Since they fail to move the burden of proof for the god claim, they try to move onto what they deem to be a valid target. This target is naturalism.
I am not going to go into a detailed explanation of what naturalism means, but in a nutshell it means that all things are natural, and there is no spiritual realm. In other words there are probably no ghosts, gods, demons or souls, unless those things are made of stuff. So there are essentially no immaterial things. I am not going to spend hours in metaphysical mental masturbation on this topic, because apologists love this. Essentially it distracts their opponents from the total lack of support they have for their position.
The theist will assert that we need evidence that the natural world is all there is. For example, the arguments usually rely on some of the following things which they might ask. Without answers for these questions, they assert that you must conclude a supernatural realm. Let's look at the questions briefly. Of course each question can be discussed at length, but I am interested in the common theme of all the following:
1. How did the universe start? How did something come from nothing?
2. How did life evolve from non-life?
3. How does consciousness arise from neurobiological processes. The so called hard problem. ( Chalmers)
4. How did rationality arise from non-rational processes?
5. How can we rely on logic in a naturalistic universe? Premises are all stacked and initial premises are not justified.
Without answers to these questions, it is apparently totally okay to conclude that an omnipotent deity did those things or in the case of 2) that our souls do it. There are three generalised problems with all these arguments. They are the same problems as before, so nobody will be surprised if they are familiar with biblical apologetics or indeed the rationalisations of any common believer.
1. Shifting the burden of proofThere is no evidence that there is a god. There is no evidence that there is not a god. We must accept tentatively that there is no god, because if we change the rules then any proposition, no matter how ridiculous, can be considered. In other words if we say that it is okay to believe something that we just asserted without any proof then we are basically opening the floodgates to any hooey, including things like astral traveling, dowsing, and alien abductions.
Why the burden of proof? Isn't this different from the god claim? Well it isn't. It is just renaming things to dress the argument up a little differently, and since some of the questions above are interesting, to the inquisitive mind it could be fun to try and think about these things and the theist just sits back and watches. The truth is though is this:
1. We know the natural world exists because we live in it
2. We have never found any supernatural phenomena
Naturalism is the default position. If a naturalist asserts that there is no supernatural it may be different. It's the same as the god claim. If you are open to good evidence for the supernatural that is all that matters. It is the responsibility of the supernaturalist to prove that this unseen realm exists.
2. God/soul of the gapsBelieving any bullshit you feel like coming up with until someone proves it wrong is not only stupid, it makes you look stupid when the actual answers are found and it closes your mind to finding the real answers. People who believed that the solar system was geocentric were hell bent on resisting the heliocentric model. Today we laugh at the idiots who held on to the stupid orthodoxy. It is pretty simple, there is no reason to just believe something when there is no evidence.
The intellectually honest position is "I don't know". Theists can always move the supernatural realm back a little as science moves on (they did this when the sublunary model was disproven and the planets were found to be natural). So you can never "prove" naturalism to them anyway, because they have set a standard of evidence that they will change at will anyway.
For instance despite showing a large amount of evidence to a theist that the mind correlates one to one with brain states, he still refused to believe that the mind could be caused by the brain. Drawing on all my knowledge of psychology and the little bit of neurobiology I know did not help. The goal posts just keep getting moved.
3. Personal incredulity"I just can't see how all of this could have come from evolution/big bang/abiogenesis". The world is a little different when you can't just plug the holes of your understanding with god everywhere and claim to have the absolute truth. Christians even spell truth with a capital T, emphasizing how utterly sure they are. It's not hard to imagine that everything could have come to be naturally. It is not hard to imagine for me that our minds are the products of our brains, and that everything we consider subjective experience is just a sum of the experiences of different mind subsystems. The theist just claims that there is no way, therefore it did not happen.
The whole situation is very unfortunate. You cannot change someone's mind if they are that willfully resistant. You can just point out that their mode of thinking is poor. One thing that holds true that I have learned is that "humans are not a rational species, humans are a rationalizing species" (I read that somewhere). That means that someone will devote a considerable amount of time to rationalize a strong belief instead of spending time trying to disprove that belief. I spend a lot of time reading apologetics blogs and they are terrible just so I can be sure that I give the other side a chance.
Essentially they are reduced to attacking scientific epistemology, because that is what sceptical atheists use to figure out which beliefs are reasonable, and at the same time they have to pretend like they still respect science. When I read apologetics, I always try to replace their proofs for god with other conclusions. Their proofs work equally well for things like solipsism in some cases, or aliens creating us in some other scenarios. If multiple alternative conclusions can be drawn and you cannot produce positive evidence for yours, then sadly there is no good reason to hold your position.