I just finished reading a very good recent paper by Nigel Goldenfeld and Carl Woese, Life is physics: evolution as a collective phenomenon far from equilibrium. http://arxiv.org/abs/1011.4125
Carl Woese of course is famous for defining the Archaea bacteria in 1977.
Below I comment on some of their writings which I found remarkable.
Goldenfeld and Woese: "In short, a unified view prevents the unnecessary multiplication of hypotheses that is the sure sign of a lack of fundamental understanding (think epicycles!)."
Yes. The field of evolution is full of ad hoc hypotheses that is good for only one or a few phenomena. The molecular clock hypothesis is one.
Goldenfeld and Woese: "Thus, in this picture, evolution is es- sentially synonymous with population genetics. Genes are assumed to be the only dynamical variables that are tracked, and are associated with a fitness benefit that is difficult to define or measure precisely, but is quanti- fied by a fitness landscape that describes how the pop- ulation fitness depends on the genotype[56–59]. Traits are simply associated with genes, and gene interactions are often ignored, or at best handled through the fitness landscape[59, 60]."
Indeed, evolution is widely treated as the same as population genetics. Michael Lynch has this at his website "Nothing in evolution makes sense except in the light of population genetics". But this is not true at all. The overlap feature of the genetic equidistance result is the best evidence for a clear distinction between population genetics and macroevolution.
Goldenfeld and Woese: "Not only is the Modern Synthesis afflicted by strong interactions, but its very foundation is questionable. The evident tautology embodied by “survival of the fittest” serves to highlight the backwards-looking character of the fitness landscape: not only is it unmeasurable a priori, but it carries with it no means of expressing the growth of open-ended complexity and the generation of genetic novelty. Thus, the Modern Synthesis is, at best, a partial representation of population genetics, but this on its own is a limited subset of the evolutionary process itself, and arguably the least interesting one."
Indeed, the modern evolution theory is only a theory of population genetics, which is the least important and interesting aspect of evolution. The more important one is the growth of open-ended complexity, which has now been described by my MGD hypothesis.
Goldenfeld and Woese: "Thus, although complexity is hard to define precisely and usefully, we regard the defining characteristic of complex- ity as the breakdown of causality. Simply put, com- plex systems are ones for which observed effects do not have uniquely definable causes, due to the huge nature of the phase space and the multiplicity of paths."
I could not agree more. No unique genes define complexity. All genes contribute to complexity by reducing their level of random mutations, as described by the MGD hypothesis. It is futile to try to find a few genes responsible for disorders of the complex brain, as has been demonstrated by the failure of the GWAS effort. We are currently studying the genetic causes of common disorders of the brain as a way of further proving the MGD hypothesis.