The Strange Inevitability of Evolution

by Philip Ball
Excerpt 1)  Natural selection supplies an incredibly powerful way of pruning variation into effective solutions to the challenges of the environment. But it can’t explain where all that variation came from. As the biologist Hugo de Vries wrote in 1905, “natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest.” Over the past several years, Wagner and a handful of others have been starting to understand the origins of evolutionary innovation.”
My comment: The origins of ecological adaptations, which Wagner attests to in the context of evolutionary innovation, are found in the biophysically constrained chemistry of nutrient-dependent RNA-directed DNA methylation and RNA-mediated protein folding that links amino acid substitutions to cell type differentiation of all cell types in all individuals of all species.
The origins of ecological adaptations are not clear in Wagner’s book or in Philip Ball’s review because Ball did not mention Hugo de Vries definition of “mutation.” De Vries definition led to use of the term in the ridiculous Modern Synthesis (neo-Darwinism) that added assumptions about cause and effect based on the definition of mutation. Those definition-based assumptions prevailed during 80+ years of research that attempted to link genetics and evolution. That research failed to establish what is known to serious scientists. Simply put, cause and effect must be linked from metabolic networks to genetic networks. Although Wagner clearly states this in the “Genetic and Metabolic Networks” section on his lab’s webpage, Wagner does not do that in his book. Indeed, as I read Arrival of the Fittest: Solving Evolution’s Greatest Puzzle, I expected that he would soon mention something about the nutrient-dependent physiology of reproduction, but perhaps he is saving that for another book. I became more puzzled. What did he think was solved?
No matter. What matters is that Philip Ball politely trashes neo-Darwinism. Without mentioning Darwin’s ‘conditions of life,’ he accurately portrays what Wagner detailed, albeit also without mentioning the need for the nutrient-dependent pheromone-controlled physiology of reproduction to link ecological variation to ecological adaptations.  Again, there is no need to consider the physiology of reproduction if all you intend to do is invent another term for ecological adaptations and portray them as innovations without linking epigenesis to epistasis. Howerver, ‘conditions of life’ must link ecological variation to protein biosynthesis and degradation and to ecological adaptations. This must be done without the pseudoscientific nonsense of population genetics and ridiculous claims that mutations, which perturb protein folding, somehow lead to the evolution of biodiversity. If the evolutionary innovations do not arise from mutations, which is what Ball suggests, he is also suggesting the evolutionary innovations are nutrient-dependent and pheromone-controlled ecological adaptatons.

Unfortunately, most people still cannot think in terms of ecological variation and ecological adaptations. “Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].” That’s close, but the evolutionary divergence is exemplified in ecological adaptations.
Despite Wagner’s book and Ball’s review, the problem with thoughts about evolutionary divergence will soon be eliminated when intelligent people realize that ecological adaptations are manifested in biodiversity, which arises via nutrient-dependent RNA-mediated amino acid substitutions.

Darwin did not know about genetics and RNA-mediated events that link nutrient uptake to the physiology of reproduction and biodiversity in species from microbes to man. If he had, his theory probably would now be referred to as the Theory of Ecological Adaptation, and it could be viewed in the context of other scientifically established facts. Wagner knows that “Genetic and Metabolic Networks“ must be linked and he probably knows he cannot link them merely by “doing the math.”

Excerpt 2) ” If you take account of the different ways that these genes might regulate one another (for example, by activation or suppression), you find that the number of possible circuits is more than 10⁷⁰⁰. That’s a lot, lot more than the number of fundamental particles in the observable universe.”
My comment: The number of fundamental particles in the observable universe limits the explanatory power of any theory about how metabolic networks and genetic networks must interact in the context of survival of the fittest or  the arrival of the fittest. Evolutionary innovability explains nothing at a time when the epigenetic landscape has been linked to the physical landscape of DNA in the organized genomes of species from microbes to man via nutrient-dependent RNA-mediated events and the pheromone-controlled physiology of reproduction.
Excerpt 3) “…manipulating this network to switch between sequential and simultaneous formation of the segments of a fly’s body is much easier to achieve than expected—it just needs a few tweaks of the regulatory mechanisms, not a wholesale reorganization of genes. “This explains much of the differences in expression patterns in different fly species,” says Jaeger. “All kinds of patterns can be produced by the same set of genes.”
My comment: In our 1996 Hormones and Behavior review article we explained all the differences in expression patterns in different fly species. In our section on molecular epigenetics we wrote: “Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.”
In his 2012 review: Alternative RNA Splicing in Evolution, Jon Lieff wrote: “…alternative splicing may be the critical source of evolutionary changes differentiating primates and humans from other creatures such as worms and flies with a similar number of genes.” Taken together, these two reviews show there is nothing strange about The Strange Inevitability of Evolution, except that fact that it is not recognized as the requirement for ecological variation to lead to ecological adaptations in species from microbes to man via the conserved molecular mechanisms of nutrient-dependent metabolism and the pheromone-controlled physiology of reproduction.