My differences with Josh in this matter of the EES is mostly one of emphasis. I agree that the EES is not a new theory, and therefore I think that comparing it to general relativity (vs. Newtonian mechanics) is a bit overblown. But there is no question that the EES has indeed provided novel insights into the mechanisms of variation. First it must be stated that the leaders of the very loose group of the Third Way are entirely disparate and diverse when it comes to their claims and their science. Shapiro, for example, claims that natural engineering replaces natural selection, which I find absurd. OTOH, Laland and his colleagues studying Niche Construction have indeed opened new avenues for exploration of evolutionary mechanisms that go beyond the Modern Synthesis. Laland and Noble (and others, including Margulis) also have in common a stress on rejection of the gene-centric view that Dawkins made a cornerstone of evolutionary theory, and since population genetics is (by definition) the mathematics of allele frequencies and mutation rates, the anti-gene centric view must to some degree appear to side step population genetics. But Noble’s call for a new mathematics that will take into account the physiology of the entire cell in its interaction with the genome betrays the fact that such formulations do not at present exist. I therefore understand why Joshua, a computational biologist, finds a great deal of this rhetoric to be troubling. And I half agree with him. I would love to see a comprehensive mathematical theory of evolution that goes beyond pop genetics, but I have strong doubts that its possible. (anyway, certainly not by me!).
To sum this all up, my view remains that the EES is potentially exciting, but that its very much a work in progress, and its true that some of its adherents (including myself, and perhaps to some extent, Perry) might have been a bit overly enthusiastic about its prospects. I think the work of Andreas Wagner on gene regulatory theory, and the Laland group, as well as Susan Rosenberg on directed (non random) mutations hold the best promise for moving forward. Meanwhile, I echo Josh’s remarks concerning the need to refrain from attacks on basic evolutionary theory and its defenders, but would also add that the vitriol from a few of the latter toward the third way folks is also unwarranted.