Following up on the quotation I gave below from Balfour, I want to address here a poor argument for dismissing apparent evidence against naturalism. It is surprising how many smart people think, or if they are not naturalists at least worry, that there is something to this argument. Here are a couple of versions of it:
Most problems which were unexplained by science in purely naturalistic terms have now been explained by science in purely naturalistic terms. So, by direct induction, any alleged evidence against naturalism has a scientific explanation in purely naturalistic terms.
Science has made and continues to make such great progress throughout history, gradually whittling away at the set of things that were previously not scientifically understood, that whatever it is that you are presently bringing forth as evidence against naturalism, I am sure that science will eventually get to that in time and explain it, as well, as entirely the product of natural causes.
There are so many things wrong with this argument that I don't know if I can fit them all into one post, but I'll make a good start, anyway.
First, notice the implication of the argument that there is some set or list of all the things that were previously (when previously?) not explained by purely natural causes and that physical science has now answered "most" of such questions, leading us reasonably to expect that it will eventually "get to" all the members of the set. Is this even remotely plausible? Let's consider a group of items not "previously" explained or well-understood scientifically and/or in terms of purely natural causes:
--How do the heavenly bodies revolve?
--Where did the mind come from?
--What is the cause of beriberi?
--Why did Napoleon try to conquer Europe?
--Why did that lump of sodium explode in water?
--What is the cause of malaria?
--How does biological inheritance of physical traits work?
--Why does your wife love you?
--Why were the disciples willing to die for the claim that Jesus rose from the dead?
--What is the cause of the spots on the moon?
--Where did the universe come from in the first place?
You get the picture. We could go on pretty much forever, listing things that were not "previously" well-understood in terms of purely natural causes. In some cases, an attempted natural explanation was given, and we now have a better one. In other cases, the phenomenon was understood to be a natural phenomenon, but the detailed cause was simply unknown. But it would be folly to say that everything on the above list fits into some natural kind, some single list of all the things science didn't used to be able to explain naturalistically, and that we have now crossed off more than half of the things on the list. Far from it. One has only to formulate the matter in these terms to see how wrong-headed such a notion is. Of course there are problems of level of specificity and of how to count, but even if we could solve those we could easily generate a list of "things" (of some sort or another) that were not previously well-explained by purely natural causes, most of which are still not well-explained by purely natural causes.
It is highly controversial to claim, for example, that most questions regarding the mind, thought, human motivations, and so forth, can now be crossed off any such list. The naturalist might try to say that they can be, but he will hardly get his opponent to agree with him on that, whereas the opponent will grant without the slightest hesitation that the causes of planetary motion are now well-understood in purely physical terms--at least proximately and so long as we don't take our questioning back to the beginning of the universe! So there is no non-question-begging way to generate such a list and to show the non-naturalist the ongoing and triumphant March of Science eating away at it and leaving only a few little remaining dark corners to be swept out eventually.
This point is closely related to the fact that science quite rightly tackles those problems that are tractable. Scientists--sane ones, anyway--don't tackle, "Why doesn't Jenny love me?" as a scientific problem, and for good reason. Progress in science there has been, but that is precisely progress in those areas where science has the best hope of making progress. (I owe these first two points to Esteemed Husband.)
So let's try a third version:
There used to be a great many things that were believed to be the result of non-natural causes but which we now know to be the result of purely natural causes. Therefore, this (whatever it is) that you are bringing up is probably also the result of purely natural causes, even though we can't right now see how.
Hmmm. Well, let's start with that passive construction "were believed." Were believed by whom? If we are going to count people's believing that fairies are responsible for rings in the grass, then I'm going to start talking about all the people nowadays who believe in Pyramid Power. And I'm going to say, "So a lot of people believe a lot of weird and stupid things. And tell me again exactly why this means I should believe that the mind is a purely natural phenomenon or that the disciples hallucinated Jesus' appearances, because I'm not seeing it." After all, I have presumably given some thought myself to the reasons for believing that the mind of man is not a purely natural phenomenon or that Jesus rose from the dead. And I would presumably not classify my reasoning with the "reasoning," if it can be called that, of people who believe in fairy rings. So this argument isn't likely to move me while I'm looking at the actual evidence.
I guess then that we have to change it to "were believed by the best-educated and most careful people of their day to be the result..." Now, right away, we have a problem with this, which is that as an historical statement, it appears to be false. There just is no long list of phenomena in the past that were definitely, by well-educated and careful people, believed to be miracles or in any recognizable sense non-natural phenomena and which are now known to be natural phenomena. Maybe epilepsy was believed to be the result of demon possession. But in all cases? And that's one example, at most. We should remember that even the casting of horoscopes and the study of alchemy were thought of as involving the understanding of the natural world. If someone had discovered the Philosopher's Stone, he would have been a rich man because of the properties of the Philosopher's Stone, not because of, say, angels. So those go in the list of "false beliefs about physical causes which have been replaced by true beliefs about physical causes," which no matter how you slice it do not confirm naturalism over non-naturalism.
And finally, again, any such meta-inductive argument simply encourages us to ignore whatever actual data or arguments we might have about the particular thing at issue. It is simply sloppy to dismiss, say, the argument from mind on the grounds that, hey, I'm an educated person, I'm inclined to believe that the mind did not originate by purely natural causes, but a lot of other educated people have been wrong about vaguely similar things.
The argument's the thing. Everything else is merely an attempt to avoid and evade the argument.
Something like this inductive naturalist/Grand March of Progress argument has been getting way too much currency for way too long. The time has come to laugh it off the stage once and for all.