I want to address some problems that various people have brought up about philosophical naturalism:
1. If you believe that your brain is just chemicals, then you can't trust your thoughts.
Well, if our brains are more than chemicals, can a schizo trust his/her thoughts? On a serious note, our brains have evolved over millions of years to accomplish two primary purposes:
I enjoy both, so I'm gonna trust my thoughts. Besides, even though I make mistakes, the majority of my decisions are good ones. I can trust my brain.
2. How can you be moral without God?
Well, let's ask the theist: Why is God moral? I suspect that most would say he just is. Same for me. I simply am moral.
3. The Universe had a beginning, therefore the universe had a cause (God).
There are a number of problems with this argument that have been addressed by many different people. One thing that must said is that the universe could be a part of a large multiverse. Lee Smolin has constructed a hypothesis that the universe was born from the black hole of another, born from the black hole of another, and so on for eternity. The theist will then argue that actual infinites are impossible. Of course, this would disprove an infinite God, but I'll roll with it. The argument to disprove actual infinites goes something like this:
If you had an infinite number of marbles, and gave every odd numbered marble to a friend, you would have an infinite number and so would he. On the other hand, if you gave him every marble with a number divisible by sixteen, you would have an infinite number and so would he. These conclusions are simply irrational, therefore truly infinite things cannot exist.
This is true, but of course why should infinite numbers behave the same as finite ones?