Empirical studies on the effects of prayer have been controversial since Francis Galton, in 1872, predicted that if intercessory prayer were efficacious then:
“members of the British Royal Family would live longer than average, given that thousands [of Anglicans] prayed for their well-being every Sunday.”
Since that time a number of different studies have been performed to assess the efficacy of intercessory prayer, and most recently some of these studies have indicated that, on average, people who are prayed for are no better off than those who aren’t, and, surprisingly, are worse off if they know they are being prayed for. Take the now famous Study of the Therapeutic Effects of Intercessory Prayer (STEP) for instance, the findings of which include that “Complications [after coronary artery bypass graft (CABG) surgery] occurred in 59% (352/601) of patients certain of receiving intercessory prayer compared with the 52% (315/604) of those uncertain of receiving intercessory prayer (relative risk 1.14, 95% CI 1.02-1.28).” It appears, according to the findings of this study, that although intercessory prayer had no effect on patients who were unaware they were being prayed for (52% faced complications) compared to patients who were not prayed for (51% faced complications), those who were knowingly receiving intercessory prayer were considerably worse off. This study seems to strongly disconfirm the hypothesis that intercessory prayer is efficacious.
Given the empirical disconfirmation of the efficacy of intercessory prayer, what can Christians (or others) offer by way of justification for retaining belief in the efficacy of intercessory prayer? In this case what the Christian needs, it seems to me, is what epistemologists refer to as a defeater-defeater; in other words, they need to regard the empirical evidence as a prima facie defeater of their belief in the efficacy of prayer, and then offer some defeater of this defeater. There are two general strategies here which we might adopt. The first is to appeal to skeptical theism, and the second is to provide some plausible reason(s) for thinking that the study is flawed.
Appealing to skeptical theism need not commit one to the claim that STEP provides no evidence against the efficacy of intercessory prayer, but merely that it provides so little evidence as to be negligible. Here some philosophers make a distinction between (moderate) skeptical theism and extreme skeptical theism, where the extreme skeptical theist believes that evil provides absolutely no evidence against God’s existence, while the skeptical theist believes that evil provides only negligible evidence against God’s existence. I think that moderate skeptical theism is sensible, and if applied in the case at hand it would suggest that STEP provides negligible evidence against intercessory prayer. Why is the evidence negligible? There are a few reasons, including the sample size, problems with the methods used, and such-like. However, the more significant reasons for being skeptical of STEP’s conclusions may be theological in nature.
On some views of God there is reason to predict that intercessory prayer would be ineffective or at least that it would remain empirically undetectable by studies such as STEP. Clearly the Deistic view of God is no less likely given STEP. However, what about the Christian view of God? Does Christianity have internal resources for motivating the prediction that STEP would yield the results it does? I think so.
If we are observing a chemical reaction or animal behaviour it becomes very easy to remove ourselves from the equation and observe what would presumably have occurred even if we had not been observing it. We can, for instance, hide from the animal so that they are unaware of our presence and surveillance. We cannot do the same with God. Just as you might get different results when observing the activities of a human person depending on whether they are aware that they are being watched, so you can reasonably suppose that God might react differently in cases where we try to detect and measure His activity with His full awareness. Does the Christian have any reason to suspect that God would act differently in the case at hand (i.e., with respect to intercessory prayer put under the proverbial microscope)? Yes, I think so.
In Matthew 13:58 we read that Jesus was unable to do miracles in his hometown because of the lack of faith among the people there (see also Mark 6:5-6). Why would Jesus be unable to perform miracles because of a lack of faith in those around him? Let us bear in mind, as we ask this question, that on the Christian worldview God’s aim is ultimately to bring us into a right relationship with him through Christ. There is no guarantee, however, that witnessing a miracle, or even merely believing that God exists, will be conducive to this aim. Thus, on the Christian view of God it is to be expected that God will refrain from doing miracles if/when they would do more harm than good. After all, with greater evidence comes less excuse, and if a person’s heart would only be hardened by finding such evidence then God has every reason for keeping it out of their hands, like a good parent keeping a child’s hand away from a hot stovetop. If God knows the state of your heart well enough (as He surely does, on the Christian hypothesis) to know that this kind of ‘evidence’ is not going to help you (and/or others) to come into a relationship with Him then He seems likely to withhold it, as Jesus did in his hometown. After all, the God of the Bible is on record, through Moses, as commanding his people as follows:
“Do not put the Lord your God to the test as you did at Massah.” (Deuteronomy 6:16)
STEP, if nothing else, seems to be putting God to the test, and that very fact gives us some reason to believe that those conducting the study don’t have their hearts in the right place to begin with.
Moreover, consider what it would mean for the spiritual welfare of believers if we knew that God did as requested in intercessory prayer only 34% of the time. This would plausibly dis-incentivize petitionary prayer, which could do real damage to indefinitely many people’s relationships with God. Further, suppose we found that intercessory prayer ‘worked’ 78% of the time. This would plausibly incentivize bargaining with God, or praying not in order to run into God’s arms, but just in order for God to do what we want Him to do (which would be to treat God as merely a means to an end). It might also induce in us a childish feeling of envy towards other people when we do not receive what we pray for, and resentment towards God for not giving us what we pray for even though most people get precisely what they want. These consequences are certainly non-trivial, and do give God morally justifying reasons for not making his activity known to us when we look for evidence of it by conducting studies like STEP.
Finally, even in the absence of such mitigating considerations, if Christians are right to think that God routinely hides Himself precisely for the sake of allowing us the free (un-coerced) choice of whether to believe in Him or not, then God may have a good reason for hiding Himself from us in this case. Blaise Pascal, the seventeenth-century Mathematician and provocative Christian thinker, once (allegedly) said:
“In faith there is enough light for those who want to believe and enough shadows to blind those who don’t.”
In conclusion, Christians do have (theological) reasons for expecting the results of studies like STEP. If one objects that the reasoning I have presented is retrospective damage control (i.e., that the reasons presented for expecting the results of STEP aren’t strong enough to have motivated Christians to actually predict the results of studies like STEP), I don’t know if I can do better than to appeal to their common sense; the reasons certainly seem strong enough to me. Clearly, at very least, STEP comes as no surprise to the vast majority of Christians.
 Although this quotation is attributed to him on seemingly every corner of the internet, it is possibly spurious. I looked hard for the precise citation and I couldn’t find it anywhere. I also thoroughly looked through the Pensées, and it certainly isn’t a quotation from there. See https://www.gutenberg.org/files/18269/18269-h/18269-h.htm and/or http://www.ccel.org/ccel/pascal/pensees.ii.html. So, just as Marie Antoinette never said “let them eat cake” and René Descartes never wrote the words “Cogito ergo sum” in the meditations (though he did write those words elsewhere), so Pascal may never have uttered/penned these words for which he is popularly remembered.