“The supernatural can never explain the physical world we observe.” complains an atheist friend.

“Of course it can’t. It wasn’t supposed to–at least in the scientific sense.” is my reply.

So my friend has this motorcycle which he really loves to fix up and ride, and I try to explain, “You might as well say that ‘love’ can never show you how to change the oil on your motorcycle.

Science tries to tell us how things work–not why they exist, or what our relationship to them should be. ‘Love’ might not tell you how to change the oil on your motorcycle, but meditating on love might help you understand why you love that motorcycle, and why you love to ride it on a beautiful Autumn day, and if the motorcycle is a gift from your wife, then love will also show you why that motorcycle has meaning beyond its mechanical genius. Love may not tell you how to change the oil, but it is the one thing that makes your motorcycle more than an ingenious lump of metal.

So with religion and science.

Believing in the supernatural realm is not some kind of philosophical ‘deus ex machina’–a God of the gaps–an answer for natural mysteries when we have no other answer. Instead the supernatural realm is a given within a philosophical view of the cosmos. It is the universal experience of the human race that the unseen realm is ‘there’. It’s part of reality. Deciding how it interacts with the visible realm and what it has to do with me and my destiny is where science ends and religion begins.
This is why it is a mistake to be too “scientific” about religion. Of course it is good to use the sciences as tools to understand the historical and physical aspects of religion. Archeology, forensics and all the tools of science and critical scholarship are terrific for helping us to understand the historical settings, the historical aspects of the sacred texts, the relics and artifacts of religion, and the human sciences of sociology, anthropology, biology and psychology can help us understand how human beings perceive and interact with religious phenomena, but what the sciences cannot do is pronounce on the validity of religious experience or explain the meaning and purpose of religious experience.
These aspects of religion must remain beyond science’s proper capabilities. I remember they once wired up the Medjugorje visionaries to electronic gadgets which monitored their physical reactions during the apparitions. The data was, no doubt interesting to scientists and students of religious phenomena and human psychology, but it had nothing to say about the validity of the apparitions, their authenticity of their meaning.
The problem with relying too much on scientific investigation of religion is that it can end up being reductionist–reducing religious experiences to some sort of measurable pop and fizzle in the brain.
That pop and fizzle may be there, but it is not the same thing as the experience any more than my increased heart rate when my beloved enters the room is that thing we call love.
Science has its methods which are well and good, but Love has its reasons which are beyond our human telling.