Beneficial microbes kill beneficial mutations

By: James V. Kohl | Published on: January 15, 2015

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Microbiology: Here’s looking at you, squid

Margaret McFall-Ngai has dissected the relationship between a beautiful squid and its live-in bacteria — and found lessons for microbiome research on the way.

Ed Yong 14 January 2015

Excerpt: “We now know that microbes make up the vast diversity of the biosphere, and that animal biology was shaped by interacting with microbes,” she says. “In my mind, this is the most significant revolution in biology since Darwin.”
My comment: I agree. Darwin’s works were bastardized by population geneticists who used de Vries definition of “mutation” and their assumptions to link natural selection and the evolution of biodiversity.
McFall-Ngai, Bonnie Bassler, Anna Di Cosmo and others, continue to show that Darwin’s ‘conditions of life’ are nutrient-dependent and pheromone-controlled by linking:
1) metabolic networks,
2) genetic networks,
3) reproduction in microbes,
and
4) reproduction in their model organisms.

Their experiments refute every aspect of neo-Darwinism by showing how cell type differentiation occurs in species from microbes to man.
Many serious scientists already know that nutrient-dependent RNA-directed DNA methylation and RNA-mediated protein folding appear to link light-induced amino acid substitutions in plants and animals to nutrient-dependent amino acid substitutions and cell type differentiation of all cells in all individuals of all species from microbes to man via conserved molecular mechanisms.
Unfortunately, most evolutionary theorists will not understand the significance of this experimental evidence, or any other experimental evidence because they’ve been taught to believe in ridiculous theories. Too bad! Their funding will go to serious scientists as physics gives way to chemistry and beneficial microbes replace the pseudoscientific nonsense about beneficial mutations.
See: Language and Communication as Universal Requirements for Life:
Excerpt: “Concepts such as genetic code, nucleic acid language, recognition sequences, translation process, amino acid language, immune responses, and cell–cell communication represent irreplaceable core concepts in molecular biology. These concepts were not introduced into biochemistry and molecular biology by linguists, communication experts, or language philosophers. Rather, they were independently coined by molecular biologists to explain observed phenomena and were clearly invoked due to the strong analogy to processes of human communication.”
My comment: McFall-Ngai’s works can now be put into the perspective above and in the perspective below. Note, however, the Kohls did not create the Laws of Biology; they merely independently incorporated what is known about them into what appears to be a cohesive series of published works.
Life is nutrient-dependent. That is a Biological Law. The ecological origin of all biological laws is apparent 1) in the context of systems biology (P. Kohl, Crampin, Quinn, & Noble, 2010); 2) in the context of the metabolism of nutrients by microbes (K. D. Kohl, 2012); and 3) in the context of how the metabolism of nutrients results in species-specific pheromones that control the physiology of reproduction (J. Kohl, Ostrovsky, Frechter, & Jefferis, 2013). Taken together, the systems biology of nutrient metabolism to species-specific pheromones, which control the physiology of reproduction, can be expressed in a summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent. See for review (J. V. Kohl, 2012; Lynch, 2007). The physiology of reproduction is pheromone-controlled. See for review (James V. Kohl, 2013). In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior (J. V. Kohl, Atzmueller, Fink, & Grammer, 2001), which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences (J.V. Kohl, 2007).
Kohl’s Laws help to explain what was missing from Darwin’s ‘conditions of life.’ Darwin knew nothing about genetics, which means he knew nothing about the epigenetic effects of food odors or pheromones. He knew nothing about the fact that microbes link metabolic networks to the genetic networks of biodiversity in species from microbes to man.
I reiterate McFall-Ngai’s claim (above): “We now know that microbes make up the vast diversity of the biosphere, and that animal biology was shaped by interacting with microbes,” she says. “In my mind, this is the most significant revolution in biology since Darwin.”
It’s a revolution that refutes neo-Darwinian evolution and unlike neo-Darwinism, the revolution arose from experimental evidence of biologically-based cause and effect. The revolution is not based on pseudoscientific nonsense. See: “[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. Assumptions, made but not verified, were taught as fact.” — Mazur (2014)
See also: “Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.” — Zimmer (2013)
My comment: John Hewitt appears to be the first science journalist to have realized the problem with the definition of “mutation.”
See: Mitochondrial DNA mutations: The good, the bad, and the ugly
Excerpt (with my emphasis): “The word ‘mutation’ is often associated with something negative, a disease causing variant or a pathogenic subsitution. The problem with these kinds of terms is that despite their different meanings, they can and will be used to describe the exact same change in any number of specific base pair alterations. This is no way to run scientific dialog, let alone research.“

Citations from the Kohl’s et al.,

Kohl, J., Ostrovsky, Aaron D., Frechter, S., & Jefferis, Gregory S. X. E. (2013). A Bidirectional Circuit Switch Reroutes Pheromone Signals in Male and Female Brains. Cell, 155(7), 1610-1623. doi: 10.1016/j.cell.2013.11.025
Kohl, J. V. (2007). The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences. In M. R. Kauth (Ed.), Handbook of the Evolution of Human Sexuality (pp. 313-369). Binghamton: Haworth Press.
Kohl, J. V. (2012). Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2. doi: DOI:10.3402/snp.v2i0.17338
Kohl, J. V. (2013). Nutrient–dependent / pheromone–controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology, 3. doi: 10.3402/snp.v3i0.20553
Kohl, J. V., Atzmueller, M., Fink, B., & Grammer, K. (2001). Human pheromones: integrating neuroendocrinology and ethology. Neuro Endocrinol Lett, 22(5), 309-321.
Kohl, K. D. (2012). Diversity and function of the avian gut microbiota. J Comp Physiol B 182(5), 591-602. doi: 10.1007/s00360-012-0645-z
Kohl, P., Crampin, E. J., Quinn, T. A., & Noble, D. (2010). Systems Biology: An Approach. Clin Pharmacol Ther, 88(1), 25-33. doi: 10.1038/clpt.2010.92
Lynch, M. (2007). The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci U S A, 104(Suppl 1), 8597-8604. doi: 10.1073/pnas.0702207104