In my previous post, I introduced this topic and gave a very simple example why He would violate the laws of physics. In addition to that, we know that God did intervene in certain circumstances. For example, He intervened at the beginning of time. He intervened at the incarnation. Jesus (and the old testament prophets before Him) performed many miracles. I don't find this to be a good answer to Ken Miller's question, however, as God had specific purposes in history to perform miracles, and these acts of divine intervention were well-documented in the Bible. Thus, it does not answer generally about the history of the universe.
My next comment is that, in a way, I sympathize with Ken Miller and Francis Collins and other theistic evolutionists on on this point. When creationists argue that God must have intervened in specially creating life, including humans on the sixth day of creation, I wonder how that would be different from a special creation of the moon. We think we know in pretty good detail how the moon was formed, from a mechanistic, laws-of-physics standpoint. However, the fact that it happened is essentially a miracle. If the moon didn't exist in a very finely-tuned fashion, neither would we. In other words, if the moon hadn't formed in just the right way from just the right materials at just the right time in just the right place with just the right mass, advanced life would not have been possible on this planet. (I can't go into the details, as I do not know them. However, take my word for it that the formation of the moon is generally accepted to be a finely-tuned event, even among atheistic scientists. Also, I found a cool movie here about this, narrated by Captain Jean Luc Picard.) The chance that the moon would form in just this way is so small as to be essentially zero. But it can be explained in a very simple way: a Mars-sized body revolving around the sun about 4.4 billion years ago at the same revolution radius as the earth was suddenly kicked out of its stable orbit. It slowly got closer and closer to the earth until the two bodies collided at a low relative velocity and at a highly oblique angle. The laws of physics can completely explain it. But they do not explain why such an event, which must have been so finely-tuned, would have happened.
Applying this to life's history, Darwinian evolution is certainly a plausible mechanism to explain life's history, given the concession that life evolving this way (i.e., in just the right way to produce us) is extremely unlikely. However, I don't see anything in direct contradiction of the laws of physics, barring a second law of thermodynamics hand-waving argument. In other words, it isn't absurd to imagine that God supernaturally superintended each of life's events such that evolution according to the natural laws would occur just as He would have it. In the same way that it isn't absurd to imagine that God supernaturally superintended the formation of the moon just as He would have it such that we could later exist. He guided an extremely unlikely set of events to get us in the end. Did He do this by setting it up from the beginning and forgetting it (like a roticerie chicken machine)? Or did He have to perform "midcourse corrections'" such as NASA ground control often must do? And what do we care?
So, this discussion leads us logically to a point that I have discussed many times, about how all theistic evolutionists should also be proponents of intelligent design, and I won't repeat them here.