I think Andrew Sullivan puts it quite well here, in his response to Sam Harris.
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. What I found insightful about your book was your openness to this possibility. You repeat that openness in your recent posting:
"While I spend a fair amount of time thinking about the brain (as I am finishing my doctorate in neuroscience), I do not think that the utter reducibility of consciousness to matter has been established. It may be that the very concepts of mind and matter are fundamentally misleading us."
So you allow for a space where the logic of science and of materialism does not lead us toward truth, but may even mislead us about it, and lead us away from it. This is a big concession, and it undermines the certainty of your entire case. Such an argument must rest on a notion of ultimate truth that is deeper than science, beyond science. It must rest on a notion that allows for the rational legitimacy of my faith.
It might even include an appreciation of other modes of rational discourse that are not empirical in origin or form. Take, for example, the question of historical truth. You rely in your books on a lot of historical facts to buttress your empirical case. But these facts are not true - and could never be proven true - by the scientific method that is your benchmark. There are no control groups in history. There are no experiments. But there is a form of truth. Discovering that historical truth is the vocation of a historian - and it is a different truth than science, and reached by a different methodology and logic.
Similarly, mathematics can achieve a proof that has no interaction with the physical world. It may even be the closest to divine truth that human beings can achieve. But it is still logically separate from empirically verified truth, from historical truth, and even from the realm of human consciousness that includes aesthetic truth, the truths we find in contemplation of art or of nature.
But that is not the sum of your argument. You argue further that even if you concede the possibility of a legitimate form of religious truth-seeking, the content of various, competing revelations renders them dangerous. They are dangerous because they logically contradict each other. And since their claims are the most profound that we can imagine, human beings will often be compelled to fight for them. For if these profound matters are not worth fighting for, what is?
I agree that this is a central problem for religion in the world. It has always been so. it will always be so. This is not a new problem. It is arguably the oldest human debate. Whether one reads Pascal or Spinoza, Locke or Montaigne, Hobbes or Leo Strauss, the religious question always prompts a political question. I think the problem is eased - if never fully solved - by a critical move that I unpack in my book, "The Conservative Soul." That move is rooted in skepticism.
In my book, excerpted in Time Magazine here, I put it this way:
If God really is God, then God must, by definition, surpass our human understanding. Not entirely. We have Scripture; we have reason; we have religious authority; we have our own spiritual experiences of the divine. But there is still something we will never grasp, something we can never know - because God is beyond our human categories. And if God is beyond our categories, then God cannot be captured for certain. We cannot know with the kind of surety that allows us to proclaim truth with a capital T. There will always be something that eludes us. If there weren't, it would not be God.
I don't think you're far away from this. That's why you've gone on retreats, explored Buddhism, experimented with psyclocybin, as I have. You see: we are closer than you might think. But you differ with me on how this translates into life. You ask legitimately: how can I, convinced of this truth, resist imposing it on others? The answer is: humility and doubt. I may believe these things, but I am aware that others may not; and I respect their own existential decision to believe something else. I respect their decision because I respect my own, and realize it is indescribable to those who have not directly experienced it. That's why I am such a dogged defender of pluralism and secularism - because I believe secularism alone does justice to the profundity of the claims of religion. The attempt to force or even rig laws to encourage others to share my faith defeats the point of my faith - which is that it is both freely chosen and definitionally dealing with matters that cannot be subject to common consensus.