If you don't mind a rather primitive question:
If I were to ask you 'which things are ontologically primitive in reality?', what kinds of things would you use to justify your answer? To be clear, I'm not just asking about what your answer is, but what kind of evidence you think is relevant to determining an answer. What, in other words, would things have to look like for you to conclude that human beings were ontologically primitive in reality (and not just in our usual models).
I ask, among other reasons, because although I'm confident that phenomena relevant to human beings, like behaviors, thoughts, biological processes, etc. are reducible to more fundamental physical systems, it's not obvious to me that this straightforwardly means that those more fundamental physical systems are more ontologically primitive than human beings. So far as I understand things, the physical, chemical, and biological theories we use to explain phenomena relevant to human beings don't purport to make claims about ontological primitiveness.
This topic probably deserves more thought than I've put into it, but it seems to me that you can tell what things are ontologically primitive in in reality by looking at what objects the fundamental laws of physics keep track of and directly operate upon. For example in Newtonian physics these would be individual particles, and in Quantum Mechanics it would just be the wavefunction. (Of course at this point we don't know what the fundamental laws of physics actually are so we can't say what things are ontologically primitive yet, but it seems pretty clear ...
In a previous post, I argued that nihilism is often short changed around here. However I'm far from certain that it is correct, and in the mean time I think we should be careful not to discard our values one at a time by engaging in "selective nihilism" when faced with an ontological crisis, without even realizing that's what's happening. Karl recently reminded me of the post Timeless Identity by Eliezer Yudkowsky, which I noticed seems to be an instance of this.
As I mentioned in the previous post, our values seem to be defined in terms of a world model where people exist as ontologically primitive entities ruled heuristically by (mostly intuitive understandings of) physics and psychology. In this kind of decision system, both identity-as-physical-continuity and identity-as-psychological-continuity make perfect sense as possible values, and it seems humans do "natively" have both values. A typical human being is both reluctant to step into a teleporter that works by destructive scanning, and unwilling to let their physical structure be continuously modified into a psychologically very different being.
If faced with the knowledge that physical continuity doesn't exist in the real world at the level of fundamental physics, one might conclude that it's crazy to continue to value it, and this is what Eliezer's post argued. But if we apply this reasoning in a non-selective fashion, wouldn't we also conclude that we should stop valuing things like "pain" and "happiness" which also do not seem to exist at the level of fundamental physics?
In our current environment, there is widespread agreement among humans as to which macroscopic objects at time t+1 are physical continuations of which macroscopic objects existing at time t. We may not fully understand what exactly it is we're doing when judging such physical continuity, and the agreement tends to break down when we start talking about more exotic situations, and if/when we do fully understand our criteria for judging physical continuity it's unlikely to have a simple definition in terms of fundamental physics, but all of this is true for "pain" and "happiness" as well.
I suggest we keep all of our (potential/apparent) values intact until we have a better handle on how we're supposed to deal with ontological crises in general. If we convince ourselves that we should discard some value, and that turns out to be wrong, the error may be unrecoverable once we've lived with it long enough.