The MicroRNAome Strikes Back: A Sokalian hoax (4)

In this Sokalian hoax series, all food energy-dependent pheromone-controlled biodiversity has clearly been linked from the speed of light on contact with water to biophysically constrained viral latency in all genera via the physiology of reproduction and autophagy, the innate phage defense mechanism.
Will water link RNA modifications to stem cell self-renewal, or will light-activated endogenous substrates and biophysically constrained RNA-mediated amino acid substitutions be tossed into the brickyard for the win?

I reiterate the most obvious facts by mentioning again:

 Virus-mediated archaeal hecatomb in the deep seafloor

Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

See also: The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition

Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding, and no net change in affinities. This phenomenon—termed enthalpy/entropy (H/S) compensation—hinders efforts in biomolecular design, and its incidence—often a surprise to experimentalists—makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting—and, perhaps, avoiding or exploiting—this phenomenon in biophysical systems.

The John Templeton Foundation typically seems to be involved in funding research reported that obfuscates facts that link science to Biblical Genesis. The claims about understanding energy-dependent biomolecular recognition in biophysical systems, which must biophysically constrain viral latency, invite more criticism of the Templeton-funded biologically uninformed theorists.

Does the “Extended Synthesis” Replace or Not Replace Neo-Darwinism? — What Has Templeton Funded?

Many terms in science have a different meaning from the public usage, because they depend on particular definitions of the phenomena to which they apply.

See for comparison: Do Human Pheromones Exist? January 23, 2018

The people interviewed are not Nobel Laureates. For comparison, LInda Buck, co-author of Feedback loops link odor and pheromone signaling with reproduction is a 2004 Nobel Laureate.
I suspect that all serious scientists have since learned that pheromones biophysically constrain food energy-dependent viral latency in species from insects to mammals via the conserved molecular mechanisms of microRNA-mediated cause and effect. Serious scientists tend to be more likely than theorists or other pseudoscientists to recognize patterns.
For instance: Insect pheromone in elephants

SIR – (Z)-7-dodecen-l-yl acetate is used by the females of more than 126 species of insects, especially Lepidoptera, as part of their pheromone blends to attract insect males1. Female Asian elephants, Elephas maximus, also use a pheromone to signal to males their readiness to mate2.

That claim links what insects eat to the pheromone-controlled physiology of reproduction of s via the food energy-dependent creation of microRNAs in species from microbes to mammals.

See: Juvenile hormone and sesquiterpenoids in arthropods: Biosynthesis, Signaling, and role of MicroRNA (with my emphasis)

Dynamic and complex mechanisms have evolved to regulate sesquiterpenoid production. Noncoding RNAs such as the microRNAs are primary regulators. This article provides an overview of microRNAs that are known to regulate sesquiterpenoid production in arthropods.

insects, arachnids, and crustaceans are arthropods. No experimental evidence of biologically-based cause and effect suggest that complex mechanisms evolved in any species. For contrast, the link from microRNAs to juvenile hormone crosses species via the molecular mechanisms that link the food energy-dependent creation of microRNAs from what is known about gonadotropin releasing hormone (GnRH) pulsatility to luteinizing horrmone secretion via the food energy-dependent GnRH-directed physiology of pheromone-controlled feedback loops in all mammals.

That fact has been placed into the context of ecological variation and biophysically constrained ecological adaptations.

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes 

…lack of genome information hinders the understanding of the adaptation

See for comparison: Differential expression of microRNAs in luteinising hormone-treated mouse TM3 Leydig cells

Results showed that miRNAs might be involved in the regulation of LH to Leydig cells.

One way to understand the adaptations revealed in the context of mussel genomes involves ignoring all claims about how complex mechanisms “evolved to regulate” anything. The overwhelming systems complexity of biophysically constraints demand that all ecological adaptations be examined from the intelligent perspective of serious scientists.

The well-detailed understanding of how the light energy-dependent creation of microRNAs is linked to all nutrient-dependent pheromone-controlled ecological adaptations. But the facts were again placed back into the context of complex mechanisms that automagically evolved in  Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs

…pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4.

The established biodiversity is obviously pH-dependent and oxidative phosphorylation was linked to the stability of organized genomes in 1964: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”. Other serious scientists moved forward in the context of the energy-dependent hydrophobicity of supercoiled DNA.
See: Structural diversity of supercoiled DNA

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

Outside the context of the epigenetic effect of anti-entropic virucidal energy from sunlight on supercoiled DNA, or perhaps in the context of minimal exposure to ultraviolet light, the metagenomic diversity of bacteria in caves with sulfur water springs led  Bautista et. al., (2018) to conclude:

…20,901 reads of bacterial 16S rRNA gene sequences spanning V1–V3 hypervariable regions corresponded to seven phyla: Proteobacteria, Firmicutes, Chloroflexi, Chlorobi, Bacteroidetes, Actinobacteria and Acidobacteria. Proteobacteria phylum dominance could be due to the increased presence of organic matter, not only of bat guano but also that caused by man and animals, directly or through infiltrations. For the UJAT5 sample, we generated 6,691 reads, which, due to the
physicochemical characteristics (Table 1) and relative frequency obtained (Figure 4), could confirm the presence of acidophilic Proteobacteria in VL caves. All the bacterial communities identified are characteristic of caves, while Acidobacteria, Proteobacteria, and Actinobacteria are typical of volcanic surface terrain.

Simply put, they seem to assume that the increased presence of organic matter is the food energy that supports the pheromone-controlled physiology of reproduction in the different species. But they do not link the creation of sunlight to differences in the food the organisms eat.
By skipping the link from the creation of sunlight — as did Nonomura (2018) in his Sokalian hoax, evolutionists have tried to convince others who are biologically uninformed that the eyes of blind cave fish exemplify evolution in the process of the fish becoming blind.
See: Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish
See (pun intended) Blind Cavefish Can Produce Sighted Offspring  (2008)

It’s a miracle! Blind cavefish, despite having adapted to their lightless environment for more than a million years, can produce sighted offspring in just a single generation, a new study reveals.

This means that even though the fish are blind, they basically have functional visual systems that have been deactivated by a few key mutations, said Jeffery, who was unaffiliated with the study.

See also: The fish evolved from surface-dwelling ancestors during the past million years. (2003)
Everything biologically uninformed theorists report must be linked toi evolution and back by mutations. They refuse to differentiate between mutations and food energy-dependent ecological adaptations because they cannot accept the fact that all biophysically constrained biodiversity is food energy-dependent and constrained by energy-dependent viral latency.
For comparison, what serious scientists see happening in the blind cave fish is the regression of food energy-dependent visual acuity in organisms that can find food without  the energy-dependent creation of G protein-coupled photoreceptors. Only the energy-dependent creation of chemoreceptors is required to link pH-taxis to survival of the microbes and the blind cave fish via what is known about oxidative phosphorylation in other species that display receptor-mediated behaviors.
What science journalists see happen is causing them to back away from their pseudoscintific claims from the past. See for example:

Hydration as a design element in biomaterials  Philip Ball January 24, 2018

John Hewitt January 24, 2018 N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications 
Will water link RNA modifications to stem cell self-renewal, or will light-activated endogenous substrates and biophysically constrained RNA-mediated amino acid substitutions be tossed into the brickyard for the win?


Food energy-dependent epigenetic adaptation (3)

Food energy-dependent epigenetic adaptation (2)

On 5/24/17 I attempted to post this to the ISHE’s human ethology group in response to the post on How concepts of God have developed: God’s shrinking role. God’s survival. Conclusions.

For comparison, see the expanding role of anti-entropic virucidal energy that theorists claim automagically emerged to sustain all evolved biodiversity.

I included a link to:

I also included a link to:

The moderator of the group responded quickly: Jay R. Feierman wrote:

What you are posting has nothing to do with the thread article.

See also: 7/25/13
Jay R. Feierman:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution. 

My summary of past interactions with Jay R. Feierman:

He refuses to accept the fact that conditions of life are energy-dependent. He refuses to accept the fact that other biologically uninformed science idiots and many anonymous fools have consistently removed Darwin’s ‘conditions of life’ and replaced them with ridiculous theories about mutations and evolution.

At a conference we both attended in 1995, Jay R. Feierman was the first to challenge the entirety of the model I presented with the question “What about birds?”

He has continued to prevent dissemination of accurate representations of energy-dependent biologically-based cause and effect since then. He exemplifies the impact that one biologically uninformed science idiot can have across an entire generation of unsuspecting anonymous fools who are likely to believe that the creation of energy has nothing to do with the claims in: How concepts of God have developed: God’s shrinking role. God’s survival. Conclusions.

See also: The general form of Hamilton’s rule makes no predictions and cannot be tested empirically

Hamilton’s rule asserts that a trait is favored by natural selection if the benefit to others, B, multiplied by relatedness, R, exceeds the cost to self, C. Specifically, Hamilton’s rule states that the change in average trait value in a population is proportional to BR−C. This rule is commonly believed to be a natural law making important predictions in biology, and its influence has spread from evolutionary biology to other fields including the social sciences. Whereas many feel that Hamilton’s rule provides valuable intuition, there is disagreement even among experts as to how the quantities B, R, and C should be defined for a given system. Here, we investigate a widely endorsed formulation of Hamilton’s rule, which is said to be as general as natural selection itself. We show that, in this formulation, Hamilton’s rule does not make predictions and cannot be tested empirically. It turns out that the parameters B and C depend on the change in average trait value and therefore cannot predict that change. In this formulation, which has been called “exact and general” by its proponents, Hamilton’s rule can “predict” only the data that have already been given.

Simply put, the authors attest to the fact that every aspect that has ever been included in mathematical models of natural selection cannot link natural selection to anything that could not be predicted by what is known about how food energy must be linked from ecological variation to ecological adaptation by the sense of smell in all living genera. The sense of smell predictably links what is known about natural selection for energy-dependent codon optimality to biophysically constrained viral latency via publication in 2005 of Feedback loops link odor and pheromone signaling with reproduction.

There has never been any experimental evidence of biologically based cause and effect that link anything but olfaction, food odor, and pheromones directly to the survival of all species. Yet Feierman’s claim continues to be echoed in the claims of all others who are biologically uninformed:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. — Jay R. Feierman

See for comparison: Scientists investigate how the sense of smell works in bacteria

…the signaling and inactive states differ only very slightly at the nitrate-binding site – by 0.5-1 angstroms, which is approximately one fifth of the size of the ion itself (1 angstrom is 10-10 meters). However, when this ion binds to the sensor, it causes huge changes in the protein: The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.


Alternative splicing of pre-mRNA

Food energy-dependent epigenetic adaptation (2)

Due to the overwhelming support for my model of top-down causation and all energy-dependent biophysically constrained biodiversity on Earth, I will replace
Food energy-dependent epigenetic adaptation (2)
with the more appropriately titled
God’s shrinking role in your salvation
See: Food energy-dependent epigenetic adaptation
and God’s shrinking role in your salvation (in prep)
before proceeding to the rest of this series on epigenetic adaptation.

Alternative splicing of pre-mRNA

Energy-dependent oscillating gene networks organize life

Nascent, innate, intrinsic, and biofunctional are among the “weasel words” used by theorists who ignore the fact that all life-sustaining energy comes from the sun via hydrogen-atom transfer in DNA base pairs in solution. See how Jon Lieff continues to misrepresent that fact, by placing everything known about RNA-mediated cell type differentiation back into the context of evolution.

Like all pseudoscientists, he starts with energy but fails to mention where the energy came from or where it goes when virus-driven energy theft is linked from mutations and genomic entropy to all pathology via base pair changes and RNA-mediated amino acid substitutions in viruses that stabilize genes in the viruses at the expense of genomic stability in all living genera.

Individual Cell Clocks and Immunity

Energy from the sun is transformed into energy and material for the cell to use in sync to these rhythms. The rhythms also are related to how the cell develops in particular organs and responses to damage and distress. It is not yet clear how these individual unique 24 hour clocks in each cell translates to the rhythms of the entire animal. In evolution, the development of these clocks appears to be vital to provide the needed resources for DNA repair at the proper time of day.

My comment to Jon Lieff’s blog site: Thank you for helping to deliver Schrodinger’s, Turing’s, and Witzany’s message about the anti-entropic virucidal effects of sunlight on alternative RNA splicings, which serious scientists know link autophagy to all biodiversity via RNA-mediated amino acid substitutions.
Please stop placing top-down causation into the context of evolution since no experimental evidence suggests that energy-dependent effects occur outside the context of the de novo creation of G protein-coupled receptors and the physiology of reproduction in species from microbes to humans.
Also, Suzan Mazur acknowledged me and my domain, as sources of information on biologically-based cause and effect for comparison to pseudoscientific nonsense about evolution in: Royal Society: The Public Evolution Summit

It would be great if you would also acknowledge my works as your source of information or acknowledge others whose life’s works are presented in your blog posts.

Thank you for your acknowledgement more than 3 years ago in:

Alternative RNA Splicing in Evolution

My comment:

In our 1996 Hormones and Behavior review, we wrote:”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 Fertilization to Adult Sexual Behavior

The alternative splicings are nutrient-dependent and appear to be enabled by the experience-dependent de novo creation of olfactory receptor genes, which enable additional receptor-mediated nutrient uptake and the metabolism of nutrients to species-specific blends of pheromones that control reproduction in species from microbes to man.

Your focus on the importance of pre-mRNA and alternative splicing is exemplary, especially in the context of neuronal plasticity.

C. elegans is the model organism of neurogenic niche construction that links nutrient-dependent ecological and pheromone-controlled social niche construction to socio-cognitive niche construction in vertebrates and invertebrates. See for review:

Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors

What you are helping to detail is self-assembly with evidence of olfactory/pheromonal self-organization that is currently missing from evolutionary theory, which attributes speciation to mutation-initiated natural selection even though there is no experimental evidence for that (as I mentioned elsewhere).

On 10/27/13 Jon Lieff wrote:

I very much appreciate your comments on pheromone communication and its rapid and critical link to the olfactory brain. I look forward to any current references and future work to help understand the immune brain connection as well as communication in general.


Jon Lieff

See for comparison: What is life when it is not protected from virus driven entropy

See the citation to: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

The full text is free. Compare the claims to Jon Lieff’s claim:

In evolution, the development of these clocks appears to be vital to provide the needed resources for DNA repair at the proper time of day.

See also Peter Berean’s claims about bio-functional information and his claims that energy is not information in the context of his denigrations of my life’s works.

See also: Guardians of the Blood Brain Barrier by Jon Lieff

Just curious where most of your information comes from? I’m a graduate student and would love the primary sources for reference!

See also: Scientists say your “mind” isn’t confined to your brain, or even your body

In math, complex systems are self-organizing, and Siegel believes this idea is the foundation to mental health. Again borrowing from the mathematics, optimal self-organization is: flexible, adaptive, coherent, energized, and stable. This means that without optimal self-organization, you arrive at either chaos or rigidity—a notion that, Siegel says, fits the range of symptoms of mental health disorders.

In biology, the idea that mathematical models are relevant to the required links from ecological variation to energy-dependent ecological adaptation is considered in the context of a joke, or parodies.
See for comparison: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
My comment: Val158Met is an amino acid substitution. Its function is known to be affected by a functional single nucleotide polymorphism (SNP) in COMT (G-to-A base-pair substitution) leading to a methionine (Met) valine (Val) substitution at codons 108/158 (COMT Val158Met). Carriers of the Met allele have been found to display a fourfold decrease in enzymatic activity compared to Val allele carriers going along with an increase of prefrontal DA activity (Lachman et al. 1996; Lotta et al. 1995).

amino acid homeostasis

Checkpoint checkmate: viruses lose if conditions of life win

Akt Kinase-Mediated Checkpoint of cGAS DNA Sensing Pathway


Innate immune receptors detect pathogens through pathogen-associated molecular patterns (PAMPs) and then elicit an immune response (Elinav et al., 2011, Medzhitov and Janeway, 2000). These germ-line-encoded pattern recognition receptors (PRRs) monitor extracellular, endosomal, and intracellular compartments for molecular signatures of microbial infection or the sometimes overlapping molecular triggers produced by abnormal, damaged, or dying cells (Latz, 2010).

Reported as: Anti-viral immune response mechanism!

This study identifies an Akt kinase-mediated checkpoint to fine-tune hosts’ immune responses to DNA stimulation.

My comment: The idea of “DNA sensing” should be placed into the context of how sensing “evolved.”
Viruses could then be linked to signals across the breadth and depth of metabolic networks to genetic networks in all living genera.
Ideas about biologically-based cause and effect could then be compared in the context of the magic of evolution. For example, neo-Darwinian theorists assume that conserved molecular mechanisms of signaling, secreting, and DNA sensing that link atoms to ecosystems concurrently arose and that life automagically emerged via abiogenesis.


Ignoring top-down causation

Dosage compensation can buffer copy-number variation in wild yeast

Susumu Ohno proposed over 40 years ago that gene duplication could provide a major force in the evolution of new gene functions, by relaxing constraint on gene sequences and allowing one or both gene copies to evolve (Ohno, 1970). The genomic era has largely borne out that hypothesis, and many studies have characterized the outcomes of whole and partial genome amplification (Jaillon et al., 2009). The immediate consequence of duplication is assumed to be increased expression of the affected genes, and in some cases the increased expression provides a selective advantage (e.g., Sandegren and Andersson, 2009; Chang et al., 2013; Edi et al., 2014). Over longer periods, the relaxed constraint afforded by functional redundancy allows one or both gene copies to evolve (Ohno, 1970), driving sub- and neo-functionalization (Lynch and Force, 2000; Lynch et al., 2001), expression divergence (Gu et al., 2004, 2005; Li et al., 2005; Wang et al., 2012), and network rewiring (Presser et al., 2008; Freschi et al., 2011; De Smet and Van de Peer, 2012).

Local chromatin environment of a Polycomb target gene instructs its own epigenetic inheritance

Epigenetic memory can be stored in the concentrations of diffusible regulatory factors that are maintained through feedback loops (trans memory) (Novick and Weiner, 1957; Ptashne, 2004; Zacharioudakis et al., 2007 ; Xu et al., 2009). Alternatively, memory could be stored locally in the chromatin environment of individual genes (cis memory), in the form of DNA methylation or post-translational modifications of histones (Moazed, 2011). While in both trans and cis memory the chromatin state is inherited, in the former case chromatin responds to the transcriptional state defined by heritable concentrations of the trans-factors, whereas in the latter case it is the local chromatin environment that instructs its own inheritance and is, therefore, the key epigenetic memory element.
My comment: The local chromatin environment links the epigenetic landscape to the physical landscape of DNA via nutrient-dependent pheromone-controlled feedback loops in species from microbes to man.
The mechanism by which one signaling pathway regulates a second provides insight into how cells integrate multiple stimuli to produce a coordinated response.
Abstract excerpt:
These studies reveal a complex interplay between reproduction and other functions in which GnRH neurons appear to integrate information from multiple sources and modulate a variety of brain functions.

Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.



Quantum correlations/pseudoscience

A quantum advantage for inferring causal structure
Preprint excerpt: “The causal inference schemes described here promise extensive applications in experiments exhibiting quantum eff ects. For instance, they can provide a test of whether the dynamics of a given open quantum system is Markovian or not [17{24]. This is because in a non-Markovian evolution, the environment acts as a common cause between the dynamical system at one time and the same system at a later time. Our inference schemes may also help to detect initial correlations between system and environment, which, if unaccounted for, can lead to
errors in the characterization of processes [15, 25-29].”
My comment: Non-Markovian evolution is exemplified by links from ecological variation to epigenetically-effected cell type differentiation manifested in ecological adaptations. For example, the light-induced de novo creation of amino acids links quantum physics to metabolic networks and genetic networks via RNA-mediated substitutions of amino acids that stabilize the organized genomes of all genera in the context of their physiology of reproduction.
Top-down causation is the sun’s biological energy (e.g., solar/spectral energy). Epigenetic effects are exemplified by photosynthesis in plants, which links top-down causation via light-induced amino acid substitutions to cell type differentiation in animals. See: Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins
RNA-directed DNA methylation and RNA-mediated cause and effect via amino acid substitutions is also recognized by serious scientists in the context of the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to man. See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
Excerpt: “…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution.”
See also my comment on: All in the (bigger) family:
Excerpt: Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.
For a summary of  what is currently known about nutrient-dependent pheromone-controlled biologically based cause and effect, see senior author Jerome Hui’s The phylogenetic utility and functional constraint of microRNA flanking sequences.
Excerpt: “Despite historic issues regarding their use for phylogenetic inference [8], miRNAs can be employed as both qualitative [9] and quantitative markers, with the latter demonstrated clearly here.”
My comment: What has been clearly demonstrated is the link from viral microRNAs and nutrient-dependent microRNAs. The balance of viral /nutrient-dependent microRNAs links viruses from entropic elasticity and nutrients to anti-entropic epigenesis and epistasis. In species from microbes to man epistasis is nutrient-dependent and pheromone-controlled by the epigenetic effects of food odors and pheromones on reproduction. See:  Feedback loops link odor and pheromone signaling with reproduction, which was co-authored by 2004 Nobel Laureate, Linda Buck.

It links top-down causation from the light-induced de novo creation of amino acid substitutions and takes the biophysically constrained chemistry of protein folding from theoretical physics and correlations to biologically-based cause and effect.
Terms like “causal inference” schemes and “phylogenetic inference” can be viewed in the context of “big bang” cosmology and evolutionary theory. These terms should not be used by serious scientists whose integrity leads them to establish patterns of biologically based cause and effect across species.
Serious scientists do that via experimental evidence. The experimental evidence must link their theories to the sun’s biological energy.
Combating Evolution to Fight Disease has led from nutrigenomics to pharmacogenomics and to clinically actionable genotypes via the conserved molecular mechanisms of biophysically constrained nutrient-dependent RNA-mediated protein folding. Causal inferences, phylogenic inferences and associated ridiculous theories have led from nothing to nowhere.


Physics, Chemistry, and Molecular biology (PCMb)

Physics, Chemistry, and Molecular biology (PCMb) link ecological variation to ecological adaptations via a model of gene-cell-tissue-organ-organ system complexity that I first presented in 1992. After adding gene activation by pheromones, I co-authored a book that linked the pheromone-controlled physiology of reproduction across species from microbes to man: The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002)
Since then, others have written books that claimed that pheromones evolved: Pheromones and Animal Behaviour (2003/2014) and one claimed that mammals don’t produce or respond to pheromones: The Great Pheromone Myth (2010).
Ignorance of biophysically-contrained biologically-based cause and effect continue to prevent scientific progress. Others have started to speak out against the pseudoscientific nonsense of evolutionary theorists and psychologists who have limited progress that could have been made by serious scientists from many disciplines. The theorists have continued to tout their pseudoscientific nonsense about mutations, natural selection and evolution, for more than 17 years after we detailed the facts about how epigenetically-effected RNA-mediated events link nutrient-uptake to the pheromone-controlled physiology of reproduction in species from microbes to man.

Many others must speak up each time they read or hear about the statistical nonsense of evolutionary theory as if it were supported by experimental evidence of biologically-based cause and effect. Tell the theorists to start making sense. Cite Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes and quote from it: “The rates of 4 types of elementary evolutionary events (hereinafter Genome Dynamics Events or GDE)…”
Help make others approach the psychology and the practice of medicine from the only perspective that makes sense: Physics, Chemistry, and Molecular biology (PCMb) — not the pseudoscientific nonsense of theorists. RNA-directed DNA methylation links RNA-mediated events to amino acid substitutions that differentiate the cell types of all individuals in all species.

See also: 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. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.