Creating nothing but a theory

By: James V. Kohl | Published on: March 29, 2015

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.

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