A lot of of events, like lightning and the origin of species, were once mysterious magic tricks, but now have been fully explained by naturalism.

Minor nitpick, but neither of those phenomena is fully explainable by naturalism yet. Last I checked there was still a good deal of debate about the rate at which evolution occurs and how gradual it is, and no physicist I've talked to is sure why lightning generates antimatter

Perhaps a better example would be something better-understood, like rain or magnetism.

EDIT: I found an unrelated, but nonetheless cool article about stimulating lightning