My “…atoms to ecosystems approach continues to be based on some speculation, but it is largely based on experimental evidence, which comes from others who also have speculated about biologically-based cause and effect in the context of the miRNA/mRNA balance and amino acid substitutions.” I have done none of the experimental “wet work.” However, I recognize that works by Svante Paabo are among the most important contributions to a cohesive representation of how the epigenetic landscape becomes the physical landscape of DNA in organized genomes.
His important contributions in monographs and in co-authored publications can now be viewed in the context of experimental evidence that eventually will remove ideas about mutations and evolution from any further consideration whatsoever. This will mean the death of evolutionary theory, and that death may come as a shock to most theorists. Perhaps that is why Paabo and others seem to be trying to slowly ease theorists into the 21st century.
For example, see: Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees. We now know that the de novo creation of olfactory receptor genes is nutrient dependent. Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates, which attests to the fact that their experience-dependent creation results only when they are required. When other sensory input helps to facilitate food selection and mate choice, the need for olfactory/pheromonal involvement is reduced. Nevertheless, the conserved molecular mechanisms that enable the de novo creation of olfactory receptor genes are not likely to be eliminated. Instead, ecological variation and the need for adaptation to ever-changing ecological and social environments appear to ensure there is no change in the way that the creation of olfactory receptor genes occurs, which explains why MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates. More than anything else I’ve read, this paper moved me away from theory, and it moved me forward to a comprehensive view of biologically-based cause and effect.
I learned about the importance of microRNAs from a conference speaker at the 2012 annual meeting of the Society for Neuroscience in New Orleans, and proceeded to discuss the microRNA/messenger RNA balance with anyone whose presentation indicated they knew more than I did about its role in ecological adaptations. At that point, of course, everyone I talked with knew more than I did about microRNAs, but no one had linked the microRNA/messenger RNA balance from the epigenetic landscape to the physical landscape of DNA in organized genomes of species from microbes to man. Then, the link from ecological niche construction to social niche construction and development of the human brain and social behavior became clear.
As it turned out, Paabo had always been there for me, and had already published Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques with co-authors in February 2012. I admit to being confused, however, by the next publication: A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes. It turned away from nutrient-dependent de novo Creation of olfactory receptor genes and touted mutations in the context of some unknown role that they supposedly played in evolution. But whatever that role might have been, it required a revision of the timescale based on genetically predisposed nutrient-dependent metabolism in cells of different species. Again, I became more confident that the end of evolutionary theory was in sight. Then, earlier today, I realized what I had missed. In 2010, Paabo published with co-authors: A functional test of Neandertal and modern human mitochondrial targeting sequences, and tentatively linked nutrient-dependent amino acid substitutions to ecological adaptations as I knew Dobzhansky had done in 1964.
However, unlike what I’ve seen others do in virtually all research that I’ve read that was published since 1964, Dobzhansky did not approach the differences between theorists and molecular biologists with caution. He wrote: “The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! ” (p. 443) It’s probably a good thing that Dobzhansky then toned it down for his audience, but it’s not so good that there are still many bird-watchers and butterfly-collectors who have ignored the serious science and experimental evidence from Paabo and others.
The end of evolutionary theory has been delayed for 50 years by the pseudoscientific nonsense touted by population geneticists, and that delay has caused many non-scientists to believe in theory instead of biological facts that explain the increasing organismal complexity that is manifested in species diversity. Finally, Paabo (with others) has done it again. Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan links the epigenetic landscape via nutrient-dependent DNA methylation to the physical landscape of DNA in the organized genomes of the Neandertals and Denisovans. This extends what is known about biologically-based cause and effect to modern humans via nutrient-dependent pheromone-controlled ecological adaptions.
Obviously, however, it will take more than the reading of just one person’s works or one group’s works to convince evolutionary theorists that the end of their time has come. Someone must publish a review that links discoveries during the past 50 years to what was reported last week. Someone must publish something like this in a peer-reviewed journal: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems. That way, the report by Paabo and others, which clarifies the role of DNA methylation in ecological adaptations, can be considered in the context of works by others that should long ago have eliminated ideas about mutations and evolution by natural selection for something — and replaced those ideas with accurate representations of the requirement for natural selection of food and its metabolism to species-specific pheromones that control the physiology of reproduction in species from microbes to man via conserved molecular mechanisms.
Paabo, or someone else with his academic standing, might be able to get reviewers to review an article that replaces evolutionary theory with established biological facts. I could not! What’s more, I knew that my invited review would encounter resistance because of past experience during publication of other articles like: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Indeed, if the title had indicated that the review was actually about ecological adaptations, it might never have been published. Others still cling tightly to their theories, no matter what experimental evidence refutes them. But Paabo’s experimental evidence, when placed into a review article — in and of itself — could readily be defended against the complaints of underinformed “peers” who are not really the peers of anyone who has learnt anything new about genetics during the past decade. Denis Noble had this to say about those who have learned what’s new in Neo-Darwinism, the Modern Synthesis and selfish genes: are they of use in physiology? He wrote: “If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based.” (p 1014)
Thank God, that Paabo’s experimental and field work has helped to move forward any additional debates so that others begin to discuss epigenetic effects on methylation and ecological adaptations and dispense with the pseudoscientific nonsense of population genetics and evolutionary theory.