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Suppose, hypothetically, that there were a positive effect resulting from prayer. This is just as likely prove that some of the people doing the praying have some kind of telekinetic healing power as it is to prove the intercession of a responsive God. A test of this would be to have prayers offered to incompatible Gods, one group to Allah, another to Jesus, another to Buddha, another to Zeus maybe, perhaps even prayers to the inactive God underlying Deism and Pandeism. Have the subjects of these prayers equally dispersed among Christians, Muslims, Pandeists, Deists, Buddhists, ...um... Zeusists? See if Muslims heal faster when Allah is prayed to for them (or if they are led to believe that prayers to Allah are made to them). See if Pandeists have any response when they think the inactive fabric of the Universe that underscores Pandeism is prayed to (not likely).

Actually, that would be an interesting experiment as well -- just tell people they're being prayed for and see if those receiving the prayers react differently from those misled to believe they are receiving the prayers!