It can now, but in the early stages it was only an assumption, that led to a theory, that turned out to work.
My opinion is, that in case of God, you could follow the same principal. It amazes me, that many people don't take this leap of thought.
First let me offer you a disclosure: I'm a scientist (albeit a political scientist) and as such I've vested a lot of trust in the scientific method's ability to help us contextualize the universe and our place in it.
The first modern scientists were monks as they were the literate and educated thinkers of their time. They operated under clear biases and lacked models and context to explain things like dinosaur fossils and meteorite deposits that began turning up all over. Later, some would even theorize that Native Americans were one of the lost tribes of Israel. Even with their biases and the incorrect inferences they drew from their work, they furthered the human wealth of knowledge by simply recording and documenting what they saw.
As science began to develop away from religion, biases still existed and tons of incorrect extrapolations continued to influence the scientific community. Darwin is a perfect example of one's whose theories biased him (he almost did not even publish Origin of a Species because of the religious grief it caused him). Darwin also could not explain the whole picture of evolution, and most of his suggestions for its mechanics have been explained better by later thinkers. However, Darwin (and others) contributed vast amounts of evidence that this process does happen.
The point is science is by no means objective, and people who claim it as such are severely misguided. It is in many ways a dialetic process, where models are proposed and replaced until we think their is no more explanation possible to offer when we call it a law. Again, it is not perfect, and there could easily be things going on in dimensions we can't understand that make these processes happen- all we can do is create a model that explains what that process is like. On Earth, for example, we know that an object will fall 9.8m/s^2 until it reaches a terminal velocity proportionate to its mass because of drag (this is basic physics and fluid dynamics). We can explain what is going, both on the micro level of an object falling and the macro level force of relative gravity and offer the evidence that explains why it happens. However it could be a giant piece of hyper intelligent pan galactic space pizza that put these functions in motion and we'd never figure that one out.
Lastly- a very quick point: most people don't understand that scientists work to disprove the null hypothesis and only offer the alternative hypothesis as theory. Even if the research disproves the null hypothesis other scientists can offer better theories based either upon the original research or constructing a test that disproves the proposed theory.
