Light-induced-conformer-intercoversion-of-hydrogen-bond

Dual genomes: exposing the evolution industry

Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes

Excerpt: “The CDP showed a significant overrepresentation of certain gene ontology (GO) groups (global tests Po0.001–0.009), using the programme FUNC23 (Methods). These groups included GPCRs, in particular olfactory receptors (ORs), and other membrane and cell-surface proteins, as well as proteins related to the immune system, such as the MHC (Class I and II), and drug metabolism…”
My comment: Biodiversity “…converges upon a ‘common diplotypic proteome (CDP)’, a distinctive subset of genes preferentially encoding two different proteins.” In that context, the importance of nutrient-dependent amino acid substitutions to the de novo creation of olfactory receptors (ORs) and other membrane and cell surface proteins cannot be overstated.
For example, this new evidence now also links the epigenetic effects of food odors associated with nutrient uptake to the de novo creation of olfactory receptors. The de novo creation of olfactory receptors links nutrient uptake to receptor-mediated behavior associated with cell type differentiation at the level of epigenetically effected  MHC / immune system differences. The differences are linked to what is currently known about the pharmacogenomics of drug metabolism and the nutritional epigenetics of health and disease.
Reported as:

Duality in the human genome

Excerpt: “More than 85 percent of all genes have no predominant form which occurs in more than half of all individuals. This enormous diversity means that over half of all genes in an individual, around 9,000 of 17,500, occur uniquely in that one person – and are therefore individual in the truest sense of the word.
The gene, as we imagined it, exists only in exceptional cases. “We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel’s time.”
My comment: We also need to rethink the interpretation of Darwin’s works, which were placed into the context of population genetics by theorists who knew nothing about biologically-based cause and effect. Observed changes in morphology were placed into the context of an invented theory that defined the changes as if they were caused by mutations in genes. I reiterate: “We need to fundamentally rethink the view of genes…” Let’s rethink the view of genes in the following context:
“[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. The anglophone tradition was taught. I was taught, and so were my contemporaries, and so were the younger scientists. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. No, it wasn’t dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact.” — excerpted from Replace the Modern Synthesis (Neo-Darwinism): An Interview With Denis Noble
That powerful recollection by Suzan Mazur, author of The Altenberg 16: An Exposé of the Evolution Industry may reflect her personal bias against evolutionary theory. Indeed, her exposé has received an abundance of criticism, as would be expected from those still touting their pseudoscientific nonsense about genes, mutations and evolution.
Does it matter if her beliefs were biased when evidence of “duality in the human genome” now attests to the fact that her beliefs are supported? Experimental evidence now links epigenetic imprinting across species via the conserved molecular molecular mechanisms that we placed into this perspective in our 1996 Hormones and Behavior review? Here’s a single paragraph from our review, which also exposed the “Evolution Industry”.
Excerpt: “Molecular epigenetics
Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.”
My comment: We now know that these alternative splicings are nutrient-dependent and that RNA-directed DNA methylation links them from from ecological variation to RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all species via conserved molecular mechanisms. It may never become clearer that cell type differentiation is nutrient-dependent and that fixation of amino acid substitutions requires the metabolism of nutrients to species-specific pheromones.
Pheromones control the physiology of reproduction, which enables fixation of the amino acid substitutions in the DNA of organized genomes. It is time to compare ridiculous theories about mutations invented by population geneticists to established facts about how experience-dependent de novo creation of olfactory receptors links ecological variation to ecological adaptations. It’s as simple as 1-2-3.
1) Amino Acid Residues Contributing to Function of the Heteromeric Insect Olfactory Receptor Complex  “Our results suggest that both the ligand-selective Or subunit and the Orco co-receptor contribute to cation channel activity and that some amino acid residues near the carboxy terminus of both subunits are important for Or-Orco channel function.”
2) orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET “orco mutant olfactory sensory neurons have greatly reduced spontaneous activity and lack odour-evoked responses.”
3) Evolution of mosquito preference for humans linked to an odorant receptor “Our results provide a rare example of a gene contributing to behavioural evolution and provide insight into how disease-vectoring mosquitoes came to specialize on humans.” Also see: “Extended Data Figure 3 | Amino acid differences of major Or4 protein alleles.  Dots represent amino acid differences with respect to the genome reference, not an inferred ancestor.”
1) amino acids and olfactory receptor complexes are important for
2) olfactory sensory function and odor-evoked responses, which are perturbed by mutations but
3) established in the context of amino acid substitutions.
In my model, nutrient-dependent amino acid substitutions link the metabolism of nutrients to species-specific pheromones that control the physiology of reproduction in species from microbes to man. In accord with the findings above, the amino acid substitutions do not infer a link to a common ancestor. Theories about common ancestors belong to population geneticists, not serious scientists who understand biologically-based cause and effect.
See for comparison: “…mutations provide the “raw material” upon which the mechanisms of natural selection can act.”
Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].
Amino acid substitutions link ecological variation and the epigenetic landscape to the physical landscape of DNA in the organized genomes of all species via conserved molecular mechanisms that are bio-physically constrained by the chemistry of protein folding. Pheromone-controlled ecological adaptations are manifested in the morphological and behavioral diversity of all species.
Mutations perturb protein folding, which is why they cannot lead to the evolution of biodiversity.
Odor-induced de novo creation of olfactory receptors links nutrient-dependent amino acid substitutions to their pheromone-controlled fixation and genome stability in species from microbes to man via conserved molecular mechanisms. See for examples: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

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Thermodynamic constraints and ecological adaptations sans evolution

Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites

Excerpt: “…a two-variable model that combines stability and stress signi ficantly improves predictions. Therefore, both the overall stability [symbol] and the stress [symbol] seem to capture distinct thermodynamic constraints on protein evolution.”
My comment: Proteins do not evolve. Nutrients are required. Metabolism of nutrients to species-specific pheromones controls the physiology of reproduction in species from microbes to man. The nutrient-dependent pheromone-controlled physiology of reproduction enables epistasis via nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate cell types in the context of thermodynamic cycles of protein biosynthesis and degradation.
Species-specific pheromones control the physiology of reproduction and “fix” the amino acid substitutions in populations. The substitutions stabilize the DNA in organized genomes and the substitutions prevent most of the damage that would otherwise result from accumulated mutations.
Nutrient-dependent DNA repair mechanisms also typically prevent the accumulation of damage that might otherwise occur during life history transitions. For example, vitamin D uptake or natural production links ecological adaptations in populations where malaria is endemic via substitution of the amino acid associated with the hemoglobin S (sickle cell) variant.
The idea of protein evolution is foreign to me because protein evolution is not exemplified in model organisms. The universal trend of amino acid gain and loss in proteins occurs when nutrient-dependent substitutions stabilize the DNA in organized genomes. Accumulated mutations that cause too much dysfunction are typically eliminated — until nutrient stress and/or social stress overwhelm the ability of organisms that might otherwise continue to ecologically adapt as if they were immortal.
Two external factors cause changes in amino acid compositions of proteins in all genera that lead to biodiversity via mortality of individuals. The external factors are nutrient uptake and the pheromone-controlled physiology of reproduction. Together, they link the epigenetic landscape to the physical landscape of DNA in organized genomes via the bio-physically constrained chemistry of protein folding. That is how protein folding can be linked to the conserved molecular mechanisms of ecological adaptations in all species via amino acid substitutions.
biomolbioandco My comment about the Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites was posted at this site after it was blocked by the moderator at the BioRxiv article site.
The stability model they detail is a model in which mutations are either neutral or completely deleterious. However, their evolutionary inferences link the mutations to biodiversity.
The same thing is done in Biophysics of protein evolution and evolutionary protein biophysics.
My comment: These are people who “…expect to witness increasing collaboration between the fields of biophysics and evolution as well as between theory/computation and experiment to decipher many aspects of the evolutionary forces that have been shaping the biological roles of proteins.”
I expect them to be humiliated by serious scientists who are less likely to think that mutations link perturbed protein folding to the increasing organismal complexity manifested in nutrient-dependent pheromone-controlled biodiversity.
See for example, a 5.5 minute video representation of: Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation)
This model refutes a book-length revision of a comparable theory: ‘Mutation-driven evolution’ [1] Chemical ecology drives adaptive evolution via ecological, social, neurogenic, and socio-cognitive niche construction. Nutrients are metabolized to pheromones that epigenetically effect hormones that affect behavior in the same way food odors classically condition behavior associated with food preferences. In mammals, the epigenetic effects of olfactory/pheromonal input are on gonadotropin releasing hormone (GnRH) neurosecretory neurons of brain tissue. For example: glucose and pheromones alter the secretion of GnRH and luteinizing hormone (LH). Secretion of LH is the measurable proxy for genetically predisposed differences in hypothalamic GnRH pulse frequency and amplitude and the downstream effects of GnRH, which is the central regulator of genetically predisposed nutrient-dependent individual survival and pheromone-controlled species survival.
This model of systems biology represents the conservation of bottom-up organization and top-down activation via the 1) thermodynamics of nutrient stress-induced and social stress-induced intracellular changes in the microRNA / messenger RNA  (miRNA/mRNA) balance; 2)  intermolecular changes in DNA (genes) and alternative splicing; 3) non-random experience-dependent stochastic variations in de novo gene expression and biosynthesis of odor receptors; 4) the required gene-cell-tissue-organ-organ system pathway that links sensory input directly to gene activation in neurosecretory cells and to miRNA-facilitated learning and memory in the amygdala of the adaptively evolved mammalian brain; and 5) the reciprocity that links the thermodynamics of gene expression to behavior and altered organism-level thermoregulation in species from microbes to man.
Examples of nutrient-dependent amino acid substitutions clarify the involvement of seemingly futile thermodynamic control of intracellular and intermolecular interactions, which result in de novo creation of olfactory receptor genes. Thermodynamically controlled cycles of RNA transcription and protein degradation are responsible for organism-level changes in pheromone production, which enable accelerated changes in the miRNA/mRNA balance and thermoregulation of controlled nutrient-dependent adaptive evolution.
In this mammalian model, food odors associated with nutrient uptake and species-specific social odors cause changes in the miRNA/mRNA balance. Those changes enable differential gene expression in GnRH neurons during developmental transitions required for successful nutrient-dependent pheromone-controlled reproduction, which occurs in species from microbes to man. Recent data extend this mammalian model of conserved molecular mechanisms across the continuum of adaptive evolution to selection for phenotypic expression associated with pheromones in a human population.
Across species comparisons of epigenetic effects on pangenomic microbial nutrient-dependent reproduction and on hormone-controlled invertebrate and vertebrate social and sexual behavior indicate that human pheromones alter the development of the brain and behavior via the molecular mechanisms conserved across all species.
It is now clear how an environmental drive evolved from that of nutrient uptake in unicellular organisms to that of pheromone-controlled socialization in insects. This makes it clearer that, in mammals, nutrients associated with food odors and pheromones associated with body odors cause controlled changes in hormones, which have developmental affects on the control of behavior in nutrient-dependent reproductively fit individuals that signal their fitness via pheromones. For contrast, in theory, mutations are not physiologically controlled, but control is required for adaptive evolution to occur [2].
An epigenetic continuum of nutrient-dependent pheromone-controlled adaptive evolution
Nematodes: Species incompatibilities are associated with cysteine-to-alanine substitutions [3]. Differences in behavior are determined by nutrient-dependent rewiring of their primitive nervous system [4].
Insects: Neurogenic niche construction in nematodes [4] is also exemplified in the honeybee model organism of nutrient-dependent pheromone-controlled adaptive evolution of the brain and behavior[5]. In flies, nutrient-dependent changes in mitochondrial tRNA and a nuclear-encoded tRNA synthetase enable the attachment an amino acid that facilitates the reaction required for efficient and accurate protein synthesis [6]. In wasps, the change in a pre-existing signaling molecule triggered by a glucose-dependent [7] stereochemical inversion [8] leads to species-specific pheromone production. In Ostrinia moth species, substitution of a critical amino acid, is sufficient to create a new pheromone blend [9].
Mammals: The association of the nutrient choline in humans and its metabolism to trimethylamine odor in different species of mice was the best example of how a change in diet becomes associated with the presence of mammalian conspecifics whose androgen estrogen ratio-associated odor distinguishes them sexually, and also as nutrient-dependent physically fit mates [10].  The mouse model makes it clearer that glucose uptake changes cellular thermodynamic equilibrium [11] and differential pathway regulation that results in adaptively evolved fitness in species from microbes [12] to mammals.
Humans: Two reports link substitution of the amino acid alanine for the amino acid valine [13] to nutrient-dependent pheromone-controlled adaptive evolution. Cause and effect was established in mice [14]. These two reports [13, 14] tell a new short story of nutrient-dependent pheromone-controlled adaptive evolution. The story begins with what was probably a nutrient-dependent variant allele that arose in central China ~ 30,000 years ago. In other mammals, like the mouse, the effect of the allele is manifested in sweat, skin, hair, and teeth, and the effect is clearly due to the epigenetic effect of nutrients on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. In the model here, the pheromones control the nutrient-dependent hormone-dependent organization and activation of reproductive sexual behavior in mammals such as mice and humans, and also in invertebrates as previously indicated [5]. Therefore, the adaptive evolution of the human population, which is detailed in these two reports, is also likely to be nutrient-dependent and pheromone-controlled sans mutations theory. See also [15] 1.     Nei, M., Mutation-Driven Evolution. 2013, Oxford, UK: Oxford Univesity Press.
2.     Noble, D., Physiology is rocking the foundations of evolutionary biology. Experimental Physiology, 2013: 10.1113/expphysiol.2012.071134.
3.     Wilson, L., et al., Fertilization in C. elegans requires an intact C-terminal RING finger in sperm protein SPE-42. BMC Dev Biol 2011. 11(1): 10.
4.     Bumbarger, Daniel J., et al., System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes. Cell, 2013. 152(1): 109-119.
5.     Kohl, J.V., Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2012. 2(17338).
6.     Meiklejohn, C.D., et al., An Incompatibility between a Mitochondrial tRNA and Its Nuclear-Encoded tRNA Synthetase Compromises Development and Fitness in Drosophila. PLoS Genet, 2013. 9(1): e1003238.
7.     Yadav, J.S., B.V. Joshi, and M.K. Gurjar, An enantiospecific synthesis of (4R,5R)-5-hydroxy-4-decanolide from d-glucose. Carbohydr Res, 1987. 165(1): 116-119.
8.     Niehuis, O., et al., Behavioural and genetic analyses of Nasonia shed light on the evolution of sex pheromones. Nature, 2013. 494: 345–348.
9.     Lassance, J.-M., et al., Functional consequences of sequence variation in the pheromone biosynthetic gene pgFAR for Ostrinia moths. Proceedings of the National Academy of Sciences, 2013. in press.
10.    Stensmyr, M. and F. Maderspacher, Olfactory Evolution: Mice Rethink Stink. Curr Biol, 2013. 23(2): R59-R61.
11.    Kohl, J.V., Nutrient-dependent / Pheromone-controlled thermodynamics and thermoregulation. http://dx.doi.org/10.6084/m9.figshare.643393, 2013.
12.    Kondrashov, F.A., Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc Biol Sci, 2012. 279 (1749): 5048-5057.
13.    Grossman, Sharon R., et al., Identifying Recent Adaptations in Large-Scale Genomic Data. Cell, 2013. 152(4): 703-713.
14.    Kamberov, Yana G., et al., Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. Cell, 2013. 152(4): 691-702.
15.    Kohl, J.V., Nutrient–dependent / pheromone–controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology, 2013. 3(20553).

terrarium-eco-system

Eliminating correlations from evolutionary ecology

De novo creation of olfactory receptor genes clearly links food odors via amino acid substitutions to cell type differentiation in mosquitoes, and in nematodes, flies, honeybees, etc. It would be surprising if cause and effect did not extend to vertebrates from invertebrates. Indeed, Elekonich and Robinson (2000) linked our 1996 model of RNA-mediated cell type differentiation to hormone-organized and hormone-activated behavior in insects more than a decade ago.
Since then, Vosshall’s lab has established the role that amino acid substitutions play in the de novo creation of olfactory receptor genes.
See: Amino Acid Residues Contributing to Function of the Heteromeric Insect Olfactory Receptor Complex . Extension of the conserved molecular mechanisms that link cell type differentiation in species from microbes to man also links the amino acid substitutions to Behavioral Responses to Mammalian Blood Odor and a Blood Odor Component in Four Species of Large Carnivores. The pattern that links metabolic networks and networks of genes is clear. It has been extended to humans via testing associated with nutrigenomics and with pharmacogenomics testing available from Alpha genomix.
Moving forward means we must rapidly distance ourselves from the practice of evolutionary medicine. Ridiculous theories about mutations that supposedly can be linked from cell type differentiation to increasing organismal complexity via the evolution of bio-physically constrained nutrient-dependent pheromone-controlled biodiversity can be eliminated from any further consideration. Serious scientists can compare silly theories to facts in the context of Experimental Food Restriction Reveals Individual Differences in Corticosterone Reaction Norms with No Oxidative Costs.
Excerpt: “A central goal in evolutionary ecology is to characterize patterns of selection on the optimal phenotype for a given environment.”
My comment: That fact places what is known about sex differences in cell types into the context of: Dobzhansky (1972) “Reproductive isolation evidently can arise with little or no morphological differentiation.” (p. 665)
Those who are familiar with the effects of food restriction present a valid complaint associated with comparisons between what is known about ecological adaptation and what is suspected about the evolution of sex via cell type differentiation. For example, changes in levels of hormones are often reported in the context of cause and effect. The changes are more likely to be correlations.

A number of studies have identified strong phenotypic correlations between plasma hormone concentrations and fitness measures and conclude that these correlations are evidence of natural selection [5]–[8]. However, these trait-fitness correlations and selection coefficients may be confounded or overestimated because of individual plasticity [9].

That nutrient-dependent plasticity is readily apparent in yeasts. “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…” Epigenetic modifications of cell types is also apparent during the life history transitions of honeybees. See: Honey bees as a model for understanding mechanisms of life history transitions.
Altering the diet of sparrows leads to accurate representations of cause and effect via the conserved molecular mechanisms that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via the honeybee model organism. This links nutrient-dependent changes in labile hormone levels to behaviors in organisms that must quickly adapt to an ecological challenge. A series of already published works have linked nutrient-dependent hormone organization and hormone activation to the pheromone-controlled behavior of birds via the innate immune system of species from microbes to man.
See, for examples:
Preen secretions encode information on MHC similarity in certain sex-dyads in a monogamous seabird
Excerpt: “At the molecular level, the link between MHC and non-peptide odours may stem from excreted odorants becoming conjugated with amino acids…”
Bird odour predicts reproductive success
Excerpt: “Our results show that the abundance and relative proportion of the volatile compounds that make up bird odour may predict genetic and social reproductive success in dark-eyed juncos.”
Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes Excerpt: “The ZAL2 and ZAL2m alleles code for 597 amino acids, with two fixed differences driving a Val73Ile and Ala552Thr polymorphism in ZAL2m. valine to alanine substitution.”
New insights into the hormonal and behavioural correlates of polymorphism in white-throated sparrows, Zonotrichia albicollis
Excerpt: “…behaviour and endocrine function may be linked to a chromosomal rearrangement that determines plumage colour.”
My comment: Unpublished works presented yesterday and today at the annual meeting of the Society for Neuroscience extend a model of nutrient-dependent pheromone-controlled ecological adaptions from birds to rodents. See:
Gene co-expression network analysis in a free-living, behaviorally polymorphic species
The effect of histone deacetylase inhibitors on the behavioral responses to social defeat in Syrian hamsters
The links to the two poster presentation abstracts may make it easier to grasp the link between nutrient-dependent RNA-directed DNA methylation in birds and pheromone-controlled histone acetylation in hamsters. Methylation and acetylation are linked to human behavioral development by the single amino acid substitution detailed in the context of Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults. Nutrient-dependent amino acid fixations obviously via the physiology of reproduction and are linked to behavioral diversity.
It may be important to connect the amino acid substitutions to a light-induced amino acid substitution in plants that links light energy as a nutrient source to nutrient-dependent amino acid substitutions in plants and animals that differentiate the cell types and animal behaviors associated with mobility.
See: Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins
Excerpt: “This strong connection between structural biology and physics means that ultrafast light-harvesting functions are under genetic and evolutionary control.”
My comment: Unfortunately, others often place their experimental results into the context of evolutionary theory, as stated above. They defy what is known about links from the laws of physics to the chemistry of protein folding and to the conserved molecular mechanisms that link amino acid substitutions from viruses to living organisms via cell type differentiation.
See the report on the “single-residue insertion”: Quantum biology: Algae evolved to switch quantum coherence on and off
Excerpt: “They found that in two species a genetic mutation has led to the insertion of an extra amino acid that changes the structure of the protein complex, disrupting coherence.”
My comment: Similarly, see: Amino Acid Substitutions in Polymerase Basic Protein 2 Gene Contribute to the Pathogenicity of the Novel A/H7N9 Influenza Virus in Mammalian Hosts If you are not too frightened to do so, also see: Identification of two amino acid residues on Ebola virus glycoprotein 1 critical for cell entry.
Facts about cell type differentiation via amino acid substitutions can then be compared in the context of social science is pseudoscience: Richard Feynman and Pseudoscience, which is an excerpt from: Richard P. Feynman – The Pleasure of finding things out [national bestseller]
What pseudoscientists never found out about quantum mechanics and quantum biology has been addressed several times. See, for example, works by Luca Turin, which include Molecular Vibration-Sensing Component in Human Olfaction. It was reported as ‘Quantum smell’ idea gains ground. Turin’s work has gained ground very slowly. Chandler Burr helped to explain why in a book that I reviewed here:The Emperor of Scent: A Story of Perfume, Obsession and the Last Mystery of the Senses. I erred by claiming that: “… Turin never attempted to work within the system.” He contacted me to let me know that his first publication was in a highly ranked journal Nature: see Carbon dioxide reversibly abolishes ionic communication between cells of early amphibian embryo.

Luca Turin has since recently published Electron spin changes during general anesthesia in Drosophila, which may link Dose-Dependent Effects of the Clinical Anesthetic Isoflurane on Octopus vulgaris: A Contribution to Cephalopod Welfare to what is currently known about the molecular mechanisms of nutrient-dependent RNA-mediated amino acid substitutions and neurotransmission exemplified in Excitatory amino acid transporters: recent insights into molecular mechanisms, novel modes of modulation and new therapeutic possibilities. In my book review, I also wrote: “Perhaps a future proponent of molecular vibration theory will manage better than Dyson, Wright and, most recently, Turin. Truly this theory may be years ahead of its time. It also may be a theory that cannot be sufficiently supported by scientific fact.’ Obviously, the theory was way ahead of its time and it has since been supported with scientific facts.

Suppression of scientific facts by pseudoscientists is addressed in: Solving Biology’s Mysteries Using Quantum Mechanics: The new field of quantum biology applies the craziness of quantum physics to biology’s most fundamental processes.
Excerpt: “In the case of the fast-adapting E. coli, that would correspond to its DNA being primed to both enable the bacteria to eat lactose and also not be able to eat lactose.”
My comment: Claims that Richard Lenski is The Man Who Bottled Evolution can now be addressed in the context of physics, chemistry, and molecular biology. Clearly the ability to eat or not eat lactose did not evolve.
Indeed, as Vosshall’s group has now shown, the ability to eat is experience-dependent, nutrient-dependent, and the ability involves the de novo creation of olfactory receptor genes. De novo creation occurs via RNA-mediated events in species from microbes to man.
That explains why Humans Can Discriminate More than 1 Trillion Olfactory Stimuli. Simply put, we are extremely well ecologically adapted in the context of RNA-directed DNA methylation and histone acetylation.
We did not evolve via mutations that perturb protein folding. That idea exemplifies the pseudoscientific nonsense of population geneticists.
Any who are interested in moving forward may want to see my comment from March, 2014, on yet another article from Leslie Vosshall’s group. The comment was published earlier today (more than 7 months later) to the Science Magazine site: Humans Can Discriminate More than 1 Trillion Olfactory Stimuli.
It was submitted and published immediately to The Scientist Magazine site: The Nose Knows.
See also: The Nose Knows: Pheromones and Human Sexuality (1995) and listen for Leslie Vosshall’s comments to Avery Gilbert, a human pheromone-denier who believes in strippers.

terrarium-eco-system

The key to science: experimental evidence

 
If it disagrees with the experiment, it’s wrong! — Richard Feynman (1964)

Two different experiments are among others from the Vosshall lab that show the theory of evolution is wrong.
1) This experiment links induced mutations in olfactory receptor genes to the inability to find a source of nutrients. orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET
The source is a human, and the presence of humans is a recent addition to the ecological variation associated with the experience-dependent de novo creation of olfactory receptor genes in experiment 2 (below).
2) This experiment links ecological variation to nutrient-dependent amino acid substitutions and the experience-dependent de novo creation of olfactory receptor genes. Evolution of mosquito preference for humans linked to an odorant receptor.
See the text from Figure 3: “Dots represent amino acid differences with respect to the genome reference, not an inferred ancestor.”
Although reported in terms that include an evolutionary inference, there is no inferred ancestor. That is probably because no experimental evidence of biologically-based cause and effect infers that there ever was a last universal common ancestor. That fact was addressed in the context of how amino acid substitutions are linked via the laws of physics and the chemistry of protein folding to the molecular epigenetics of biologically-based cause and effect in species from microbes to man.
See, A universal trend of amino acid gain and loss in protein evolution
“We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.”
The Vosshall lab experiments establish a the existence of a metabolic link from the epigenetic landscape to the nutrient physical landscape of DNA in the organized genomes of species from microbes to man. The metabolic link is obviously  receptor mediated.
Mutations in olfactory receptors perturb all aspects of biodiversity that might otherwise link them to increasing organismal complexity via evolution. For example, organisms that cannot find food and metabolize it cannot fuel the diversity of  increasingly complex genetic networks. First, the organisms must have metabolic networks that link their receptor-mediated nutrient-uptake to their genetically predisposed receptor-mediated behaviors.
The need to link metabolic networks to genetic networks via amino acid substitutions has been exemplified in mosquitoes. However, another group established the obvious connection from the de novo creation of olfactory receptor genes in insects to nutrient uptake in mammals. Behavioral Responses to Mammalian Blood Odor and a Blood Odor Component in Four Species of Large Carnivores  “The results of the present study demonstrate that a single blood odor component can be as efficient in eliciting behavioral responses in large carnivores…”
Apparently, there are differences in the nutrient-dependent amino acid substitutions of blood cells that link them via epigenetically-effected RNA-mediated events to detectable differences in cell type differentiation in insects and mammals.  Detection of those differences appears to involve the de novo creation of olfactory receptor genes and to exclude mutations. Thus, the 1964 Feynman video “The key to science” can be linked from physics to the chemistry of protein folding and to molecular biology by what Dobzhansky wrote in 1964. “Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule.”
This historical link also includes an error. In 1964, Dobzhansky also wrote “Self-reproduction plus mutation make possible natural selection. Natural selection makes possible evolution.” However, in 1973, Dobzhansky 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.”  The Vosshall lab’s experimental evidence shows that nutrient-dependent amino acid substitutions link the de novo creation of olfactory receptor genes to detectable differences in odor produced by insects and mammals. So does all other experimental evidence of biologically-based cause and effect that links physics to the chemistry of protein folding. See for review:

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

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

No experimental evidence of biologically-based cause and effect links mutations to increasing organismal complexity. Evolutionary theorists and human ethologists should quit claiming that evidence from population genetics has anything to do with “The key to science.” Evidence from population genetics is the pseudoscientific nonsense the Vosshall lab has exposed for what it has always been.
See also: Amino Acid Residues Contributing to Function of the Heteromeric Insect Olfactory Receptor Complex
Excerpt: “…the biophysical properties of the channel vary according to subunit composition, even with highly similar proteins such as BmOr-1-Orco and BmOr-3-Orco. Second, because ligand-selective Or sequences within and between insect species are extremely divergent, the primary amino acid sequence of the ion-conducting pore is likely to differ according to the subunit composition of the Or-Orco complex.’
My comment: Ecological adaptations are bio-physically constrained and so is the de novo creation of olfactory receptor genes. Pattern recognition is also a key to science. It’s a key that has gone missing from this claim: “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.”
Similarly, in a book review of ‘The Meaning of Human Existence’ by Edward O. Wilson, pattern recognition is also missing.
We read:
Excerpt 1) “…the scientific view that humans have evolved, along with millions of other species, from earlier life forms, entirely by natural processes…”
Excerpt 2) “…roughly two-thirds of Americans reject this view of evolution, which undergirds all of modern medicine and the life sciences.”
RNA-directed DNA methylation and RNA-mediated events link nutrient-dependent thermodynamic cycles of protein biosynthesis and degradation in metabolic networks. The metabolic networks link amino acid substitutions to protein folding that stabilizes DNA in the organized genetic networks of all cell types of all individuals of all species.
What is currently known about the laws of physics; the chemistry of protein folding; and the conserved molecular mechanisms of biology links species from microbes to man via the conserved molecular mechanisms of nutrient-dependent pheromone-controlled cell type differentiation.
The epigenetic landscape is linked to the physical landscape of organized DNA via nutrient uptake and the metabolism of nutrients to species-specific pheromones that control the physiology of reproduction. That fact “undergirds all of modern medicine and the life sciences”. EO Wilson obviously needs a “fact-checker.” He’s an expert on ants who has somehow failed to realize their behavior is nutrient-dependent and pheromone-controlled.
Others who want information on biological facts that can readily be compared to the pseudoscientific nonsense of evolutionary theory can read anything written in the past decade about pharmacogenomics or nutrigenomics (i.e., nutritional epigenetics).
Physics, chemistry, and biology are linked to the meaning of human existence via the de novo creation of receptors, which links the de novo creation of genes to our ability to find food and reproduce. That is what the nutrient-dependent de novo creation of new genes does in all species. Creation links the epigenetic landscape to the physical landscape of DNA via nutrient-dependent amino acid substitutions. For comparison, the “…view that humans have evolved, along with millions of other species, from earlier life forms, entirely by natural processes…” has never been supported by scientific facts, which require experimental evidence.
If you grasp nothing else that’s been learned about biologically-based cause and effect during the past 50 years, you probably can still understand this, so I reiterate: If it disagrees with the experiment, it’s wrong! — Richard Feynman (1964)
Indeed, if it’s social science, it’s pseudoscience. Richard Feynman and Pseudoscience
 

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Ecological adaptations reported as evolution in insects and mammals

Evolution of mosquito preference for humans linked to an odorant receptor
Excerpt: “Our results also provide insight into the molecular basis of behavioural evolution.”
See their diagram in Extended Data Figure 3: Amino acid differences of major Or4 protein alleles.

Excerpt: Dots represent amino acid differences with respect to the genome reference, not an inferred ancestor.
Reported as:

Study suggests how mosquitoes evolved an attraction to human scent

Excerpt: The switch from preferring animals to humans involves a variety of behavior adjustments: Mosquitoes had to become comfortable living around humans, entering their homes, breeding in clean water found in water jugs instead of the muddy water found in tree holes. “There’s a whole suite of things that mosquitoes have to change about their lifestyle to live around humans,” Vosshall says. “This paper provides the first genetic insight into what happened thousands of years ago when some mosquitoes made this switch.”
My comment: In my model, nutrient-dependent amino acid substitutions stabilize DNA in the organized genome of species from mosquitoes (and microbes) to man but the substitutions are not linked via to any ancestor via evolution.What happened thousands of years ago is most readily attributed to a nutrient-dependent amino acid substitution and metabolism of nutrients to species specific pheromones that control the physiology of reproduction, which results in fixation of the amino acid substitution in the populations that were studied. Fixation of beneficial amino acid substitutions can be compared to the detrimental effects of mutations on protein folding that prevents the de novo creation of olfactory receptor genes associated with food odors.

See also: orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET
Excerpt: “We conclude that the odorant receptor pathway is crucial for an anthropophilic vector mosquito to discriminate human from non-human hosts…”
Reported as:

Genetic engineering alters mosquitoes’ sense of smell

Their diagram and Excerptorco mutants exhibited severely impaired electrophysiological responses
My comment: I reiterate (from above) “There’s a whole suite of things that mosquitoes have to change about their lifestyle to live around humans…” Mutations appear to eliminate the suite of things that must occur in the context of nutrient-dependent pheromone-controlled fixation of amino acid substitutions linked to the behavior of mosquitoes.
Our 1996 model of RNA-mediated events links the molecular epigenetics of the nutrient-dependent pheromone-controlled physiology of reproduction to increasingly complex morphological and behavioral phenotypes in species from microbes to man. Nothing suggests mutations are beneficial or that they could be linked to biodiversity via natural selection and evolution. Instead, the model forms the basis for claims made in Elekonich and Robinson (2000), which link the model to insects and claims made in Elekonich and Roberts (2005) that link the model to life history transitions in the honeybee model organism. Additional evidence that supports our link from pheromones to the physiology of reproduction in mammals is was reported in

Neuroscientists reveal mechanism crucial to molding male brains.

Excerpt: “…we now show how in the first hours of drawing breath it also triggers our brains to develop differently according to our sex.”
The need for pre-natal and post-natal development of sexually dimorphic olfactory systems that respond to similar food odors but differences in pheromones was clarified in the context of The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences.
LeVay summarized his thoughts on extension of our 1996 model to sexual preferences in Gay, Straight, and the Reason Why: The Science of Sexual Orientation. (p. 210)P
“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…”
Few people would foolishly argue that food odors associated with nutrient uptake and pheromones associated with controlled reproduction could be less important that any other sensory input that might somehow link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. Similarly, it is not likely that anything  is more important than species-specific pheromones to the control of reproduction. Thus, the role of food odors and pheromones can be compared in the context of a recently reported link between blood-sucking mosquitoes and predatory mammals. See:

Odor that smells like blood: Single component powerful trigger for large carnivores

Excerpt: “…the results demonstrate that a single blood odor component can be as efficient in eliciting behavioral responses in large carnivores as the odor of real blood, suggesting that trans-4,5-epoxy-(E)-2-decenal may be perceived by predators as a “character impact compound” of mammalian blood odor.”
My comment: Food odors, which epigenetically effect hormones that affect behavior are considered in the context of ‘character impact compounds.’ Will pheromones continue to be considered in the context of anything that does not directly link the nutrient-dependent odor-controlled physiology of reproduction to epigenetically-effected hormones that affect species-specific behaviors via conserved molecular mechanisms of RNA-mediated amino acid substitutions and cell type differentiation in species from microbes to man? If so, the word-play of evolutionary theorists and semi-serious scientists will have won their game. Few people will learn that ecological variation is linked to ecological adaptations only via nutrient uptake and the pheromone-controlled physiology of reproduction. Most may continue to think that mutations and/or natural selection can somehow be linked to the evolution of biodiversity because that is what they have been taught to believe.
For comparison see:

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

Conclusion: “Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans…”

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

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

human-evolution

Sexual differentiation of cell types in plants

Antheridiogen determines sex in ferns via a spatiotemporally split gibberellin synthesis pathway
Excerpt: “Homosporous ferns have evolved a mechanism to favor cross-fertilization by controlling the sex ratio among individuals or prothalli within the population with the aid of antheridiogens. Antheridiogens are pheromones…”
Reported as:

Researchers find ferns communicate with one another to decide gender

Excerpt: “The intercommunication abilities demonstrated by the ferns is an example of a growing field in botany that some have taken to calling plant neurobiology—when plants exhibit behavior that resembles activities of animals.”
My comment to Science Magazine
Biologically-based cause and effect in these ferns appears to parallel what is known about biophysically-constrained thermodynamic cycles of nutrient-dependent protein biosynthesis and degradation in other genera, which is controlled by the metabolism of nutrients to species-specific pheromones.
From an atoms to ecosystems perspective this links nutrient uptake to RNA-directed DNA methylation; RNA-mediated amino acid substitutions; and to pheromone-controlled chromosomal rearrangements associated with ecological speciation but not necessarily associated with mutations, natural selection, and the evolution of biodiversity.
Have homosporous ferns somehow evolved a mechanism that appears to link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man? To me it seems more likely that ecological variation led to RNA-mediated ecological adaptations like those that are manifested in the morphological and behavioral phenotypes of other living organisms with cell types that are differentiated by amino acid substitutions.
For examples, see: Signaling Crosstalk: Integrating Nutrient Availability and Sex “The mechanism by which one signaling pathway regulates a second provides insight into how cells integrate multiple stimuli to produce a coordinated response.”
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932994/
See also: Feedback loops link odor and pheromone signaling with reproduction “Indications that GnRH peptide plays an important role in the control of sexual behaviors suggest that pheromone effects on these behaviors might also involve GnRH neurons.” http://www.ncbi.nlm.nih.gov/pubmed/16290036
The link from microbes (yeasts) to mammals seems to be nutrient-dependent amino acid substitutions, like those Dobzhansky (1973) reported in Nothing in Biology Makes Any Sense Except in the Light of Evolution “…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.” http://www.jstor.org/stable/4444260
If what others are reporting in the context of mutations in the Ebola viruses are ecological adaptations, our response to the threat may need to be reconsidered in the context of reports like this one: Identification of two amino acid residues on Ebola virus glycoprotein 1 critical for cell entry. http://www.sciencedirect.com/science/article/pii/S0168170206001882
My comment to the phys.org site:

“…plants exhibit behavior that resembles activities of animals.”

That suggests conserved molecular mechanisms of the nutrient-dependent pheromone-controlled physiology of reproduction extend across all genera, as does everything else currently known about the physics, chemistry, and molecular

biology of biophysically-constrained protein biosynthesis and degradation. Indeed, it would be incredibly odd if these “…ferns have evolved an antheridiogen-mediated communication system“The communication system clearly exemplifies how ecological variation leads to ecological adaptations via RNA-directed DNA methylation and amino acid substitutions that differentiate cell types, which are manifested in the morphological and behavioral phenotypes and ecological speciation in all other genera.
If ferns somehow evolved that level of organism-level complexity, their evolution would seem like a miracle that could be compared to their ability to ecologically adapt.
achiral-glycine

No understanding of biodiversity

No single explanation for biodiversity in Madagascar

Excerpt: “The study is part of a larger body of research aimed at identifying the climate, geology and other features of the environment that help bring new species of plants and animals into being in an area, and then sustain once they’re there.”
My comment: Like many studies, this one posits that new species automagically arise and are somehow sustained in ecological niches.
Excerpt: “What governs the distribution of, say, a particular group of frogs isn’t the same as what governs the distribution of a particular group of snakes,” Brown said. “A one-size-fits-all model doesn’t exist.”
My comment: Apparently, these researchers do not understand the fact that RNA-directed DNA methylation links the epigenetic landscape to the physical landscape of DNA in the organized genomes of all species via conserved molecular mechanisms that lead to ecological, social, neurogenic, and socio-cognitive niche construction manifested in increasing organismal complexity. Alternatively, they want others to believe there is no model of how nutrient-dependent pheromone-controlled biodiversity arises. For example, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. “Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.” If the model is ignored, the claim can be made that one model links nutrient uptake to RNA-mediated biodiversity doesn’t exist.
Excerpt: “…each group of animals experiences its environment in a way that is unique to its life history and other biological characteristics,” Yoder said.”
Cell type differentiation in each individual of all groups of animals is nutrient-dependent. RNA-mediated events leads to amino acid substitutions that differentiate all cell types in all tissues of all organs in all organ systems that arise in the context of the pheromone-controlled physiology of reproduction that links biodiversity from ecological variation in nutrient availability to ecological adaptation via reproduction.
Abstract excerpt: A necessarily complex model to explain the biogeography of the amphibians and reptiles of Madagascar
“We conclude that patterns are influenced by a combination of diversification processes rather than by a single predominant mechanism. A ‘one-size-fits-all’ model does not exist.”
My comment: The model of nutrient-dependent pheromone-controlled RNA-mediated biodiversity has existed since 1996. It has been used to explain all biodiversity in the context of systems biology and niche construction based on details of conserved molecular epigenetics: “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…” There is no other way that cell type differentiation occurs in any cell of any species.
See also: Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors.
“Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”

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Systems biology and memory disorders

Reversal of cognitive decline: A novel therapeutic program

Reported as:

Memory loss associated with Alzheimer’s reversed: Small trial succeeds using systems approach to memory disorders

News Article Excerpt:

(1) eliminating all simple carbohydrates, leading to a weight loss of 20 pounds;
(2) eliminating gluten and processed food from her diet, with increased vegetables, fruits, and non-farmed fish;
(3) to reduce stress, she began yoga;
(4) as a second measure to reduce the stress of her job, she began to meditate for 20 minutes twice per day;
(5) she took melatonin each night;
(6) she increased her sleep from 4-5 hours per night to 7-8 hours per night;
(7) she took methylcobalamin each day; ( Methylcobalamin (MeCbl), the activated form of vitamin B12)
(8) she took vitamin D3 each day;
(9) fish oil each day;
(10) CoQ10 each day;
(11) she optimized her oral hygiene using an electric flosser and electric toothbrush;
(12) following discussion with her primary care provider, she reinstated hormone replacement therapy that had been discontinued;
(13) she fasted for a minimum of 12 hours between dinner and breakfast, and for a minimum of three hours between dinner and bedtime;
(14) she exercised for a minimum of 30 minutes, 4-6 days per week.
Seven items are associated with nutrient uptake and five items are associated with stress reduction via exercise and sleep. Hormone replacement — for a total of 13 out of 14 items — also links the epigenetic landscape to the physical landscape of DNA in the organized genomes of all vertebrates via the same neuronal system.
The honeybee model organism can now be linked to epigenetically-effected human health and disease via the conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated cell type differentiation. The link is the gonadotropin releasing hormone neuronal (GnRH) system. For example, Feedback loops link odor and pheromone signaling with reproduction via the GnRH neuronal system in mammals.
We linked the nutrient-dependent pheromone-controlled feedback loops across species from microbes to man via the conserved molecular mechanisms of cell type differentiation in our Hormones and Behavior review: From Fertilization to Adult Sexual Behavior.
Elekonich and Robinson (2000) “Organizational and activational effects of hormones on insect behavior” extended hormone-organized and hormone-activated behaviors to invertebrates and Elekonich and Roberts (2005) Honey bees as a model for understanding mechanisms of life history transitions extended our 1996 ‘microbes to man’ model to life history transitions in the honeybee.
In my 2012 review Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors, I noted that: “The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, and diseases of the X chromosome (Honeybee Genome Sequencing Consortium, 2006). Included among these different aspects of eusocial species survival are learning and memory, as well as conditioned responses to sensory stimuli (Maleszka, 2008; Menzel, 1983).”
See: How Do We Answer Fools? Clearly, this new n=10 study, which has not been replicated, shows evolutionary theorists that — if honeybees had teeth — improved oral hygiene might be the most important intervention of all to help them avoid Alzheimer’s disease symptoms. Indeed, the theorists may even link their ideas about the evolution of pheromones to the evolution of teeth in predatory nematodes via mutations and/or natural selection, which they think somehow leads to the evolution of biodiversity.
For contrast, the 14 step intervention shows serious scientists how important it is to link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms. Attempts to treat pathologies based on the pseudoscientific nonsense of evolutionary theories without considering their basis in nutrient-dependent pheromone-controlled cell type differentiation has led to 18 years of wasted research dollars that could have been better spent developing a model of biologically-based cell type differentiation, which is clearly involved in 13 of the 14 interventions listed above. See also: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis.

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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.

neuronal-plasticity

Physics denied; pseudoscientific nonsense accepted

 

The events depicted are now portrayed in the context of Genome Dynamics Events, which are biophysically-constrained RNA-mediated events. RNA-mediated events lead to amino acid substitutions that differentiate the cell types of species. For example: “…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.” Dobzhansky (1973)
See also:

God, Darwin and My College Biology Class

Excerpt: “Since Darwin, however, we have come to understand that an entirely natural and undirected process, namely random variation plus natural selection, contains all that is needed to generate extraordinary levels of non-randomness.”
My comment: Only those taught to believe in pseudoscientific nonsense continue to claim, like many unenlightened theorists, that “…random variation plus natural selection…” leads to the evolution of biodiversity. They ignore the Laws of Physics and what is known about the biophysically constrained chemistry of cell type differentiation.
For contrast, serious scientists understand that
1) RNA-directed DNA methylation leads from ecological variation and
2) nutrient-dependent thermodynamic cycles of protein biosynthesis and degradation to
3) RNA-mediated events such as
4) amino acid substitutions that
5) differentiate all cell types of
6) all individuals of
7) all species via
8) conserved molecular mechanisms of
9) nutrient-dependent
10) pheromone-controlled ecological adaptations.
The ecological adaptations link ecological variation to to nutrient-dependent ecological speciation, which is biophysically constrained, via the production of species-specific pheromones that epigenetically control the nutrient-dependent physiology of reproduction in species from microbes to man.
Pseudoscientists skip the steps that link creation from nutrient-uptake to controlled reproduction and claim that “…random variation plus natural selection, contains all that is needed to generate extraordinary levels of non-randomness.”
That’s where their ridiculous ideas about mutations, natural selection, and the evolution of biodiversity came from: IGNORANCE! Serious scientists continue to add experimental evidence of each successive step in the linear series of RNA-mediated events that refutes the pseudoscientific nonsense of evolutionary theorists each step of the way (e.g., from Let there be Light-induced amino acid substitutions in plants and animals to ecological speciation.)
Pseudoscientists skip the “Let there be light” part, and proceed with claims that species evolve via random variation plus natural selection. However, they have not described any biologically-based evolutionary event that links one species another. Instead, they look at morphological phenotypes and claim that morphological and behavioral phenotypes must have evolved outside the context of the Laws of Physics.
For consideration of physics, chemistry, and the molecular biology of ecological speciation see my 5.5. minute-long ISHE 2013 poster presentation video:
Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation)

Click on the photo