Ecological law, cooperation, and DNA repair

By: James V. Kohl | Published on: January 10, 2016

Ecological laws: what would they be and why would they matter?

Abstract excerpt:

… I argue, the existence of ecological laws would make ecological explanations irreducible to even the most complete possible physical explanations of the same phenomena. Ecological laws would make ecology genuinely autonomous from physics.

My comment: This is a fool’s argument.  Serious scientists know physics and chemistry must be linked to biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry. The links must be placed into the context of ecological variation linked to ecological adaptation. Variation is linked to adaptation in all living genera via the physiology of reproduction.

The Evolution of Cooperation


The key to harnessing such cooperative relationships is to understand them at the most basic biological levels. Continued research on within- and between-species cooperation will be necessary to make the most of our social world.

My comment: Across-species cooperation is nutrient-dependent and controlled by the physiology of reproduction. Weekend evolution of the bacterial flagellum exemplifies what can happen when there is no competition.

Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

My comment: Nutrient-dependent RNA-mediated DNA repair is obviously required for adaptation.

DNA repair in species with extreme lifespan differences


The results of this study support the hypothesis that the longer-lived species, human and NMR, have superior DNA repair than the short-lived mouse, and confirm that DNA repair is indeed a longevity assurance system.

My comment: RNA-directed DNA methylation and RNA-mediated amino acid substitutions link competition for energy across all individuals of all species.

  1. Competition for energy-dependent hydrogen-atom transfer in DNA base pairs links nutrient energy-dependent base pair changes to microRNAs.
  2. The nutrient dependent microRNAs are linked to adhesion proteins.
  3. The adhesion proteins act as stress buffers against nutrient stress and/or social stress.
  4. Thermodynamic cycles of protein biosynthesis and degradation link the stress buffers to from amino acid substitutions in histones to supercoiled DNA
  5. The supercoiled DNA protects the organized genomes of all living genera from virus-driven entropy.

The anti-entropic virucidal effects of the sun’s biological energy  have been linked to the stability of organized genomes in bacteria in an answer the question “What is Life?”
See: Virome-associated antibiotic-resistance genes in an experimental aquaculture facility and also: Study of the Viral and Microbial Communities Associated With Crohn/’s Disease: A Metagenomic Approach
Life is the absence of virus-driven entropy. The answer was placed into its proper context, albeit in reverse order, by Schrodinger (1944).

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight)

See also: Prolegomenon to patterns in evolution


The concept of “function” lifts biology irreducibly above physics, for as we shall see, we cannot prestate the ever new biological functions that arise and constitute the very phase space of evolution. Hence, we cannot mathematize the detailed becoming of the biosphere, nor write differential equations for functional variables we do not know ahead of time, nor integrate those equations, so no laws “entail” evolution. The dream of a grand theory fails.

Scientific Seeker Stuart Kauffman on Free Will, God, ESP and Other Mysteries


He proposed that our scientific understanding of reality is radically incomplete, and that some sort of anti-entropy, order-generating force remains to be discovered.

My comment: The order generating anti-entropic force is the sun’s biological energy. It links hydrogen-atom transfer in DNA base pairs from microbes to humans via the physiology of their nutrient-dependent pheromone-controlled reproduction.

  1. Ecological laws would make ecology genuinely autonomous from physics.
  2. The concept of “function” lifts biology irreducibly above physics…

If you let them, neo-Darwinian evolutionary theorists and theoretical physicists will make ecology autonomous from physics with claims like this from Mutation-driven evolution:

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements” (p. 199).

See also:

Memo To PZ Myers: Damage is Random. Repair is Not

My comment: Only an intellectually immature teleophobe would not admit that gut microbes are the link from metabolic networks to genetic networks. The network connections include links to all morphological and behavioral biodiversity in all invertebrates and vertebrates. It is past time for all serious scientists to move forward by ignoring all neo-Darwinian teleophobes.
They were “outed” more than 50 years ago, when Dobzhansky (1964) wrote:

“It is a striking and profoundly meaningful fact that organisms are so constructed, so function, and so behave that they survive and perpetuate themselves in a certain range of environments frequently enough for their species not to become extinct for long periods of time. Furthermore, the ranges of the environments propitious for survival and reproduction are widely different for different forms of life. A biologist who chooses to ignore this widespread adaptedness overlooks a fundamental and very nearly universal characteristic of all that can be meaningfully studied on every level of biological integration, from the strictly molecular to the highest organismic the ecosystem level.” — p. 450

See also:

Researchers Map How Scientific Misinformation Spreads On The Internet


…this phenomenon is driven by the brain’s confirmation bias, which is the natural tendency to seek out and interpret information in a way that confirms our pre-existing beliefs. Social media, which allows us to carefully curate our news exposure, makes it easier than ever to indulge this bias.


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