Either the world was deliberately created, so that some sort of theism is true, or else atheism is true, but both options involve us in such mysteries (as the two below) that to choose either, given only such evidence as is publicly available (and so worthy of being called ‘evidence’), would be to favour irrationally one mystery over another, whence agnosticism (i.e. the absence of a belief either way) is to be preferred.
......The obvious problem with theism is that, when we look at the world we see only mundane things, no gods and not even angels or fairies. We don’t even see any clear evidence that the world was deliberately created, or is being guided from above, or even watched over. But more importantly our language is so orientated towards the world that we are unable even to form a clear idea of what its creator might be like.
......Conversely we know a lot about the world. We even know that our brains are composed of many brain cells, each of which is composed of a lot of organic molecules, many of them highly complicated but all of them composed of atoms. Atoms themselves have a very tidy structure (as shown, for example, by the Periodic table of the elements), and they are the building blocks of, not just brain cells but rodents and radishes, rocks and raindrops, robots and radios.
......But it is precisely because we know so much about how atoms behave that it is so troubling that (although we can see how information-processing mechanisms can be composed of them) we are unable to make much sense of the idea of their giving rise to such conscious individuals as we know ourselves to be. We might deduce that there must be more to them than we know at present, but it is quite mysterious even what sort of stuff there would need to be (or even its whereabouts, given how much we already know about atoms).
......Perhaps the way that organisms have atoms is akin to how they have skeletons—if the X-ray photograph of an organism shows only its skeleton (which could account for all its scientific properties, had few enough of its properties been observed and measured) that does not mean that there is not more to the organism. But again it is difficult (and not so much because of the complexity as the conceptual obscurity) to make much sense of that idea, not without introducing some sort of non-physical substance (akin to the flesh on the skeleton).
......Still, prima facie we are non-physical individuals, and the mysteries of how and why such mental beings interact with physical structures would seem less of a problem (less of an unlikely coincidence) were the world created because then both the mental and the physical would have had a common origin in a deliberate creation (cf. inventing trains and tracks together). So were we to reject the obscure possibility of atoms giving rise (via natural processes) to conscious beings like ourselves, then we might conclude that the physical world is (probably) a deliberate creation.
......But of course, were we to reject the possibility of a creator for its obscurity, we could instead conclude that there must be some way in which atoms do give rise to us. After all, the considerable evidence that the world is Newtonian turned out to only be evidence that it is approximately Newtonian, and so it is not unreasonable to suppose that atoms might also be only approximately how we think of them, deviating from our simplest picture of them in some similarly unforeseeable way.
......But similarly, neither would it be unreasonable to suppose that we might have been created (e.g. as below). So, it being completely obscure (at present) how either theism or atheism could be consistent with what we know of the world, it is surely impossible to tell, from the publicly available evidence, which one is most likely. And so although (for various reasons) each of us is actually quite likely to presume one of them, the more objectively rational option is surely agnosticism.
......I shall end with an example of one such reason (evolution) for preferring one of those two options (atheism) that seems to be fairly common amongst philosophers (for fairly obvious reasons, e.g. see ScienceBlogs). (This example was suggested by Aaron's comment on the recent post that inspired this post.) Suppose that modern accounts of the evolution of life are (at least approximately) true (as a lot of quite varied evidence indicates). Even so, only such ideas of creation as a too-literal reading of Genesis would consequently be false (and even then, only correspondingly approximately). (In this post I considered one possible motive for creating a world via evolutionary processes, but of course any actual motive is likely to lie well beyond our imaginations.)
......Similarly a simplistic, billiard-ball style of materialism is rendered improbable by our self-awareness, but I’m here considering theism vs. atheism, not literalism vs. materialism. It was once said (fallaciously) that incremental evolution could never explain our eyes, but we now have mathematical models of how eyes might arise incrementally. Nonetheless the likelihood of our being unable to provide any such explanation would surely (had it existed) have undermined this reason for preferring atheism. And so we return to the lack of any indication whatsoever of how an evolutionary explanation of consciousnesses such as ours might go.