This is a trope that's very difficult to think round, for both atheist and theist alike.
In this post PZ Myers links to a critique of theism by someone called Greta Christina who finds four reasons why any form of theism (not just the anti-evolution type) is untenable. I haven’t got time to do justice to these posts so here are some quick thoughts on the four points.
ONE: It (theism) contradicts a central principle of the theory of evolution…. in evolution, there is no direction
My Comment: Wrong; evolution is very, very directional; if it wasn’t it simply wouldn’t work. The argument presented here is a bit like saying that railway rolling stock doesn’t have any direction because it can go both backward and forward. The line about “contradicting a central principle” smacks of the evangelical atheist tendency to sniff out what it thinks to be scientific heresy.
TWO: If there really were a Divine Tinkerer mucking about with evolution,…. we don’t see any signs whatsoever of outside intervention.
My Comment: Bad theology. Straight in with the false dichotomy of God vs Nature, the tinkerer vs. insentient physical processes! IDist V J Torley will be pleased that this atheist probably agrees with him on something! True, there is little or no evidence for such a being! But here’s a thought to chew on: The first person sense of conscious cognition is immanent to the brain, but try as I might the third person observer such as myself never sees consciousness in the brains of other people but only neural activity. We may as well complain that there is no evidence for consciousness!
The last two points which now follow are interesting because they are basically bound up with the theology of the problem of pain and suffering, with an additional problem of “inefficient design” thrown in:
THREE and FOUR: You’ve got kangaroo molars, which wear out and get replaced — but only four times, after which the animals starve to death. You’ve got digger wasps laying their eggs in the living bodies of caterpillars — and stinging said caterpillars to paralyze them but not kill them, so the caterpillars die a slow death and can nourish the wasps’ larvae with their living bodies……. Evolution doesn’t give a damn about any of this. But God supposedly does. So why did he do it this way? If God is so powerful that he could bring all of existence into being simply by wishing it; if he’s so powerful that he can tinker with the genetics and circumstances of evolution simply by wishing it — why would he wish it to be so clumsy, half-assed, inefficient, jury-rigged, superfluous, and brutal?
And evolution is brutal. It’s not just that the results of the process are often uncomfortable, frustrating, even painful. The process itself is inherently brutal. The process ensures that most animals die in dreadful suffering and terror: they die from starvation, from injury, from disease, from birth defects, from being torn to pieces and devoured by other animals
My comment: The same old, same old lament: Why doesn’t God stop the pain (and the design bodging!) if he really exists? I don’t think I’m going make much impression on that problem here! But let me just say this: It is our cosmos with its logic of pain and bodging that has been dragged out of platonic possibility; you take it or leave it, and draw your theological conclusion accordingly. (The argument by fundamentalists about the Fall fails even on Biblical grounds – the serpent, the chaos beast, pre-exists man’s fall). Interestingly the reference to "God is so powerful that he could bring all of existence into being simply by wishing it" is very close to the fundamentalist magical idea that "God spoke" the universe into existence. That there might be some kind of obliging process logic and cost to a creation such as ours is never once considered.