The second issue is surprising since it seems, at first glance, so simple. Evolutionist and cat-lover Jerry Coyne has made the point several times recently that science can, indeed HAS, disproved supernatural claims. On the face of it this is obvious- open the Bible, read its account of the earth's creation, and then consider that in light of accumulated geologic and cosmological evidence about how our planet formed. Simple indeed. However, some (Pigliucci again!) maintain that the supernatural can not, by definition, be scientifically disproven or even interrogated. This seems only to be true if we ignore the history of supernatural and religious belief. Overall the vast majority of religious beliefs have been things subject to investigation; they have been physical phenomena that have been claimed to have occurred (such as God creating species directly in their present form) or alleged states of the world/human nature (such as that prayer will have an effect). Both of these are equally amenable to empirical investigation. We can looks at the facts gathered in paleontology and evolutionary biology and, using this evidence, falsify the religious claim that God woo-wooed whales into existence in their current form.
Pigliucci's walling off of scientific investigation from supernatural phenomena only works for the most arid deism. That's to say, it's a truism that the tools of rational investigation can't be brought to bear on phenomena that aren't even phenomena, that don't interact in any way with the material world. The moment they do, however, they are subject to investigation (and would presumably be in the Pigliuccian definition ipso facto NOT supernatural). But really, what is this religion that has no interaction or influence upon the world? When has any religious ideology like that existed? Even the desperate retreat of wanna-believers such as Karen Armstrong into a polite, ill-defined and ecumenical deity won't cut it: their God must poke his head up somewhere. Besides, that type of playing-it-safe deism is light years away from the religion of almost all believers today and especially when we consider what adherents and their churches have historically believed. The doctrines of Catholics, Protestants, Muslims, Jews, Hindus, etc have all contained specific claims of supernatural intervention in the material world. This has happened again and again in their history as knowledge structures. Most of these claims have been proven false, with two responses from the religions themselves. Some religions modified their knowledge structures to remove/abstract/coverup the falsified claims as the Catholic church has done in the case of its acceptance of evolution. It's no surprise this is often the response of larger, more powerful and thus more “materially invested” religions. The other approach was initially to legislate away the problem and forcefully maintain orthodoxy, but the erosion of religious power in many states has closed this option off. The result is “guerilla tactics”, trying to attack the scientific consensus and sow confusion about the status of the evidence itself that has overturned the previous claim (i.e. the Discovery Institute).
Whatever occurred, at the time each of these claims were made they certainly had the status, within doctrine, of being an example of supernatural influence in the world. When heliocentrism was going down in flames under the evidence brought to bear by various Copernicans, the church certainly acted as if the very truth of revealed doctrine was at stake. In other words, they saw the situation as the possible disproving of a supernatural claim!