Hi Lev,
Yes I am *assuming* that set theory is a place to start - sort of. It is actually the methodology I have developed since encountering several formalisms (mostly in the computation context) which claim to be Foundational - and which then ask for comments. To make sense of such formalisms I have tried to develop a better understanding of the foundational classics: set theory, automata theory, lambda calculus - and then see what the new formalism offers.
Having now read a 96 page paper on ETS theory (only once though) I think that I would now describe the situation a little differently. There is a straw man argument that:
Set Theory is a foundation for Mathematics;
Mathematics is a foundation for Physics;
Physics and Mathematics is a foundation for Biology
implies that
Set Theory is a foundation for Physics and Biology. (ditto with Peano arithmetic)
Having studied Set theory for some time I have no idea whether Set Theory has anything to say about physics or biology, although it does have remarkable logical things to say.
The ETS theory seems to be challenging Set theory for this straw man role of "foundation of physics and biology" - except in ETS theory we might have a genuine candidate for that latter role. However this also assumes that a single framework can fullfill all the tasks ETS seems to have set itself:
1. Foundation for Quantum Processes
2. Foundation for Epigenesis and biology
3. Foundation for Space-Time and cosmic inflation
An earlier post asked to apply ETS theory to protein folding. For me, still trying to understand how much is in the theory, I would ask (for the biology case) "where is the DNA?" That is could ETS theory have predicted the need for DNA if we didnt already know about DNA - and if so where does the strut formalism "hide" the parameter that is DNA?
Also a video presentation of ETS theory would be helpful to make sure that we are grasping it propertly.