Junk DNA: A Journey Through the Dark Matter of the Genome

Hardcover – April 14, 2015 by Nessa Carey

New Book on “Junk DNA” Surveys the Functions of Non-Coding DNA

Review by Casey Luskin

Excerpt: “We now know that in some cases just a single base-pair change in an apparently irrelevant region of the genome can have a definite effect” (p. 201)

My comment: A single base-pair change “… appears to result in species-specific organism-level changes in skin, glands, and hair, through pheromone-controlled reproduction.” Pheromones link the effect of the single-base pair change to affects on behavior. See the section from my 2013 review: Mathematical models vs. biological facts

Excerpt: “Random mutations that somehow cause one or more amino acid substitutions are not likely to simultaneously cause adaptive evolution from the bottom up via the thermodynamics of chromatin remodeling and control of adaptive evolution from the top down via organism-level thermoregulation. However the nutrient-dependent substitution of alanine for valine (Grossman et al., 2013; Kamberov et al., 2013) appears to result in species-specific organism-level changes in skin, glands, and hair, through pheromone-controlled reproduction.

Increased apocine gland secretions associated with the amino acid substitution in mice links smaller human breasts capable of more milk production and more pheromone production to sex differences in imprinting on the species-specific odor of the mother and classical conditioning of associated hormone-organized and hormone-activated behaviors throughout life. For example, sex differences in preferences for breast size are probably classically conditioned via associations with the unconscious effect of odor from human female breasts that differentially alters hormone-dependent neurogenesis from birth. Fos protein expression from pubertally born neurons that are integrated into region-specific areas of the brain activated by socio-sexual behavior in the Syrian hamster (Mohr & Sisk, 2013), more strongly suggests that the role of nutrient-dependent pheromone-controlled regulation of GnRH pulse frequency and amplitude is the biological core of mammalian reproductive sexual behavior.” — Kohl (2013)

See also: Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant

Abstract excerpt: “An adaptive variant of the human Ectodysplasin receptor…  has been associated with increased scalp hair thickness and changed tooth morphology in humans… We identify new biological targets affected by the mutation, including mammary and eccrine glands.”

Identifying Recent Adaptations in Large-Scale Genomic Data

Journal article excerpt: These data suggest that only a minority of recent adaptations are due to amino-acid changes and that regulatory changes are likely to play a dominant role in recent human evolution.

In their model of recent human evolution, they confuse the effect of an “adaptive variant” and “biological targets affected by” a mutation. Biological targets may be effected by adaptive variants, but affects of adaptations on behavior are attributed to amino acid changes. The changes require RNA-mediated amino acid substitutions to be fixed in the organized genomes of species from microbes to man via the physiology of their pheromone-controlled reproduction.

The difference between effect and affect is important enough to require a correction, as in this Correction for McEwen, Brain on stress: How the social environment gets under the skin

The authors note that on page 17184, right column, first paragraph, line 4, “effect” should instead appear as “affect.”

Mutations and amino acid substitutions effect the nutrient-dependent stability of organized genomes. Mutations cause perturbed protein folding and pathology. Amino acid substitutions are linked from RNA-directed DNA methylation to metabolic networks and genetic networks, which are linked from nutritional epigenetics and pharmacogenomics to affects on behavior during life history transitions. See for example: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults.

Excerpt: DA availability in the PFC is critically dependent on its degrading enzyme catechol-O-methyltransferase (COMT) (Yavich et al. 2007). Its function is known to be affected by a functional single nucleotide polymorphism (SNP) in COMT (G-to-A base-pair substitution) leading to a methionine (Met) valine (Val) substitution at codons 108/158 (COMT Val158Met).

My comment: DA (dopamine availability) is effected by the base-pair substitution. Behavior is affected by a single amino acid substitution. The confusing misrepresentations of cause and effect attributed to evolutionary theorists continue to arise in the context of their attempts to link the effects of base-pair substitutions to affects on behavior without realizing that effects do not lead to affects on successful species-wide behaviors unless RNA-mediated fixation of amino acid substitutions occurs via the physiology of reproduction, which affects behavior.

Nutrient stress and social stress act on the same epigenetically-effected RNA-mediated pathway that links effects on hormones to affects on behavior in mammals and insects. Understanding cause and effect in the context of affects on behavior is not part of what evolutionary biologists have helped others to do.  At best, they have confused others. At worst, they have forced others to combat evolutionary theory and disease by integrating what is known about the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding into their accurate representation of how ecological variation effects hormones that affect behaviors that are required for ecological adaptation. See: Combating Evolution to Fight Disease.

Abstract: Molecular biology and evolutionary biology have been separate disciplines and scientific cultures: The former is mechanistic and focused on molecules; the latter is theoretical and focused on populations. However, these domains are beginning to converge in laboratories addressing molecular mechanisms that explain how evolutionary processes work, and bring these processes to bear on medical problems such as cancer and infectious disease. Each discipline can be viewed as a missing link in the other’s description of biology, and in medicine.

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