Chris,
I have downloaded your two papers and the one from Nature. At the risk that I am making excuses, I am in the middle of writing a book, and the current section deals with enormously complicated chemical kinetics (some with >600 equations); I trust you will be patient and eventually I will provide you with a response. I should re-state that I am not pro-, or against ToE; my position has always been that the theory(s) is nowhere near adequate to justify revision of orthodox theology (eg Adam, Eden, personhood, etc), and if theology were not involved, I would be extremely happy to leave the thing to biologists.
Just as (from the top of my heat) teaser, the Nature paper mentions it is not ‘detracted’ by neutral drift, while on this site, neutral drift is suggested to be central to common ancestry.
I cannot accept you analogy with chemistry - the various disciplines deal with specialised areas and are not in conflict, and theoretical chemistry undergoes all the rigour demanded by physics and maths. This constant appeal to Newton and now chemistry to bolster ToE is unseemly - if anyone can derive maths from variation and natural selection, from first principles (and I am sure you understand this) then all scientist (including myself) would celebrate that day.
Fuller has written many books that also deal with the history of science, paradigms and associated matters. I think you and others may show inordinate disrespect to his achievements, by the hubris inherent in the observation that he is not a biologist. I have looked to other PoS books (Rosenburg, a total materialist, Gerhard, Fuller, Polanyi, to name a few). I cannot find anyone who professes such unreserved acceptance of evolution, evident on this site, whatever their personal position.
Best wished,
George