For centuries, chemists have written equations representing chemical reactions by using symbols for atoms and molecules; for example, 2H2O + 2Na → 2NaOH + H2. This short notation shows only four reacting particles, but even in a classroom demonstration where a small piece of sodium is dropped in water, the total number of reactants will be on the order of Avogadro’s number (∼6 × 1023). On page 900 of this issue, Liu et al. (1) instead study a chemical reaction taking place between a minimal number of participants. In their experiment, exactly two atoms collide, absorb a photon, and form a molecule in the excited state. And this time, the reaction equation, Na + Cs → NaCs* (where the asterisk denotes an excited molecule), describes exactly the process that takes place in the laboratory.
The link from quantum physics to classical physics was placed into the context of quantum chemistry via the link from the collision of two atoms that link the absorbed photon to a biophysically constrained molecular state.
Biophysically constrained molecular mechanisms of cell type differentiation link the difference in the energy of two photons to all morphological and behavioral diversity in species from microbes to humans. The molecular mechanisms are the same. They link the creation of the sun’s anti-entropic virucidal energy from microRNA biogenesis to the microRNAome and every aspect of microRNA-mediated cause and effect.
Most representations of top-down causation are still framed in the context of the microbiome rather than the microRNAome.
See for example: The Human Microbiome: Colonization in Health and Disease
…microbial colonization changes throughout our life and is impacted by where we grow up, and what we touch, eat, and experience. Events like a fever or a course of antibiotics can cause sudden shifts in our microbiomes, with effects that may last for years or even a lifetime.
Top-down causation links environmental selection from natural selection for energy-dependent codon optimality to the fixation of the amino acid substitutions that biophysically constrain viral latency in all living genera.
The fixation of amino acid substitutions is linked to hemoglobin variants hbVar via the creation of G-protein coupled receptors such as olfactory receptors in olfactory receptor genes, which have been linked to the abundance of other genes or gene losses in all species.
Based on the information about energy-dependent fixation of amino acid substitutions and cell type differentiation that was available at the time, in 1995, I co-authored The Scent of Eros: Mysteries of Odor in Human Sexuality. We linked ecological variation to ecological adaptation via the food energy-dependent pheromone-controlled physiology of reproduction. After that, some peers hated us then. Some still do.
Here is a report that indicate why some peers still hate us. Typically, the hate-mongers are evolutionary theorists.
“With billions of years of evolutionary experience, bacteria are adept at surviving in changing environments,” said Robert Gennis, a University of Illinois professor emeritus of biochemistry who led the new research with biochemistry professor Emad Tajkhorshid.
“Most have the ability to modify, replace or combine molecular tools to suit the new demands—sometimes within a single cell’s lifetime,” Gennis said. These tools include enzymes, which catalyze chemical reactions to perform specific tasks.
The energy required by the bacterium is obtained by transporting electrons from high energy food molecules to oxygen, similar to what occurs in plant or animal cells, Gennis said. Electrons pass from one enzyme to another until finally reaching oxygen.
Typically, an enzyme passes an electron on during a random collision with another enzyme. The researchers showed that in some conditions, nature eliminates the need for random collisions by sticking the enzymes together to form a “supercomplex.” Each part of the supercomplex can generate a voltage, but all parts must function in sequence,” Gennis said.
“It makes sense that they will function as a single unit to make sure the electron transport is rapid and the electrons end up where they belong,” he said. “Supercomplexes are probably important in all electron transport chains, but in most cases, attempts to isolate them fail because they fall apart. We were lucky to be studying an organism called a Flavobacterium, in which the supercomplex is stable.”
Rather than relying on detergents to extract the proteins from the membrane, as is typically done in such experiments, the team tried an industrial polymer—a kind that plastics are made from. Using this polymer, they extracted and isolated the supercomplex in a single, rapid step. The process embedded the supercomplex in a small disc of membrane shaped like a coin.
With the help of their collaborators at the University of Toronto and the New York Structural Biology Center, the team used cryo-electron microscopy to determine the configuration of the supercomplex components.
No experimental evidence of top-down causation has been linked to theories about bacteria that supposedly have “billions of years of evolutionary experience.” Nothing suggests that the quantized energy-dependent transfer of electrons leads to random collisions with other enzymes. Instead, the quantized energy differences of two photons have been linked from quantum chemistry to quantum biology via niche construction at every level of biological organization and every level of investigation by serious scientists. For example, stem cells do not create themselves.