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Sniffnoy comments on Belief in Belief - Less Wrong
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Think of the relation between the magisteria as a one-way relationship. The supernatural can affect the natural but there is no way to move backwards into the supernatural.
This is flat wrong and doesn't accurately describe the theology/cosmology of most theists, but it helps when using the concept of magisteria. Personally, I don't think the term magisteria is completely useful in this context.
There is a deep problem behind all of these things where one layer or set of beliefs trumps another. In a framework of map/territory beliefs this makes little sense. It certainly doesn't translate well when talking to someone who doesn't adhere to a map/territory framework.
An example: If you asked the person why God didn't make your son get better you will get a bazillion answers. Likewise, if you asked about taking your son to the hospital they will tell you that you should. These two beliefs aren't in conflict in their system.
I have watched an entire congregation pray for someone who had cancer. They earnestly believed that their prayer was having some effect but if you asked for particulars you will get the bazillion answers. These people are not trying to explain away a future answer. They have seen what appears to be a bazillion different endgames for the scenario they are now in. That, mixed in with the crazy amount of factions within Christian theological circles, isn't going to make sense with a map/territory framework. But they aren't using that framework.
The weak assumption in the dragon example is that the believer of the dragon hasn't already tried using a CO2 meter. Don't underestimate the amount of historical questions packed behind the confusing answers you get when you ask someone to prove their dragon exists.
That being said, the dragon example does bring up a very awesome and valid point. If I took a few of those people who were in that congregation who prayed about cancer and asked them years later about the prayee's status... what would they say? Would they expect a change in their state? Would the cancer be gone? What do they expect from the prayer? My guess is that they wouldn't make any prediction.
As a specific example of Eliezer's larger point, prayer is a natural attempt to influence the supernatural; so by that account, prayer must be futile.
Er, I am not defending the idea of one-way relationships between magisteria. The point was meant to highlight that magisteria is very much the wrong term.
As far as the one-way relationship, the term was not used to mean communication, causality, or anything else in particular.
The easiest example is a write-only folder on my computer. I can drop a file in that folder but do not have any direct measurement of its success or what happens to it after I drop it there. This relationship is "one-way" in the same way that my original statement was using "one-way." Likewise, a read-only file can be opened and viewed but not modified. This is also "one-way" in the same manner that I meant "one-way" in the original statement.
Both of these examples are not one-way in the manner that magisteria would describe one-way.
And again, I am not trying to defend this view. I am merely trying to describe why magisteria is the wrong term.
Prayer would be an example of dropping a file into a write-only folder. We do something and assume that something happens to it later. We don't have access to whatever happens because we don't have read access.
This statement wouldn't make any sense in the cosmology of a typical theist. That cosmology may be completely wrong but using this statement to tell them that prayer is futile would make you sound like a complete nut. The discussion needs to start somewhere else.