It's supernatural. Perhaps the hardest reason to quantify, it's also one of the most powerful. Praying people believe in supernatural forces and in a God's ability to heal and that seems to have a strong effect on people's health - even if the real mechanism of effectiveness is through one of the three previous reasons. Now, no two mystics describe their other worldly experiences in the same way, and it can be difficult to distinguish among the various types of mystical experiences, be they spiritual, traditionally religious, or simply awe-inspiring. If you're an atheist and you live a certain kind of experience, you will relate it to the magnificence of the universe. If you're a Christian, you'll associate it with God. The point isn't the differences between the spiritual experiences, but rather the similarities - that we can get to that place in lots of different ways.
I think it's likely that future tests and studies will continue to show the relationship between health and prayer. That said, this kind of unexplained energy we feel is the next big frontier in medicine. That is, we define life at the level of the cell. As long as the membrane maintains an energy gradient between the inside and outside world, our cells are alive. When you aggregate cells into organs and then put these in the right spot to make a human, you have life. That's why we're interested in adjusting energy in the body through such vehicles as acupuncture, homeopathy, and hard-to-explain methods like reiki and prayer. After all, everything that matters in life - like love - can't always be measured with blood, machines, and complex calculations. They're measured in the way you live.
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