The author’s argument in the third chapter is that the laws of classical mechanics only operate in a closed system, and because science does not claim the universe is a closed system, divine intervention is not a violation of those laws.
It must first be said that there is no point in defining a system unless you can specify the boundaries of that system. If modern science does not define the universe as a closed system it is because we know that the boundary is not fixed; the universe is expanding at a great rate. This is entirely different from an otherwise closed universe that is merely able to opened by god at his whim.
Truthfully, though, Plantinga makes no attempt to define system boundaries, for either the universe or god. It’s as if the concept of an open system means that energy and mass can intrude from just about anywhere, which isn’t the case. Left unanswered is how god would interact with the system of our universe. Why would god want to intervene? What if god doesn’t want to intervene? What if there is no god? Why assume that the god-system is in close enough proximity to our system to affect us?
Certainly no evidence is given to show where it has been observed that a transfer of mass or energy from outside our universe has made any difference, on earth, or within the solar system, or in the Milky Way, or in the next galaxy over. Where’s the evidence?
The universe is open as a matter of its expansion, but the boundary is understood, and any energy and matter coming into being or being destroyed as the universe expands will only have local effects, 45 billion light years away. I suppose it is possible that an occurrence at this boundary right now could affect us in 45 billion years. Perhaps god is timing energy and matter transfers 45 billion years in advance to affect earth, but we don’t see evidence of that.
Keep in mind that if god was intervening in the process of evolution, every intervention would have to be a miracle; if it wasn’t, it could be explained by natural laws. So Plantinga paints a picture of god allowing evolution to take place and then working miracle after miracle after miracle to get it the way it ought to be. Wouldn’t it be easier and more logical to just create it all in a week, like a literal reading of Genesis 1 would give us?
I should also point out that just because people hold on to religion and science, it does not follow that they can be harmonized. It is likely many such people compartmentalize, perhaps with the aid of the NOMA principle.