In response to a post by Peter Bokulich over on Massimo's blog (see my post here of Oct. 13, 2012 @ 08:53 GMT), I've now posted the following response:
Hi Peter,
I appreciate your approach. The key issue for me is that you agree that there are real high-level causes. Good. I agree that given the lower level dispositions of states resulting from those higher causes, the lower level physics gives a complete causal account; but overall, the causal account is incomplete without taking into account the way higher level causes lead to those specific lower level dispositions. A good example is a digital computer, where an engineering computation is taking place because a) C++ has been loaded as the current high level software, b) simulation software incorporating the relevant finite element algorithms has also been loaded, and c) specific initial data to run the relevant algorithms has been entered via the keyboard. The outcome that occurs is then a unique result of the lower level electronic states resulting from a), b) and c). However there is no way that the numerical algorithms embodied in the patterns of lower level excited states can be derived in a purely bottom up way from the underlying physics. It's a category error to assume that purely physical processes can lead to existence of any such algorithms.
Whether we agree on causation or not depends on the weight you put on the words "nothing but" in the phrase "are nothing but constrained, structured, microphysical causal features". I think the explanation above says it's a mistake to use the phrase "nothing but", because significant other causal effects are at work. Part of the problem for a true reductionist is that the electronic gate states are "nothing but" specific states of quarks and electrons; and these again are "nothing but" excitations of superstrings - if they exist, which may or may not be the case. Which level are you claiming is the true microphysical level? The embarrassment for a true reductionist is that we don't know what the lowest level structure is - we don't have any viable theory for the bottom-most physical states. Thus if we take your phrase at face value, all physics is "nothing but" we know not what. Why not leave those words out?
As to quantum indeterminism: it plays two significant roles. Firstly, it ensures that outcomes on Earth today cannot have been uniquely determined by initial conditions in the early universe, inter alia because cosmic rays have altered our genetic history significantly, and emission of a cosmic ray photon is (assuming we believe standard quantum physics) an inherently indeterminate process. The complex structures that exist have come into existence through emergent processes with their own logic that is independent of the underlying physics. Secondly, the most important such process is adaptive selection, which is guided by selection effects operating in a specific ecological context; and that is an inherently top-down process (see "Natural Selection and Multi-Level Causation" by MartÃnez and Moya in Volume 3 (2011) of Philosophy and Theory in Biology, available from Massimo's website). In the example just given, quantum uncertainty plays a key role in providing the repertoire of variant states on which adaptive selection can operate (without the cosmic rays, there would have been fewer such states to choose from). The conjecture is that perhaps something similar might be true in the way the brain works. But that's very hypothetical.