You seem to have taken particular offense at my imputing self-deception and/or dishonesty to the faithful. I make no apologies for this. One of the greatest problems with religion is that it is built, to a remarkable degree, upon lies. Mommy claims to know that Granny went straight to heaven after she died. But Mommy doesn't actually know this. The truth is that, while Mommy may be rigorously honest on any other subject, in this instance she doesn't want to distinguish between what she really knows (i.e. what she has good reasons to believe) and 1) what she wants to be true, or 2) what will keep her children from grieving too much in Granny's absence. She is lying--either to herself or to her children--but we've all agreed not to talk about it. Rather than teach our children to grieve, we teach them to lie to themselves . . .
I believe I can offer an adequate response. It may not be adequate to you; but it is adequate to me, and to many, many others - in fact, to the vast majority of human beings who have ever lived. My response rests on an understanding of truth that is not exhausted by empiricism or materialism. I do not believe, in short, that all truth rests on scientific premises and can be 'proven' by empirical or scientific methods. I believe science is one, important, valuable and respectable mode of thinking about the whole. But there are truth questions it has not answered and cannot answer . . .
One thing I appreciate about atheists is how they force you to consider whether your faith is as silly as they make it seem, or whether it is based upon something more than just a fairy tale fancy. It is one thing to go out and do "apologetics" for the purpose of evangelism, sounding smart, or just saving face. It's another thing to ask, "Why do I believe?" privately and honestly within your own heart and mind.
Someday I will be lying on my death bed facing the great unknown beyond, if there is a great beyond. In that moment I will be alone with my faith, and none of the people I've wrapped my life around, whether family, friends or church, can help me through it. None of the things I've done to try to impress people with my knowledge or deeds or great Christian witness will count for anything once the finality of death draws near. The thought of death is a reality check for a Christian. And so are the criticisms of atheists who think that I've entrusted my soul (except that they don't believe in souls) to something akin to the Flying Spaghetti Monster.
I'm still trying to get caught up in reading the entire debate. If you want to read the whole thing, you can start from the beginning here.
Update: The morning I posted this I wrote to Andrew Sullivan and shared similar thoughts with him. On 1/27 he posted my email on his blog here.