Originally posted by saizai
If the significance says that the probability of error (i.e. results due to chance) is 5%, then it's 5%.
If the level of significance is 5%, this means that,
assuming prayer has no effect, the probability is 5% that a future study will show a positive result anyway purely by chance.
But that probability is not directly relevant. We don't know whether prayer has an effect or not; that's what we're trying to determine. Rather, what we know is that the study showed a positive result (supposing that it did). Now, the question we're faced with is, given the study's positive result, what's the probability that prayer is not effective and that the positive result was due just to chance? This is not the same question, although it sounds the same ("what's the probability that a positive result is due to chance?"), because the assumptions are different. Before, we assumed that prayer was ineffective and we didn't yet know the result of the study; now, we know the result of the study but we don't know whether prayer is effective.
It is a different question, and in general it has a different answer. The answer does depend on the level of significance of the test and its power, but it also depends on the prior probability of the effectiveness of prayer.
You could argue that 5% is not enough, and call for a repeat or a study with higher significance threshold, but this would simply drive that 5% down (assuming the successive ones are correct). You must, if you are to retain self-consistency as a skeptic, be willing to assign a priori some level of significance at which you will believe the results, no matter what your previous belief on the subject.
I should be able to decide on a level of significance that would convince me, but the level I pick will depend on my previous belief. The surer I previously am that prayer doesn't work, the stronger evidence of its effectiveness I will require before I change my mind. That makes sense, no?
And if I'm more sure that prayer by designated healers won't result in a difference between the test group and the control group when others might be praying for the control group than when it's certain that no others are praying for them, which I am (aren't you?), then I'm justified in requiring stronger evidence for the former hypothesis than the latter.
69dodge: To put it bluntly, if one studies a sufficiently silly hypothesis, any positive result of the study is more likely to be due to chance than to the silly hypothesis actually being true.
saizai: This way, as explained above, lies dogmatic disbelief.
Yes, I wasn't very precise. I don't mean that one should ever simply ignore a study. But, depending on one's prior belief and the power and level of significance of the study, a positive result might only have the effect of changing one's opinion about the hypothesis tested from 'almost certainly false' to 'very probably false', rather than from 'probably false' to 'probably true'.
(I would like to reiterate, FWIW, that I make no claims about how, why, mechanism, etc., for this to work. I would suggest that you do likewise; you can state your a priori belief as a skeptic that it doesn't since it has no known avenue, but you have no foundation on which to argue - again, as a skeptic - anything whatsoever concerning how it would work or what its limits might be. That would require you to assume the major point to be conceded - i.e. that prayer works at all.)
We shouldn't assume that it works. But we need to make some assumptions about how it would work if it did work, so that we can devise an appropriate study to test it. If we don't decide what it is we're looking for, we won't know whether we've found it or not.
You don't get to make the argument "if prayer works in way X, then you will get a false positive". Because, if it does work in way X, then it works... which is a true positive. And if it doesn't, then the argument is vacuous. You can certainly argue for a false negative, and I think I've already agreed that that might be the case; a necessary risk, given the vast number of (mutually exclusive) theological frameworks available in this world.
I agree that if prayer works, a false positive is impossible by definition. But that's not the argument. The argument is that if, on the assumption that prayer is (in some sense) effective, a false negative is nevertheless very likely, then an actual positive result provides only weak evidence in favor of prayer's effectiveness.
Here's one way to think about it: if, on the assumption that prayer works, the study is anyway likely to result in a false negative, then the study isn't really studying prayer, to any great extent. Other unknown factors have much more of an effect than prayer on the study's outcome. Therefore, a positive result from the study doesn't tell us much about prayer, either, because mostly it wasn't a study of prayer to begin with.
The extreme case is a study in which the probability of a negative result is the same whether prayer works or not, as in my previous example where the outcome of a coin flip is taken to be the result of the study. Obviously, in such a case, one can conclude nothing about prayer from the study, because the study was designed in such a way that prayer could have no effect on its outcome. Similarly, if a study is designed so that prayer could possibly affect its outcome, but is unlikely to---i.e., there is a high probability of a false negative---then one can conclude something about prayer from the study, but not much.
All that said, I am highly curious to hear your logical basis behind the argument you just gave. You seem quite convinced in it - though I see it as fallacious at core - and I would rather like to understand why.
It's standard Bayesian reasoning.
http://www.trinity.edu/cbrown/science/bayes.pdf
http://en.wikipedia.org/wiki/Bayesian_inference