Daniel:
You make some good points.
Regarding your physics examples, I think we have to bear in mind context.
I don’t think the “yet” in your physics examples, given the context in which such things are usually said (especially the second one), has any obvious bearing on the MN/PN distinction regarding origins. In the second example, which clearly has nothing to do with origins, the “yet” may merely indicate a hopefulness about technical progress, rather than rigid prediction. I grant that “yet” can be used in that looser way.
But when we are talking about origins, there is powerful social context (Scopes trial, Hume on miracles, Huxley vs. Wilberforce, fundamentalism, YEC, etc.); most people who participate in American origins debates think and speak from within that context, and have it in mind when they make claims.
So if someone says, “Science has not yet established how life began”, given the context (that a large number of Americans do not believe that a scientific answer to the origin of life will be or can be found, and that scientifically educated people in America often think of themselves as above the religious nonsense of the rabble), there is a good chance that the speaker is tacitly rejecting the possibility that the first life could have been created miraculously; there is a very good chance that the speaker is endorsing not just methodological but philosophical naturalism.
If the speaker wanted to guard against this inference, he could have left out the “yet”, or said, “We (not “science”) do not know whether life began miraculously or through natural causes, and if the latter, what were the natural causes.”
In short, my argument about the use of “yet” is not entirely based on a strict construal of the word by itself, but is connected with context, with knowledge of alternatives regarding origins that are likely in the minds of speakers and hearers.
But setting aside this point, let’s look at your point about the Gospel stories. Yes, they treat the events as miraculous, as signs of Jesus’s power and mission, etc. Yet if we want to be precise, the Gospels don’t use Greek words for “nature” or “natural order”, and while the events are certainly portrayed as marvelous, they aren’t explicitly said to be violations of any rigid causal nexus (as opposed to being just darned unusual). That sort of Humean language (miracles are things that break natural laws) comes much later.
And if we put ourselves back into the Biblical frame of mind, and abandon our instinctive urge to try to make Genesis not conflict with modern science, it appears to me very likely that the Jews of Jesus’ day would have regarded God’s actions in the Genesis creation story as special deeds of extraordinary power, much like the deeds done by Jesus. It’s true that Genesis does not explicitly say that God’s actions violate any natural laws; but then, neither do the Gospels say that Jesus’s actions violate any natural laws. In both cases you have mighty deeds of God which show God’s mastery over his creation.
I think the typical Jew of Jesus’s day would be very surprised by an exegesis of Genesis which said, “God didn’t really do any of those things in the creation story directly; rather, he equipped nature with the natural powers to evolve stars, planets, life, and man by itself, with him remaining in the background “sustaining” all that natural activity, but not intervening or breaking any of the laws he created.” I think most of them would have trouble even understanding the language of such a claim. I think their “explanation” of what Jesus did in Galilee, and what God did in creation, would be much the same, and whether terms like “miracle” or “natural laws” are used in either case is beside the point.
Regarding your other points, yes, I grant that some miracles might be miracles of timing that don’t break any natural laws, but I think there are too many cases in the Biblical stories where there is clearly more than fortunate timing involved for that to be very useful as a general explanation. And yes, if we use a non-Humean, Biblical meaning of miracle as “wondrous event” or the like, it is not necessary to insist that miracles can have no scientific explanation, but again, I think that over-eagerness to find scientific explanations for Biblical miracles is suspect, because it springs from modern sensibilities which the Biblical writers and their audience didn’t share.
I’ve seen some of the extremely complex and rather forced attempts to explain the Red Sea episode solely in terms of geological and meteorological phenomena, and they don’t ring true, when all the details of the Biblical story are taken into account. Yes, God uses a wind, but no merely natural wind could account for all the details of what happened to the waters in the story. And given that this episode follows just after the Ten Plagues, to be consistent one would try to find purely natural causes for all ten of the plagues, and while some of them might be explicable in natural terms, it seems unlikely that all of them can be. Or the rods turning to snakes.
Similarly, I’ve seen it claimed that Jesus could walk on the sea because of a very rare weather condition which can create a thin sheet of invisible ice on a lake, but that seems a desperate attempt to avoid concluding that Jesus violated what we now call natural laws, and I don’t find such inventions, no matter how ingenious, to be convincing or in the spirit of the text.