5th-6th Sept 2018 Dublin, Ireland

Abiogenesis vs microRNA biogenesis (3)

by with No Comment Adaptationsbase editingDiseases & DisordersEcologymicroRNA editingModel OrganismsPhysicsRNA DirectedRNA editingRNA interferenceRNA-directed DNA methylationRNA-mediated epigenetic regulation of gene expressionRNA-mediated gene silencingRNA–Mediated Epigenetic Heredity
 

My comment to BioRxiv (Hold on, this is waiting to be approved by BioRxiv)

Thank you for helping to show what has been missing from neo-Darwinian theories and other claims that were based on de Vries 1902 definition of mutation. Theorists may now want to learn more about the energy-dependent molecular mechanisms of recombination.

Most of them will not like the findings you have provided. The peer-review process is especially deadly to those who challenge the current dogma. But since you have made the quantum leap see also:

Mechanisms of Recombination conference  Start: Sunday, May 20, 9.00am Finish: Tuesday, May 22, 6.45pm

Natural selection for codon optimality link quantized energy-dependent RNA-mediated DNA repair from biophysically constrained viral latency to sympatric speciation and all biodiversity.

When people who you thought were your peers reject your findings, you need only wait until after “Schrödinger at 75 – The Future of Biology” – September 2018 to resubmit and publish in a top-tier journal (if you have not already done so).

Until then, see also: Systematic analysis of complex genetic interactions

Reported as: How Many Genes Do Cells Need? Maybe Almost All of Them
Theorists failed to note that the creation of genes in yeasts is quantized energy-dependent and biophysically constrained by the physiology of reproduction. Most of their ridiculous claims try to link abiogenesis to genome evolution.
See for example:  Genome evolution across 1,011 Saccharomyces cerevisiae isolates
The origin of the yeast species in China has been linked to all biophysically constrained sympatric speciation via the section on molecular epigenetics from this 1996 review of RNA-mediated cell type differentiation.
From Fertilization to Adult Sexual Behavior

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

From the Discussion:

Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995).

See also: Correction of β-thalassemia mutant by base editor in human embryos
See for comparison: Nothing in Biology Makes Any Sense Except in the Light of Evolution (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.

Theorists must now face the facts about mitochondrial DNA that also attest to their ignorance. They will be forced to link the creation of anti-entropic virucidal energy to the creation of ATP synthase, the creation of ATP, and the creation of RNA, which links microRNA biogenesis from naturally occurring energy-dependent base editing and the origin of microbial yeasts in China to morphological and behavioral phenotypes in humans via biophysically constrained changes in the microRNA/messenger RNA balance.
After comparison to these “Levels of Biological Organization” (See slide # 6) and the examples from all species, anyone left touting ridiculous theories will be dismissed.

5th-6th Sept 2018 Dublin, Ireland

Polymaths and paradigm shifts: from Asimov to Bear (4)

by with No Comment AdaptationsDiseases & DisordersEcologyRNA Directed

Saying Goodbye to the RNA World Theory

RNA has a limited ability for catalysis compared to peptides, and would have struggled to maintain its catalytic activity under the changing temperature conditions of early Earth. Carter and Wills also argued that if an RNA world existed, it would have been unlikely for it to incorporate peptides later on.

See for comparison: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).

The energy-dependent creation of ATP synthase has since been linked to this claim from McEwen et al., (1964):

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

By starting with the energy-dependent de novo creation of enzymes, others have linked Schrödinger’s claims from “What is Life” (1944)  to all biophysically constrained biodiversity.
Say Hello again to Schrödinger at 75 – The Future of Biology
Let Timothy J. Cunningham, who disappeared from the CDC last month, reintroduce you. See his publications on:
1)”Racial Disparities in Age-Specific Mortality”
2) “Sex-specific relationships between adverse childhood experiences”
3) “Associations between antioxidants and all-cause mortality”
and
4) “Health and Safety Issues for Travelers”
Serious scientists know that all racial/ethnic disparities are food energy-dependent, RNA-mediated, and pheromone-controlled  in the context of enymes, metabolism, and amino acid substitutions. Fixation of the RNA-mediated amino acid substitutions differentiates all cell types in all living genera — including sex differences in cell types.
See for examples our section on molecular epigenetics from this 1996 Hormones and Behavior review of RNA-mediated cell type differentiation. From Fertilization to Adult Sexual Behavior

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

Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus…

See for comparison, this nonsense: Caenorhabditis elegans glia modulate neuronal activity and behavior

Introduction: a brief on evolution of neuroglia

“Nothing in biology makes sense except in the light of evolution”. — Theodosius Dobzhansky (1900–1975)

Evolution of the nervous system proceeded through an increase in number and complexity of the nervous elements and through their specialization into electrically excitable neurons connected through defined synaptic contacts and electrically non-excitable neuroglia forming networks through intercellular gap junctions. Intercellular chemical neurotransmission is, however, characteristic for both forms of the neural cells that express appropriate receptors and are capable of secreting neurotransmitters. The evolution of the nervous system was not a straight journey from less complex and accomplished networks to the more refined ones; at the turning point between invertebrates and vertebrates, a fundamental metamorphosis occurred that changed the overall structure of the central nervous system (CNS).

The difference in the energy of two photons has since been linked from the proton motive force to the creation of enzymes and metabolism of food. The pheromone-controlled physiology of reproduction in species from bacteria to humans has linked DNA methylation from the creation and fixation of RNA-mediated amino acid substitutions to viral latency and all biodiversity. Timothy J. Cunningham placed that fact into the context of his history of published works.
For comparison, see: On the Difference between Physics and Biology: Logical Branching and Biomolecules (2018) and The Large Scale Structure of Space-Time(1975) George FR Ellis was a coauthor of both published works.
He, and others like him, failed to link Physics and Chemistry from molecular epigenetics to what is known about energy-dependent RNA-mediated biophysically constrained cell type differentiation to all biodiversity on Earth. Framing what is known to all serious scientists about cell type differentiation in the context of what Ellis might think is a logical representation of biomolecules attests to his lack of logic across the time-space continuum of his life.
See for comparison: Olfaction Warps Visual Time Perception (2017).
See also Odor-induced mood state modulates language comprehension by affecting processing strategies (2016)
The 2016 citation to The impact of natural odors on affective states in humans can now be linked to the accurate representations of top-down biophysical constraints on food energy-dependent pheromone-controlled feedback loops. The feedback loops are required to biophysically constrain viral latency.
See: What is life when it is not protected from virus driven entropy (video)

The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

See for comparison: Gay, Straight, and the Reason Why: The Science of Sexual Orientation (2011)

Still, even in fruit flies, other sensory input besides pheromones — acoustic, tactile, and visual stimuli — play a role in sexual attraction, and sex specific responses to these stimuli appear to be innate rather than learned by association [36.]. We simply don’t know where the boundary between prespecified attraction and learned association lie in our own species, nor do we have compelling evidence for the primacy of one sense over another. (pp. 210- 211)

See also: Gay, Straight, and the Reason Why: The Science of Sexual Orientation, 2nd edition (2016)
From the second edition of LeVay’s book:

… chemosignal enthusiasts point to a variety of studies in which sniffing body secretions or substances purified from secretions appears to have some psychological effect… (p. 115)

LeVay cites Kohl et al., (2001) Human pheromones: integrating neuroendocrinology and ethology.
He has never mentioned the fact that the effects of virus-driven entropy on cell type differentiation were linked human sexual orientation in The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002) and in the book chapter he cited in the first edition of Gay, Straight, and the Reason Why: The Science of Sexual Orientation.
See for comparison: Always follow your nose: the functional significance of social chemosignals in human reproduction and survival (2015) This article is part of a Special Issue “Chemosignals and Reproduction”
John Cacioppo, a Founder of Social Neuroscience, Dies

The University of Chicago psychology professor made fundamental contributions to understanding the neural mechanisms of social experiences.

My comment to The Scientist:

See also: Evolution of neuroarchitecture, multi-level analyses and calibrative reductionism (2012)

I hope John Cacioppo is remembered for this refutation of neo-Darwinian pseudoscientific nonsense:

Although peptide chemistry has been with us since amino acids first formed, the social role of oxytocin did not exist prior to the evolutionary sculpting of the vertebrate brain.

He may have been one of the first social scientists to recognize the fatal flaw that others continue to include in their works. All other serious scientists, like him, start with the energy-dependent creation of enzymes and amino acids. Only pseudoscientists still start with the evolution of the vertebrate brain.

I remember when he and his wife turned towards me and smiled — after I asked the speaker from Argentina about the role of oxytocin in a rodent model. No studies were being done for the obvious reason that few people knew where oxytocin came from.

I invited the speaker to lunch and we laughed a lot about the works that tried to link oxytocin to differences in behavior without linking the differences to altered  RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse

RIP John Cacioppo

See also: Multilevel integrative analyses of human behavior: social neuroscience and the complementing nature of social and biological approaches (2000)
Nothing published during that 12-year period and nothing published before or since then suggests the the neuroarchitecture of intelligent creatures somehow evolved.
For comparison, see: Human pheromones and nutrient chemicals: epigenetic effects on ecological, social, and neurogenic niches that affect behavior (2012) Presented at the Society for Social Neuroscience Annual Meeting 2012
See also: Neuroglia in C. elegans (2018)

The nematode C. elegans is one of the most important model organisms for understanding neurobiology. Its completely mapped neural connectome of 302 neurons and fully characterized and stereotyped development have made it a prototype for understanding nervous system structure, development, and function. Fifty-six out of C. elegans‘ total of 959 somatic cells are classified as neuroglia. Although research on worm glia has lagged behind studies focused on neurons, there has been a steep upswing in interest during the past decade. Information arising from the recent burst of research on worm glia supports the idea that C. elegans will continue to be an important animal model for understanding glial cell biology. Since the developmental lineage of all cells was mapped, each glial cell in C. elegans is known by a specific name and has research associated with it. We list and describe the glia of the hermaphrodite form of C. elegans and summarize research findings relating to each glial cell. We hope this lecture provides an informative overview of worm glia to accompany the excellent and freely available online resources available to the worm research community.

The worm research community seems to be largely unaware of this fact: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
The have failed to link food odors from the pheromone-controlled physiology of reproduction to ecological adaptatation manifested in morphological and in behavioral diversity.

Alternative splicing of pre-mRNA

The overwhelming ignorance of sex researchers (2)

by with No Comment AdaptationsAlternative SplicingsAutophagyDiseases & DisordersEcologyModel OrganismsRNA DirectedVariations

Conclusion: There is a clear link from Estrogen receptor α polymorphism in individuals and in species with differences in behavioral phenotypes. The differences are food energy-dependent and RNA-mediated. The differences link the sense of smell and the pheromone-controlled physiology of reproduction in soil bacteria from The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression to the report on the Obligatory role of hypothalamic neuroestradiol during the estrogen-induced LH surge in female ovariectomized rhesus monkeys

Reported on December 12, 2017 as: Estrogen discovery could shed new light on fertility problems

Estradiol builds in the bloodstream until it reaches a concentration that causes a surge of the hypothalamic and pituitary hormones, including one called luteinizing hormone, which in turn trigger an ovary to release an egg.

“It’s a feedback loop…

From our section on “Neurosteroids” in this December 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior

Perhaps significantly, neuron-specific transcription regulation of neurosteroidogenic enzymes and subsequent neurosteroids production suggest clues to mechanisms that allow some persons to develop in accord with typical gonadal male-pattern or female-pattern hormones and have appropriate male-typical or female-typical physiques nonetheless have parameters of their sexual behavior profile quite opposite to their physical phenotype. For instance, it might be possible for local neurosteroid action in CNS loci specific for sexual orientation to operate independently of other hormonal production and separately from gross body morphology in general. This could, for instance, account for different manifestations of transsexualism and homosexuality.

The “gay agenda” served its proponents well as they attempted to bury the facts that link feedback loops from odors and pheromones to biophysically constrained viral latency.

See: Feedback loops link odor and pheromone signaling with reproduction

Most sex researchers still live in fear that the biologically uninformed masses will learn that homosexual orientation is nothing more than another variation of what happens in the context of transgenerational epigenetic inheritance.

See: The overwhelming ignorance of sex researchers (December 8, 2016)

All serious scientists link food energy to the pheromone-controlled physiology of reproduction and autophagy, which protects all organized genomes from the virus-driven degradation of messenger RNA. The virus-driven degradation of messenger RNA links mutations to all pathology in species from microbes to humans.

If you try to make any aspect of pathology specific to any group of individuals in any human population, you challenge the totality of experimental evidence that links top-down causation to healthy longevity. You be forced to admit that you are not perfectly healthy, which means you are not qualified to judge the mental health or judge the physical health of others. The take home message is stop judging anyone based on your ignorance.

See also the author’s copy of this award-winning review: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences

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.

Conclusion:

ISSUES FOR FURTHER CONSIDERATION

    Rarely do sex researchers address the ongoing philosophical debate between canonical neo-Darwinism and Biblical creation.  Perhaps this is because any debate between scientific theory and religion arises from distinctly different domains of cognitive thought.  Does the acceptance of Darwin’s theory represent the glorification of Science pitted against religion, or is it a means by which Science and religion might be integrated?  Integration of Science and religion might be achieved by recognizing that the key components of this olfactory/pheromonal model appear to be as irreducibly complex as the basic tenets of evolution and the basic tenets of religion.

    From an evolutionary perspective, highly conserved GnRH peptide ligand/receptor signaling mechanisms are the molecular biochemical mechanisms for sexual reproduction in all organisms.  These signaling mechanisms also appear to play an integral role in the development of sexual preferences.  From a religious perspective, these signaling mechanisms dictate that the creation of life, which begets life, also allows for the creation of diversified life through the same mechanisms.  These mechanisms allow life to recognize the difference between self and non-self and to respond to this difference.

    Perhaps the creation of diversified human life gave us the ability to recognize differences between our sexual behavior and the sexual behavior of others.  Since all life does not beget diversified life, those who judge sexual preferences that do not seem to result in diversified life may be judging creation itself.

    It is easy to understand how someone could judge a particular sexual preference, without thought.  Unconscious affects that are manifest in the development of human sexual preferences are, by their nature, a part of diversified life that few people think about.  What we think about human sexual preferences becomes less meaningful when we realize that most of sexual behavior is not what we cognitively think it should be.  Indeed, the largest contributor to sexual preferences that are manifest in the sexual behavior of any species appears to be unconscious affect.  This also appears to be the basis for diversified life.

See this claim about diversified life for comparison: New Zealand discovery of fossilised ‘monster bird’ bones reveals a colossal, ancient penguin

Insights into penguin evolution

The other startling thing about the new colossal fossil is its ancient age. At 55 to 60 million years old, it is nearly as old as the earliest penguin ancestors ever found. It would have lived during a geological period known as the Paleocene, just after the mass extinction 66 million years ago that wiped out non-bird dinosaurs.

The most startling thing about this ridiculous claim is that it cannot be linked from anything known to serious scientists about biophysically constrained viral latency to all biodiversity on Earth via the pheromone-controlled physiology of reproduction and chromosomal rearrangements in birds.

See for comparison: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes 

Two fixed differences among 597 amino acids drive a Val73Ile and Ala552Thr (valine to alanine) polymorphism in ZAL2m that distinguish its morphological and behavioral phenotype from ZAL2.

See also: Autophagy.pro

There is a clear link from Estrogen receptor α polymorphism in individuals and in species with differences in behavioral phenotypes. The differences are food energy-dependent and RNA-mediated. The differences link the sense of smell and the pheromone-controlled physiology of reproduction in soil bacteria from The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression to the report on theObligatory role of hypothalamic neuroestradiol during the estrogen-induced LH surge in female ovariectomized rhesus monkeys

Difference in the network of hydrogen bonds between high- and low-altitude Hb variants, HH-H and LL-L, respectively The α1 and β1 subunits of HH-H (light blue) and LL-L (light red) are superimposed, and van der Waals radii are shown for α-chain residues that are in atomic contact with β-chain residues of the opposing α2β2 dimer.

The overwhelming ignorance of sex researchers

by with One Comment AdaptationsDiseases & DisordersEcologyHuman BrainHuman PheromonesLight EnergyModel OrganismsNeuronal PlasticityPhysicsRNA DirectedRNA-directed DNA methylationRNA–Mediated Epigenetic HeredityVariations

Summary: J. Michael Bailey, and others like him, pretend to not know how non-coding variants are epigenetically linked from differences in hydrogen bonds to all energy-dependent biophysically constrained morphological and behavioral phenotypes.

Genome-Wide Association Study of Male Sexual Orientation [Energy-dependent changes in biophysically constrained viral latency]

We identified several [energy-dependent changes in] SNPs with p < 10−5, including regions of multiple supporting SNPs on chromosomes 13 (minimum p = 7.5 × 10−7) and 14 (p = 4.7 × 10−7). The genes nearest to these peaks have functions plausibly relevant to [biophysically constrained viral latency and] the development of  sexual orientation.

Reported as: Gene variants identified that may influence sexual orientation in men and boys

The findings by the team do not settle the argument of whether homosexuality in people is biology-based, but instead offers more evidence that suggests it is likely the case. Prior studies that looked at family histories have also offered some evidence of biology playing a role while other studies have found some differences in chromosomes. In this study, the number of samples tested was too small to offer conclusive evidence—larger studies will have to be undertaken to solidify the evidence.

I was not surprised to see J. Michael Bailey listed as a co-author. He is a biologically uninformed pseudoscientist and a passive/aggressive antagonist.

It’s been more than 4 years since food energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution were linked to biophysically constrained viral latency and all biodiversity via the pheromone-controlled physiology of reproduction in all living genera.

An external file that holds a picture, illustration, etc. Object name is nihms675257f2.jpg
Sex researchers like J. Michael Bailey, are still among the majority of those who have paid no attention to the extant literature since the time we published this 1996 review in Hormones and Behavior (with a section on molecular epigenetics.)

From Fertilization to Adult Sexual Behavior

Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995).

All serious scientists know that everyone else must also start with differences in the quantized energy of hydrogen to get from epigenetic modifications to differences in morphological and behavioral phenotypes. Serious scientists also know that social science is pseudoscience and that pseudoscientific nonsense is the cause of all preventable unnecessary suffering and premature death.

See for instance:

1) Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin
2) Mutation-Driven Evolution
and my refutation of neo-Darwinian pseudoscientific nonsense. All three were published on June 14, 2013.
3) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Please join the other serious scientists who have been quietly ridiculing people like J. Michael Bailey for more than 20 years.

QuEBS workshop has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has been developed in Lithuania for more than 20 years already. The beginnings could be associated with a series of “Light-harvesting Physics” international conferences, which were held in Lithuania (in Preila, 1992 and 1994, and in Birštonas, 1996). During these conferences, discussion of notable scientists and pioneers of Quantum Biology, such as Graham R. Fleming, Shaul Mukamel, Rienk van Grondelle, Richard Cogdell, Alfred Holzwarth and others, established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.

Light harvesting is the source of energy-dependent changes in hydrogen that link physics, chemistry, and molecular epigenetics to accurate representations of RNA-mediated cell type differentiation. All aspects of energy-dependent RNA-mediated cell type differentiation have been virtually ignored by J. Michael Bailey, who is the proud owner of the Sexnet listserver. It has been a consistent source of misinformation for all participants during the past two decades.
See for comparison my comments on: Evolution of a Vertebrate Social Decision-Making Network
1)

Re: Cause and effect. How could it not be the adaptive evolution from yeasts of the ligand-receptor binding exemplified across species by the conservaton of gonadotropin releasing hormone (GnRH) and diversification of its receptor? Model organisms like the threespine stickleback make clear the involvement of ecological niche construction. The honeybee invertebrate model organism makes clear the involvement of the nutrient dependent ecological niche in construction of the pheromone-dependent social niche. Invertebrate and vertebrate models collectively attest to the common molecular biology of adaptively evolved social decision-making networks. In mammals, the hypothalamic neurogenenic niche (probably located in the MPOA) responds to nutrients to enable fertility and responds to pheromones to enable sexual reproduction that has adaptively evolved from its origins in brewer’s yeast. Never before has there been such a clear reprentation of cause and effect across species from microbes to man, where nutrient chemicals calibrate the intracellular signaling and their metabolism to pheromones standardizes and controls the stochastic gene expression required for reproduction. Gene expression enables adaptive evolution of the brain and ensures that our ability to acquire nutrient chemicals is the first priority for reproduction via appropriate social behaviors, as it is in every species. For example, microbes eat the DNA of heterospecifics but not conspecifics, which indicate more social sense than what some people today are capable of recognizing in the design of biology (the evolved gene, cell, tissue, organ, organ system pathway that directly links sensory input to the mammalian neuroendocrine system and the hormones responsible for our behavior, which activates the same ‘organized’ pathway).

2)
Re: The Intersection of Neurotoxicology and Endocrine Disruption. NeuroToxicology, Bernard Weiss

Abstract excerpts: …hormones help steer the process of brain development.

…sex differences in behavior are primarily the outcomes of differences in how the brain is sexually differentiated during early development by gonadal hormones (the Organizational Hypothesis).

… environmental chemicals are capable of altering these underlying events and processes. Among those chemicals, the group labeled as endocrine disrupting chemicals (EDCs) offers the clearest evidence of such selectivity… —————– I have terminally argued to conclusion that the clearest evidence of chemicals that alter the underlying events and processes of brain development and its sexual differentiation are the nutrient chemicals and pheromones responsible for the adaptive evolution of species from microbes to man.

Focus on endocrine disruption establishes what happens when toxic chemicals alter the same events and processes of brain development and its sexual differentiation via epigenetic effects on gonadotropin releasing hormone (GnRH) pulsatility, luteinizing hormone, olfactory bulb neurogenesis, hippocampal neurogenesis, learning, and memory in vertebrates.

For contrast, I’ve modeled the epigenetic effects of food odors and pheromones on homeostasis and species diversification, and for many years, my friend Teresa Binstock and co-author (e.g., with Milton Diamond)stressed the importance of endocrine disruption (specifically due to bisphenol A and phthalates) on J. Michael Bailey’s “Sexnet”. Now that the basic principles of biology and levels of biological organization, which link sensory input from the environment directly to behavior via intracellular signaling and stochastic gene expression, have been clarified by work with model organisms, I look forward to learning if there are any reasons to avoid the incorporation of current information on endocrine disruption into existing studies of the homeostatic development of human sexual behavior.

Comparing typical and atypical epigenetic effects that appear to extend to those that are transgenerational seems even more important now than in 1996.

Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338

See also: Open Chromatin Profiling in hiPSC-Derived Neurons Prioritizes Functional Noncoding Psychiatric Risk Variants and Highlights Neurodevelopmental Loci

Our study shows that noncoding disease variants in OCRs can affect neurodevelopment, and that analysis of open chromatin regions can help prioritize functionally relevant noncoding variants identified by GWAS.

After Alan R. Sanders and others published this, the claims in Genome-Wide Association Study of Male Sexual Orientation can be viewed in the context of two decades of false claims and pleas for more funding.

Conclusion:

In this study, the number of samples tested was too small to offer conclusive evidence—larger studies will have to be undertaken to solidify the evidence.

rp_tumblr_ngykp0yfND1r5gzz6o1_500.jpg

Energy-dependent epigenetic translation to mRNA stability

by with One Comment AdaptationsbiophotonicsCytosisDiseases & DisordersEcologyHuman PheromonesLight EnergyModel OrganismsNutrigenomicsPhysicsRNA DirectedRNA-directed DNA methylationVariations

Negative selection in humans and fruit flies involves synergistic epistasis

Negative selection against deleterious alleles produced by mutation influences within-population variation as the most pervasive form of natural selection.

Naturally occurring positive selection for energy-dependent codon optimality replaced every aspect of neo-Darwinian theories that linked natural selection from mutations to evolution of increasing organismal complexity. Positive selection for epigenetically-effected beneficial alleles links the epigenetic landscape to the physical landscape of supercoiled DNA via nutrient-dependent pheromone-controlled metabolic networks and genetic networks.
Everything from atoms to ecosystems was included in this invited review of nutritional epigenetics because all serious scientists know that organisms survive on food energy and that species exemplify the pheromone-controlled reproduction and chromosomal inheritance that ensures survival of all living genera.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction.

See also: Transcriptome-wide Discovery of microRNA Binding Sites in Human Brain

This interactome points to functional miRNA:target pairs across >3,000 genes and represents a valuable resource for accelerating our understanding of miRNA functions in brain. We demonstrate the utility of this map for exploring clinically relevant miRNA binding sites that may facilitate the translation of genetic studies of complex neuropsychiatric diseases into therapeutics.

See also: Connections Underlying Translation and mRNA Stability

…intimate connections between mRNA and the ribosome can drive biological regulation. In closing, we consider the likelihood that these connections between protein synthesis and mRNA stability are widespread or whether other modes of regulation dominate the mRNA stability landscape in higher organisms.

No experimental evidence of evolution includes biophysically constrained biologically-based cause and effect, which integrates the required link from ecological variation to the physics, chemistry, and molecular epigenetics of what Darwin presciently linked from his “conditions of life” to ecological adaption via energy-dependent changes in messenger RNA (mRNA).
See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (with my emphasis)

…the ribosome interprets two codes within the mRNA: the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.

Natural selection for energy-dependent codon optimality conserves the amino acid substitutions in the context of the stability of supercoiled DNA. That stability protects all organized genomes from virus-driven energy theft and genomic entropy. Protection from viruses occurs via the pheromone-controlled biophysically constrained physiology of reproduction in all living genera. Experimental evidence of that fact was included in our section on molecular epigenetics from this 1996 Hormones and Behavior review.
From Fertilization to Adult Sexual Behavior

Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995).

See for comparison: Tracing the Enterococci from Paleozoic Origins to the Hospital

Host energy-dependent speciation

Graphical abstract from “Tracing the Enterococci from Paleozoic Origins to the Hospital”

Reported as: Enterococci may have evolved antimicrobial resistance millions of years ago

…researchers have traced evidence of the bacteria’s evolutionary history back 425 million years and theorize that the same traits that allow the bacteria to thrive in hospitals likely emerged when they were carried onto land in the guts of the world’s first terrestrial animals. The study was funded in part by the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health.

The physiology of reproduction in bacteria and all other living genera is nutrient-dependent and pheromone-controlled. Researchers who think they have traced evidence back to the bacteria’s evolutionary history across 425 million years have not considered the weekend resurrection of the bacterial flagellum to be proof of their pseudoscientific nonsense. Instead, they report “Speciation: Host energy source driven” in their graphical abstract.
Where did the energy come from?
See: Evolutionary Rewiring
The nutrient-dependent pheromone-controlled physiology of reproduction in P. fliuorescens was linked to the weekend evolution of the bacterial flagellum.
See also for an invertebrate example of nutrient energy-dependent pheromone-controlled top-down causation: Inhibition of miR-274-3p increases BmCPV replication by regulating the expression of BmCPV NS5 gene in Bombyx mori  From: Virus Genes. 2017 May 10. doi: 10.1007/s11262-017-1466-7
See also: Two fatty acyl reductases involved in moth pheromone biosynthesis

Studies over the last two decades have pinpointed that the epigenetic effect of pheromone-driven adaptive evolution is one of the major factors driving the successful diversification of Lepidopteran insects10. In moths, a few substitutions in critical amino acids in the key pheromone biosynthetic enzymes are sufficient to create a novel pheromone component11,12.

Facts about pheromones in species from microbes to humans have now been placed into their proper context.
Poor human olfaction is a 19th-century myth, which was reported as: “The human sense of smell: It’s stronger than we think” May 11, 2017
See for comparison: Human pheromones: integrating neuroendocrinology and ethology

The ‘affective primacy hypothesis’ [5] asserts that positive and negative affective reactions can be evoked with minimal stimulus input and virtually no cognitive processing. Olfactory signals seem to induce emotional reactions whether or not a chemical stimulus is consciously perceived. We theorize that the importance of human non-verbal signals is based upon information processing, which occurs in the limbic system, and without any cognitive (cortical) assessment. Affect thus does not require conscious interpretation of signal content. Underlying this fact is that affect dominates social interaction and it is the major currency in social interactions [6]. Affective reactions can occur without extensive perceptual and cognitive encoding. They are made with greater confidence than cognitive judgments, and can be made sooner [5, 7]. Olfactory input from the social environment is well adapted to fit such assertions. For example, chemical cues allow humans to select for, and to mate for, traits of reproductive fitness that cannot be assessed simply from visual cues.

See also: The RNA Age: A Primer
What is currently known about energy-dependent biophysically constrained RNA-mediated cell type differentiation refutes every aspect of neo-Darwinian evolution by placing natural selection for codon optimality and the pheromone-controlled physiology of reproduction first.
All published works and reviews of RNA-mediated events must be placed into the context of the paradigm shift that led to the development of this game.
Cytosis: A Cell Biology Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

Some researches may continue to ignore details about energy-dependent RNA-mediated protection from virus-driven energy theft; the degradation of messenger RNA; and the pathology that is linked from mutations to the loss of enzymes, hormones and receptors in all living genera.
Others will obfuscate what is known to serious scientists.
See for comparison: Ontological Systems In Cognition

There is investigated the possibility of cognition of everything that somehow and other is able to influence to the cognizer – its Existing, which exists for him and may be cognized by him. It is proved that all parts of the Existing are interconnected, it is closed and is the only one for all cognizers in it, and everything differed from the Existing is indistinguishable for the cognizer from non-Existing and cannot be cognized by him. It is shown that the surrounding world of the cognizer, understood as a collection of objects and interconnections identified by him, corresponds to the cognizer’s `nature’ – its ontology and are only a part of the Existing. Objects and interconnections of different ontology differ from each other on level of notions, so are uncertain, inconsistent and paradoxical in relation to each other, and corresponding systems of representations with definite ontology cannot be unified in frames of one system, so are irredundant with each other. There are found the correlations of physical objects of quantum theories, also as cosmological dark matter and dark energy with objects with different ontology. There are analyzed the methods of mathematical description of objects with different ontology, the so-called `correlation principle’ of physical theories in irredundant systems of representations, the `principle of freedom’ for formation of the universe understood as the surrounding world of the cognizer. There are considered the philosophical aspects of the existence of irredundant representations, the physical picture of the world, which this concept leads to. The surrounding worlds corresponding to irredundant representation systems, being parts of the one Existing, are closely interconnected, mutually complemented and form each other, without mixing and being different `by nature’, and contradictions between them stand as moving forces of their evolution.

All aspects of anything that has ever been linked to the “moving forces” of evolution have clearly been linked from food energy and movement to biodiversity and from stress-related virus-driven energy theft to mutations that link the lack of movement at the molecular level to all pathology.
See for instance: Valerie Horsley Gets Under Skin

The Yale University cell and molecular biologist is probing the deep mysteries of epidermal cells.

My comment:
See also: Brain on stress: How the social environment gets under the skin

The authors note that on page 17184, right column, first paragraph, line 4, “effect” should instead appear as “affect.”

The failure to provide a neurobiological framework for understanding natural selection for energy-dependent codon optimality, which is the basis for the biological embedding of epigenetically-effected positive health, positive affect, self-efficacy and self-esteem via effects on reactive alleles in the genome, continues to link all pathology from the virus-driven degradation of messenger RNA to the negative supercoiling of DNA.
No one asked me to establish that framework for healthy longevity or pathology, but I did it anyway after I was told to start with gene activation in GnRH neuroscrectory neurons by Bruce McEwen.
See also: Genome Digest

What researchers are learning as they sequence, map, and decode species’ genomes

The researchers found that genes involved in key survival functions, such as the removal of cellular toxins, the stabilization of proteins, and the activity of the innate immune system, were expanded in deep-sea mussels.

Anna Di Cosmo’s group presciently placed these finding into the context of General and Comparative Endocrinology in Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000). — p. 61

The fact that the energy-dependent stability of RNA-mediated protein folding chemistry links physics from autophagy to biophysically constrained viral latency went missing during the past 4 years, but is not likely to continue to be ignored.
See why: 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’.

There is still no other model for comparison, despite the publication of Mutation-Driven Evolution on the same day my 2013 review was published.

(1) Mutation is the source of all genetic variation on which any form of evolution is dependent. Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation.

That claim differentiates ridiculous theories from my model of biophysically constrained biologically-based cause and effect. The differences were noted in 1991 when Roger Penrose wrote:

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? – From What is Life? (reprint edition)

See also: The Latest Discovery In Quantum Physics Shows Reality Is Not What It Seems

New experiments and studies conducted in laboratories such as CERN seem to suggest that everything is actually composed of energy rather than material particles, including human beings.
rp_levels-of-organization.jpg

Selective reporting of inferences: examples of pseudoscience

by with One Comment AdaptationsAutophagybiophotonicsDiseases & DisordersEcologyHuman BrainModel OrganismsNeuronal PlasticityPhysicsRNA DirectedRNA-directed DNA methylationRNA-mediated epigenetic regulation of gene expressionRNA-mediated gene silencingRNA-mediated toxicityRNA–Mediated Epigenetic HeredityVariations

In the narrative of this presentation on RNA mediated molecular epigenetics and virus driven entropy, I mentioned that Cori Bargmann is scheduled to deliver a lecture entitled “Genes, neurons, circuits and behavior: an integrated approach in a compact brain.” An integrated approach will help others understand what is currently known about how ecological variation leads to ecological adaptation.

Works, like hers, with the nematode model organism will help others understand how ecological adaptation leads to biodiversity in the morphological phenotypes and behavioral phenotypes of all living genera. For example, P. pacificus is an ecologically adapted C. elegans. It is like a C. elegans with teeth that eats other nematodes.

Anyone who continues to report differences in the two nematodes context of selective inferences based on theories about mutations and evolution should promptly be dismissed from the ranks of serious scientists. People like that are biologically uninformed and they seem to know nothing about biophysically constrained RNA-mediated cell type differentiation.  Many of them have built careers on funding from the evolution industry, which supports ridiculous misrepresentations of biologically-based cause and effect by placing them into the context of statistical analyses. The representations omit what is known about biologically-based facts, and report inferences as if the inferences wer based on something besides the definitions and assumptions of others who are biologically uninformed.

It’s not the p-values’ fault – reflections on the recent ASA statement (+relevant R resources)

Excerpt 1)

…the selective reporting of inferences problem is serious enough a problem in our current industrialized science even when no omission takes place.

Excerpt 2)

What, then, went wrong in the last decade or two? The change in the scale of the scientific work, brought about by high throughput experimentation methodologies, availability of large databases and ease of computation, a change that parallels the industrialization that production processes have already gone through. In Genomics, Proteomics, Brain Imaging and such, the number of potential discoveries scanned is enormous so the selection of the interesting ones for highlighting is a must.

My comment: The selection of interesting discoveries led serious scientists to link everything known about physics, chemistry, and the conserved molecular mechanism of RNA-mediated protein folding from hydrogen-atom transfer in DNA base pairs in solution to biologically-based ecological adaptation in species from microbes to humans. Ecological variation has been linked from nutrient-dependent microRNAs and microRNA flanking sequences to all biodiversity in all invertebrates and vertebrates via supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy.
See for comparison:

Krauss, Meyer, Lamoureux: What’s Behind it all? God, Science and the Universe

  1. PROF. DR. LAWRENCE M. KRAUSS, is an internationally known theoretical physicist…
  2. DR. STEPHEN C. MEYER …has expanded the scope of the case for intelligent design to the whole sweep of life’s history.
  3. DR. DENIS O. LAMOUREUX… academic specialty focuses on the modern origins controversy.

My comment: The controversy that some people think exists is the focus of this inference: Young Earth Creationists killing Christian credibility? Perry Marshall, like many other biologically uninformed people who are not scientists, failed to grasp the systems complexity that has been detailed in my works, which include citations to the works of those who have established biologically-based cause and effect at every level of examination from angstroms to ecosystems. Perry Marshall’s ignorance led to this attack on Ken Ham’s creationist claims.
When all else fails to detail what theorists know about how mutations lead to evolution, young earth creationists are easy targets. Theorists, like Perry Marshall, attack what they think people like Ken Ham believe. They do not look at experimental evidence that proves how nucleic acids and cells were created in the context of biophysically constrained RNA-mediated protein folding chemistry. The biophysically constrained chemistry of protein folding links supercoiled DNA to protection from virus-driven entropy in all cell types of all individuals of all living genera that have organized genomes. (Note to theorists: All living genera have organized genomes.)
Excerpt (from Perry Marshall’s inferences):

When folks like Ham stand up and claim to speak for all Christians, we lose face in the debate.
The good news is, there’s another narrative that allows for God and evolution — religion and science — to coexist. One where all of modern science’s discoveries only support the mystery of God, not debunk it.

My comment: Perry Marshall does not tell us which discoveries he believes support the mystery of God. Does he believe fossil record discoveries that some researchers claim link what is known about dead organisms to genome organization in living genera? Does Perry Marshall have evidence of biologically-based cause and effect that can be placed into the context of his inferences and the simultaneous emergence of hens and eggs?
See, for example: Was ribosome the first self-replicator?
Excerpt:

…does it make sense to talk about dark variants of cell and cell membrane? Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously.

My comment: The claim that ‘Hens and eggs emerged simultaneously’ can be compared to Perry Marshall’s inference that young earth creationists may be killing Christian credibility. See my comments to Perry Marshall’s site, but also see the support for Ken Ham’s scientific/Biblical perspective which begins with atomistic insight, not evolutionary theory:
For example:
1) The phylogenetic utility and functional constraint of microRNA flanking sequences

The approach allows rapid resolution of relationships between both closely related and rapidly evolving species, and provides an additional tool for investigation of relationships within the tree of life.

2) Structural diversity of supercoiled DNA

Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function.

3) Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity
Reported as: Reprogramming Cancer Cells Back to Normal Cells

…adhesion proteins — the glue that keeps cells together — interact with the microprocessor, a key player in the production of molecules called microRNAs (miRNAs). The miRNAs orchestrate whole cellular programs by simultaneously regulating expression of a group of genes. The investigators found that when normal cells come in contact with each other, a specific subset of miRNAs suppresses genes that promote cell growth. However, when adhesion is disrupted in cancer cells, these miRNAs are misregulated and cells grow out of control. The investigators showed, in laboratory experiments, that restoring the normal miRNA levels in cancer cells can reverse that aberrant cell growth.

My comment: More than 48,000 published works that link atomistic insight to supercoiled DNA are indexed here: “microRNA.” Taken together there is no doubt that nutrient-dependent microRNAs biophysically constrain protein folding in the context of the physiology of reproduction that links supercoiled DNA to protection from virus-driven genomic entropy and all biomass and all biodiversity in all living genera. The published works also are beginning to show that virus-driven energy theft links mutations to all pathology (see below).
See for comparison:

Human adaptation and population differentiation in the light of ancient genomes
Excerpt:

…our results provide clear evidence that local adaptation contributed to these allele frequency changes in European populations, as strongly differentiated alleles in Europeans are enriched in likely functional variants: genic, previously constrained and putatively regulatory.

Reported as: Stone Age hunters contributed adaptive variants to present-day Europeans
Excerpt:

…the team speculates that these variants may be beneficial in populations living at high latitudes with limited exposure to UV light. However, Key is cautious, commenting that: ‘We have to note that our functional understanding of human genetic variants is still limited.’

My comment: Neo-Darwinian theorists consistently fail to grasp any of the experimentally established facts that link ecological variation to nutrient-dependent ecological variations via top-down causation. Key phrases such as “variants may be beneficial” in the context of  “local adaptation” manifested in “allele frequency changes”are not linked from top-down causation to biodiversity. Top-down causation links the speed of light on contact with water from UV light to energy-dependent hydrogen-atom transfer in DNA base pairs in solution.
See also: Many long intergenic non-coding RNAs distally regulate mRNA gene expression levels
Excerpt:

Using Mendelian randomization, we found that there is evidence for lincRNAs having distal effects on the expression levels of protein-coding genes in a dosage-dependent way across the genome in similar proportions to distal effects of mRNA.

My comment: They link what organisms eat from metabolic networks to genetic networks and obesity, but attribute the obesity to genetic predispositions linked from expression quantitative trait loci (eQTLs) to obesity-linked pathology in the context of Mendelian randomization. In this regard, Mendelian randomization can be thought of as a “natural” randomized controlled trial. From a statistical perspective, it is an application of the technique of instrumental variables (Thomas & Conti 2004, Didelez & Sheehan 2007), with genotype acting as an instrument for the exposure of interest.
In other words, Mendelian randomization allows them to report selective inferences in the context of biologoically-based caues and effect without mentioning the fact that nutrient-dependent microRNAs have been linked to biophysically-constrained RNA-mediated cell type differentiation via what is known to serious scientists about protein folding in all living genera.
When people like Perry Marshall stop attacking others, and start learning what serious scientists know about UV light and energy-dependent cell type differentiation, they may also learn that young earth creationists were among the first to recognize how viruses would be linked to all pathology.
See: Viral Genome Junk Is Bunk
Excerpt:

…the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6

Works cited by the young earth creationists include:
Holmes E. C. 2003. Molecular Clocks and the Puzzle of RNA Virus Origins. Journal of Virology. 77 (7): 3893–3897.
Chuong, E. B. et al. 2013. Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nature Genetics. 45 (3): 325-329.
See also: Regulatory evolution of innate immunity through co-option of endogenous retroviruses
Conclusion:

Regardless of how these sequences originated, our study illuminates how selfish genetic elements have contributed raw material that has been repurposed for cellular innovation.

Reported as: Viral ‘fossils’ in our DNA may help us fight infection
See my comment:

Re: “The work suggests that these viral fossils probably played a key role in the evolution of our species…”
The work shows that Greg Bear accurately portrayed virus-driven energy theft when he linked it to the creation of new species. In 1999 and 2003, he linked what is now known about the anti-entropic effects of sunlight and hydrogen-energy transfer in DNA base pairs in solution to the creation of a new human subspecies.
What’s currently known outside the context of science fiction also links Einstein’s math and physics to molecular mechanisms of adaptation via Schrodinger’s claims about sunlight when paired with Dobzhansky’s claims about amino acid substitutions in the context of transgenerational epigenetic inheritance.
For example, the Zika virus clearly links primate craniofacial morphology and brain development. DNA damage linked to variations can be compared in the context of the fossil record and what is known about how cell type differentiation occurs. Nutrient energy-dependent RNA-mediated DNA repair and amino acid substitutions are linked to species-wide ecological adaptations.
The energy-dependent adaptations link ecological variation to morphological and behavioral phenotypes in species from microbes to humans. Virus-driven energy theft links a single amino acid substitution to increased virulence when nutrient-stress and/or social stress cause changes in pH that favor viral replication instead of nutrient-dependent immune system-support of controlled cell type differentiation.
Simply put, Dobzhansky’s claims can be placed into the context of what is known about all virus-driven pathology. He wrote: “…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)” — See: Nothing in Biology Makes Any Sense Except in the Light of Evolution
The “light” is sunlight and it is linked to hydrogen-atom transfer in DNA base pairs in solution to fixation of amino acid substitutions and supercoiled DNA by everything currently known to physicists, chemists, and molecular biologists about biophysically constrained chemistry and the nutrient-dependent biological basis of the physiology of reproduction in all living genera.
Viruses increase their virulence via energy theft linked to a single amino acid substitution. All nutrient-dependent life must ecologically adapt by at least one nutrient-dependent amino acid substitution, which must be linked to supercoiled DNA via the physiology of reproduction in all living genera.
What some people call “viral fossils” are clear indicators of how the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding prevents virus-driven entropy of organized genomes in the context of the physiology of reproduction.

Summary: Claims that include statements like this: “Regardless of how these sequences originated…” invariably lead to claims that link pseudoscientific nonsense to the evolution of what serious scientist understand about the origin of the innate immune system. It is called the innate immune system for a reason. It it did not exist to protect the organized genomes of all living genera from virus-driven entropy, there would be no claims about “…how selfish genetic elements have contributed raw material that has been repurposed for cellular innovation.”
Viruses may be used to frame arguments that include claims about “selfish genetic elements.” But virus-driven energy theft cannot contribute any raw material that can be repurposed for cellular innovation. Cellular innovation is nutrient-dependent, and only the innate immune system can enable repurposing via nutrient energy-dependent feedback loops that link supercoiled DNA to the innate immune system’s protection from virus-driven entropy in the organized genomes of all living genera.
See for examples from the past few days.
2016 Mar 15 Downregulation of the stress-induced ligand ULBP1 following SV40 infection confers viral evasion from NK cell cytotoxicity.
2016 Mar 16 Non‑invasive prostate cancer detection by measuring miRNA variants (isomiRs) in urine extracellular vesicles
2016 Mar 16 MicroRNA-1229 overexpression promotes cell proliferation and tumorigenicity and activates Wnt/β-catenin signaling in breast cancer

2016 Mar 15 Phenotypic switching of vascular smooth muscle cells in the ‘normal region’ of aorta from atherosclerosis patients is regulated by miR-145
2016 Mar 15 A preliminary microarray assay of the miRNA expression signatures in buccal mucosa of oral submucous fibrosis patients
2016 Mar 14 Role of cancer stem cells in racial disparity in colorectal cancer
Excerpt:

Our findings suggest that an increase in CSCs, specifically the CD44+ CD166– phenotype in the colon could be a predisposing factor for the increased incidence of CRC among AAs. MicroRNA 1207-5p appears to play a crucial role in regulating stemness in colonic epithelial cells in AAs.

My comment: Each of the articles linked above links stress perturbed changes in pH from virus-driven energy theft to mutations and pathology. Serious scientist have arrived at conclusions that link everything known about RNA-mediated cell type differentiation to the nutrient energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution. Energy-dependent changes in base pairs link atoms to ecosystems in the context of supercoiled DNA and the physiology of reproduction.
Links from atoms to funcitonal ecosystems do not include mutations and evolution except in the context of virus-driven energy theft, genomic instability, and pathology. That fact will lead to the public humiliation of any neo-Darwinian theorist who continues to tout their pseudoscientific nonsense about beneficial mutations. The careers of the pseudoscientists already have begun to end. Do not let them take your career with them or kill anyone else with their theories as they make a hasty exit. At the same time, watch them change the terms they have used to link mutations to evolution.
Learn the difference between a nutrient-dependent RNA-mediated amino acid substitution and a mutation and you won’t get caught making ridiculous claims about weekend evolution of the bacterial flagellum.
Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Excerpt:

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).

See for comparison:



I reiterate, see also: Young Earth Creationists killing Christian credibility?

Perry Marshall says:
March 19, 2016 at 10:04 am
James, you are one step away from being banned because of your disingenuous comments, your accusations, and your unnecessary combativeness. I am getting tired of it. People accuse you of being a troll for a reason.
This is your final warning.
My comment: Obviously, I can say nothing more about Perry Marshall’s attacks on the credibility of young earth creationists — on his blog site.  And there is no reason to reassert my claim that all serious scientists are Combating Evolution to Fight Disease.
My comments to the Science Magazine site:
1) “An alternative theory proposes environmentally induced change in an organism’s behavior as the starting point (1), and “phenotypic plasticity” that is inherited across generations through an unspecified process of “genetic assimilation” (2).” http://www.sciencemag.org/content/332/6034/1161.short
This is now more than merely an alternative theory of genetic assimilation. It links transgenerational epigenetic effects from nutrient uptake and RNA-mediated events to amino acid substitutions that differentiate the cell types of all cells in all individuals of all organisms. See, for example: Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans http://www.cell.com/cell/abstract/S0092-8674(14)00806-X The nutrient stress-induced RNA-mediated events, which link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man, also link morphological and behavioral diversity via conserved molecular mechanisms exemplified in the context of biologically plausible ecological speciation in nematodes.See: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes http://linkinghub.elsevier.com/retrieve/pii/S0092867412015000
A difference in their feeding behavior and in the anatomy of their mouth parts is linked from nutrient-dependent pheromone-controlled feedback loops to ecological, social, and neurogenic niche construction. The change in focus from mutations, natural selection, and the evolution of biodiversity via unknown evolutionary events to nutrient-dependent pheromone-controlled RNA-mediated events that differentiate cell types may be required for others to realize the difference between evolutionary theories and biologically-based facts about RNA-mediated events.RNA-mediated events are biophysically constrained, which means they are a biologically plausible way to link the physics and chemistry of protein folding to increasing organismal complexity via molecular biology. RNA-mediated events can also be compared to any unknown evolutionary events that might arise in the context of an alternative theory about constraint-breaking mutations, or other theories that include no mention of RNA-mediated events. Submitted on Sat, 09/13/2014 – 08:58
2) Re: “Molecular biology and evolutionary biology have been separate disciplines and scientific cultures: The former is mechanistic and focused on molecules; the latter is theoretical and focused on populations.”Now see: A mechanistic link between gene regulation and genome architecture in mammalian development http://www.sciencedirect.com/science/article/pii/S0959437X14000495 for the refutation of neo-Darwinian pseudoscientific nonsense.Experimental evidence of biologically-based cause and effect does not support ideas about mutations, natural selection, and the evolution of biodiversity.Experimental evidence of biologically-based cause and effect supports the fact that ecological variation leads to nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man via conserved molecular mechanisms. Submitted on Tue, 07/15/2014 – 22:13
3) Re:”…the driver of evolution is not mutations or variation but selection, be it natural, artificial, kin or sexual selection. Mutation is but one of the factors that contribute to variation.”I thought Robert Frye knew better than that, because he attended a 1993 symposium I organized and my 2007 Reiss Plenary session of The Mind’s Eyes: Modeling the Development of Diverse Sexual Preferences.Perhaps this is a different Robert Frye or one who thinks that sexual orientation arises via mutations and natural selection in human males but via nutrient-dependent pheromone-controlled cell type differentiation in yeasts as we reported in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior “Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus…”Robert: What about Anne’s rams. Are they among the selected mutants that you think may have evolved their exclusive homosexual orientation? Submitted on Sun, 09/07/2014 – 20:51
4) Darwin probably anticipated the insemination of population genetics that led to the bastardization of his detailed observations in the “Modern Synthesis.” He politely insisted that ‘conditions of life’ be considered before natural selection. There are two ‘conditions of life.’ It is nutrient-dependent and pheromone-controlled. Rosenberg and Queitsch now note the work with Dobzhansky’s rarely acknowledged claim: “I am a creationist and an evolutionist.” They also declare the need for “Deep understanding of the mechanisms that generate variation at the molecular level…”Deep understanding of the ‘conditions of life’ does not come from theory. Problems with the “modern synthesis” now lead us back to the facts about biologically-based cause and effect that Darwin and Dobzhansky approached with humility, which are the same biological facts that evolutionists approached with ignorance about behavioral affects and the arrogance that accompanies that ignorance. Rosenberg and Queitsch echo the sentiments of those who have been subjected to academic suppression. Clearly, however, “nothing in evolution makes sense except in the light of biology” is not an exaggeration. It is a common sense statement about the biologically plausible genesis of functional cell types. Population genetics and evolutionary theories abandoned the biophysical constraints of ecological variation and the physiology of reproduction, which enable epigenetically-effected nutrient-dependent pheromone-controlled receptor-mediated ecological adaptations and species diversity via the complexities of protein folding and niche construction. It’s time for biophysicists to tell theorists and pathologists how to differentiate between theories about the genesis of different cell types and the biological facts about the nutrient-dependent pheromone-controlled ecological adaptations that enable the genesis of different cell types in individuals of different species. Simply put, it’s time to stop trying to explain ecological adaptations in the context of mutations and evolution. Submitted on Fri, 03/07/2014 – 12:07
Addendum: With his book, and on the FB page and blog site that he controls, Perry Marshall, has joined the ranks of many others who are fighting to keep evolution and disease. The evolution industry has been successfully built from the pseudoscientific nonsense of theory, and Perry Marshall is riding the wave of success with Evolution 2.0.
See also:

James V. Kohl says:

Your comment is awaiting moderation.

March 19, 2016 at 11:10 am

I apologize, Perry. I thought you were attacking my beliefs. Typically, I am not combative, but I am not defenseless, either.
What aspect of my model are you willing to discuss?
For example, I presented this poster at the Labroots Neuroscience 2016 Virtual event last week:
From hydrogen atom transfer in DNA base pairs to ecosystems
https://www.youtube.com/watch?v=5CN2a0Z1fQI

For comparison to my model:
Here is a recent representation of the never-ending focus on visual input, which ignores the fact that chemotaxis must precede phototaxis during the integration of sensory input in the developing brain: Building A Brain: Mysteries of the Brain.
When someone like Perry Marshall, attacks Ken Ham, or anyone else for their beliefs, ask yourself what beliefs they are trying to sell you with their marketing campaign. Perry Marshall, for example, seems to be trying to sell you his belief that hybrids created in the lab are examples of God’s creation of different species.
Dobzhansky (1972)
Conclusion:

As a category of classification, species was and is being applied to all organisms, and this has led to futile search for universal biological properties of all species. What is actually found is a remarkable variety of different kinds of species. Even confining our attention to sexually reproducing and outbreeding forms, we find more or less monolithic “good” species, superspecies, and semispecies. Finally, it begins to look as if reproductive isolation may sometimes follow and at other times precede the adaptive divergence of gene pools of populations.

My comment: In either case, the physiology of reproduction is nutrient-dependent and must link what is known about the innate immune system from feedback loops to biodiversity via supercoiled DNA, which protects all organized genomes in all living genera from virus-driven entropy.
 

rp_levels-of-organization.jpg

Organic Compounds and the Miracle of Smell and Taste

by with No Comment AdaptationsAlternative SplicingsbiophotonicsDiseases & DisordersEcologyHuman BrainHuman PheromonesLight EnergyModel OrganismsNeuronal PlasticityNutrigenomicsPharmacogenomicsPhysicsRNA DirectedRNA-directed DNA methylationRNA-mediated epigenetic regulation of gene expressionRNA-mediated gene silencingRNA-mediated toxicityRNA–Mediated Epigenetic HeredityVariationsWhat's in the News

Neo-Darwian evolutionary theorists and human ethologists seem to ignore the fact that reproductive isolation is nutrient-dependent and controlled by the physiology of reproduction.

…reproductive isolation may sometimes follow and at other times precede the adaptive divergence of gene pools of populations. — Dobzhansky (1972)

Those who cite Dobzhansky’s (1973)  claim that Nothing in Biology Makes Any Sense Except in the Light of Evolution, have failed to explain why

…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.

Single amino acid substitutions that differentiate species appear to arise only in the context of de novo gene creation that begins with the creation of olfactory receptor genes in all invertebrates and vertebrates. Therefore, de novo gene creation appears a miracle linked to the chemical senses of smell and taste.

The Miracles Of Smell And Taste (free book)
Excerpt:  

…the sense of smell developed in order to identify amino acid-like chemical substances soluble in water. The ability to determine molecules floating in the air is an adaptation of that original mechanism.96″ (p. 106)

See also:  How The Nose Knows: Research On Smell Boosted
Excerpt:

“Amino acids are the signature of life,” he said. “Every living thing sheds amino acids. The olfactory system evolved to pick up information. Odors help an animal find food, avoid predators and locate a mate.”

See also:  Same switches program taste and smell in fruit flies
Excerpt:

One way to get many types of cells or proteins from the same genetic starting material is by mixing and matching different parts of one gene to produce multiple gene readouts, a phenomenon known as alternative splicing. The team’s results point to another strategy, however: using the same genes in different combinations, or “combinatorial coding.”
By tweaking different fly genes and counting how many neuron types were produced as the flies matured, the team identified a network of five genes that work together like coordinated control switches to guide the precursor cells’ transformation to mature neurons. The genes regulate each other’s activity, interacting in unique combinations to set each precursor cell on a distinct path by turning on different olfactory receptors in each cell.

My comment: 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.
Conditioned hormonal and behavioral responses to odors associated with food selection and conspecifics in mammals require something like the collective ‘neural networks’ of beehives. Philosophically and metaphorically, these neural networks extend to mammalian brains. The concept that is extended is the epigenetic tweaking of immense gene networks in ‘superorganisms’ (Lockett, Kucharski, & Maleszka, 2012) that ‘solve problems through the exchange and the selective cancellation and modification of signals (Bear, 2004, p. 330)’.

See also: Table of Organic Compounds and their Smells: revised edition


See also: On the Origins of Chemophobia – Part 1
Excerpt:

“Chemicals are the sinister and little-recognised partners of radiation entering into living organisms, passing from one to another in a chain of poisoning and death” – Rachel Carson’s Silent Spring, 1962

My comment:  If not for nutrient-dependent pheromone-controlled RNA-mediated DNA repair, we would have much more to fear from radiation than chemophobic pseudoscientists have to fear from others who have learned about human pheromones.
The Hellstrom Chronicle (1971)
Excerpt:

A fictitious scientist called Dr. Nils Hellstrom (played by Lawrence Pressman) guides viewers throughout the film. He claims, on the basis of scientific-sounding theories, that insects will ultimately win the fight for survival on planet Earth because of their adaptability and ability to reproduce rapidly….

My comment: Nutrient-dependent metabolic networks are linked to genetic networks via the pheromone-controlled physiology of reproduction in species from microbes to humans.  However, facts about human pheromones are typically ignored by pseudoscientists.
A Fear of Pheromones (1971)
Excerpt: 

WHAT are we going to do if it turns out that we have pheromones? What on earth would we be doing with such things? With the richness of speech, and all our new devices for communication, why would we want to release odors into the air to convey information about anything? We can send notes, telephone, whisper cryptic invitations, announce the giving of parties, even bounce words off the moon and make them carom around the planets. Why a gas, or droplets of moisture made to be deposited on fenceposts?

On Smell (1980)
Excerpt:

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  (p. 732).  — Lewis Thomas as cited in “The Scent of Eros: Mysteries of Odor in Human Sexuality“

See also: Genes with monoallelic expression contribute disproportionately to genetic diversity in humans reported as:

The Spice of Life 

Excerpt:

…in a gene with monoallelic expression, there’s an equal chance for either of the two copies to be expressed during early development—but only one of the copies will be expressed. This random decision doesn’t change the DNA in that cell, but the decision to express only one allele is “inherited” by the offspring of that cell, through what is called an epigenetic process. In other words, the identical genes in the daughter cells will also be monoallelic.

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.

My comment: Jim Pfaus is one of many other biologically uninformed sex researchers. He knows nothing about physics, chemistry, or RNA-mediated amino acid substitutions and cell type differentiation. He can’t link link metabolic networks and genetic networks via the physiology of reproduction. He works with rodents, but doesn’t realize that the de novo creation of olfactory receptor genes must link species from microbes to humans via the conserved molecular mechanisms of cell type differentiation we detailed in the molecular epigenetics section of this 1996 review: From Fertilization to Adult Sexual Behavior
Excerpt:

Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995).

See also: 40 million years before butterflies existed, this creature evolved with strikingly similar looks.
Excerpt:

It’s thought that Oregramma illecebrosa last shared a common ancestor with modern butterflies more than 320 million years ago. The fact that two quite unrelated insects developed these markings millions of years apart from one another is a perfect example of convergent evolution: Oregramma illecebrosa might not have shared space with owls, but plenty of big-eyed creatures — perhaps even dinosaurs, the prominent predators of the Jurassic period — could have served as inspiration for the markings.

My comment: No serious scientist I have ever met thinks that convergent evolution occurs in any two species. There is only experimental evidence that links ecological variation to lineage specific variation and ecological adaptation via energy-dependent hydrogen-atom transfer in DNA base pairs in solution. I am never surprised when Rachel Feltman or other journalist fail to link what is known about nutrient-dependent pheromone-controlled biodiversity in butterflies to nutrient-dependent pheromone-controlled biodiversity in all living genera via the same molecular mechanisms.
Like other biologically uninformed reporter, Ms. Feltman reports findings that she links to millions of years of evolution, instead of what is known about links from atoms to ecosystems in the context of metabolic networks linked to genetic networks. No matter how many serious scientists she interviews, pseudoscientists like Jim Pfaus will deter her from learning any facts about pheromones and the physiology of nutrient-dependent reproduction.
The fear of pheromones among sex researchers causes most of them to deny all the facts about RNA-mediated cell type differentiation that are known to serious scientists. For example, see: Feedback loops link odor and pheromone signaling with reproduction.
See also: Gay, Straight, and the Reason Why: The Science of Sexual Orientation (p. 210 – 211)

This model is attractive in that it solves the “binding problem” of sexual attraction. By that I mean the problem of why all the different features of men or women (visual appearance and feel of face, body, and genitals; voice quality, smell; personality and behavior, etc.) attract people as a more or less coherent package representing one sex, rather than as an arbitrary collage of male and female characteristics. If all these characteristics come to be attractive because they were experienced in association with a male- or female-specific pheromone, then they will naturally go together even in the absence of complex genetically coded instructions.”
Still, even in fruit flies, other sensory input besides pheromones — acoustic, tactile, and visual stimuli — play a role in sexual attraction, and sex specific responses to these stimuli appear to be innate rather than learned by association [36.]. We simply don’t know where the boundary between prespecified attraction and learned association lie in our own species, nor do we have compelling evidence for the primacy of one sense over another.

My comment: The primacy of olfaction has been linked from metabolic networks to genetic networks via hydrogen-atom transfer in DNA base pairs in solution, which link the virucidal effects of UV light to the stability of supercoiled DNA in all living genera via the physiology of reproduction and species-specific chromosomal rearrangements. All this has since been placed into the context of links from stress to cell type differentiation via microRNAs.

See:  Neuro-Epigenetic Indications of Acute Stress Response in Humans: The Case of MicroRNA-29c

Reported as: Targeting the mind/body connection in stress
Excerpt:

The research for this study was conducted on 49 healthy young male adults. Researchers integrated the analysis of fMRI images of brain function during an acute social stress task and also measured levels of microRNAs—small RNAs that exert potent regulatory effects—obtained in a blood test before and three hours after the induced stress.

My comment: Again, researchers from Israel take the lead by providing even more information that links microRNAs and adhesion proteins to the stability of organized genomes via RNA-mediated protein folding chemistry in the context of hydrogen-atom transfer in DNA base pairs in solution, which is linked to supercoiled DNA that protects all living genera from virus-driven entropy.

If students in other countries learned more about how ecological variation must be linked to ecological adaptation, they could not possibly be taught to believe in the pseudoscientific nonsense of neo-Darwinian theories.

 
 

amino acid homeostasis

Keep the gay gene theory?

by with No Comment AdaptationsEcologyHuman PheromonesModel OrganismsNeuronal PlasticityRNA DirectedRNA-mediated epigenetic regulation of gene expressionRNA-mediated gene silencingVariations

See first: Supercoiled DNA constrains virus-driven genomic entropy

The data that links small molecules, such as microRNAs, from metabolic networks to genetic networks, makes the claims of neo-Darwinian theorists the theme of this parody. It is an accurate representation of how nutrient-dependent base pair changes link ecological variation to ecological adaptation and all biomass on earth via what is currently known to serious scientists about base pair changes and RNA-mediated DNA repair.

For example: This gene-centric theory has been eliminated.

Gene May Prompt Male-to-Male Attraction in Worms

Excerpt 1) “…the gene variant, known as plep-1, may somehow be altering the chemical profile of the excretions in a way that makes them more attractive to other males.”

Excerpt 2) Next, the researchers want to learn what it is about a mutation in the plep-1 gene that makes males attractive to other males.

My comment: Anyone who wants to keep the gay gene theory will need to link the mutation to male homosexuality in humans.

rp_levels-of-organization.jpg

Is photic-zone ribosomal diversity linked to all biodiversity?

by with No Comment AdaptationsEcologyModel OrganismsRNA Directed

Yeast cells optimise their genomes in response to the environment

Excerpt:

The ability to sense environmental nutrient availability and act accordingly is a critical process for all organisms. Changing behaviour in response to nutrients can occur at many levels: the activity of proteins can be varied or new genes can be activated to produce a different set of proteins.

My comment: Could photic-zone eukaryotic plankton ribosomal diversity be linked from the light-induced de novo creation of amino acids to RNA-mediated gene duplication and the RNA-mediated amino acid substitutions that appear to differentiate all cell types of all individuals of all living genera via the physiology of their reproduction?
If so, this research report might link the speed of light on contact with water to nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation at the advent of sexual reproduction in yeasts to sexual orientation in all species that sexually reproduce.
See for review: 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.

 
 

rp_levels-of-organization.jpg

Methylation maintains cell type differences (2)

by with No Comment AdaptationsHuman PheromonesNeuronal PlasticityNutrigenomicsPharmacogenomicsRNA DirectedVariations

Follow up to:  Methylation maintains cell type differences

Brain’s ‘gender’ may be quite flexible: Mechanism that plays key role in sexual differentiation of brain described

Excerpt: “Prof. McCarthy is now doing additional research on the links between the immune system and brain sex differences.”

See also: An immune hypothesis of sexual orientation

Excerpt: “…this ICS-hypothesis is consistent with the fact that many mfTSs can have children and does not preclude effects of odors and pheromones, but elucidates why those substances are less effective for individuals with sexual orientation altered by immune-mediated mechanisms. Importantly, Peeters et al. elegantly demonstrated that familial does not necessarily imply genetic (148). Their findings are relevant to immune-mediated alterations of SoGo because ± in the context of fetal and postnatal critical periods of immune development ± infections during pregnancy and/or early infancy might lastingly shape an individual’s sexually significant ICS.”
Excerpt from the 1996 review she co-authored: “Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995).”

My comment (added to my comments at The Scientist):
RNA-directed DNA methylation links nutrient-dependent RNA-mediated cell type differentiation via amino acid substitutions in all cell types of all individuals of all genera via their physiology of reproduction. In species from microbes to man, cell type differentiation is nutrient-dependent and pheromone-controlled via fixation of the amino acid substitutions in the organized genome.
The human pheromone-deniers delayed the scientific progress on RNA-mediated cell type differentiation by at least two decades. During the same time they have delayed explanations of biologically-based cause and effect that link metabolic networks and genetic networks via the conserved molecular mechanisms of the biophysically constrained chemistry of protein folding.
What’s known has been detailed by others in the context of nutrigenomics and pharmacogenomics. It is great to see those who study sexual differentiation of the brain begin to catch up.
If someone asks why they did not know this, perhaps they will read 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).
————————-
See:  Pharmacogenomics at Mayo Clinic  (2.5 minutes) and Nutrient-dependent / Pheromone-controlled thermodynamics and thermoregulation (5.5 minutes)
2010 Powerpoint presentation 20 minutes International Society for Human Ethology
2007 Powerpoint presentation 45 minutes Society for the Scientific Study of Human Sexuality