It is simple, once you realize what it means that science is methodological naturalism and based on a set of assumptions for which there are no proof or evidence.
- Nature is orderly, and the laws of nature describe that order.
- We can know nature.
- All phenomena have natural causes.
- Nothing is self evident.
- Knowledge is derived from acquisition of experience.
- Knowledge is superior to ignorance.
That is the definition of God as used by science. None of these assumptions can be proven because they run into Agrippa's Trilemma. In short as for the history of science as related to philosophy once it was realized that there is no Truth in practice, you don't have to hunt for Truth. You go with what appears to work and forget about the problems of epistemological solipsism, Descartes' evil demon and that rationalism doesn't work; and simply state what appears to work.
Now for those of you,, who want to have your cake and eat it too, you can't. Science is not about Truth and there is no proof possible for these assumptions. They are the basis for knowledge, but not knowledge, truth, proof or evidence themselves. That is what, it means, that science is methodological naturalism.
They also explain, how knowledge is cognitive or a model and thus the difference between the model and the landscape in the fundamental sense. In other words for the practical use of science, you explain your model of knowledge and what you find when you use that model, Truth or no Truth.
That is the dirty secret of science. It doesn't prove or otherwise shown that reality is natural. It assumes it. Now add the limitations in practice of science:
Science has limits: A few things that science does not do
And that includes that you can't with strong justification show, that religion is wrong, because science doesn't deal in that kind of wrong, you get a certain kind of non-religious person, who argues beyond science and ends up doing morality/useful/philosophy.
So for the set of non-religious people just as I have to "defend" the religious belief that is okay to eat babies, non-religious people don't have as a double standard to defend anything. Science is self-evidently True with Reason, Logic, Proof and what not and we don't go near that one, because science is scared. You can't point out that it in practice can't solve morality or useful and that it is limited in practice. Oh, yes and that the Big Bang is not a fact. It is one possible set of theoretical models.
Some people in practice can't differentiate between the philosophy of science and their belief that it is a fact, that reality is natural, physical and what not.
Now for those of you , who get this and know this. Fine!
But it was never about you. It is about those who confuses methodological naturalism with philosophical naturalism or overdo the usefulness of science.
Regards and love
Mikkel