Actually we do see it happen, in organisms that have fast generational times, like bacteria. The tuberculosis bug has evolved to become resistant to most traditional antibiotics...
But to get to your original point, as a matter of fact, it is a kind of faith. To believe in science as the best means to achieving knowledge about the natural world, is indeed axiomatic. There's no way to "prove" that it's the best way, because the very concepts of logic and proof are part of it.
If one believes that knowledge comes from a divine revelation, there is no way to prove them wrong, since proofs are not the means by which they are persuaded. I freely admit to having faith in the scientific method and logic as a means to understand the universe.