>What form does this intolerance to heat changed proteins >take? Does it
account for GI diseases as Cordain suggests?

off the top of my head i can't remember. it is the whey proteins which are
easily-altered.  my own experience is that i cant take any amount of
pasteurised milk, but can drink a litre of raw milk daily. proteins are
broken down into peptide chains if incompletely digested and can mimic
endogenous peptides.

that said, cheese should be ok since whey proteins are removed and you are
left only with caseins. but then some people react negatively to the amines
[proteins developing in the ripening process].

andrew