Just speaking very generally, it seems that in many of your
interests, you would be assisted by a general theory of
"complex functionally-defined systems". (So would I!)
Perhaps the first step in making such a theory would be
to identify all the possible elementary functions, and
"rules of combination" - ie ways in which elementary functional
systems can be combined to make more complex ones.
The theory of computation offers some precedent for this
sort of theory, but it ignores functions which have some
physical component (e.g. "energy production"). I also think
that existing computational theory doesn't really address
the semantic level very much. Someone called James Miller
wrote a book, _Living systems_, advancing a "general
theory of living systems" which claims that each living
system must contain 19 (!) types of subsystems at least,
or at least must have access to such subsystems (which
might be located in another organism, or externally).
I have a list of Miller's subsystem types at
http://www.thehub.com.au/~mitch/systems.html. I don't
recall anything in Miller's book which said that these
are *all* the types of functional systems there can be.
Identifying *all* the possibilities for elementary
functional systems I think requires some metaphysical
assumptions, about what sorts of relationships are
possible. Maybe one could find prototypes for such
arguments somewhere in the philosophical literature;
I think Kant claimed that his enumeration of judgment-types
(in _Critique of Pure Reason_) was necessarily complete
(although I never found the actual argument demonstrating
this).
-mitch
http://www.thehub.com.au/~mitch