In reply to my comment about YEC and MN, Ted Davis, a Senior Fellow for the History of Science for the BioLogos Foundation and Professor of the History of Science at Messiah College, offered his own thoughts in the comment section of his thread, which I thought were worth repeating:
"Re #1: If one accepts methodological naturalism (MN), then (as you say) one might be faced with data that cannot presently be “explained” fully—not a novel situation in any science. It seems to me that we identify at least 4 possible approaches to MN, in general.
(a) ALL events have “natural” explanations, whether or not we can produce them now, based on our limited knowledge. It is *never* legitimate to invoke “supernatural” agency. We might perhaps call this the strong form of MN; it’s not held provisionally and not open to supernatural agency in any way.
(b) A weaker form of MN: we should always do the best we can to find a “natural” explanation, since we know from experience that “natural” explanations almost always work well to explain events. Science must confine itself to such explanations, but we cannot rule out the possibility that certain events simply do not have scientific explanations.
(c) A strong rejection of MN: MN is appropriate for the experimental sciences, but absolutely inadmissible in the historical sciences. The Bible tells us what God actually did, and we must interpret all data in light of this.
(d) A weaker rejection of MN: MN is generally valid, even in the historical sciences, but it must not be used arbitrarily to rule out design; it must allow the possibility that an intelligent cause (whether acting “naturally” or “supernaturally”) is a necessary part of the complete explanation of the data."
Naturally, I think (d) is the most reasonable approach.