The God of the Abyss
In the beginning there was nothing. The beginning of human knowledge about the universe, that is. Things happened without any particular rhyme or reason. As long as the universe was an orderless Abyss that didn't appear to be playing by a set of consistent rules, a person could conclude either that 1) the world is fundamentally random and devoid of reason or 2) events can be explained by the caprices of a deity. The latter notion at least provides the universe with an organizing principle, an indication that there's some intelligence behind events. This is a comforting thought to the organized mind of a human being, even if knowing that offers no predictive power. This deity--that which separates us from an orderless, incomprehensible universe--is what I'll call the God of the Abyss.
The God of the Gaps
With the benefit of hindsight, we now identify the God of the Abyss as the God of the Gaps. Today we know that recurring patterns--underling laws--are responsible for natural events. Thus the God of the Gaps argument posits that religion has always served as a placeholder whose utility disappears as the body of scientific knowledge grows. Religion's God of the Gaps offers explanations in the absence of genuine understanding; but the order it brings to an otherwise orderless universe is only temporary. It is supplanted by scientific knowledge as the gap--which we recognize to be a gap in that scientific body of knowledge--shrinks. The God of the Abyss, dating from a time when it was not known that there were laws governing the universe, did not, strictly speaking, fill gaps because it was not recognized at the time that there was another side to the chasm.
Thus, the argument goes, just as science has shown us that the God of the Abyss was actually the more limited God of the Gaps, it has also indicated that in the limit that those gaps shrink to zero there is no need for god. Science slays god.
Chess
But there is another way to view this progression. Physicist Richard Feynman once described our quest to understand the underlying laws of the universe by using the analogy of a chess game:
One way, that's kind of a fun analogy in trying to get some idea of what we're doing in trying to understand nature, is to imagine that the gods are playing some great game like chess, let's say, and you don't know the rules of the game, but you're allowed to look at the board, at least from time to time, in a little corner, perhaps, and from these observations you try to figure out what the rules of the game are, what the rules of the pieces moving are.
The God of the Abyss arises from the assumption that there are no rules that the pieces on the chess board obey, merely an intelligent hand moving them around as it sees fit. Once we recognize that the pieces do obey laws, the mysterious intelligent hand is invoked only to explain chess moves that do not yet conform to our understanding of the rules (e.g. we might be absolutely befuddled the first time we observe castling). The recognition of underlying rules reduces the God of the Abyss to the God of the Gaps, as long as we regard god as a fundamentally pragmatic tool. But ultimately we will understand all of the rules and we won't need to assume that any sentient hand is guiding any of the pieces.
However, one might also look at the chessboard and muse on how extraordinary it is that the pieces follow any rules at all. If they moved randomly it might be psychologically comforting to "explain" their motions as occurring due to the actions of an intelligent player with designs of his own that remain mysterious to us. But the simplest explanation under those circumstances would simply be that the pieces are drifting around without any organizing principle accounting for their movements. The very lack of apparent purpose behind their movements could easily be taken to indicate the lack of an intelligence behind the game. Thus a rule-less chess game lends itself to both arguments: 1) that it must indicate that an intelligence with independent will (some cosmic rebel without a cause) is moving the pieces or 2) that the pieces move the way they do precisely because the chess game lacks any intelligent force driving it. This is the issue faced by a person living in the Abyss.
But a person living in an ordered universe with gaps--areas of incomplete knowledge of the laws that we trust can and will disappear as we learn more--faces the same problem. On the one hand, one can argue that things happen because they're obeying the laws. A chess game on autopilot doesn't require a chess player. But the mere existence of underlying rules can also be taken to indicate the existence of an intelligence somewhere in the process. If we take this interpretation, then the steady march of scientific progress merely vindicates faith because it demonstrates that something ("the laws of physics") is governing the universe. And that's a very curious fact. Why should a godless universe be governed by mathematically elegant rules?
Which way do we lean on this one? Sadly, the question is unresolvable. Is there an intelligence at work somewhere, is there not--the answer you prefer depends on your world view. The facts don't favor either one because what's at stake here is merely an interpretation of the facts. We know that the chessboard has rules. The question is whether that relieves us of the burden of having to worry about a deity or whether the chessboard is gesturing frantically in the direction of some chess-playing deity watching--or perhaps not watching--its game play out according to the rules it devised.
And therein lies the intellectual honesty of the agnostic position: fuck if I know.
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