Energy-dependent structure and function: Until death (5)

In 1996, I proposed to my publishers a novel about the coming changes in biology and evolutionary theory. The novel would describe an evolutionary event happening in real-time–the formation of a new sub-species of human being. What I needed, I thought, was some analog to what happens in bacteria. And so I would have to invent ancient viruses lying dormant in our genome, suddenly reactivated to ferry genes and genetic instructions between humans.

To my surprise, I quickly discovered I did not have to invent anything. Human endogenous retroviruses are real, and many of them have been in our DNA for tens of millions of years. Even more interesting, some have a close relationship to the virus that causes AIDS, HIV.

…under natural conditions, a newly emergent, highly lethal pathogen that kills very rapidly is expected to evolve lower virulence. At the same time, however, the host species is evolving resistance to the infection…

Natural selection for energy-dependent codon optimality biophysically constrains viral latency in the context of the physiology of pheromone-controlled reproduction. See: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition and Olfaction Warps Visual Time Perception
My comment to The Scientist:

Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution (2013)

“The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.”

One nutrient energy-dependent change in a base pair is linked to fixation of the amino acid substitution in the virus and one nutrient energy-dependent change in a base pair is linked from the physiology of pheromone-controlled physiology of reproduction to fixation of amino acid substitutions in the organized genomes of hosts. Fixation is a function of the innate immune system, which  biophysically constrains viral latency.

Simply put, it’s “All about that base” See also: Structural diversity of supercoiled DNA

Nutrient stress and social stress act on the same molecular mechanisms that link the virus-driven degradation of messenger RNA to mutations and all pathology. That fact can now be examined in the context of everything know about how the cryo-EM technology links energy-dependent changes in electrons to ecosystems via the physiology of reproduction. Alternatively, everything known to serious scientists about ecological variation and energy-dependent ecological adaptations can be place back into the context of ridiculous theories about evolution.

See for example, these claims about a model for how the brain controls foraging.
Brain modelling: Does the brain control foraging?

The brain might instead act as a mediator between controlling factors in the environment and behavioural output. Perhaps, like evolution, it functions as a tinkerer, equipped with a range of signalling or other mechanisms that allow adaptation (see F. Jacob Science 196, 1161–1166; 1977).

Claims that the brain evolved have been replaced by claims that the brain is an energy-dependent ecological adaptation. Claims about its ability to function as a tinkerer have been replaced with facts that link electrons to ecosystems via the 2017 Nobel Prize-winning technology called cryo-EM. Developers of the technology won the Prize in Chemistry.
Cryo-EM can now be viewed in this context of biophyiscally constrained protein folding chemistry and claims from 2005.
See: Feedback loops link odor and pheromone signaling with reproduction
The claims about feedback loops can be placed into the context of what anyone who is 10 years-old can learn about cell biology and virus-driven energy theft by playing the game “Cytosis.”
If a player starts with evolution instead of the creation of energy that links ATP to the creation of RNA, the player is a loser.