Ah, yes, the God of The Gaps. Your argument is identical to the "we don't know how it was done. so God done it" argument of the creationist crowd (whatever they call them selves this week). It's a bad argument, and it should certainly not be used to make drastic, and very, very expensive change.
It's not even remotely the same. His argument is based on evidence and data, not ignorance. He's asking for an alternate hypothesis that has as much explanatory power as his evidence-based model.
FORTUNE'S FUN FACTS TO KNOW AND TELL: A firefly is not a fly, but a beetle.