An excellent article by Godless Mama on the simple error that theists make when they ask, “Well, how do you explain XXX?” It’s supposed to be a “Ha! Gotcha!” kind of argument generally, in which the atheist suddenly realizes that s/he doesn’t have an explanation for XXX and maybe suddenly is saved.
The problem with the whole set of questions, though, is that atheists are generally not concerned with knowing EVERYTHING, because we’re generally aware that, in fact, humanity DOESN’T know everything yet, but that doesn’t mean we jump to saying, “Oh, it must be God!” No, we just say, “Well, we don’t know yet. Hopefully someone will figure that out soon,” or “Apparently there are some good hypotheses on that, but the evidence is just so-so, ” or something along those lines. We’re fine with not knowing or being able to explain. And sometimes, of course, there is a perfectly good explanation already, of which the theists simply aren’t aware or don’t want to acknowledge or don’t understand.
So what if we don’t know everything? That’s the excitement and wonder of exploring and learning and never ceasing to ask questions. Saying, “Oh, that’s God,” for us……that would actually be boring.