What conclusion is it that I don't like? Is it that macroevolutionists don't agree with my conclusions. And what level of biology have I failed at?
So you want me to explain the thermodynamics behind this biology (again)? OK, for an ME, why not?
Darwinian evolution consists of two thermodynamic processes, evolutionary competition (what Darwin calls the struggle for existence, the selection of the most relatively fit variant in a given environment) and evolutionary adaptation (improvement in reproductive fitness).
Evolutionary competition occurs because it takes energy to replicate and in an environment (MEs would call this the "system") with a limited carrying capacity (energy available for reproduction), the different variants compete for this limited amount of energy. The variant that is the most effective user of this limited energy in this environment may in some cases drive the less fit variants to extinction such that the only variant remaining in the environment is this most fit variant. This is what biologists call "fixation". This is a first law of thermodynamics process (conservation of energy). Biologists have done a decent job describing this process. Two of the most famous models of evolutionary competition were written by Kimura and Haldane. Kimura's model is given in this paper:
ON THE PROBABILITY OF FIXATION OF MUTANT GENES IN A POPULATION
You as an ME should recognize that Kimura's equation (1) is a stardard heat transfer equation with an energy storage term, energy diffusion term, and an energy convection term. I find this formulation too complicated and difficult to use in any real situation because of the difficulty in defining boundary conditions and constants used in the equation. A different, simpler, and more elegant way of modeling evolutionary competition was published by Haldane in his cost of natural selection paper:
THE COST OF NATURAL SELECTION
His model is simple, when selection of the most fit variant occurs, the frequency of the most fit variant increases, and the frequency of the less fit variant(s) decrease, a simple conservation principle. Note that Haldane uses different terminology. He uses the word "substitution" instead of "fixation". Haldane's model was demonstrated as a conservation of energy principle by Flake and his coauthor in this publication:
An Analysis of the Cost-of-Selection Concept
Haldane's model can be easily modified for variable population sizes which I do when modeling the Lenski experiment. But what about evolutionary adaptation, what thermodynamic principle is operating here?
Evolutionary adaptation is a second law of thermodynamic process. This can be recognized physically by considering how DNA evolution operates. One starts with a particular genome. On replication, random mutations accumulate in that genome over time. Without natural selection, that genome over time would consist of nothing but random mutations, the genome would diverge to a totally random sequence. However, natural selection tends to remove variants with detrimental mutations and increase the number with adaptive mutations. Mathematically this can be modeled as a random walk process using Markov Process mathematics which can be shown to be an entropy process. Natural selection acting with a Markov model can be shown to give the same results (number of replications for a reasonable probability of an adaptive mutation occurring) as the nested binomial probability model that I've presented (does a beneficial (adaptive) mutation occur or not).
Now, you should understand that evolutionary competition and evolutionary adaptation are distinct physical processes. Depending on the environment, evolutionary competition can be interfering with evolutionary adaptation or not. It depends on the carrying capacity of the environment.
Since I've given you an introduction to the thermodynamics of biological evolution (which as an ME, you should easily understand), why does superimposing evolutionary competition slow evolutionary adaptation? In other words, why are the adaptive mutations in the Kishony experiment accumulated much more rapidly than in the Lenski experiment?
