Biology to a Physicist

Tweaking the story to fit the theory

Reported May 12, 2015 They linked a crucial part of the avian feeding apparatus to the nutrient-dependent pheromone-controlled physiology of reproduction that enables fixation of RNA-mediated amino acid substitutions in the organized genomes of species from microbes to man, and placed their findings into the context of evolutionary theory and the fossil record.

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


The concept that is extended is the epigenetic tweaking of immense gene networks in ‘superorganisms’ (Lockett, Kucharski, & Maleszka, 2012) that ‘solve problems through the exchange and the selective cancellation and modification of signals (Bear, 2004, p. 330)’. It is now clearer how an environmental drive probably evolved from that of food ingestion in unicellular organisms to that of socialization in insects. It is also clear that, in mammals, food odors and pheromones cause changes in hormones such as LH, which has developmental affects on sexual behavior in nutrient-dependent, reproductively fit individuals across species of vertebrates.

Turning back clock on dinosaur evolution

Reported May 23, 2015

The birds’ palates reverted to their ancestral states as well, indicating that small molecular changes can have big consequences on anatomy.

A flap of skin covering their altered skulls obscured the ways the birds’ beaks had changed. But by creating digital models of the embryos’ skeletons, they were able to examine the ways the birds’ manipulated jaws more closely resembled those of ancient creatures like Archaeopteryx and Velociraptors than a modern-day chicken’s beak.

Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links

My comment: In the structured abstract they link a distant ortholog of yeast to DNA repair. Their “…mechanistic insights into the pathways that ensure genomic stability during perturbed DNA replication” link nutrient-dependent RNA-mediated cell type differentiation from the origin of sexual reproduction in yeasts to their pheromone-controlled physiology of reproduction. The physiology of reproduction enables fixation of nutrient-dependent RNA-mediated amino acid substitutions in the organized genomes of all genera.

Their mechanistic insights help to explain how ecological variation links RNA-mediated protein biosynthesis and degradation from fixation of amino acid substitutions to ecological adaptations via DNA repair, not via mutations that perturb protein folding and lead to pathology.

Turning back the clock on dinosaur evolution by creating digital models of birds’ jaws does not address any aspect DNA repair, which enables “beak tweaking.” Placing nutrient-dependent RNA-mediated DNA repair, the physiology of pheromone-controlled reproduction, and the “beak tweaking” into the context of the fossil record or into a story about the evolution of dinosaurs that became birds, exemplifies pseudoscientific nonsense. RNA-mediated amino acid substitutions differentiate cell types. Mutations perturb protein folding and link failed DNA repair to pathology, not to evolution of birds from dinosaurs.

Addendum: 5/28/15 (A creationist perpective).

Dinosaur-faced chickens?


What possible selection pressure would cause the creation of new information that is useless until all the parts come together into a working whole? This is an old evolutionary puzzle, and we feel that it has remained unanswered because it shines light on the great gulf between evolutionary theory and scientific reality (see Can Mutations Create New Information?).

See also (my comments on) the “[p]ervasive dual encoding of amino acid and regulatory information: Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution.

Additional comment: Simply put, no experimental evidence of biologically-based cause and effect suggests that proteins evolve. All experimental evidence has repeatedly showed that proper RNA-mediated DNA organization is required for cell’s normal functioning.

See also: The Histone Chaperones FACT and Spt6 Restrict H2A.Z from Intragenic Locations


Chromatin organization and composition are very plastic because cells need to modulate DNA accessibility to several proteins in space and time for regulation of various nuclear transactions, such as gene expression, DNA replication, and DNA repair. This is achieved by at least three different mechanisms.

My comment: All molecular mechanisms that epigenetically effect nuclear transactions can be linked to nutrient-dependent RNA-mediated cell type differentiation. Fixation of nutrient-dependent RNA-mediated amino acid substitutions in the organized genomes of all genera is controlled by the physiology of their nutrient-dependent reproduction.

In species from microbes to humans the plasticity of chromatin organization and composition is biophysically constrained by the nutrient-dependent chemistry of RNA-mediated protein folding and the pheromone-controlled physiology of reproduction.  This makes the misrepresentation of mutation-driven re-evolution of the bacterial flagellum in 4 days, as ridiculous as the misrepresentation of how tweaking the beak of chickens links the evolution of dinosaurs to birds.

See also: Spag17 Deficiency Results in Skeletal Malformations and Bone Abnormalities


Spag17 encodes a protein present in cilia and flagella with a “9+2” axoneme structure.

This was reported as: Researchers identify unexpected functions in the determination of height for a gene expressed in sperm


“This was an unexpected finding,” Boyan said. “It is not a protein that anybody in my field would have thought to look at.”
Researchers emphasize that more studies are needed to fully understand how SPAG17 affects bone and bone structure.
“Our findings are very important because they have revealed functions for SPAG17 that extend the role of this gene to regulation of skeletal development, growth and mineralization,” Teves said. “This was just the beginning. The next step is trying to find the mechanisms of why this gene influences skeletal development.”

My comment: Their unexpected finding links the report of re-evolution of the bacterial flagellum in 4 days to sex differences in cell type differentiation that clearly also are nutrient-dependent and pheromone-controlled in species from yeasts to mammals via RNA-mediated links from metabolic networks to genetic networks.  See: From Fertilization to Adult Sexual Behavior.

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (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: Mutations, which perturb protein folding and are linked to pathology, are not likely to ever be represented in the extant literature that links biologically-based nutrient-dependent RNA-mediated cell type differentiation to DNA organization. The organized DNA is required for the normal functioning of all cell types in all individuals of all genera.
The fact that theorists continue to misrepresent biologically-based cause and effect in the context of mutation-driven re-evolution of the bacterial flagellum or in the context of the evolution of dinosaurs to birds would make them the laughingstocks of creationist’s jokes — if creationists had ever joked about experimentally established scientific facts.

I reiterate: Researchers identify unexpected functions in the determination of height for a gene expressed in sperm


“This was an unexpected finding,” Boyan said. “It is not a protein that anybody in my field would have thought to look at.”

My comment:  It would be interesting to ask someone like this if they never looked for the protein because they thought it was a mutated protein that had somehow “evolved.”

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