I've never believed in a religion, even when I was younger and (I think) there was daily prayer in school. I have written in my journal before about being "rationally and logically agnostic but practically atheist." I am rationally agnostic because we cannot prove a negative; we cannot prove that God doesn't exist unless we search the entire universe (and that's under the assumption that there's physical evidence for God). The other main problem which I admit natural philosophy has trouble explaining is the beginning of the universe. It's hard to imagine someone spring out of nothing; although of course, if you say God is eternal, that's just begging the question of how God came to be.
A recent thought I had, however, is more an argument against religion or philosophy in general than against the existence of God. I'm not particularly well read in the debate between atheism and religion, but I do believe this has been mentioned somewhere before. Some people argue that religion (and God) should not be put under scientific scrutiny, since there are things which science could not explain. Therefore, God does not require a reason for existence, and people cannot ask for "proof" of His existence.
My new thought was that this is a version of the mind body problem. Under Cartesian dualism, the mind is a completely non-physical entity, on a utterly different realm than the body, which is entirely physical. This famous problem in philosophy tries to find the answer to the question: if the mind has not relation to the body at all, how can we move our body simply when our mind wants to? By setting up a dichotomy between the mind and the body, which seems logical, we lose the mechanism through the mental is tied to the physical.
How does this relate to religion? Well, some people say God is not a physical being. I've never heard of people saying He's completely non-physical, but since if he is physical there would be evidence, let's assume for now that He is entirely on a different plane of existence. This sets God up in the same position as the mind, completely dissociated from the physical world.
Well, not completely, or we wouldn't have any problems. The mind-body dilemma arises when we hear stories of God creating the world, or parting the Red Sea, or setting a bush on fire. Science, as a discipline and a philosophy, studies what happens in the physical world. Clearly, parting the Red Sea is a physical phenomenon, and therefore should be subject to the same scrutiny as we give to say, the Newtonian physics of two pool balls. Physical phenomenon, therefore, is the analogical body of a person.
The question is clear: how does God, as a non-physical entity, influence the physical world? Hence we have the religious analog of the mind-body problem, which has been around for several hundred years without resolution.
There is another problem, unique to religion, if God has the power to influence the world. By changing objects in the world, God is essentially opening Himself up to scientific scrutiny. After all, if the water in the Red Sea parted, there must have been some force which prevented the water coming down. Given the amount of water, the water level of the sea would have risen, flooding some coastal areas. I don't suppose Moses's staff is a force field generator.
In the same way that the scientific method has been extended to study the mind (also known as the field of psychology), God, by interacting with the world, is open to scientific study. Of course, this would be a lot easier if the Red Sea parted every day, so we could do experiments. But God has refused to do anything in the last 2000 years or so, since his son came down, so it has been kind of hard for us to collect experimental data.
I apologize if that sounded sarcastic. Going back to religion, there is one way in which God is closed to scientific inquiry: if He does not affect the physical world at all. The problem facing religion then is not science, but of practicality. If God cannot affect the world, well, why do you even believe in God? I can believe that a chain of keys will help me get through life, but if that believe can't change anything, then the belief is unfounded. Similarly, a religion believing in a God who has no influence in the world means nothing.
Which brings us back to the mind-body problem. Some people would argue that God cannot influence the world, but can influence people's minds. With a belief in God, people are more confident, optimistic, kind, etc. These are all great things, and it is through the power of the people which God acts in the world. Which is great, but hidden there is the question, how does being "optimistic," a state of mind, create physical changes in the body? And we're back to square one.
What I just wrote is based on several assumptions, which I will state here explicitly. It is my believe that God will not hold up to scientific scrutiny, and hence religions will attempt to bar such investigations from extending to God. The point of this piece is to show that such an attempt is without grounds.