If you're talking about proving the metaphysical from the physical, perhaps. But one can certainly prove things within one sphere of thought starting with axioms from within that sphere, insofar as they can be reduced to logical or mathematical constructs/algorithms. One can prove quite readily that within a given frame of reference any number of physical laws hold true, by looking at what those laws predict and confirming empirically that the predictions are correct. One can prove with equal ease any number of logical propositions about the metaphysical nature of the universe, given agreed-upon axioms.
The trick is finding the right frame of reference, and the right axioms.
The difference is that in the physical world improvements in empirical observation can force changes in our understanding of the physical laws involved. That doesn't mean the law changed, only that our previous understanding was limited by our observational capability.