Dear Ian,
Very well written! In addition to the interesting nature of the topic (particularly to someone like me), I appreciate the general viewpoint and broad historical and philosophical context. I have a few questions and remarks:
1. On page 2, you note the close relationship between causality and the "reduction" of a system to its "constituent parts," and on page 4, you mention several possible views on the independence of "emergent behavior" from "underlying processes." You then proceed to offer two objections to what you call the "anti-constructionist view" asserting a degree of independence in this sense. In this context, and avoiding for the moment quantum-theoretic complications, I would offer a third objection, which I also mentioned to George Ellis. Causality is also closely linked to "the" arrow of time, and causality is often described in terms of a binary relation on the set of events (this relation is defined in terms of the light cones in special relativity, for instance). Now if emergent systems exert causal influence independent of their constituent events, then one must model causality not as a binary relation on the set of events (of a classical universe), but as a binary relation on the much larger set of subsets; i.e., the power set. Causality would then represent an "arrow" (i.e., a single dimension) only from the perspective of the power set of the universe, while at the level of the universe itself, it would appear vastly more complicated and nothing like the arrow of time we seem to observe.
2. I am not sure what you mean by the statement that mathematics is purely reductionist? Your brief explanation is that mathematics is "built on logic and is thus internally completely self-consistent." Ignoring possible Godel-type objections to this, I would point to the structure I described above (a binary relation on a power set) as something I would call a non-reductionist mathematical system: by definition you cannot tell what is happening by looking at pieces of a given subset, since the subset is assigned its own "point" in the power set, and information can be assigned to this point which has nothing to do with the information assigned to the points representing the individual pieces. An analogous example in a totally different field of mathematics is the concept of a positive-dimensional point in an algebraic scheme in algebraic geometry; one of the most important conceptual aspects of Grothendieck's program was the realization that working only with the zero-dimensional points leaves out important information.
3. It seems that all this becomes much more complicated when one attempts to combine quantum theory and general relativity. In his 1948 paper, Richard Feynman discussed summing over particle trajectories in Euclidean spacetime and thereby recovered "standard" quantum theory, with its Hilbert spaces, operator algebras, Schrodinger equation, etc. Feynman was able to take all the trajectories to be in the same space because he was working with a background-dependent model; the ambient Euclidean space is unaffected by the particle moving in it. Now, if GR has taught us anything, it is that "spacetime" and "matter-energy" interact, so that different particle trajectories mean different spacetimes. Hence, in a background-independent treatment, Feynman's sum over histories becomes a sum over "universes," with a different classical spacetime corresponding to each particle trajectory. His original version is a limiting case in which the effect of the particle on the spacetime is negligible. Now, from such a perspective, the phases associated to the paths, and hence the amplitudes, a priori depend on the entire universes involved. Thus, it seems that holism can arise as a quantum phenomenon even with a completely reductionist classical theory.
4. These two features, complete reductionism at the classical level, with holism in the above sense arising at the quantum level, represent the only way I can think of to move toward a suitably relativistic and quantum theoretic picture, as I describe here in my essay: On the Foundational Assumptions of Modern Physics. Reductionism seems necessary at the classical level to make sense of time and causality. Holism seems necessary at the quantum level because the sum over histories method is the only version of quantum theory I know of that seems to generalize in a suitable manner to the nonmanifold models of spacetime that seem likely to be relevant for quantum gravity.
Evidently you have thought about these issues deeply and in a wide range of contexts, and I would be grateful for any further remarks you might have. Take care,
Ben Dribus