Gondolinian comments on The Galileo affair: who was on the side of rationality? - Less Wrong
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We have alternative hypotheses for a lot of things we didn't have then. We know a lot more things that don't make much sense with a God than we knew then. Science and religion weren't always in conflict. The conflict doesn't occur until you have empirical evidence against religeon.
If you define God as "an invisible bearded wizard living on the top of the clouds", then yes, we have empirical evidence against that. But that's not the only definition of God. But as I said, there are much better places of coming up with proofs and disproofs about the existence of God that this article.
I find more sophisticated theologies as unconvincing. The fundamental problem is the more coherent and logically provable your god is, the less she matters, until it's nothing left that could be thought of as a god at all, let alone produce any real consequences that we should worry about. It's like the driving paradox - to paraphrase George Carlin, everyone that drivers slower than you is an idiot, everyone that drives faster is a maniac. If someone has a more literal god than you (you in the general sense) they're clearly just a straw man or an idiot. If someone has a less literal god than you, they're misguided or heretical or cowardly.
In this analogy, I choose not to drive.
We have disproven a higher portion of hypotheses that include God than that do not.