But science, natural-science, was never, ever, intended to give the whole picture.
No pretense was made historically that "natural philosophy" was the only philosophy permitted.
Instead naturalism referred simply to the natural component of the overall "big picture" which always included God's spiritual realm.
Indeed, it was understood that God both created and ruled over the natural realm.
Science then was simply hoping to understand, as some believers said, "the mind of God".
Only in recent generations have some (most?) scientists begun to insist that the natural word is the only world that truly exists, that there is no spiritual realm and no God to create & rule over it.
But the fault here is not science itself, rather it's that atheists attempt to define away all other forms of knowledge.
Aspasia: "And who is to say?
If you get to choose what science is, you're not exactly beginning with a blank slate.
That choice functions as a presupposition, and you've begun as a philosopher or theologian."
Not me, certainly, but science writ large, historically what our Founding generations understood by terms like "natural philosophy" and "natural science".
The name of Enlightenment philosopher, Unitarian William Paley, has been mentioned on this thread.
He invented the "watchmaker" analogy to support the idea of God the Creator, and our Founders were perfectly happy with that.
Again, my argument here is not that natural-science itself is philosophically atheistic, only that philosophical atheists deny any realm outside the natural one.
That's a peculiar bird's-eye view. But at least you note its limitation. Still, how did it ever get out of control? Friedrich Hayek in The Counter-Revolution of Science, Studies in the Abuse of Reason describes scientism: "the mechanical and uncritical application of habits of thought to fields different from those in which they have been formed."
It's now gone beyond "-ism" for Darwinism. The dialogue must be turned off, especially if anyone suggests that Darwin took his idea too far to describe the whole picture.