protein-folding Archives

Light-controlled cell biology (revisited)

March 21, 2018

by James Kohl with No Comment Adaptations Autophagy biophotonics Cytosis Diseases & Disorders Ecology Light Energy microRNA editing Model Organisms Nutrigenomics Physics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations What's in the News

See Sci-Bay Scholar for citations and downloads of more than 3300 published works that link viruses to microRNAs
Summary: …either the organized genomes of all cell types use the energy source, or viruses use the biophysically constrained energy of the cell types. No extant species can be used as an example of how the virus-driven theft of quantized energy can be linked from natural selection to the evolution of a new species.
See also, with my emphasis:

Light Offers New Way to Control Cell Biology (3/16/17)

…the power of light-sensitive proteins is that they can be used to study the inner workings of any living cell.

Archaea:

Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no known species of archaea does both.

See: A Conversation With George Church At 15:10

…the cyanobacteria turn out that they fix light ah as well or better than land plants…

From the transcript:

The cyanobacteria fix [carbon via] light as well or better than land plants. Under ideal circumstances, they can be maybe seven to ten times more productive per photon.

The difference between the fixation of light and the fixation of carbon is that (see above) no known species of archaea does both. That fact supports the claim that the ability to fix light is an ecological adaptation that links the quantized energy of sunlight to all biophysically constrained biodiversity in the context of energy-dependent viral latency.

Archaea that do not use sunlight as their energy source probably become L-forms in the context of the virus-driven degradation of their messenger RNA, which has been linked from mutations to all pathology in the context of one-carbon metabolism. Quantized energy is the obvious link from the fixation of light to the fixation of carbon in all carbon-based life forms on Earth.

Simply put, either the organized genomes of all cell types use the energy source that fixes carbon, or the viruses use the biophysically constrained energy of the cell types. For comparison, no extant species can be used as an example of how the virus-driven theft of quantized energy can be used in the context of natural selection and evolution.

Diet-driven RNA interference and cancer prevention (3)

January 18, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy Cytosis Diseases & Disorders Ecology RNA Directed

Excerpt: They claim to have found novel autoregulatory feedback loops that link changes in microRNAs to the alternative splicing factors SRSF1 and SRSF2. Ectopic expression of SRSF1 can automagically repress the level of multiple microRNAs and SRSF2 can automagically upregulate miRNA expression.

The fact that a peer-reviewed work published in 2018 links autoregulatory feedback loops to automagically altered gene expression and apoptosis via alternative splicings of pre-mRNAs suggests it is time for all serious scientists to retire. The magic of pseudoscientists has prevailed for more than 2 decades.

See for comparison: In clinical trial, cream reduces squamous cell carcinoma risk

Results of a new randomized, double-blinded, controlled clinical trial in veterans showed a 75 percent reduction in the risk of needing surgery to treat a squamous cell carcinoma for a year after applying a skin cream for up to four weeks.

How Fluorouracil Works: (with my emphasis)

The ability of chemotherapy to kill cancer cells depends on its ability to halt cell division. Usually, the drugs work by damaging the RNA or DNA that tells the cell how to copy itself in division. If the cells are unable to divide, they die. The faster the cells are dividing, the more likely it is that chemotherapy will kill the cells, causing the tumor to shrink. They also induce cell suicide (self-death or apoptosis).

Chemotherapy drugs that affect cells only when they are dividing are called cell-cycle specific. Chemotherapy drugs that affect cells when they are at rest are called cell-cycle non-specific. The scheduling of chemotherapy is set based on the type of cells, rate at which they divide, and the time at which a given drug is likely to be effective. This is why chemotherapy is typically given in cycles.

Chemotherapy is most effective at killing cells that are rapidly dividing. Unfortunately, chemotherapy does not know the difference between the cancerous cells and the normal cells. The “normal” cells will grow back and be healthy but in the meantime, side effects occur. The “normal” cells most commonly affected by chemotherapy are the blood cells, the cells in the mouth, stomach and bowel, and the hair follicles; resulting in low blood counts, mouth sores, nausea, diarrhea, and/or hair loss. Different drugs may affect different parts of the body.

Fluoruracil belongs to the category of chemotherapy called antimetabolites. Antimetabolites are very similar to normal substances within the cell. When the cells incorporate these substances into the cellular metabolism, they are unable to divide. Antimetabolites are cell-cycle specific. They attack cells at very specific phases in the cycle. Antimetabolites are classified according to the substances with which they interfere. Fluoruracil is classified as a pyrimidine analog because it interferes with DNA and RNA synthesis by mimicking the building blocks necessary for synthesis.

The term antimetabolites is confusing. Metabolism is enzyme-dependent. Cell type differentiation is energy-dependent and the creation of microRNA links ATP to the creation of enzymes that metabolize food to the species-specific pheromones.
Pheromones biophysically constrain viral latency. That is how they prevent all pathology in the context of metabolism. Enzyme-dependent cycles of metabolism are the key to healthy longevity. Simply put, pheromones prevent the transgenerational epigenetic inheritance of nearly all viruses that have not been biophysically constrained by food energy-dependent metabolism.

Hardin, Hall and Rosbash (1990) put that fact into the perspective of Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels. The feedback loops are food energy-dependent and biophysically constrained by naturally occurring RNA interference (i.e., natural selection for energy-dependent codon optimality). The feedback links the metabolism of food to pheromone-controlled biophysically constrained viral latency.

Rosbash shared the 2017 Nobel Prize in Chemistry, which attests to the fact that all serious scientists probably know how to prevent or to effectively treat cancer as a disorder of cyclic changes in the chemistry of energy-dependent RNA mediated cell type differentiation. Prevention should include limiting exposure to nutrient stress and/or social stress because stress alters microRNA-mediated alternative splicings that link food energy to the biophyiscally constrained chemistry of protein folding.

See: Microrna-mediated regulation of splicing factors SRSF1, SRSF2 and hnRNP A1 in context of their alternatively spliced 3’UTRs

The microRNAs targeting SRSF1 and SRSF2 are involved in a regulatory feedback loop. microRNAs miR-183-5p and miR-200c-3p that target SRSF2, affect the expression of genes involved in apoptotic regulation.

They claim to have found novel autoregulatory feedback loops that link changes in microRNAs to the alternative splicing factors SRSF1 and SRSF2. Ectopic expression of SRSF1 can automagically repress the level of multiple microRNAs and SRSF2 can automagically upregulate miRNA expression.

See for comparison:

From Fertilization to Adult Sexual Behavior (1996)

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 [model organisms.]

See also:
Feedback loops link odor and pheromone signaling with reproduction (2005)
The feedback loops are food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans.

Sarcasm alert: The treatment of automagically dysregulated apoptosis should probably begin with a change in diet.

Changes in diet have been linked from the energy-dependent creation of enzymes that specifically link an energy-dependent base pair change to microRNA-mediated DNA repair via fixation of an RNA-mediated amino acid substitution. The substitutions are linked to energy-dependent cell type differentiation and healthy longevity without the magic.

Just add food energy or the virus-driven theft of quantized energy to eliminate the term autoregulatory and you could prevent or effectively treat all virus-driven pathology.

Energy-dependent RNA interference links the enzyme-dependent metabolism of food and drugs to cell type differentiation via feedback loops that link pheromones to biophysically constrained viral latency.

Do not claim to have a logical philosophy if you cannot link the creation of the sun’s anti-entropic virucidal energy to every aspect of the biophysically constrained pheromone-controlled physiology of reproduction in species from microbes to human by starting with the obvious need to control viral replication in the ocean and linking the control to healthy longevity in modern human populations via fixation of RNA-mediated amino acid substitutions in all differentiated cell types.

Transfer RNAs (tRNA) are abundant short non-coding RNA species that are typically 76 to 90 nucleotides in length. tRNAs are directly responsible for protein synthesis by translating codons in mRNA into amino acid sequences.

RNA polymerase III (Pol III) and transcription factor IIIB (TFIIIB) assemble together on different promoter types to initiate the transcription of small, structured RNAs.

Nothing happens without the energy-dependent creation of the enzymes and the biophysically constrained viral latency that links the creation of G protein-coupled receptors to the functional structure of supercoiled DNA. The claims about molecular mechanisms of promoter opening appear to be deliberate attempts to obfuscate cause and effect.
Activation of G protein-coupled estrogen receptor signaling inhibits melanoma and improves response to immune checkpoint blockade

Female sex and history of prior pregnancies are associated with favorable melanoma outcomes. Here, we show that much of the melanoma protective effect likely results from estrogen signaling through the G protein-coupled estrogen receptor (GPER) on melanocytes. Selective GPER activation in primary melanocytes and melanoma cells induced long-term changes that maintained a more differentiated cell state as defined by increased expression of well-established melanocyte differentiation antigens, increased pigment production, decreased proliferative capacity, and decreased expression of the oncodriver and stem cell marker c-Myc. GPER signaling also rendered melanoma cells more vulnerable to immunotherapy. Systemically delivered GPER agonist was well tolerated, and cooperated with immune checkpoint blockade in melanoma-bearing mice to dramatically extend survival, with up to half of mice clearing their tumor. Complete responses were associated with immune memory that protected against tumor rechallenge. GPER may be a useful, pharmacologically accessible target for melanoma.

Sex-specific cell type differentiation links yeasts to primates via the nutrient-dependent pheromone-controlled physiology of reproduction that links the food energy-dependent structure and function of enzymes and G protein-coupled receptors to the biophysically constrained Structure and dynamics of GPCR signaling complexes, which are required to biophysically constrain viral latency in the context of effect of androgens and estrogens on difference in the cell type of males and females.
Any focus on G protein-coupled estrogen receptors compared to G protein-coupled androgen receptors should be viewed with suspicion in the context of what has been known to all serious scientists about hormones and behavior since our Hormones and Behavior review of RNA-mediated cell type differentiation. From Fertilization to Adult Sexual Behavior (1996)
Simply put, the alternative splicings of pre-mRNAs, which are now called microRNAs, biophysically constrain energy-dependent viral latency and prevents the transgenerational epigenetic inheritance of nearly all virus-driven pathology until excess nutrient stress or social stress takes its toll on the innate immune system.
Eventually, our food energy-dependent RNA-mediated DNA repair fails, and the accumulation of viral microRNAs predicts the failure of cell type differentiation in the tissues that are required to sustain our physical health and mental health.

Energy-dependent pheromone-controlled entropy (3)

March 15, 2017

by James Kohl with No Comment Adaptations biophotonics Diseases & Disorders Ecology Light Energy Physics RNA Directed RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Variations

See: Energy-dependent pheromone-controlled entropy (2)
Let’s make peer review scientific

…peer review is often biased and inefficient. It is occasionally corrupt, sometimes a charade, an open temptation to plagiarists. Even with the best of intentions, how and whether peer review identifies high-quality science is unknown. It is, in short, unscientific.

Here’s another failed attempt to put top-down causation back into the context of peer review.
Electron transfer between anatase TiO2 and an O2 molecule directly observed by atomic force microscopy

Molecular oxygen is an inert species, unable to enter chemical reactions. Activation occurs through the acceptance of an extra electron; this catalytic step plays a major role in applications such as heterogeneous catalysis and fuel cells. It is also used by all living organisms.

The energy dependent catalytic step used by all living organisms was reported as: Switching oxygen molecules between a reactive and unreactive state

The news report claims all living organisms use a trick to link light to the addition of electrons and chemical reactions in the context of photocatalysis (i.e., light energy as information-induced chemical changes). The researchers demonstrate the trick at the level of atomic force via changes in oscillations during the transition from the inactive to the active state of titanium oxide.
They claim that they can control the trick during investigation of the inner workings of photocatalysts. They do not link femtosecond blasts of virucidal UV light to RNA-mediated DNA repair and all biodiversity via the trick.
If they did that, others would realize it is not a trick. It is the link from the creation of the sun to all biodiversity via what is known to all serious scientists about the simultaneous creation of nucleic acid precursors, which also create the starting materials needed to make natural amino acids and lipids.
See: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
A single set of [light activated] reactions appears to link the creation of most of life’s building blocks, simultaneously.
Reported as: Researchers may have solved origin-of-life conundrum

…slight variations in chemistry and energy could have favored the creation of one set of building blocks over another, such as amino acids or lipids, in different places.

The slight variations in the energy-dependent chemistry of biophysically constrained RNA-mediated protein folding are not something that should be placed into the context of any peer-reviewed journal article that lends itself to being reported as a trick or reported as if the trick solved the origin-of-life conundrum.

George Church refutes theistic evolution (2)

February 10, 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 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

See: George Church refutes theistic evolution

George Church may not know that he refuted every aspect of theistic evolution in his presentation on February 8, 2017. Hopefully, someone will tell him how he linked quantum physics from chemistry to biophysically constrained protein folding and all biodiversity, or explain to others how he did that. Here is my explanation of his admissions. I placed the explanation into the context of this poster session submission.

Title: Energy as information and constrained endogenous RNA interference
Abstract:

Sunlight-induces energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution. Changes in the potential of hydrogen (pH) link quantum physics to classical physics via chirality (manifested in chemistry). Energy-dependent biophysically constrained protein folding chemistry links what is known about molecular epigenetics to what is known about autophagy. For instance, energy-dependent changes in pH link ecological variation from angstroms to ecosystems via base pair changes and RNA-directed DNA methylation (endogenous RNA interference). That is how the sun’s anti-entropic virucidal energy is linked from the physiology of reproduction to all life on Earth.

Base pair changes link microbial quorum sensing from the nutrient energy-dependent pheromone-controlled physiology of reproduction to the National Microbiome Initiative. Endogenous RNA interference (RNAi) links the base pair changes from the innate immune system to supercoiled DNA and chromosomal inheritance. Sunlight is linked from the National Microbiome Initiative to the Precision Medicine Initiative via genome wide inferences of natural selection for nutrients and the pheromone-controlled energy-dependent fixation of amino acid substitutions in all organized genomes.

This presentation explains how natural selection for energy-dependent codon optimality links biologically-based cause and effect from the de novo creation of G protein-coupled receptors (GPCRs) to fixation of RNA-mediated amino acid substitutions. GPCRs link metabolic networks and genetic networks to the amino acid substitutions that differentiate all cell types in all individuals of all species.

Ecological variation is linked to energy-dependent metabolic networks and genetic networks, which link alternative RNA splicings from supercoiled DNA to polycombic ecological adaptations. Ecological adaptations, which are manifested in morphology, are linked from supercoiled DNA and chromosomal inheritance to healthy longevity via energy-dependent differences in behavior.

For contrast, virus-driven energy theft links messenger RNA degradation to negative supercoiling and constraint-breaking mutations. Virus-driven hecatombic evolution links energy theft from biophysical constraint-breaking mutations to all pathology. For example, the viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA in human infants, which typically is repaired by energy-dependent endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

A link to the poster session and narrative summary should be available within the next two weeks.

Theories vs facts about polycombic adaptation

December 6, 2016

by James Kohl with No Comment Adaptations Alternative Splicings Diseases & Disorders Ecology Model Organisms Nutrigenomics 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

See: Demoncrats fight polycombic ecological adaptation

Exosomes as miRNA Carriers: Formation–Function–Future

Important aspects will be highlighted as a take-home message (THM) at the end of each paragraph.

THM: Extracellular vesicles transport miRNA in a paracrine and endocrine manner. Questions regarding the cellular options of producing either microvesicles or exosomes and their difference in miRNA composition and number are still unknown.

In my 2014 invited review, the four F’s, Formation–Function–Future and Copulation were included in details about how the nutrient energy-dependent de novo creation of microRNAs must be linked to nutritional epigenetics. My invited review was returned without review by the guest editors of a special issue of “Nutrients.”
I realized the guest editors had “baited me” into providing them with all the available current information and published my submission to Figshare. That’s how I show the level of deception that biologically uninformed theorists still use to obfuscate what is known to serious scientists about biologically-based cause and effect.

See for example: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (April 10, 2014)

Abstract: “This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.”

Lynnette Ferguson, was one of two guest editors that invited my review.

She is the co-author of The Interaction between Epigenetics, Nutrition and the Development of Cancer This article belongs to the Special Issue NutritionalEpigenetics

Conclusion:

…it is imperative to understand the implications of diet on epigenetic modifications, and the effect of those modifications on the development of cancer today and in future generations. Such an understanding and an appropriate resultant response would help decrease the level of risk in future generations.

There would be no future generations if diet could not be epigenetically linked from metabolism to the pheromones that control the physiology of reproduction in species from microbes to human via energy-dependent changes in the microRNA/messenger RNA balance. The microRNA/messenger RNA balance biophysically contrains RNA-mediated protein folding chemistry.

Protein folding chemistry links energy-dependent changes from angstroms to ecosystems in all living genera via the innate immune system and fixation of RNA-mediated amino acid substitutions in supercoiled DNA. Supercoiled DNA exemplifies natural section for energy-dependent codon optimality, but theorists will not accept that fact. They would rather believe that the mutations in DNA are naturally selected and that mutation-driven evolution automagically occurs outside the context of energy or the virus-driven energy theft that causes all mutations and all pathology.

This scenario challenges the assumed value of extant blastoporal behaviours for explaining the evolutionary origin and diversification of Bilateria that has been presumed for over 100 years^{4,5,6,7,9,10,11}. Freeing the constraint that the mouth and anus have a necessary association with the embryonic blastopore will help in understanding the developmental events underlying the evolution of an alimentary canal^5,20,21,50, and ultimately the appearance and diversification of bilaterian body plans.

All scenarios that failed to link energy-dependent behavior to the physiology of reproduction and also failed to link virus-driven energy theft to all pathology have always been based on questionable assumptions. The assumptions fall outside the context of Darwin’s “conditions of life,” which require links from what organisms eat to signaling and sensing and the behavior of other organisms.

For example, Schrodinger (1944) linked excretion from mammals to sunlight as the source of anti-entropic virucidal energy used to support all ecosystems. All serious scientists have done that since Thomas Hunt Morgan won the 1933 Nobel Prize in Physiology or Medicine for linking chromosomes to transgenerational epigenetic inheritance long before most people understood what the term autophagy means.

Filtering light through a prism to identify tissue type

Epigenetics and autophagy vs mutations and evolution (5)

November 11, 2016

by James Kohl with No Comment Adaptations Alternative Splicings Diseases & Disorders Ecology Model Organisms RNA Directed RNA methylation Variations

Two-Photon Microscopy’s Historic Influence on Neuroscience

Excerpt:

Yuste says he’s proud of what he and Denk accomplished. “But now I go to meetings where everyone is presenting two-photon calcium imaging, and no one knows, or remembers, or cites our work,” he says, laughing.

My comment: What else can be done but laugh? Most researchers still have not linked the anti-entropic energy of virucidal ultraviolet light from the biophysically constrained RNA-mediated chemistry of protein folding to all biodiversity in all genera despited the advances that link biophotonics and femotosecond blasts of UV light to DNA repair and to supercoiled DNA via the physiology of reproduction.

Many still seem to be largely unaware that supercoiled DNA protects all organized genomes from virus-driven entropy because they cannot see the femtosecond blasts. They decide to link mutations to the evolution of all biodiversity, instead.

See for comparison the molecular epigenetics section of our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior

I stopped attending meetings where everyone is presenting on molecular epigenetics and no one knows, or remembers, or cites our work. Neo-Darwinian theorists have continued to present findings in the context of pseudoscientific nonsense and the are now trying to link the molecular mechanisms of energy-dependent polycombic ecological adaptation to a new ridiculous theory of evolution, which they refer to as adaptation.

Unified theory of evolution

Introduction:

The unifying theme for much of modern biology is based on Charles Darwin’s theory of evolution, the process of natural selection by which nature selects the fittest, best-adapted organisms to reproduce, multiply and survive. The process is also called adaptation, and traits most likely to help an individual survive are considered adaptive.

My comment: The process of evolution was not called adaptation until people like Michael Skinner realized there is no such thing as mutation-driven evolution. They know it is obvious that nutrient energy-dependent pheromone-controlled biophysically constrained protein folding chemistry controls cell type differentiation because otherwise life could not exist on Earth.

Glutamine is the amino acid coded for by the genomic trinucleotide CAG. Repeating glutamines, called polyglutamines, are normal in huntingtin proteins, but when the DNA is copied incorrectly, the repeating sequence of glutamines can become too long. The result can be diseases like Huntington’s or spinocerebellar ataxia.
The number of repeats of glutamine can grow as the genetic code information is passed down through generations. That means a healthy parent whose huntingtin gene encodes proteins with 35 repeats may produce a child with 36 repeats. A person having the longer repeat is likely to develop Huntington’s disease.

My comment: The number of repeats is nutrient energy-dependent and longer repeats link virus-driven energy theft to all pathology.

Epigenetics and autophagy vs mutations and evolution

November 10, 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 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 What's in the News

RNA interfernce in “evolution”

My comment: What evolved?
See for comparison: Energy-dependent RNA-mediated biophysically constrained protein folding chemistry in the context of ecological adaptation.

From Precis to Proof in 6000 years

November 5, 2016

by James Kohl with One Comment Adaptations Alternative Splicings biophotonics Diseases & Disorders Ecology RNA Directed

Religious texts, such as The Holy Bible appear to be like a Precis of works from God. He seems to be explaining energy-dependent creation in the context of what is currently known to serious scientists about biophysically constrained RNA-mediated protein folding chemistry, healthy longevity and RNA-mediated biodiversity.
God made it perfectly clear, in advance, that all miraculous biodiversity is energy-dependent. Energy as information is the theme that extends to the weekend resurrection of the bacterial flagellum in P. fluorscens. Biologically uninformed theorists are beginning to realize the importance of a simplistic version of biologically-based systems complexity.
Energy as information can be understood by non-scientists whether or not they are interested in further examination of top-down causation at every level of subsequent interactions among subatomic particles and macroscopic biodiversity.
See for instance: Protein Folding Using Quantum Topology which is linked to this video as a part of a series from “Serious Science”
Description:

Matematician Jørgen Andersen on local geometry of hydrogen bonds, quantum states of proteins and future methods of predicting the macromolecules structure.

Excerpt:

There are about 2000 local patterns that we’ve seen popping out now and we are trying to understand what is the correlation between the primary sequence of these patterns. Some of them have a clear significance. We’re trying to devise energy contributions for each of such patterns and then trying to see if we can create algorithms that generate all structures with a certain sequence of patterns. And this is a combinatorial problem that we’ve actually solved very recently.

My comment: Does he realize he is giving the bird to all pseudoscientists with both fingers?

See also: Jørgen Ellegaard Andersen publications

See for comparison: Precis: The Scent of Eros: Mysteries of Odor in Human Sexuality

The book was written for the general readership (as indicated by the Table of Contents). This precis is designed to elicit responses from the scientific readership.

This Precis provides an overview of the book “The Scent of Eros: Mysteries of Odor in Human Sexuality,” which details for a general audience a five-step biological pathway that allows the social environment to influence the genetic nature of mammalian behavior. This pathway is: gene-cell-tissue-organ-organ system. Moreover, though there are many environmental influences on genes, mammalian pheromones are the only known social-environmental stimuli that appear to activate gene expression in neurosecretory cells of tissue in the brain, an organ that is essential to any organ system involved in behavior. Human pheromones appear both to elicit a homologous “neuroendocrine” response and to influence behavior. Thus, human pheromones may fulfill the biological criteria required to link at least one aspect of a sensory-based, nurturing, social environment: olfaction, to the genetic nature of human behavior through a five-step pathway common to all terrestrial mammals and to many other vertebrates.

Full text:

1. This book incorporates both non-human animal and human models of reciprocity among odors, olfaction, neuroendocrinology, and behavior. It details the likely influences both of human chemical communication and of olfaction on genes in neurosecretory neurons. These neurons are found in brain tissue responsible for integrating, coordinating, and directing reproductive endocrine function in organs that comprise the organ systems known to influence mammalian reproductive sexual behavior and human sexuality. Though this book is not written to meet any requirements of a “hard scientific” approach to interdisciplinary topics, it is fully referenced for the knowledgeable scientist and for those interested either in further study or in support for any conclusions. Also included are chapter notes, a glossary, and an index.

2. After a Foreward by William E. Hartman and Marilyn A. Fithian and an Introduction by the co-author, Chapter 1 begins with commentary on previously published works by various scientific authorities who have offered their insights into the importance of human chemical communication. Among these authorities are Havelock Ellis, Irving Bieber, and Lewis Thomas, who offered the following statement: “I should think we might fairly gauge the future of biological science, centuries ahead, by estimating the time it will take to reach a complete, comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece all the mysteries.” (Thomas, 1980)

3. In Chapter 1, there are fourteen examples of the many questions that may be answered when one considers the likelihood of odorous human communication. Most of these questions concern different aspects of human sexuality. Briefly deliberated are concerns about an ineffective “language of olfaction” and errors in the logic that has been used in the past to deny the importance of odor in human sexuality. The introductory focus then turns to biological consistency among species; the common basis for scientific advancements; and the development of the working hypothesis that odors are a primary influence on human sexuality.

4. Chemical communication and its importance in other species from insects to mammals is more fully detailed in Chapter 2. The term pheromone is defined, with added emphasis of one basic causal relationship, namely, that mammalian pheromones appear to influence the secretion of gonadotropin releasing hormone (GnRH), a hormone with both short-term and long-term effects on neurotransmission. Distinguishing characteristics of pheromones like species-specificity, and the differences between signalling and releasing pheromones are added to the definition. After a brief discussion of mammalian pheromones, the natural production of human odors is discussed and anecdotal evidence of some of their effects are offered as support for the concept of human pheromones.

5. Chapter 3 alludes to Greek mythology; the story of Ariadne’s thread, which metaphorically addresses the issue of biological consistency among species. The development of the mammalian sense of smell is detailed from its beginnings in single-celled organisms. Olfactory transduction is briefly discussed. Four crucial turning points in the development of mammalian chemical communication systems, which contribute to species survival, are: (1) the release of pheromones to attract another organism, which occurs in single-celled non-motile organisms, (2) the ability to detect and respond to chemical messengers with movement, which occurs in motile single-celled organisms (3) the development of neural networks devoted to processing chemical signals, which occurs in brainless invertebrates, and (4) phylogenetic advances in the development of these neural networks to include development of the vertebrate brain. Species-specific comparisons and contrasts in structure and function are provided.

6. Chapter 4 offers an ontogenetic perspective on development, both of the mammalian olfactory systems and of the GnRH neuronal system. The ontogenetic connection between the structure and function of olfactory sensory systems and brain development ascends in its significance because it allows the odorous social environment to directly and indirectly influence brain function by acting on GnRH, which in turn has short-term effects on neurotransmission and long-term effects on the hypothalamic-pituitary-gonadal (HPG) axis.

7. Kallmann’s syndrome represents a failure of GnRH neuronal migration. Correlates with anosmia and the inability to fall in love are noted, as are correlates with the GnRH neuronal system and brain development in other species. Additional aspects of olfactory transduction and signal processing are discussed. There are differences between the main olfactory system and the accessory olfactory system. The importance of the vomeronasal organ (VNO) for pheromone detection in other species and renewed interest in the recently confirmed presence of the human VNO add to the argument for the influence of odors on human sexuality.

8. Chapter 5 begins with anthropological folklore associated with odor and human behavior and progresses to a discussion of empirical evidence for this link. The metabolism of hormones into pheromones is noted. Specifically addressed are experiments with putative human pheromones and the likelihood of causal physiological and behavioral relationships. Comparisons and contrasts among species again are offered in this regard. The use of mammalian pheromones in fragrances designed to enhance the sexual appeal of humans is examined. The naturally occurring fragrance of musk, present in the secretions of many species, is held in high regard for its universal sex-attractant properties.

9. Chapter 6 reports on experiments with consciously processed human odors, beginning with the classically-conditioned response of infants to their mothers’ naturally-scented or artificially-scented breasts. Olfactory imprinting and the importance of the mother-infant bond are linked through non-human animal models to the development of neural templates and the human “love map”. Aspects of odor hedonics are detailed.

10. Children can determine the genetic sex of adults, and adults can distinguish between different people using their sense of smell. The importance of mammalian odors in aggression and in other contexts besides the mother-infant bond suggests human correlates. Similarly, clinical and anecdotal evidence that humans are culturally aware of odor-associated customs enhances a more scientific approach to the link between sex and the human sense of smell. Odors and fetishism are linked. The natural superiority of women’s olfactory acuity and specificity is linked to estrogen levels and to an important role in female choice: What human beings lack in acuity they make up for in powers of discrimination, which rival those of any other mammal.

11. Chapter 7 is a simplistic overview of prenatal GnRH neuronal system development. Included are genetic predisposition and the importance of GnRH pulsatility in the regulation of the HPG axis. This chapter begins, however, with the importance of chemical communication between ovum and spermatozoa and progresses through basic genetics, neuroanatomy, endocrinology, and endocrine aspects of neurotransmission. Postnatally, odor input is linked to human HPG axis function. Pheromone input appears to be indirectly measurable in assays of luteinizing hormone.

12. Beginning with the “nature” versus “nurture” controversy, Chapter 8 proceeds to the important issue of finding a link between the social environment and genes. The likelihood that genes are involved both in physiological and in behavioral cause and effect relationships is detailed. The influence of pheromones on genes and on concurrent neuroendocrine, reproductive system, and central nervous system development is proposed.

13. Twin studies are discussed, as is recent evidence of master genes that may allow chemical communication at the cellular level to play a primary role in behavioral development and in sexual orientation. Genetic conservation among species, specifically with regard to chemical communication, is addressed. Enzymes and chemical responses are linked with human behavior, as are genes and G protein-coupled receptors through an example of familial precocious puberty. Correlates between adrenal androgen metabolism, pheromone production, sexual dimorphism in the human hypothalamus, and human sexual orientation are offered.

14. Chapter 9 details aspects of human consciousness and of limbic learning and memory. Olfaction plays a key role by providing input to the medial preoptic area of the hypothalamus. Comparisons and contrasts among species and among theories of consciousness are offered.

15. The importance of linking specialized research in diverse disciplines is made known, namely, how a “gay gene” might influence both human neuroanatomy and human sexuality. Dean Hamer has proposed the following: “The most simple hypothesis would be that the Xq28 makes a protein that is directly involved in the growth or death of neurons in the INAH-3. Alternatively, the gene could encode a protein that influences the regulation of this region by hormones.” (Hamer & Copeland 1994).

16. Effects of pheromones on other species are favorably compared to the effects of putative human pheromones. A consciously-processed odor stimulus has been used as an adjunct to classically condition the human immune response, thereby adding clinical significance to the effects of odors.

17. Chapter 10 reveals evidence of odor-driven hormonal effects on human behavior and on sexuality, again using cross-species comparisons that link information provided in earlier chapters. Examples supporting a link between pheromones and human sexuality are discussed. The “Law of Propinquity” appears to be invalidated by experience with pheromones that create more of a friendship or kinship bond, perhaps also creating an antibond effect on love. There is evidence that humans mate for genetic diversity on the basis of unconscious odor associations, and that odors may be involved in the Coolidge effect.

18. The sources of human pheromones are detailed in Chapter 11, with a discussion of the role of glandular secretions, fatty acids, bacteria, skin cells, and the relationship between levels or ratios of sex hormones and pheromone production. Important aspects of pheromone distribution are then linked to intimate behavioral associations. Androgenization appears to stimulate secretion of a more masculine pheromone signature. Odors can be used in clinical diagnostics. The inherent difficulties of human pheromone research are briefly discussed.

19. Chapter 12 links human pheromones to various courtship behaviors (e.g., dancing, kissing, et al.,) that appear to become progressively more intimate with increasing exposure to pheromones. Stereotypic attractive qualities (e.g., large breasts or hair color and distribution) with anecdotal evidence of causal relationships between pheromones, attraction, and intimacy are represented both positively and negatively. Culturally, negative representations often appear to correlate well with sexual repression. Racial differences in odor production that may contribute to racial prejudice are briefly addressed.

20. Included in Chapter 13 is a discussion of results from the National Geographic Smell Survey. Data was collected from approximately one and a half million people worldwide. Causes of anosmia and its link both to genetics and to the GnRH neuronal systems are detailed, as are links between damage to the VNO, age-related disorders, olfactory deficits, and behavior.

21. Chapter 14 provides both a historical and a modern-day overview of aromatherapy. Cultural differences in odor hedonics are explained by odor-associated classical conditioning. The roles of chemicals now known to function as human pheromones and of putative human pheromones in fragrances for commercial use is discussed. A brief summation of current research supporting the hypothesis that human pheromones are a primary influence on human sexuality is provided.

22. I believe that “the pheromones of other mammals are the only social-environmental stimuli to influence genes [in GnRH neurons].” Accordingly, human pheromones are the most likely link between the “nature” and the “nurture” of human sexuality. However, a typographical error: insertion of “not” on page 189, in paragraph 2, line 4 (intended to read as above) detracts from the concluding paragraphs.

REFERENCES

Thomas, L. (1980) Notes of a biology-watcher: on smell. New England Journal of Medicine 302: 731-733.

Hamer, D. & Copeland, P. (1994) The Science of Desire, Simon & Schuster: 163.

My comment: Claims that my Precis is linked to proof of biophysically constrained energy-dependent causd and effect can be viewed in the context of the video representation by Jorgen Anderson for comparison to this detailed representation of my model and/or this video:

See the discussion attempt here before it is removed via suggestion by an unfriendly administrator who claims he is my friend. I’ve already given him the bird (in the cartoon representation from this blog post).

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.

The Mind's Eyes (revisited)

June 12, 2016

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

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

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

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

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

Book description:

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

Available 6/12/16 from Amazon books
Description:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See page 141

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

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

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

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

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

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

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

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

——————————————-

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

Excerpt:

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

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

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

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

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

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

See also: Viral Nucleic Acids
Abstract excerpt:

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

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

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

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

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

Excerpt:

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

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

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

For comparison, see:

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

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

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