There are many different kinds of stories and ways to put them together. Science is driven by the evidence found in experiments and by disproving old theories and replacing them with newer ones that are almost as true. Other systems, like religion, nationalism, paranoid thinking, and art, are based on what people have done or seen (faith, inspiration, paranoia, etc.).
Experience-based and fact-based stories can and do interact with each other.
For example, some scientists who believe in God see science as a way to "look at God's cards" and get closer to Him. Another example: pursuing scientific goals makes people feel more proud of their country and is driven by that pride. Science is often messed with so that nationalistic and racist claims can be made.
The most important parts of any story are the things that happen to the environment. In this way, God is exactly the same as electrons, quarks, and black holes. All four constructs can't be seen with the naked eye, but their effects show that they do exist.
Granted, God's effects can only be seen in the social and psychological (or psychopathological) realms. But the fact that He is limited doesn't make Him less "real." The idea that God exists simply explains a lot of things that don't seem to go together, so it follows the rules for how scientific theories are put together.
God's supposed existence is clearly and only in the minds of people who believe in him. But again, that doesn't mean He's not real. What we think is just as real as anything "out there." In fact, it's hard to tell the difference between epistemology and ontology.
But is God "real," or is He just something we make up out of our own neediness and imagination?
Truth is measured by how well our models can describe and predict events. In people's minds, the fact that God exists does both of these things. For example, if we assume that God exists, we can figure out how many people who say they believe in God will act. Because of this, there is no doubt that God exists (in this formal and strict sense).
But does God exist outside people's minds? Is He a thing that exists on its own, no matter what people think about Him? Even if all living things died in a terrible disaster, the Sun would still be there, spinning as it has since the beginning of time.
If a terrible disaster killed every living thing, would God still exist? If every living thing, including every human, stopped believing in God, would He still exist? Does God being "out there" make religious people believe in God?
Things that are known don't depend on whether or not there are observers (although the Copenhagen interpretation of Quantum Mechanics disputes this). Things that are believed depend on there being people who believe them.
We know the Sun is out there. We don't know for sure that God is real. We think God exists, but in the scientific sense, we don't and can't know for sure.
We can set up tests that will show that electrons, quarks, and black holes don't exist (and, thus, if all these experiments fail, prove that electrons, quarks, and black holes exist). We can also set up experiments to show that electrons, quarks, and black holes exist.
But we can't come up with a single experiment that would disprove the existence of a God that people don't think about (and, thus, if the experiment fails, prove that God exists "out there"). Also, we can't come up with a single experiment that would show that God exists outside of the minds of people who believe in him.
What about the "design argument"? The universe is so big and full of different things that it must have been made by a supreme intelligence, which some people call "God." On the other hand, modern scientific theories like evolution and the big bang can fully explain how rich and varied the world is. There's no reason to add God to the equations.
Still, it's possible that everything is God's fault. The problem is that we can't think of a single experiment that would disprove the idea that God made the world (and, if the experiment fails, show that God really did make the world). Also, we can't come up with a single experiment that would show that God made the world.
We can, however, design many experiments to show that the scientific theories about how the Universe came to be are wrong (and, thus, if these experiments fail, lend these theories substantial support). We can also make experiments to test the scientific theories that explain how the Universe came to be.
It doesn't mean that these ideas are always right and can't change. Not at all. Our current scientific theories are only partly right, and they are likely to change as we learn more through experiments. New, better scientific theories will replace the ones we have now. But in the future, every scientific theory will be able to be proven wrong and put to the test.
Knowledge and belief are like oil and water. Don't go together. Knowledge doesn't lead to belief and belief does not yield knowledge. Belief can lead to strong convictions or opinions. But believing can't lead to knowing.
Still, there are things that are known and things that are believed. The first ones exist "out there," while the second ones only exist "in our minds." But that doesn't make them less real.
