It's not broken, mind you, but the important question got distorted.
Above is a video of Richard Feynman explaining his take on science in comparison to religion. I'm probably biased, because I respect the guy a ton and he's one of my biggest role models, but what he says in it is exactly correct. I'm stealing his thoughts in this post because I never really found a good way to state my frustration with the theism debate until now.
The current debate, relegated largely to frustrated forums, relay chats, and Reddit, deals with two frameworks.
One, from the side of theism, is that God is the ultimate truth and in order to see that, you must be engaged in the ritual to become closer to God (worship, prayer, what have you). Through miracles, or emotional connections, you will eventually become so close to God that it no longer matters that the scientific grounding is loose because it is not the logical understanding of the nature of the universe that matters but the emotional connection, simply because religion was clearly not made for making structure in the chaos of nature but for emotional and social guidance. People worship religions because it helps mold their behavior and not because it explains why the Earth orbits around the Sun. I don't agree with this view because I don't believe in compromising logic for emotional convenience but I understand why people would believe in it.
The second (more muddled side) is atheism, which I'm going to define here as the solid belief that no God exists. There are many confused variants of it, especially with agnosticism (which claims that the existence/non-existence of a deity is by definition unknowable) and religious skepticism (which claims that one is unbelieving in a certain deity until further evidence gives significant doubt otherwise). In this framework, atheism is an assertion in its own right; it is the assertion that "no god, or at least none of the gods proposed by currently-standing religions, exist in our universe," as opposed to the theistic belief that a god does exist. And this is fine, albeit ugly.
My problem with this is when atheists claim it is against the spirit of the scientific method to believe in a God because it shows that they do not understand the scientific method at all. It is impossible to understand the whole of the universe simply because there is no way to verify that one's knowledge of the universe is complete. Even if all of the proposed questions have been answered, there is no way to verify with 100% certainty that those answers are true. One can only make progress if they accept that certain assumptions will have to be taken for granted; we can only proceed with logic once we assume that our understanding of logic is correct. Of course, it's unscientific to simply assume something is correct, but we do so because it is the only means we have of making progress.
Since we cannot understand the whole of the universe, it is reasonable to say that the importance of science is not to find the end result of our pursuit for knowledge. (You could argue that the "end result of science" -- that is, modern science -- has a lot of practical applications that benefit mankind, but if it wasn't clear by now I'm speaking from a theoretical point-of-view and not a practical one). If it isn't about reaching the end, then the only possible explanation for the purpose of science, by process of elimination, is that science is about the pursuit itself. Scientists don't look for the answer to reality, but rather they pose questions about reality and attempt to make structure out of them based on some precepts that they have assumed to be true as a baseline. This process, called the scientific method, is useful because it creates more structure out of what we have.
It serves no purpose for science whatsoever to assume the end result that "there is no God." What benefit does that have for science? Will we be able to solve the absence of dark matter from the non-existence of God? Will we find the relationship with gravity to the electromagnetic force because we accept that there is no God? You could argue that, yes, it would help us pose such questions in the first place. But given that the scientific community already poses those questions, it does not help us at all.
Theism, at least, has some purpose, as the proof of a deity would dramatically alter our understanding of science, and create new structure. Theists, however, have a bad habit of claiming that structure is not necessary as long as you have faith, and that's not particularly helpful either.
If you didn't get any of that:
- Science exists so we can understand more science.
- Accepting certain assertions in science help us create structure so we can understand more science.
- The assertion that God does not exist does not help us create structure apart from denying the structures proposed by theism.
- Therefore, the proposal that "there is no God" is more scientific than "what if there is a God?" is completely bogus because the former has no potential to create structure while the latter has does.
- That being said, the convenient theistic response of "there is a God, and all of your questions will be answered through your ambiguous faith in God" also has no potential to create structure and is equally useless to science.