Collecting facts from many sources, I tried to assemble the outline of a modern appendix to Darwin, using ideas derived from disciplines not available in Darwin’s time: theories of networks, software design, information transfer and knowledge, and social communication–lots of communication.
My primary inspiration and model was variation in bacteria. Bacteria initiate mutations in individuals and even in populations through gene transfer, the swapping of DNA by plasmids and viruses.
My comment: Greg Bear and I share a similar approach. I collected facts from work in different departments of medical laborartories to help determine what was going to kill the next person who would die. It was always the same, a problem with the transfer of energy as information. Cell types stopped communicating effectively and failed energy-dependent communication signals the death of all living organisms. What prevented effective communication? Blood gas analyses always suggested the problem was a change in pH, which is an assessment of hydrogen-atom transfer in DNA base pairs in solution. How did subatomic particles get into the hydrogen atom, and when did they do that so that the transfer of energy could lead to phosphorylation, or autophosphorylation (without the energy)?
What is causing my trouble communicating facts about energy-dependent cell type differentiation to others? Are they neo-Darwinian theorists who believe in the magic of autophosphorylation? Are they young earth creationists who also are physicists, chemists, or molecular biologists? No matter who they are, except for family members, atheists, and pseudoscientists, I have no trouble communicating with others who are not scientists.
For example, Greg Bear appears to be an inspired Deist who is much more informed than Dobzhansky was when Dobzhansky (1973) claimed this in Nothing in Biology Makes Any Sense Except in the Light of Evolution:
…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.
How can we compare Greg Bear’s claims to the claims of others, whether or not they are scientists? Why was I one of the people he invited to fact-check his representations before he sent the manuscript for Darwin’s Children to the publisher? How can anyone else tell the difference between a Deist, an atheist, a secular humanist, or an old earth creationist?
Do secular humanists, atheists, and old earth creationists think that what physicians refer to as a natural death is not caused by virus-driven energy theft? Where does the energy of life go when someone you love is “gone.” Did an oncocer steal it? Did an oncohistone cause them to die of “natural causes?” Have neo-Darwinian theorists cause the death of millions? Does it matter?
I can compare some differences between life and death to what I know about young earth creationists who have linked everything known about nutritional epigenetics to healthy longevity and everything known about virus-driven energy theft to all pathology. Is there an easier way to explain what I think is the lack of any differentiating characteristics between secular humanists, atheists, and old earth creationists?
If they do not believe the facts about energy-dependent autophagy that serious scientists believe in, what do they believe about creation and how biodiversity arose? Do they believe in the emergence of energy and autophosphorylation?
Phosphorylation links autophagy to energy-dependent RNA-mediated protein folding and healthy longevity, or from virus-driven energy theft to all pathology. Have you ever wondered where the energy comes from that enables autophosphorylation, which is a type of post-translational modification of proteins. Autophosphorylation is generally defined as the phosphorylation of the kinase by itself.
You can place that definition into the context of reports that must link autophosphorylation and autophagy to cell type differentiation in all cell types of all living genera. If you use the definition, you may understand why Vries 1902 definition of mutation led all pseudoscientists to believe that the automagical phosphorylation of kinase by itself led to endothelial sprouting, branching and pruning during angiogenesis.
If you substitute mutation-driven evolution for an explanation of everything known to serious scientists about PDGFB/PDGFRß signalling and all other signaling among all other cell types in all living genera, you will be accepted among those who claim that life emerged and “living organisms have evolved” the ability to phosphorylate their kinases. You can tell others that evolution must be true because pseudoscientists claim it is.
But if you claim scientists say evolution is true, prepare yourself to submit your experimental evidence to support your ridiculous claim, or present the experimental evidence that you think led any serious scientist to claim that evolution is true.
Compare your evidence to the evidence cited in Nutrient-dependent/pheromone-controlled adaptive evolution: a model and we can compare models. Most pseudoscientists clearly have missed out on this fact:
See: Phosphorylation of basic amino acid residues in proteins: important but easily missed
See for comparison: Young phosphorylation is functionally silent
Evolutionary cell biology is still in its early days (1).
My comment: There is no such thing as evolutionary cell biology because cell types do not evolve. Cell types must adapt to viruses by biophysically constraining them in supercoiled DNA. That occurs only in the context of energy-dependent phosphorylation and autophagy.
See also: Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees
Our identification of GO categories related to protein phosphorylation that were enriched for genes with methylated splice junctions is consistent with a similar finding in a recent study of species-specific alternative exons . The authors present evidence that argues that alternative splicing is used to alter protein phosphorylation, which can alter protein stability, subcellular localization, activity, and other properties . Further research is needed to determine the mechanism by which splice junction methylation and hydroxymethylation affect mRNA splicing.
My comment: Autophagy is the obvious mechanism that alters the speed of virus-driven mRNA degradation via energy-dependent DNA repair.
See also: Drivers of evolution hidden in plain sight
“This study is about understanding how evolution works, which tells you how species adapt to changing environments over many generations,” says Pedro Beltrao, a research group leader at EMBL-EBI. “For example, when you compare humans and chimps, they are obviously different, even though a good part of their genetic makeup is more or less the same. Our task is to figure out how diversity is generated, so that we can see in detail how life evolves. That helps us understand how plants and animals adapt and change, and how cancers or bacteria find their way around drugs.”
My comment: The difference in the cell types of chimpanzees and humans compared to gorillas is a single amino acid substitution, which was reported by Dobzansky in 1964 and 1973. This study links ecological variation to energy-dependent ecological adaptation via phosphorylation and RNA-mediated fixation of amino acid substitutions in the context of autophagy, which links supercoiled DNA and chromosomal rearrangements to protection of organized genomes from virus-driven entropy.
That protection is called biodiversity when it links ecological variation from the energy-dependent de novo creation of the innate immune system to ecological adaptation via the energy-dependent de novo creation of G protein-coupled receptors.
Calling it evolution or inventing evolutionary cell biology is something only biologically uninformed theorists will continue. Alternatively, if the invention of evolutionary cell biology is an attempt to support the evolution industry or big bang cosmology industry, pseudoscientists can keep referring to ecological adaptation as evolution for as long as they want.
All serious scientists already know how to link energy-dependent changes from angstroms to ecosystems in all living genera, and no species has ever evolved from another species.