The question of can science explain miracles is not an effort to explain them away by providing a naturalistic explanation. Rather, in this case, it is dealing with the question of how they might actually happen. That is a completely different question, and one that is often not asked. In fact, the most common argument against miracles refers to them as magic. What we are exploring here is how science can offer a potential mechanism that allows miracles to occur.
If all we had in physics was classical physics with its totally mechanistic nature, calling miracles magic would tend to make sense. After all they would require somehow breaking this mechanistic nature of reality. However, classical mechanics is not all that we have; we also have quantum mechanics, which changes the picture of reality completely. It does so by ending the idea of a purely mechanistic and materialistic nature behind reality.
One of the things that quantum mechanics ultimately does is end the idea of a purely mechanistic reality. This at once ends mechanistic arguments against both the idea of free will and miracles. In fact, once the idea that our reality is fundamentally an information system, as suggested by quantum mechanics, is considered, the mechanism by which miracles can occur clearly presents itself.
This mechanism is simply an act of God changing the information in the system, altering what is happening. In other words, a miracle ends up being a change in the information behind our reality that changes that reality. With God as the programmer and operator of the system, it is perfectly reasonable to expect that he would be able to make changes in it when he wants to. Such changes, from our perspective, would be miracles because they do not operate according to the regular laws of nature.
There are likely to be those that object to any contemplation of how miracles work after all in their thinking doing so might diminish God’s power in their minds. However, it is logical to consider that miracles would have some form of mechanism behind them. Figuring out the basic process does not diminish God's power or majesty one single bit; after all, it does not mean that we could ever fully understand or manipulate the system ourselves.
This approach has the advantage that it does answer the big objection frequently touted by atheists, that God is nothing but a magical sky daddy. This is because it clearly indicates that miracles are not magic but temporary alterations in the programming necessary for the universe to operate on a regular basis as it does. Miracles are simply cases where God temporarily intervenes in the regular operation for a particular purpose.
In conclusion, quantum mechanics does provide a possible way of explaining the way that miracles work. It does so by changing the process from magic to programming. This does not diminish the power and majesty of God at all; it simply provides a glimpse at how the process works. This glimpse is on a relatively simple level, but it provides a way the miracle can be scientifically understood to operate.
