Miracles and materialism
There are many ways in which we can say something is a "miracle". There are secular uses of the word - a miracle being something positive and extraordinary, or something that has tremendous emotional impact - which have no bearing on this discussion. Although people have very little understanding of probabilities and can come to believe that extraordinary events must have a greater explanation, we know that the improbable must happen to a lot of people every day, by simple mathematical necessity. Miracles in this sense are the expression of the extremes of natural law.
The theological meaning of "miracle", however, is of great interest to us. A miracle in this sense is commonly defined as an event which breaks natural law because it is created by God's will. For example, God can pop everything from nothing, send an avatar to Earth to be born of a virgin, or send magical plagues. These are all "miracles" because they are impossible from the materialist standpoint, and they are "acts of God".
Obviously the first problem with these events is that, as I said, they are impossible. As such, taking a page from Hume's playbook, we should reject testimonies of such events as being less likely than the possibility that, for example, all the testimonies are lies, fabrications, delusions, or honest but misguided recountings. In the same way, I would not believe someone who said he saw me at this or that place, when I was lying sleeping on my bed, unless I had very good reason to mistrust my memories in this case. But I would never believe, in any circumstance, that this person saw me come back from the dead and rocket into the sky, like "Jesus". I would dismiss any number of such testimonies as either lies, fabrications, delusions, or honest but misguided recountings of a mundane event (such as, perhaps, a cleverly-made hologram of myself). Likewise, I must reject out of hand the Christian stories of the universe popping from nothing, an avatar coming to Earth, or magical plagues, as mythical fabrications.
This is all well and good. But now look at the issue from a materialist perspective. For a miracle to be a miracle, it must be miraculous, that is to say, it must break natural law. And natural law is the result of materialist causation. So the definition of a miracle itself implies that materialism is true ! For it includes both material causation and its "break" for a specific event. If there is no material causation, then the concept of miracle is meaningless.
Let me make this point as clear as possible, as some believers have invoked the notion of "regularity" to try to explain this problem away. The argument goes like this : if there are no "natural laws" but merely "regularities", then there would be no problem with miracles.
But this is mind-numbingly absurd. Consider that natural laws exist because of the law of causality - things change in accordance with their nature. If there are no natural laws, then there is no more causality, and everything is basically random.
Now, take the law of gravity. We know the law of gravity reflects a fact about mass. Things always fall down when we thrown them up, at least on Earth, because of the Earth's gravity field, and proportionally to that field. We can measure it easily. Now, if there is no more causality, only a regularity, we are supposed to believe that the Earth randomly generates a gravity field that is somehow always exactly proportional to its mass. This is the equivalent of rolling a million dice, and rolling a specific, pre-determined distribution of numbers. Then doing it again, and again, and again, and again...
The idea that regularities in nature are merely regularities and not the product of natural law is so absurdly improbable that it merits no examination beyond realizing how absurd it is.
So it turns out that the concept of miracles implies atheism. And since natural law is how we understand reality, this also brings up the question of how we could possibly know that a miracle is happening. For one thing, it would require us to be omniscient and know that natural law is not operating, which is impossible. At best we can say that an event breaks natural law "as far as we know it". But that's not nearly enough.
Finally, as TANG proved, the notion of miracles contradicts the operation and validity of science, most notably in cosmology and biology. Given the tremendous success of science, any position that contradicts it would seem to be very unwise indeed.
There is also an alternate position on miracles that is sometimes used, and that is the exact opposite - that God acts in the universe through natural law. This is more commonly used by the ignorant believers, to say for instance that natural disasters are God's way of expressing its anger, and so on. However, from an ontological standpoint, we can easily see that such a position is completely contradictory. If divine intervention is expressed as natural law, and natural law is a materialist process, then it cannot possibly be "divine". At best, the believer is saying absolutely nothing when he says the event is the product of divine intervention, as adding this label adds no meaning to the explanation, unless one wants to contend that God is very, very material, and is made of tectonic plates or low pressure zones. Ultimately, adding the "God" label to anything cannot possibly be justified, and cannot possibly be meaningful, regardless of one's belief system.