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Wasted Templeton Funding (2)

See also: Wasted Templeton Funding (1)

Templeton grant funds evolution rethink

Excerpt:

The extended evolutionary synthesis is a term coined in 2007 to imply that the preeminent current evolutionary theory, the so-called modern synthesis, needed to broaden its focus because it concentrated too much on the role of genes in evolution and lacked adequate incorporation of new insights from development and other areas of biology.

My comment: That is an understatement! The problems with the so-called modern synthesis are perfectly clear:
1) [W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. 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…. Assumptions, made but not verified, were taught as fact.
2) The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…
3) …evolutionary science has now “moved on to such an extent” that she and Peter Saunders don’t really care anymore about “trying to convince the neo-Darwinists.”
All serious scientists have since linked angstroms to ecosystems via what is known about the biophysically constrained chemistry of energy-dependent protein folding and links from the innate immune system to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and entropy in the context of the physiology of reproduction.
See for example:

See also: Precision Medicine Program to Get $9.3M in NHLBI Funding for Omics Research
One of the things they are asking for is:

“Causal modeling using whole genome sequences and functional genomics data to enhance discovery of influential genetic and epigenetic variants that influence [heart, lung, blood, and sleep] HLBS disorders;”

My comment: They are asking for what has already been included in every model of biologically-based cell type differentiation that has ever been detailed by serious scientists.  Now, the  Templeton Foundation has awarded $8.7M to fund research that can only benefit humanity by answering Schrodinger’s question “What is Life?” in the context of what is known about how the energy-dependent RNA-mediated innate immune system and supercoiled DNA protect life from virus-driven energy theft.”How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” — Roger Penrose
 

Sunlight as information

Creating nothing but a theory

De novo design of a transmembrane Zn2+-transporting four-helix bundle

Excerpt 1) The de novo design of proteins is an important endeavor that critically tests our understanding of the principles underlying protein folding and function, while also laying the foundation for the design of proteins and molecular assemblies with desired properties. Much progress has been recently demonstrated… but no designed membrane protein has been experimentally shown to adopt the desired fold at atomic resolution.
Excerpt 2) Nevertheless, these findings… provide support for the view that transporters may have evolved from very simple pseudo-symmetric precursors (42).
My comment: Similarly, “[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. 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….  Assumptions, made but not verified, were taught as fact.” Replace the Modern Synthesis (Neo-Darwinism): An Interview With Denis Noble

See also: What I cannot create, I do not understand

Excerpt: “Life today depends on the chemical activity of proteins.”
My comment: The chemical activity of proteins is biophysically constrained by the Laws of Physics. That may be why the quote “What I cannot create, I do not understand” was borrowed from Richard Fenyman. It was written on his blackboard around the time of his death.
Theorists might believe he meant that if he could not create a formula that helped him to understand a problem, he could not solve the problem. Creationists might believe that he realized mathematics explained nothing about creation. No matter what anyone believes, mathematics has never explained anything about the de novo creation of any membrane receptor or the creation of any other functional protein. That forces theorists to believe in a theory about how membrane receptors, membranes, and all other cell structures evolved. For example, theories about evolution have never explained the de novo creation of an olfactory receptor.
An atoms to ecosystems model of ecological variation linked to ecological adaptation also explains the de novo creation of olfactory receptors. See: The Miracles Of Smell And Taste. Thank God.
Excerpt: “Professor of Biology John T. Caprio of Louisiana State University states that initially, the sense of smell developed in order to identify amino acid-like chemical substances soluble in water. The ability to determine molecules floating in the air is an adaptation of that original mechanism.96” (p. 106)  Originally reported here: How The Nose Knows: Research On Smell Boosted.
Since the time of that report, others have linked odor exposure to the de novo creation of olfactory receptor genes and mutations to loss of function.
See: orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET
Excerpt: orco mutant olfactory sensory neurons have greatly reduced spontaneous activity and lack odour-evoked responses.
In November 13, 2014, I contacted Leslie Vosshall about this. I wrote:

“If you are attending SFN, “Gene co-expression network analysis in a free-living, behaviorally polymorphic species may be of interest.” Prior works from Donna’s lab linked feeding patterns of the different morphs via an amino acid substitution and chromosomal rearrangements. They did not portray the substitution as if it were a mutation.
The forthcoming presentation (Tue. Nov 18) by Wendy Zinzow-Kramer, includes preliminary data that link genetic networks and metabolic networks via at least one enzyme. It appears to also be linked to odor-induced receptor-mediated chromatin remodeling and chromosomal rearrangements via a nutrient-dependent amino acid substitution, which is linked to the physiology of pheromone-controlled reproduction across species from microbes to man.
She will need encouragement from someone like you to focus on the across-species link from invertebrates to vertebrates, and is currently a wonderfully personable post-doc.”

See also: Evolution of mosquito preference for humans linked to an odorant receptor
Excerpt: 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.
My comment: No inferred ancestor and no experimental evidence for a designed membrane protein that adopt the required fold at atomic resolution suggests the mosquito preference for humans is a nutrient-dependent pheromone-controlled ecological adaptation.

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

Abstract: This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.
Excerpt: Nutrient-dependent epigenetic effects on histone modifications and DNA methylation play an important role in stabilizing cell type identity and in orchestrating many developmental processes. For example, vitamin C appears to stimulate histone demethylases, which appear to alter the de novo creation of functional olfactory receptor genes (Adipietro, Mainland, & Matsunami, 2012; Blaschke et al., 2013; Jazin & Cahill, 2010; Lyons et al., 2013; Tan, Zong, & Xie, 2013).
See also: Seeing the (UV) light: Previously undetected difference in human mutation rate unique to Europeans
Excerpt: “These so-called population-private mutations…”
My comment: I am reminded of Dobzhansky (1973) “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla” (p. 127).

Apparently, some theorists still haven’t learned the difference between a so-called ‘population-private mutation’ and an amino acid substitution linked to the so-called alpha chains of hemoglobin, a molecule that carries oxygen to all tissues of species with circulating blood cells. For example, nutrient-dependent RNA-directed DNA methylation and the circulation of blood leads to RNA-mediated amino acid substitutions that are fixed in the organized genomes of all genera via their physiology of reproduction.Mutations in blood cells — or in other tissues and organs of organ systems in all mammals — perturb protein folding and are linked to pathology, which means they are not beneficial. UV light-induced amino acid substitutions in plants and animals may confuse some theorists who link excess exposure to mutations but do not link the sun’s anti-entropic biological energy to ecological adaptations in all populations of all primates via RNA-mediated amino acid substitutions.
Light-induced-conformer-intercoversion-of-hydrogen-bond

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’.”