PhilGoetz comments on Belief in Belief - Less Wrong
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It is not possible to interpret "separate magisteria" as different kinds of stuff, one "empirical" and one "non-empirical". What they are, rather, is different rules of thinking. For example, prayer can often help and never hurt in individual cases, but have no effect in the aggregate (e.g. when surveys are performed). There's no consistent model that has this attribute, but you can have a rule for thinking about this "separate magisterium" which says, "I'll say that it works and doesn't hurt in individual cases, but when someone tries to survey the aggregate, I won't expect positive experimental results, because it's not in the magisterium of things that get positive experimental results".
Mostly, "separate magisterium" is the classical Get-Out-Of-Jail-Free card. It can't be defined consistently. Mostly it means "Stop asking me those annoying questions!"
This division, needless to say, exists in the map, not in the territory.
If, in quantum mechanics, we can say that something doesn't happen unless it's observed, why can't we say that prayer works only if it isn't observed (in the aggregate)? They seem equally mysterious claims to me.
Indeed, certain interpretations of quantum mechanics (for example, non-local action at a distance) point to dualism. You don't even need to be quite so exotic: spontaneous particle creation in a vacuum would be evidence that X isn't closed or complete. These are real and interesting problems at the interface of science and philosophy. It doesn't minimize physical materialism to acknowledge this.
(I keep saying that I agree that dualism is incoherent -- likewise I think that some interpretations of quantum mechanics and the existence of any truly random processes would be incoherent as well for equivalent reasons. )