energy theft that links gene losses to loss of function via differences in G protein-coupled receptors.
Dopamine Neuron-Specific Optogenetic Stimulation in Rhesus Macaques
G protein-coupled receptor kinases as regulators of dopamine receptor functions
Subsecond Regulation of Synaptically Released Dopamine by COMT in the Olfactory Bulb
Programmable RNA-binding protein composed of repeats of a single modular unit
Excerpt from the conclusion:

… Pumby may present a simplified context in which to insert Pumilio modules to study how specific amino acids contribute to the emergent properties of modular RNA binding, independent of position-specific effects.

Wasted Templeton Funding (3)

April 22, 2016

by James Kohl with No Comment Adaptations Diseases & Disorders Ecology Human Pheromones Model Organisms 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

Templeton grant funds evolution rethink

Excerpt:

…parents can influence offspring not just through their DNA but by passing on the microorganisms they host or by transmitting epigenetic marks to subsequent generations. “Innovation may be a developmental response that becomes stabilized through genetic changes,” explains Armin Moczek, an evolutionary developmental biologist at Indiana University, Bloomington.

My comment: He has not explained how nutrient energy-dependent changes in base pairs link hydrogen-atom transfer in solutions from microRNA flanking sequences and adhesion proteins to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. But, when I first saw the name Moczek, I was reminded of Danesh Moazed, who has been linking biologically-based cause and effect from RNA-mediated cell type differentiation in yeasts to humans for as long as I have.
1996 A Deubiquitinating Enzyme Interacts with SIR4 and Regulates Silencing in S. cerevisiae
2015 RNA-mediated epigenetic regulation of gene expression
See for comparison:
1996 From Fertilization to Adult Sexual Behavior
2013 Nutrient-dependent/pheromone-controlled adaptive evolution: a model
2015 You are already here: Welcome to RNA-Mediated

A Message From J.V.Kohl:

Here you will find information that links physics, chemistry, and molecular epigenetics via RNA-mediated events such as the de novo creation of olfactory receptor genes in order to encourage a public discussion of a paradigm shift.

See also this invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
This abstract has already been accepted in the context of a poster session I plan to present at: Genetics and Genomics

RNA-mediated physics, chemistry, and molecular epigenetics

Olfaction and the innate immune system link energy as information from the epigenetic landscape to the physical landscape of supercoiled DNA. The sun’s biological energy is the source of the information that links angstroms to ecosystems via physics, chemistry, and molecular epigenetics.
RNA-mediated protein folding chemistry and amino acid substitutions link the anti-entropic quantized energy of sunlight from the virucidal effects of ultraviolet (UV) light to healthy longevity via biophysically-constrained energy-dependent hydrogen-atom transfer in DNA base pairs in solution and cell type differentiation.
Biomarkers link energy-dependent differences in base pairs and amino acid substitutions to biosignatures across the healthy life span. RNA-mediated amino acid substitutions also reveal the increasing complexity of interactions among cell types as pathology progresses. For comparison, successful reproduction links energy from supercoiled DNA to protection of all organized genomes from virus-driven energy theft and pathology.
This model links the sun’s biological energy from top-down causation in microbes to the most recent model of bottom-up gene activation and cell type differentiation in vertebrates. Citations to extant literature provide examples of what is currently known about how ecological variation leads to biophysically constrained cell type differentiation in the context of nutritional epigenetics and Precision Medicine, which clearly link metabolic networks and genetic networks to pharmacogenomics.
See also: Virus fighter may have played a key role in human evolution

Ignore the evidence: Rachel Feltman

March 15, 2016

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

“There is incontrovertible evidence that Alzheimer’s Disease has a dormant microbial component. We can’t keep ignoring all of the evidence”

–Professor Douglas Kell, Manchester University

Experts Say There’s a Herpes-Alzheimer’s Link

Excerpt:

…herpes has been linked to damage in the central nervous system and the limbic system, which is associated with mental decline and personality changes, the Telegraph reported. The experts called for a deeper investigation into the connection.

Calm down: Herpes probably isn’t going to give you Alzheimer’s

Excerpt:

…implicating HSV — a disease that already gets way more stigma than it is due — as the dastardly culprit behind a devastating disease is not based on sound science.

My comment: It wasn’t an implication. Their claims also linked HSV and other microbes from loss of olfactory acuity and specificity to all neurodegenerative diseases:
(iii) Olfactory dysfunction is an early symptom of AD [58]. The olfactory nerve, which leads to the lateral entorhinal cortex, the initial site from where characteristic AD pathology subsequently spreads through the brain [59, 60], is a likely portal of entry of HSV1 [61] and other viruses [62], as well as Chlamydia pneumoniae, into the brain [63], implicating such agents in damage to this region.
Rachel Feltman seems to keep suggesting that all evidence of virus-driven energy theft, which is linked from olfaction to entropy in all organized genomes, should be ignored.

See for comparison:

In the second part of this poster, four citations link virus-driven energy theft to all pathology. Part 3 links nine more citations and examples of biologically-based cause and effect from the Zika virus to differences in human craniofacial and behavioral phenotypes.

Zika Update

Summary: Virus found in breastmilk; another disease linked to Zika infection; some mosquitoes resistant to pesticide; genetically engineered–mosquito field trials could proceed

My comment: Will Rachel Feltman suggest that others also ignore facts about transgenerational epigenetic inheritance of the Zika virus in hopes that she can maintain some degree of credibility as a science journalist?

What Do We Actually Know About Pheromones?

Excerpt:

If you, as a human, don’t have a sense of smell, it doesn’t render you behaviorally incapable.

Excerpt:

But Kohl’s products, which he likens to food spices (“They give you an extra kick!”), make some researchers roll their eyes. Dr. Jim Pfaus, professor of psychology at Concordia University in Montreal, is one of them.

Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
My comment: The nutrient-dependent production of species-specific pheromones links everything known about the development of the gonadotropin releasing hormone (GnRH) neuronal system in mammals from luteinizing hormone and the proliferation of neural stem cells to neurogenesis during life history transitions in humans via humanized mouse models and immune therapy research.
Everything known about cell type differentiation in all living genera starts with the innate immune system of all cell types and links atoms to ecosystems. If nutrient-dependent RNA-mediated events do not lead from microRNAs to adhesion proteins and supercoiled DNA via the physiology of reproduction, individuals die and species become extinct.

A simple physical mechanism enables homeostasis in primitive cells

Excerpt:

We suggest that such systems, wherein short oligonucleotides reversibly inhibit functional RNAs, could have preceded sophisticated modern RNA regulatory mechanisms, such as those involving miRNAs.

My comment: That suggests energy-dependent hydrogen-atom transfer must already have occurred, since there is no other way currently known to link the sun’s anti-entropic virucidal energy to the supercoiled DNA that protects organized genomes from virus-driven entropy in all living genera in the context of their nutrient-dependent physiology of reproduction.
Reported as: Simple mechanism may have allowed primitive cells to maintain internal conditions
See also: Base-pairing protects DNA from UV damage
and Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution
Szostak’s group seems most likely to be the next to report the link from energy-dependent hydrogen-atom transfer in DNA base pairs in solution to the creation of all cell types and the survival of all species via nutrient-dependent RNA-mediated DNA repair linked to supercoiled DNA that protects organized genomes from virus-driven entropy. For example, he already appears to know about the importance of nutrient-dependent amino acid substitutions.

Electrostatic Localization of RNA to Protocell Membranes by Cationic Hydrophobic Peptides

Excerpt:

With peptides that have phenylalanine as the hydrophobic amino acid, there appears to be a minimum number of arginine residues necessary to enable localization to oleic acid membranes…

My comment: If others would simply start from the creation of the first cell in the context of quantum physics and the de novo creation of the receptors that let nutrients pass through the cell wall, they might better understand how pH-dependent life and death are determined by the balance of nutrient-dependent microRNAs that contribute to RNA-mediated DNA repair that is needed to prevent the virus-driven entropy of all organized genomes.
For comparison, see: Mitonuclear Epistasis for Development Time and its Modification by Diet in Drosophila
Abstract excerpt:

…mitonuclear epistases are context-dependent; suggesting the selective pressure acting on mitonuclear genotypes may vary with food environment in a genotype-specific manner.

Conclusion:

We found evidence for pervasive mitonuclear effects and 3-way interactions for development time in the panel, and suggest that mitochondrial DNAs (and the genes they contain) act as capacitors to release cryptic genetic variation in alternative environments. We have uncovered interesting genotypes that will be the focus of future quantitative genetic mapping, and identified a sexual dichotomy in the relationship between phenotypic and genotypic expression. A striking outcome of these studies has been the unpredictable fitness consequences of different mitonuclear combinations. Efforts to test the vigor of mitonuclear combinations in human cell lines from diverse backgrounds could provide important information about genetic risk factors associated with mitochondrial replacement therapies in humans.

My comment: They appear to have found evidence that nutrient energy-dependent changes must be linked from microRNA flanking sequences and hydrogen-atom transfer in DNA base pairs to the physiology of reproduction, which links ecological variation to ecological adaptation in all living genera.
Darwin suspected that and stated his evidence in the context of his “conditions of life” at a time when he knew nothing about mitochondria, genes, or risk factors associated with gene editing.
See also: You are what your parents ate!
Excerpt:

In their theories on heredity and evolution, both Jean-Baptiste Lamarck and Charles Darwin explicitly stated that characteristics and traits that parents acquire during their lifetime through interaction with the environment could be passed on to their offspring. It was not until the neo-Darwinist “Synthetic Theory of Evolution,” which combines the theories of natural selection by Darwin and of genetics by Gregor Mendel, that the inheritance of acquired traits was rejected. “From the perspective of basic research, this study is so important because it proves for the first time that an acquired metabolic disorder can be passed on epigenetically to the offspring via oocytes and sperm- similar to the ideas of Lamarck and Darwin,” said Professor Johannes Beckers.

My comment: If not for the pseudoscientific nonsense about mutations and evolution touted by neo-Darwinists and human ethologists, all pathology would by now have been linked from stress to changes in pH and to viral replication via energy theft of hydrogen-atoms the must be transfered in DNA base pairs in solution to link RNA-mediated amino acid substitutions to the supercoiled DNA that protects all organized genomes in all living genera from virus-driven entropy.

From angstroms to ecosystems and entropy

February 24, 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-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations

Text with these references to follow. The two submissions should be available within the month. I will announce the availability and add the text with links to the citations at that time.
From hydrogen-atom transfer in DNA base pairs to ecosystems
[1] Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
[2] Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution.
[3] Photonic Maxwell’s Demon
[4] Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
[5] Observation of Gravitational Waves from a Binary Black Hole Merger
[6] Re-criticizing RNA-mediated cell evolution: a radical perspective
[7] From Fertilization to Adult Sexual Behavior
[8] Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing
[9] Long non-coding RNAs in innate and adaptive immunity
[10]Defective control of pre–messenger RNA splicing in human disease
[11] What is Life?
[12] Conditional iron and pH-dependent activity of a non-enzymatic glycolysis and pentose phosphate pathway
[13]Structural diversity of supercoiled DNA
[14] Metabolic Reprogramming with a Long Noncoding RNA
[15] New insights into the hormonal and behavioural correlates of polymorphism in white-throated sparrows, Zonotrichia albicollis
[16] The metabolic background is a global player in Saccharomyces gene expression epistasis
[17]Dynamics of epigenetic regulation at the single-cell level
[18] A new view of transcriptome complexity and regulation through the lens of local splicing variations
[19] Pan-neuronal imaging in roaming Caenorhabditis elegans
[20] Distinct Circuits for the Formation and Retrieval of an Imprinted Olfactory Memory
[21] System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
[22] Nutrient-dependent/pheromone-controlled adaptive evolution: a model
[23] Role of olfaction in Octopus vulgaris reproduction
[24] Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems
[25] Mitochondrial functions modulate neuroendocrine, metabolic, inflammatory, and transcriptional responses to acute psychological stress
[26] Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity http://dx.doi.org/10.1038/ncb3227
[27]Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
RNA-mediated molecular epigenetics and virus-driven entropy
[1] The phylogenetic utility and functional constraint of microRNA flanking sequences
[2] Structural diversity of supercoiled DNA
[3] UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair
[4] Phosphorylation-Mediated Regulation of Alternative Splicing in Cancer
[5] An Epigenetic Signature for Monoallelic Olfactory Receptor Expression
[6] Cyanobacteria use micro-optics to sense light direction
[7] Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function http://dx.doi.org/10.1038/nature16955
[8] Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution
[9] RNA-Mediated Regulation of HMGA1 Function
[10] An expanded sequence context model broadly explains variability in polymorphism levels across the human genome
[11] The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
[12] miR-30e controls DNA damage-induced stress responses by modulating expression of the CDK inhibitor p21WAF1/CIP1 and caspase-3
[13] Redefining part of 300 year-old classification system for grouping members of the animal kingdom
[14] Systematic microRNAome profiling reveals the roles of microRNAs in milk protein metabolism and quality: insights on low-quality forage utilization
[15] Human milk miRNAs primarily originate from the mammary gland resulting in unique miRNA profiles of fractionated milk
[16] Neuroscience of Early-Life Learning in C. elegans
[17] Differential Odour Coding of Isotopomers in the Honeybee Brain
[18] Breast Milk Sugars Support Infant Gut Health
[19] C. elegans lifespan extension by osmotic stress requires FUdR, base excision repair, FOXO, and sirtuins

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.

The Light and Darkness of "Evolution 2.0"

February 9, 2016

by James Kohl with One Comment Adaptations Diseases & Disorders Ecology Light Energy Model Organisms 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

The light of evolution in the oft-cited work by Dobzhansky (1973) is the energy from sunlight. 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.
Excerpt from Dobzhansky (1973)

…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: Viruses steal the energy that is required for nutrient-dependent RNA-mediated cell type differentiation in the context of RNA-mediated amino acid substitutions.
Authors’ comment on Koel et al., (2013): The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
My comment: When a virus steals energy from a cell, it uses the energy to support viral replication, and viral replication perturbs nutrient-dependent cell type differentiation.
Excerpt from Taylor et al (2015):

After 96 hours of incubation of AR2 and Pf0-2x at room temperature on SMM, two breakout mutations were visible, conferring first slow (AR2S and Pf0-2xS) and then fast (AR2F and Pf0-2xF) spreading over the agar surface (Fig. 1A). The AR2F strain produces flagella, but we could not detect flagella in electron microscopy samples for AR2S (Fig. 1B). Genome resequencing revealed a single-nucleotide point mutation in ntrB in strain AR2S, causing an amino acid substitution within the PAS domain of the histidine kinase sensor NtrB [Thr97→Pro97 (T97P)] (13). The fast-spreading strain AR2F had acquired an additional point mutation in the σ54-dependent EBP gene ntrC, which alters an amino acid (R442C) within the DNA binding domain (Table 1 and table S2).

My comment: Collectively, three articles established the link from sunlight to RNA-mediated cell type differentiation via microRNAs and adhesion proteins linked to supercoiled DNA and chromosomal rearrangements in the context of the physiology of reproduction. But, they individually and collectively reported their findings in terms of mutations and evolution.
See for comparison: Feedback loops link odor and pheromone signaling with reproduction and What is Life?
My comment: An intelligent person need look no further than what is known about life in the context of the nutrient-dependent physiology of reproduction, which links all invertebrates to all vertebrates. After a brief review, they could still probably grasp the fact that supercoiled DNA protects organized genomes from virus-driven entropy. If an intelligent person did not look at the role of viruses, they might make the claims made by neo-Darwinian evolutionary theorists. That is why it is important to note that:

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

I was informed by the Royal Society science program office that there will be no formal presentations on viruses, per se, which seems peculiar considering viruses are now understood to be the biggest part of the biosphere, and a key reason for paradigm shift. Viruses and microbes — both organisms — were left out of the modern synthesis.

My comment: Why is a meeting that supposedly will address the evolution paradigm shift not going to include anyone who knows about virus-driven genomic entropy? Most serious scientists already know that …gradual mutation followed by selection has not, as a matter of fact, been demonstrated to be necessarily a cause of speciation.
That fact makes the motives of the meeting organizers increasingly suspicious. Clearly, the role of virus-driven genomic entropy msut be discussed in the context of a paradigm shift. The paradigm shift must also include what is known about nutrient-dependent RNA-mediated DNA repair. The nutrient-dependent repair mechanisms link metabolic networks to genetic networks in all living genera via the innate immune system.
See: Noncoding RNA –NORAD– Regulates Genomic Stability by Sequestering PUMILIO Proteins
Excerpt:

Interestingly, it was recently reported that NORAD (LINC00657) is induced by hypoxia in human endothelial cells (Michalik et al., 2014), suggesting broader roles for NORAD in cellular stress responses. How NORAD influences the functional outputs of these and other stress response pathways, and the broader roles of NORAD in normal physiology and disease, represent important areas for future research.

My comment: The immune system is the interface between stress-related effects on cell types vs healthy longevity. Stress-related proliferation of viruses links viral microRNAs to perturbed RNA-mediated protein biochemistry that is typically constrained by hydrogen-atom transfer in DNA base pairs. Constraint-breaking mutations show up quickly and are consistently linked to outcomes via changes in thermodynamic cycles of protein biosynthesis and degradation that can be measured via changes in the pH of human body fluids or via spectophotometry. Both types of measurements assess nutrient-energy theft by viruses.
See for example: Molecular requirements for a pandemic influenza virus: An acid-stable hemagglutinin protein
Excerpt:

These studies link a fundamental property, activation energy of a fusion protein measured as its pH of activation (acid stability), to the ability of zoonotic influenza viruses to cause a human pandemic.

Reported as: Acid-sensitive molecular changes contribute to the emergence of pandemic influenza
Excerpt:

“The hemagglutinin protein plays a central role in human flu pandemics, yet until now the molecular properties required for pandemic viruses have remained largely undefined,” Russell said. “Our findings suggested that one requirement for a pandemic influenza A virus was an acid-stabilized protein with an activation pH of 5.5 or less, which was sufficient to allow airborne human-to-human transmission at the start of the 2009 H1N1 pandemic.”

Koel et al., (2013) revisited: The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
My comment: In the context of my model, virus-linked energy theft from specific cell types led to the stability of an acid-stabilized protein in the virus with an activation pH of 5.5 or less via a single amino acid, which allowed “…airborne human-to-human transmission at the start of the 2009 H1N1 pandemic.”
See also: The Quest to End the Flu
My comment:

See also: “Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution”
The idea of biophysical constraints seems antithetical to the idea of nature somehow selecting mutations that cause amino acid substitutions. However, I am not a biophysicist or evolutionary theorist.
The problem may be my focus on nutrient-dependent receptor-mediated amino acid substitutions in species from bacteria to humans (non-viral organisms). Since I am not a virologist or physicist, I’m not sure that the laws of physics apply to viruses and their replication.
If they do, natural selection for random mutations is not likely to result in amino acid substitutions because the thermodynamics of changes in organism-level thermoregulation preclude such randomness. Stability of protein biosynthesis and degradation that probably depends on protein folding must somehow be controlled. Besides, I don’t know how random mutations in viruses could be naturally selected for inclusion in the human virome (or in the virome of any organism capable of thermoregulating its thermodynamic intercellular signaling).
If the Second Law of Thermodynamics does not apply to viruses, which means the chemical bonds that enable the amino acid substitutions can form at random and somehow be naturally selected, the details of biophysical constraints in this article seems out of place, since I do not think in terms of constrained random mutations and natural selection in mutation-driven evolution.
Hopefully, someone with a background in biophysics will address my confusion in case others are confused. In addition, I wonder if the consequences of understanding the evolutionary mechanisms that govern viruses extend to consequences important to understanding the evolution of species from bacteria to humans via constrained random mutations and natural selection?

The comment above was also published to the “Science Magazine” comments section, but it was removed and replaced with the authors’ comment. Obviously, they knew that anyone familiar with the laws of physics and chemistry of nutrient-dependent RNA-mediated protein folding would link virus-driven constraint breaking mutations to the antigenic change in the virus without claims about evolution.
Viruses don’t evolve! Antigenic changes don’t evolve! Proteins don’t evolve! Researchers must make it clearer that they know the difference between neo-Darwinian theory and facts about cell type differentiation. That is the only way serious scientists can avoid being removed from positions where their ignorance may cause a pandemic.

See also: It is not clear in any representation that a virus-driven change in a base pair could be linked from the theft of energy and perturbed hydrogen-atom transfer in DNA base pairs in solutuion to pathology. Although only one base pair change and one amino acid substitution may make a difference to the cell type, nutrient-dependent RNA-mediated healthy longevity is not placed into the context of one amino acid substitution linked to pH and spectophotometric assays of hydrogen ion concentration in body fluids. Thus, the accumulated knowledge fron every test that I ever performed during ~60,000 hours of testing in my career as a medical laboratory scientist is dismissed by the claims of evolutionary theorists.
However, the changes in hydrogen-atom transfer in DNA base pairs in solution have now been placed into the context of bacteria the move towards the light.
See: How slime can SEE where it’s going: Single-celled pond bacteria act like ‘microscopic eyeballs’ to sense light and move towards it
Excerpt:

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
See also:
Comparative Proteomics Reveals Important Viral-Host Interactions in HCV-Infected Human Liver Cells
Theoretical investigation of hydrogen atom transfer in the cytosine-guanine base pair and its coupling with electronic rearrangement. Concerted vs stepwise mechanism
Wheeler’s delayed-choice gedanken experiment with a single atom
Effect of Methylation on the Properties of the H-Bridges in DNA. A Systematic Theoretical Study on the Couples of Base Pairs
Photoinduced amino–imino tautomerism of 2-aminopyridine in a low-temperature argon matrix
My comment: Even those who claim to be trying to reconcile the differences between theorists and creationists contribute to ongoing misunderstanding.
See: Darwinists Underestimate Nature. Creationists Underestimate God
Excerpt:

You say that “We can produce new species at will and it happens all the time”.

My comment: February 7, 2016 at 7:21 am
Like many others, you seem to be confused about what can happen in the lab compared to what does not happen outside the lab.
For example: Re: “1) Hybrids, where Species 1 crossed with Species 2 gives you Species 3. ”

For comparison: Species of Drosophila

Excerpt:

Hybrids of Drosophila pseudoobscutra and D. persirnilis are easily obtainable in the laboratory, but they are absent in localities where both species occur side by side (14).

My comments: Perry Marshall seems to be siding with those who think hybrids are proof that evolution may occur over millions of years, albeit without the pseudoscientific nonsense about mutations and natural selection.

James V. Kohl says: January 26, 2016 at 3:24 pm
My 2012 Templeton Grant Proposal:

Nutrient chemicals are required to sustain life and for transgenerational epigenetic inheritance of biological populations. This fact is exemplified in the honeybee model organism and other model organisms. The nutrient chemicals cause receptor-mediated events. The receptor-mediated events allow nutrient chemicals to enter though the cell wall. Electrostatic changes then alter intracellular signaling as nutrient chemicals are metabolized to species-specific chemicals called pheromones.
The metabolism of nutrient chemicals to pheromones exemplifies the apparent design of biology. Bottom-up (genetically predisposed organization) and top-down reciprocity via sensory activation is what allows nutrient chemicals and pheromones to control survival of the species. The nutrient chemicals support individual fitness and the pheromones control reproduction. From the bottom up, their ability to control species survival is enabled by their epigenetic effects of nutrient chemicals that cause stochastic gene expression. Similarly, from the top down, pheromones epigenetically effect stochastic gene expression (in cells of organisms from microbes to man).
All extant organisms show a clear pattern of genetic predispositions that enable nutrient chemical-dependent and pheromone-dependent adaptive evolution via ecological, social, neurogenic, and socio-cognitive niche construction. Adaptive evolution is facilitated via the expression of new genes, including those that are important to the development of language abilities and human brain development.
The ability of cells containing genes to produce de novo genes does not seem to have developed via random mutations. Although gene expression is stochastic, organisms that choose the wrong nutrient chemicals are less reproductively fit and doomed to suffer and die. One organisms choice also may determine downstream down-stream epigenetic effects on other organisms that selfishly compete for life-sustaining nutrient chemicals in same ecological niche. Only when some level of cooperation is achieved can individuals or species survive in the same ecological niche, and species-specific pheromones ensure that two species do not share the same social niche.
Ecological and social niche construction collectively enabled evolved nutrient-dependent and pheromone-dependent neurogenic niche construction, which is exemplified in vertebrates by conservation of the GnRH molecule, and diversification of its receptor across 400 million years of adaptive evolution that first required nutrient-dependent and pheromone-dependent sexual reproduction in unicellular and multicellular organisms, with molecular origins as the alpha-mating pheromone in brewer’s/baker’s yeast.
The ecological and social niches constructed by one species that eats another exemplify how that advent of multicellularity and cooperation in different species enabled the cascade of diversity that is readily evidenced across Creation, as it always has been. When viewed from a model of complexity, Creation of the diversity of life does not appear to involve random events, but instead involves the common molecular biology of receptor-mediated events is species from microbes to man.
The concept that is extended is the epigenetic tweaking of immense gene networks in ‘superorganisms’ that ‘solve problems through the exchange and the selective cancellation and modification of signals. It is now clearer how an environmental drive probably evolved from that of food ingestion in unicellular organisms to that of socialization in insects. It is also clear that, in mammals, food odors and pheromones cause changes in hormones that have developmental affects on sexual behavior in nutrient-dependent, reproductively fit individuals across species of vertebrates.
Thus, simply put: “Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans.” And there is nothing random about that!

My comment: I did not receive the grant and as of 2/9/16, I had not received a response from Perry Marshall to my post, which addresses many of his claims. I held this blog post for several weeks to give Marshall and others a chance to respond to what is currently known to serious scientists about how physics, chemistry, and molecular epigenetics must be linked to healthy longevity or to virus-driven pathology. Obviously, it is not only the neo-Darwinists and theoretical physicists who want to continue to ignore the obvious links from atoms to ecosystems via the sun’s anti-entropic energy.

Perry Marshall says:

February 9, 2016 at 3:39 pm

No argument that living things use sunlight in processing of information.Show me a non-living thing that turns sunlight or chemicals into code and then we’ll have something to talk about. Thus far nothing you have presented so far meets the specification of the prize.

James V. Kohl says:

February 9, 2016 at 5:51 pm
Thanks. I think others can see what is happening with the specifications of the prize.
From page 206 of “Evoluton 2.0.”
You wrote: “But I could find no formula or transformation that turns matter or energy into information. This is precisely what the Evolution 2.0 Prize seeks to discover.”
Sunlight is the energy that links information to matter. Now it’s not a formula that you want; it’s an example of a non-living thing that links sunlight from quantum physics to the chemistry of protein folding via the de novo creation of nucleic acids.
Why not simply admit that you will not accept any accurate representation of biological facts that link the de novo creation of nucleic acids (the code) to all RNA-mediated biodiversity. You’re stuck with your claims about hybrids and Shapiro’s nonsense.
Addendum: Shapiro’s nonsense was published as Evolution: A View from the 21st Century
Excerpt: Proteins operate as conditional microprocessors in regulatory circuits.
Excerpt: The concept of most proteins as systems of domains exemplifies the new combinatorial thinking frequently emphasized in this book. It makes good sense a priori to expect that a protein will make a successful functional change by acquiring an existing intact binding or catalytic capability. Intuitively, this has a far higher probability of proving effective than does a random process of changing one amino acid at a time and gradually selecting modest improvements in catalysis or binding specificity.
My comment: The processes that link RNA-mediated amino acid substitutions to cell type differentiation in all living genera via the physiology of reproduction are nutrient-dependent. They are not random processes that change amino acids one at a time. The processes link atoms to ecosystems via hydrogen-atom transfer in DNA base pairs in solution in the context of microRNAs, adhesion proteins, DNA repair, and the stability of organized genomes that links supercoiled DNA to protection against virus-driven entropy.
Shapiro’s book (2011) and Nei’s book (2013) Mutation-Driven Evolution were more than a decade past their due dates. As is common with all textbooks, by the time they are published, new information makes them increasingly worthless to anyone who needs to learn more about what is known to serious scientists. For that knowledge, you must follow the extant literature and try to keep up. Good luck catching up before you try to keep up with what is being published on the role of microRNAs in cell type differentiation.
See, for example: Items: 1 to 20 of 47233

Perry Marshall says:

February 9, 2016 at 9:45 pm

James, if you think you have a solution then fill out a proper prize submission and show that you have met the specification.
My comment: Perry Marshall removed my response. I asked where to find the prize submission form and asked again about the Non-Disclosure Agreement (NDA), which he claims is not yet available. He contacted me via email. He claimed that he would send the submission form and asked me to be patient while waiting for the NDA. It seems clear to me that the prize is part of a scam. One that provides an opportunity for Perry Marshall to market his book with his opinions about how biologically-based cause and effect are linked to nutrient-dependent biodiversity. But, as every serious scientist knows, Perry Marshall’s opinions are worth no more than the opinions of others who are biologically uninformed.
—————————————————–

James V. Kohl says:

Your comment is awaiting moderation.

February 10, 2016 at 2:30 am

Thanks. I’m disgusted by your claims and the missing “proper prize submission” form, and the unavailable non-disclosure agreement.
The delay has left others with the opportunity to move forward with publications that address your questions in the context of the same experimental evidence I intended to provide several weeks ago.
You should have admitted that the forms weren’t available, so that everyone would be aware of the delay you caused in my attempt to win the prize.

Intelligent RNAs vs evolved genes

January 11, 2016

by James Kohl with No Comment Adaptations Alternative Splicings Ecology RNA Directed RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Variations

Intelligent RNAs in the Brain

Excerpt: Alternative RNA splicing and non-coding RNA particles have evolved unusually rapidly. Intelligent RNAs in the brain have fostered rapid human evolution.
Tom Robbins
Do we have to say “evolved” for everything? The complexity here is intelligent, no matter what you call it, evolved implies with no direction, an mainly by chance, which is an outmoded term for this level of complexity. I get so tired of trying to latch on a dead end theory of chance and necessity, somehow driving things – it is obvious to me, and I think any intellectually honest person, that we are GIVEN what we need to progress and adapt.. Or alternatively our consciousness pushes us forward. And important – when they say CHANCE and necessity, they are talking about winning the lotto, continuously every day, over and over and over. There is no chance.

Xeroxed lung gene helps salamanders breathe through their skin

Excerpt: A copy of a key lung gene shifted where it is active, rendering skin capable of efficient gas exchange, they reported here this week at the annual meeting of the Society for Integrative and Comparative Biology. The loss of lungs represents major evolutionary change

Meeting Abstract

75-6 Wednesday, Jan. 6 09:15 Neofunctionalization of a lung-gene paralog may facilitate respiration in lungless salamanders LEWIS, Z.R.*; DORANTES, J.A.; HANKEN, J.; Harvard University, Cambridge, MA; Harvard University, Cambridge, MA; Harvard University, Cambridge, MA zlewis@oeb.harvard.edu http://www.people.fas.harvard.edu/~zrlewis/
Most terrestrial vertebrates use lungs to breathe. The few exceptions include lungless amphibians (hundreds of species of salamanders, but only two other amphibians), which breathe entirely through the skin and buccal cavity. How lungless amphibians are able to meet metabolic demands is a topic of considerable speculation. Lunglessness places theoretical limits on thermal tolerance and body size, but lungless salamanders paradoxically live across diverse thermal environments and reach relatively large body sizes. Lungless salamanders display a slight increase in vascularization of extrapulmonary tissues (the skin and buccal cavity) compared to some lunged species, but morphological differences alone do not explain observed increased extrapulmonary respiratory capacity. Molecular differences between lungless and lunged species may account for greater extrapulmonary respiratory capacity. We have discovered a novel paralog of a lung-specific gene that likely evolved in salamanders and may serve a unique function in lungless species. This paralog is expressed solely in the lungs in lunged salamanders, resembling the expression pattern of its ancestral gene. However, the expression site of this paralog in a lungless salamander is dramatically divergent: in embryos and larvae of Desmognathus fuscus, the paralog is expressed throughout the skin. At metamorphosis, expression shifts to the buccal cavity. We propose that the salamander-specific paralog is neofunctionalized in lungless salamanders to facilitate cutaneous and buccal respiration. Neofunctionalization of this gene and its dynamic expression pattern may help lungless salamanders adapt to shifting life history-related demands for gas exchange and may help account for the remarkable adaptive radiation of lungless salamanders.
My comment: The presenters reported the nutrient-dependent de novo creation of a gene via energy-dependent hydrogen-atom transfer in DNA base pairs and gene duplication that links the physiology of reproduction to ecological adaptations via fixation of RNA-mediated amino acid substitutions that are required during life history transitions.

We have discovered a novel paralog of a lung-specific gene that likely evolved…

My comment: No experimental evidence of biologically-based cause and effect suggests that any gene has ever evolved.

Scent of Eros

Posts tagged: Hydrogen-Atom Transfer

Sal Giardina: apologetics revisited

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

Energy as information and constrained endogenous RNA interference (3)

Polycombic ecological adaptation as a science, not a theory (2)

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

Hydrogen-atom energy in DNA base pairs

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

Supercoiled DNA is the link to viral latency, which is the link to healthy longevity.

Wasted Templeton Funding (3)

Templeton grant funds evolution rethink

A Message From J.V.Kohl:

Ignore the evidence: Rachel Feltman

“There is incontrovertible evidence that Alzheimer’s Disease has a dormant microbial component. We can’t keep ignoring all of the evidence”

Experts Say There’s a Herpes-Alzheimer’s Link

Calm down: Herpes probably isn’t going to give you Alzheimer’s

Zika Update

What Do We Actually Know About Pheromones?

A simple physical mechanism enables homeostasis in primitive cells

Electrostatic Localization of RNA to Protocell Membranes by Cationic Hydrophobic Peptides

From angstroms to ecosystems and entropy

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

The Light and Darkness of "Evolution 2.0"