The Second Axiom of Construction and the Second Axiom of Biology posit that any system can allow a certain degree of random noises or errors in its building blocks, and such limited degree of random errors may confer zero, negative, or positive values to the functioning/survival of the system under certain random environmental circumstances.
This axiom underlies the whole of the modern evolution theory composed of Neo-Darwinism and Kimura’s Neutral theory and is the foundation for microevolution and population genetics where there is no change in system complexity over time. (In contrast, the First Axiom of Biology is the foundation for macroevolution where there is change in system complexity over time.)
For the neutral errors that confer zero values to the functioning/survival of the system under a certain random environmental circumstance, the accumulation of such errors is determined by random drift and linearly related to time, as described by Kimura’s neutral theory. For the non-neutral errors that confer either negative or positive survival values, the survival values are dependent on the environmental circumstances, which are and can only be random in nature. Thus, the accumulation of non-neutral errors is determined by random natural selection by random environmental circumstances. Since natural selection is overall a completely random process (see my post on April 9, 2009 and other posts on the random nature of natural selection), the fixation of non-neutral mutations by natural selection is effectively no different from that of neutral mutations and is therefore also linearly related to time given long enough time that allows for multiple rounds of selection and de-selection. Thus, the genetic distance between any two species is linearly related to time like a clock, regardless whether the errors that contribute to such distance are fixed due to random drift or random natural selection. Evidence for beneficial mutations to behave in a clock like manner has been shown recently (Barrick et al., 2009). Our recent molecular dating study has also shown a remarkable concordance between molecular dating and fossil dating. Thus empirical evidence supports the notion that there is a strong linear correlation between genetic distance and time of divergence even if such distance is largely contributed by non-neutral mutations. In theory, as long as we correctly view natural selection to be what it really is (it really is random), we can easily make sense of the clock like behavior of the non-neutral mutations within the neutral theory framework. The fixation of the non-neutral mutations has one fundamental property in common with that of the neutral mutations. They are both random. Over long periods of time and numerous random environmental changes, the number of positive selections will roughly equal the number of negative selections. Thus, the canceling out of each other the positive and negative selections makes non-neutral mutations to effectively behave as no different from neutral mutations.
So, the modern evolution theory (Neo-Darwinism plus the Neutral theory) is not completely counter-intuitive or non-sensible. As a theory of microevolution and population genetics, it is completely sensible or intuitive and flows readily from the self-evident Second Axiom of Biology. But as a macroevolution theory, it is completely non-sensible or counter-intuitive as it must negate the First Axiom of Biology. The more complete MGD hypothesis takes into account both of the Axioms of Biology and fully grants the modern evolution theory to be what it really is or has been proven to be (a theory of population genetics and microevolution or the microevolutionary phase of macroevolution).
I may formally introduce The Second Axiom of Construction and Second Axiom of Biology in a future paper.
Barrick, J.E., Yu, D.S., Yoon, S.H., Jeong, H., Oh, T.K., Schneider, D., Lenski, R.E., and Kim, J.F. (2009). Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 7268, 1243-1247.