Thanks for commenting again Conrad - and I'm very glad to hear it had an impact.
As to your point, I actually generally agree with you on this. It may *not* be the case that all of science can be described in terms of a non-broken hierarchy of supervenience. Perhaps very strange stuff is going on at the microscale and causal structure of any kind can only exist at some level above the ultimate microscale anyways. However, causal emergence is relative to levels; so for instance, if biology does supervene on chemistry, biology could causally emerge from chemistry (regardless of whatever is going on beneath chemistry). It's also very probably that causal emergence can apply to non-strictly supervening scales - because again it's just comparing the macro to the micro causal structures. So these are really great questions - I'm not going to a priori ruling anything out. This is just the clearest way to present the idea without getting into all sorts of caveats about whether and where supervenience holds and how strict it is; which is, in a sense, a different (although just as interesting) problem. Certainly in the systems I'm working with supervenience always holds, which I view as the most difficult scenario in which to make a strong case for emergence, so that's why I always enforce that.
EPH