One answer, from a naturalistic perspective, is something like this: 1. The mutations that led to speciation were either directed by intelligence, or they happened randomly. 2. It's outside the realm of science to consider the existence of some intelligence that manipulates the mutation of organisms. 3. Therefore, from a scientific point of view, the mutations in question must have happened randomly.
This line of reasoning, of course, has holes in it you could fly a C-5 through. The first of these is that point 1 is a false dichotomy; just because a process happens naturally, without exterior guidance, emphatically does not mean that the process is random. A large subset of science is devoted to the derivation of mathematical formulae that describe the operation of the universe, and there's no reason to believe that speciation doesn't operate according to its own attendant formulae.
I didn't go through this exercise to construct a straw man, however. I just mean to point out what I see may be inarticulated assumptions in the common naturalistic point of view.
As long as you're busy building false assumptions, here's another one. Science does this sort of stuff all the time, including with guided mutation of organisms. So it's clearly not outside the realm of science to do this stuff.
One wonders why science is therefore claimed to be utterly incapable of detecting what science can do. Dogmatic convenience, perhaps?