It is important to remember as atheists that we can never really disprove god per se with science. At best, science will be able to show that god is redundant by providing a natural alternative explanation. As our scientific knowledge increases and natural explanations grow greater and greater, the theist who stakes his foundation for god on a current gap in our knowledge, like the origin or DNA, or consciousness, has his days numbered. And if you think about it, resting your "proof" for god in a current gap in our knowledge is a pretty lousy reason to believe in god anyway.
But there exists the world of logic and philosophy. And through this medium, I think we can indeed disprove certain specific concepts of god on pure logic alone, because let's face it, god is as far as we know, is just a concept.
I've always had trouble digesting the idea that an all-loving god could be compatible with the cruelty and suffering required by the evolutionary process, and how no loving god could prefer that such a drama unfold. Over the years I've heard many wild assertions to try to get out of this problem ranging from fundamentalist denials of evolution, to beliefs that all animals have souls and go to heaven, or that non of them were ever meta-conscious.
Over at SkepticInk, I've been going back and forth with a theist named Vincent Torley from the intelligent design site Uncommon Decent, who responds to my Evolutionary Argument Against God:
1. Any creature capable of third-level pain awareness is self-aware and therefore has an immortal soul of some sort. 2. The claim that it's wrong to create humans using a method that involves conscious suffering is not necessarily true, if the creatures that consciously suffer also have an immortal hereafter.
The theist knows that there is a logical problem with an all-loving god and a long, slow evolutionary process in which millions of animals consciously suffer. Theists like Torley it seems can always just make up ad hoc excuses to retrofit evolution with their all-perfect deity. Since I don't see how it's plausible to say that no non-humans are capable of being meta-conscious given what we've researched and discovered, I think the theist's only way out of this dilemma, as Torley demonstrates, is to say that conscious animals have immortal souls.
But now we're on shaky theological grounds because no Abrahamic scripture makes such a mention as far as I know. Animals were put on earth for man to have dominion over. Only people have souls. That's been standard Abrahamic orthodoxy since the beginning. If animals had souls, we probably wouldn't have been told to use them as god instructed us. And what good is having a soul for a neanderthal, or a chimpanzee anyway? If the standard monotheistic belief is that our soul gives us our free will and our ability to be rational and moral and to know god, why don't animals exhibit this behavior?
The problem here is this: ardent theists will simply just move the goal posts once they're handed a good counter argument to their faith. If animal suffering is a problem, they'll just say all animals have souls and go to heaven! How convenient. And saying so doesn't require any proof or evidence. All that's required is that you say it. It's a testament to the unfalsifiable nature of religion. When things are looking bad, make up some new theology!
I can say however, that I really like the idea of backing all theists into this corner to force them to take the position that conscious animals have souls, because it allows me to get them to say on record beforehand whether they do or don't, and then I can hold them accountable to make sure that they don't contradict themselves when trying to get out of this dilemma.