Elegantly put by David Friedman:
Consider, for an obvious analogy, the scientific view of the nature of light. A critic could argue that some scientists describe light as particles, some as waves, and they cannot both be true. The response is that they can both be true–we can write down a mathematical description of light that is consistent with all of the experimental evidence. What we can’t do is to clearly intuit that description. We can intuit the wave version, we can intuit the particle version, to our intuition they seem inconsistent, but in fact each is a partial description of a single consistent reality.
Part of my skepticism with regard to the efforts of my fellow atheists to demonstrate how absurd the opposing position is comes from knowing a fair number of intelligent, reasonable, thoughtful people who believe in God–including one I am married to. Part comes from weaknesses I can perceive in the foundations for my own view of the world. At some point, I think, each of us is using the superb pattern recognition software that evolution has equipped us with to see a coherent pattern in the world around us–and since the problem is a harder one than the software was designed to deal with, it isn’t that surprising that we sometimes get different answers.
The Dish 