The Living Set

Mathematical and computational approaches are making strides in understanding how life might have emerged and organized itself from the basic chemistry of early Earth.

By Wim Hordijk | June 1, 2015


Put some E. coli in a dish with appropriate nutrients, and after a few days the dish will be teeming with new bacterial offspring.

My comment: Put some genetically altered P. fluorescens in a dish and leave them “over-the-weekend” with their missing flagella over-the-weekend. Forget to remove them from the incubator and 4 days later learn they have “re-evolved” their missing flagella.

See: Evolutionary Rewiring. Try to convince serious scientists “re-evolved” flagella exemply how autocatalycic processes link ecological variation to ecological adaptations via mutations that perturb the thermodynamic cycles of protein biosynthesis and degradation. Parenthetically, the thermodynamic cycles link the nutrient-dependent physiology of reproduction to RNA-mediated cell type differentiation in all cell types of all individuals of all genera. See this 5.5 minute-long review.


If you can successfully link mutations and evolution via a mathematical model, you can teach neo-Darwinian theory to unsuspecting students who may think you are teaching them more about biodiversity than they might otherwise have learned if they knew that: “[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.


If a living system is indeed an autocat­alytic set, then the next question to ask is whether an ecosystem, a network of inter­dependent organisms, can be considered an autocatalytic superset of autocatalytic sub­sets.

My comment: If you asked whether ecosystems evolved to link autocatalytic sets to cell type differentiation in in all cells of all individuals of all genera via anything except the natural selection of nutrients, you would find that Darwin answered that question when he warned others they must first consider his “conditions of life.”  If you ignore the “conditions of life” on this planet, you can probably link everything to anything via definitions and mathematical models. However, teaching that pseudoscientific nonsense to students who are biologically informed will require you to show them experimental evidence that mathematical models have more explanatory power than models of how ecological variation lead to ecological adaptations. That happens in models of biologically-based cause and effect. Those models are being used by the serious scientists who are Combating Evolution to Fight Disease.

The Living Set cites: S. Kauffman, “Autocatalytic sets of proteins,” J Theor Biol, 119:1-24, 1986. It could also have cited: Prolegomenon to patterns in evolution. Kauffman has since gone on to help others learn that “…our scientific understanding of reality is radically incomplete, and that some sort of anti-entropy, order-generating force remains to be discovered.” When theoretical physicists and evolutionary theorists discover the anti-entropic epigenetic effects of the sun’s biological energy, they will discover what is missing from their ridiculous theories of emergence.

See also:

Early Code

New research points to key properties of transfer RNA molecules and amino acids that may have supported the origin of life on Earth.

By Jef Akst | June 3, 2015


“Dr. Wolfenden established physical properties of the 20 amino acids, and we have found a link between those properties and the genetic code,” Carter said. “That link suggests to us that there was a second, earlier code that made possible the peptide-RNA interactions necessary to launch a selection process that we can envision creating the first life on Earth.”

My comment to The Scientist:

Simultaneous emergence was suggested by Matti Pitkanen who pirated my model of biophysically constrained RNA-mediated cell type differentiation and claimed that “Hens and eggs emerged simultaneously.”

Serious scientists now appear to have discovered the link from the light-induced de novo creation of amino acids to the de novo creation of receptors that link RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of genera via the nutrient-dependent chemistry of RNA-mediated protein folding.

The nutrient-dependent physiology of metabolic networks and genetic networks link reproduction to fixation of the amino acid substitutions, which enables all extant biophysically constrained biodiversity, which is exemplified in differences in morphological and behavioral phenotypes.

Claims of simultaneous emergence should be supported by experimental evidence of biologically-based cause and effect, or abandoned along with claims of Mutation-Driven Evolution, like this one: “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.” (p. 199)

For comparison, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which was published on the same day as Nei’s textbook.

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