1) –with my emphasis Re: “There’s nothing here that is revolutionary or requires rethinking of our assumptions about how the immune system functions…”
My comment: They removed assumptions about cell type differentiation by linking differences in metabolic networks to genetic networks. They indirectly showed that ecological adaptations are nutrient-dependent and the adaptations are controlled by the metabolism of nutrients to species-specific pheromones.
The pheromones control the nutrient-dependent physiology of reproduction in species from microbes to man. See: Microbiology: Here’s looking at you, squid
Perhaps this additional news about epigenetics will clarify the fact that all beneficial cell type differentiation begins with self vs other immune system recognition and that cell type differentiation facilitates nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions. The substitutions link metabolic networks to genetic networks via conserved molecular mechanisms. For example, the biophysically constrained chemistry of protein folding establishes nutrient-dependent feedback loops linked to chromatin loops and protein folding.
McFall-Ngai helps to put these facts into a microbes to man perspective that includes thermodynamic cycles of protein biosynthesis and degradation in the gut microbes of squid. Epistasis in the microbes and the squid supports the nutrient-dependent pheromone-controlled physiology of reproduction of both species. Her works also represent symbiotic interactions across species that link the epigenetic landscape to the physical landscape of DNA in all other organized genomes.
2) –with my emphasis Re: “There’s nothing here that is revolutionary or requires rethinking of our assumptions about how the immune system functions…”
Mutations perturb protein folding, which is why claims that mutations lead to the evolution of biodiversity should be reserved for the biologically uniformed. No experimental evidence of biologically-based cause and effect links what is currently known about physics, chemistry, and conserved molecular mechanisms to cell type differentiation in all cells of all individuals of all species via assumptions. What’s revolutionary is the experimental evidence that establishes what is known about olfaction, pheromones, and the immune system. Olfaction and pheromones enable self vs other immune system recognition.
Combining the representations from the studies of twins with representations made in the article about McFall-Ngai’s work shows how physics, chemistry, and beneficial microbes eliminate claims by theorists who think in terms of assumptions about beneficial mutations. For example, “Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995).” — see for review: From Fertilization to Adult Sexual Behavior https://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html
Attempts to link genetics and evolution have caused the stagnation of research across disciplines. Serious scientists should have recognized that the link from metabolic networks to genetic networks was required to make sense of cell type differentiation.
3) –with my emphasis Re: “There’s nothing here that is revolutionary or requires rethinking of our assumptions about how the immune system functions…”
Repeat it many times. It sounds like something an evolutionary theorist would say when faced with experimental evidence that all cell type differentiation is nutrient-dependent and pheromone-controlled in all cells of all individuals of all species, whether or not the differences in cell types are found in maternal or paternal twins with difference in their sexual orientation. No matter how many more times someone tries to tell you that “There’s nothing here that is revolutionary or requires rethinking of our assumptions about how the immune system functions…” it is clear to serious scientists that this research changes the assumptions of evolutionary theory, and that evolutionary theorists don’t want their ridiculous assumptions about cell type differentiation to change.
Four years ago, they opted for this gene-centric claim: “Genes, via their influences on morphology and physiology, create a framework within which the environment acts to shape the behavior of an individual animal. The environment can affect morphological and physiological development; in turn behavior develops as a result of that animal’s shape and internal workings. Genes also create the scaffold for learning, memory, and cognition, remarkable mechanisms that allow animals to acquire and store information about their environment for use in shaping their behavior.”
Genes create. Get it? Not if you’re a serious scientist. Epigenetic effects on cell type differentiation link ecological variation to genetically predisposed biodiversity. You start with epigenetic effects on the cell; you don’t start with the automagical creation of something from genes.
“Nonheritable influences, particularly microbes, seem to play a huge role in driving immune variation,” said Davis. “At least for the first 20 or so years of your life, when your immune system is maturing, this amazing system appears able to adapt to wildly different environmental conditions. A healthy human immune system continually adapts to its encounters with hostile pathogens, friendly gut microbes, nutritional components and more, overshadowing the influences of most heritable factors.”
That’s much more complicated than claiming “genes create.” It’s also what is required to meet Darwin’s ‘conditions of life’ in the context of physics, chemistry, and conserved molecular mechanisms.