Yes Dave, that was what I was trying to get at - if the data doesn't fit, figure out a better model where the data *does* fit.
Amos, I don't entirely rule out the existence of duality. I'm simply asserting that it's something we have no way of proving or disproving, which makes it practically useless. In fact it's worse than useless, because an experience might be ascribed to the "spirit" as an explanation when a physical explanation is actually correct. But because the "spirit" explanation exists, it discourages anyone looking for another explanation - after all, we already have one, right? That's how we get to the "just because" point. Actually it's not "just because", it's that it's "spirit", but for all practical purposes the two are the same - it's saying "spirits just do that" and that's the explanation.
If people figure out every part of the brain and find that there *is* some kind of control from outside, and there's no mechanism for that control, I'm good with Holmes's "you have excluded the impossible, whatever remains, however improbable, must be the truth". I personally suspect that won't be the case, but it's not something anyone will know for a while yet.
The problem is though that if you want to figure out and fix depression, schizophrenia, chronic pain and all the other woes that a malfunctioning brain can dump on you, you'll need more than "it's the spirit". The most basic assumption to be made is that it *might* be possible to fix them, and since the spirit is untouchable, that *might* put these down to physical problems (otherwise it wouldn't be possible to fix them). It seems obvious, but it's a point which eluded all religions until very recently - they assumed that it *was* the spirit, so the person was irrevocably damned (or holy, depending on what attributes the religion ascribed to their behaviour), with appropriate consequences for them and for society as a whole.
And once you start looking, you may find that certain manifestations are reproducable by particular malfunctions. This doesn't require nihilism to accept it, simply an awareness that our brains can be fooled and that what we perceive is not necessarily the truth. Think optical illusions - if you take a pair of straight lines and draw concentric circles over the top of them, the lines seem to be bent, but all you've actually done is fooled your brain's perception of them. In other words, you've revealed a malfunction in the brain. And if you accept the possibility of a malfunctioning brain for vision, why not for other illusions, including spiritual experiences? I don't say it's the only game in town, but if someone finds a brain malfunction which reliably causes this, it's not too big a leap to suppose that people in the past who've experienced this were having that brain malfunction and not a spiritual experience.
The classical explanation of perception is a "dusty mirror". I think a better explanation is a warped fairground mirror. A whole bunch of people might look into the mirror and say "hey, we all have really short legs and deformed heads". They're all experiencing the same thing, but it doesn't make it true.