If you've ever been involved in, or witnessed a debate between a theist and an atheist on the issue of God's existence, you may have encountered the 'God of the Gaps' argument. The argument usually takes the form of this:
1. Ancient peoples often attributed explanations of physical phenomena to direct interactions by God or gods. i.e. Rainbows occur because the god of rainbows shoot them out of his belly
2. As scientific knowledge increases explanations for the mechanisms behind these physical phenomena are discovered. i.e. rainbows occur due to refraction of the light spectrum when passing through water molecules (or something like that)
3. God's explanatory role is diminished, and his existence becomes progressively less likely. God retreats into gaps of understanding, once the gaps are filled, he is forced to retreat further and further.
Sam Harris is a popular atheist who often make this argument (his professional atheist contemporaries don't make it nearly as often as he does). Stressing the strengths of modernity, and the idea that religion is a 'failed science'.
The key problem with this argument is right in the title. "God of the gaps". Clearly, if we look at the argument in the form presented God himself does not have a diminished role, God himself is not forced to retreat, God himself is completely unaffected by the increase in information. If God exists, then he exists in exactly the same form that he did prior to the increase in information. If God does not exist, then he didn't exist prior to the increase in information and still doesn't.
The only thing that is affected by the increased information is people's perception of God (or gods) and how He interacts with his creation. Clearly these advances in knowledge and understanding have the capacity to falsify a particular belief about the specific manner in which God behaves. Clearly God doesn't shoot Rainbows out of his belly. Clearly God doesn't physically grasp the 'edge' of the Earth and shake it to cause an Earthquake. So any person who believed these things, was wrong, and their false conception of God's nature is forced to retreat.
Also notice that the argument does nothing to decrease the likelihood that God is ultimately behind, and ultimately responsible for any particular physical phenomena. If the ancient person said 'God created rainbows' rather than 'God makes rainbows BY shooting them out of his belly', then the ancient person is just as likely to be correct once we understand the physical mechanisms involved in making rainbows as he was before we did. God is still just as likely to have created rainbows (or created the mechanisms that cause rainbows) before and after our increase in understanding. The likelihood that he exists, and the likelihood that he created rainbows, is exactly the same before and after. The only thing that is falsified are claims that God created rainbows using some specific methodology that has been shown to be false.
That pretty much completely neutralizes the argument. The argument is more appropriately titled "people's-conception-of-God-of-the-gaps". And yes, admittedly, as the limited beings that we are, our conception of God and how he works is always changing, always incomplete, and often flat out wrong. This is not evidence against his existence, however. Merely evidence of our own shortcomings.