Questions about God and Science

[Darkstar]

Scientists believe in all manner of entities that cannot be directly perceived: protons, electrons, quarks, bosons, black holes, nuclear forces, etc. They believe in these things because they help them understand natural phenomenon which they do perceive. Correct?

But God isn't one of those things that scientists can believe in because... why?

Not with the naked eye, but with a powerful microscope, perhaps. We cannot directly percieve some of them, but we can discern them from their effects. These effects are well documented and behave in predictable manners. The 'effects' of god simply aren't there. If god ever did something, even indirectly, in this world we would know about it unless he were deliberately hiding himself. Studies have shown that prayer doesn't work, so I don't see any 'effects of god'.

What are the respective intellectual advantages and disadvantages of believing in things like protons versus believing in god, or gods or intelligent design or a universal intelligence or something like that?

There is no disadvantage in 'believing in' protons, etc. They are proven to exist, and they fit perfectly into all of the calculations, etc. involving them. God only fits anything because he is a 'one size fits all' cop out.