Across the world, religion is at the root of violent confrontations. Here at home, religious dogma threatens vital stem-cell research and the teaching of evolution in schools.

A new wave of atheists --- including biologist Richard Dawkins and philosopher Daniel Dennett --- has emerged to champion rationalism. Leading the charge, in books and lectures, is Sam Harris.

Harris, who is pursuing a doctorate in neuroscience ("when," he says, "I can step away from my day job as an infidel") is putting a fresh, positive face on atheism. His first book, "The End of Faith," has reclaimed a spot on the New York Times' paperback best-seller list, while his new book, "Letter to a Christian Nation," is on the hardcover Top 10.

In contrast to screaming television antagonists, Harris is disarmingly polite as he lays out his case. He's so reasonable that on Fox News, Bill O'Reilly ends an interview with him by instructing viewers: "Buy the book."

If they do, they will find a clear, concise, and logical argument --- and it may clash with everything they hold sacred.

Scrutinizing the Bible or the Koran, Harris doesn't pull punches. He believes we can do a lot better than to live our lives according to the wisdom of men who thought the world was flat. And he doesn't gloss over the violent passages of either book.

Harris believes we waste a great deal of human energy on what he believes issupernatural nonsense. Beyond that, he warns, in an age of chemical weapons and suicide bombers, blind adherence to ancient mythologies could bring the end of civilization.

He finds "elements of reasonableness" in the Bush administration's "war on terror," and while he has harsh criticism of the president, he says that liberals need to recognize the danger posed by Muslim extremists.

In a recent interview, Harris discussed all that. The following is an edited version of our conversation.

City: How does your study of neuroscience inform your views about religion?

Harris: If you want to understand the human mind, you have to know something about the brain. There's no question that religion emerges from deeply ingrained cognitive traits: a desire to understand our circumstance, a desire to predict the future and to have our belief order our experience in a way that is useful and confers emotional, behavioral, and ultimately adaptive advantages for the species.

There is clearly an evolutionary explanation for the tools we have cognitively, and this is being studied at the level of the brain. You could certainly argue in evolutionary terms that religion has served an important purpose, if not for ourselves in the immediate past, for our distant ancestors. It probably allowed large groups of people, larger than kin, to cohere. It does not seem far-fetched to say that any group tightly bound by its religious dogmas would have had advantages over groups that were not.

But you can't move from an evolutionary explanation like that to argue that religion is useful now. In fact, I think it's one of the principal impediments to developing a genuinely sustainable global civilization at this point.

What do you hope to accomplish with your new book?

I think it's worth focusing on our indigenous problem of right-wing Christianity. I couldn't let Islam go unmentioned, and my criticism is against religious faith in principle, but I think some emphasis on the problems posed by the political empowerment of the religious right in our country is definitely warranted. It also reflects the response I got to "The End of Faith." It was not a surprise that most of the criticism I got was from rather committed Christians.

You point out that everyone is already an atheist in one way or another; no one believes in Poseidon anymore. Do all Christians understand this?

Amazingly, they don't. It strikes them as utterly preposterous that anyone could compare the God of Abraham to a dead god of Greece or Rome or any other god. What seems an apt, accurate, and devastating analogy to secular people seems like a non sequitur to Christians. It's also strange that I now get hate mail from people who actually believe in Poseidon.

Christians think there's something about the Christian tradition and the contents of the Bible that puts the God of Abraham on a completely different footing epistemologically. It's a sign that it's very difficult to see your circumstance with fresh eyes when you've been taught from the moment you acquired language that the word "god" means something robust, intelligible, and beyond criticism and these other words are names of mythical figures.

For many people, the tsunami, Hurricane Katrina --- not to mention the Holocaust --- raise the question of what difference God makes.

In terms of the obvious examples of God's failure to protect good human beings, moderates basically respond that they would never expect God to make decisions of that scale. They don't have an interventionist God in mind. Then they resort to notions of mystery and the inscrutability of God's will. It's almost a kind of agnosticism.

Fundamentalists bite the bullet and tell you why they think God is angry and victimizing these specific people. Occasionally they'll resort to notions of God's inscrutability when the evil being done is so patently at odds with the notion of a benign and omnipotent God.

When you talk about little girls getting crushed by farm equipment, they tend not to say God is punishing us for supporting gay marriage and abortion. Even they are somewhat chastised by how ludicrous it is to suppose that a good God was overseeing accidents of that sort. It's odd. It seems to me to be utter disproof of the notion of an omnipotent, loving, and moral God.

The standard line is that religious extremists cause problems. You believe religious moderates are also problematic. Why?

Religious moderates insist that we respect people's religious beliefs no matter how unreasonable and divisive they are. We respect this basic claim that it's legitimate to organize your life around the contents of a single book. This mode of discourse gives immense cover to fundamentalists.

We really can't call a spade a spade when it's religious dogma getting people killed, because moderates want their faith claims off the table of criticism. And they also want raising their children to believe they are Christians, Muslims, or Jews to remain off the table. The other problem is, by virtue of being moderates, they don't understand the degree to which fundamentalists and extremists are moved by their theology.

They don't take their theology seriously; therefore they're rather perversely the least able to understand that people really do fly planes into buildings because they think they're going to paradise. People really do live in the Christian West with this expectation that Jesus is going to come down and Rapture them and their families into the sky in a few years.

I know many good people who say religion gives structure to their lives and links them to generations past.

We can get our structure without pretending to know things we don't know. If false certainty were a good principle of structuring one's life, it would take five minutes to conjure a religion better than Christianity or Islam in terms of structuring lives and creating happy, non-neurotic, peaceful people. You could simply take the best things from these religions and jettison the rest. You'd have a better dogmatism to live by, but it wouldn't suggest that this dogmatism were true.

What if a religion said: "Treat everyone well, don't lie, raise your children to excel in science and mathematics and if you don't do that, you're going to be tortured for eternity by a green-headed demon"? This would be a benign religion to spread when you compare it to the jihadist lunacy that goes on under the name of Islam or many of these end-time beliefs that animate Christianity at the moment.

This would be a good religion, yet it wouldn't lend the slightest bit of credence to the claim that there's a demon who's going to enforce its precepts. People would recognize that immediately. It's based on this false notion that you can believe things simply because they're useful. You should only be able to believe things because you have reason to believe that they're true. Usefulness and truth are quite distinct. We can get our useful structures without deluding ourselves about the nature of the universe.

Some say religion supplies a moral foundation. Religious groups are at the center of charities, soup kitchens, and other good causes.

Even if religion made people good, it would not provide the slightest evidence for the specific claims of Christianity, Islam, or Judaism. It's a non sequitur to say this grants some credence to the claims of religious people.

But I think you can argue that it's not as useful as is being alleged. It's not a good basis for morality, because real moral concerns have to be focused on questions of the suffering of conscious beings. The moment you focus on suffering, you see that many of the moral concerns religious people press have nothing to do with morality.

Christians debate gay marriage as though it were the question upon which the greatest swing in human suffering is going to turn. But they're arguing based on a conception of morality born of religious dogmatism. It's not born of a real concern for the living reality of human suffering.

Is there any place for spiritualism in the world?

There's no question that people have real experiences that we can call spiritual or mystical, and there are ways to have these experiences. What should be open to debate is what is reasonable to conclude about the universe on the basis of these experiences. If you go into a cave and spend a year praying to Jesus, there's no question that there's a way of doing that that will radically change your experience of the world. You could come out the most loving and compassionate and well-adjusted person around.

But it's also true that a Hindu could go into a cave and achieve the same thing thinking about Krishna. On the basis of those two experiments, you have to admit that the claims of Christianity or Hinduism are not really the best interpretations of the data. There are deeper principles of human psychology and our potential to transform our experience that we have to talk about rationally, in the spirit of science.

If it's done in that spirit, there will be disagreements but always with respect to evidence and argument. The conversation remains open. That's precisely what does not characterize religion. In religion, we have absurd claims to certainty married to incredible passions that get people killed and leave us in a world where if you draw a cartoon depicting the prophet Muhammad, you can get crowds 100,000 strong seething with rage and calling for the deaths of newspaper editors. It's time we noticed the difference between that mode of discourse and the discourse we demand of every other area of our lives.

Ann Coulter's recent bestseller was titled "Godless," as if that's the ultimate insult. Why do people hate atheists?

I can count on one hand the memes that define this animosity toward atheism. One is they think atheism brought us the Nazis and the Communists and the Killing Fields of Pol Pot. I can't tell you how many times I've heard that atheism is responsible for the greatest crimes of the 20th century. Auschwitz was an expression of reason run amuck. This is where they think these events came from: a lack of faith in God.

There is not the slightest sense in which those events were born of people thinking too clearly about the nature of the universe. People also suggest that atheism is itself a faith, the least reasonable faith: "You can't prove that God's not there, so atheists are making the most outrageous claim."

You write that political correctness has helped to allow forced marriages, honor killings, and loathing of homosexuals to take place in Europe.

It's been disastrous, and this recent canceling of the German opera is another example. It's easy to see why they canceled it. Who wants to sit in the audience wondering whether a bomb will go off? But this kind of capitulation is a bad strategy, given the pretensions to power so many Muslims have in Europe. There's got to be some unified front that all civilized people present.

Essentially it's the Salman Rushdie dilemma. He wrote his book and was hung out to dry by liberal Europe. What there should have been the next day is 100,000 Salman Rushdies. The fatwa would not have been a problem if everyone stood shoulder to shoulder with him.

Given your views about the threat of Muslim extremists, what are your thoughts on the "war on terror"?

There are elements of reasonableness to it, but it's been executed so ineptly that it's almost the worst possible situation. What we've done is alienate --- with some exceptions --- all of our necessary allies. We've allowed the Ahmadinejads of the world to drive a wedge between us and our European allies.

We're doing everything possible, it seems, not to have the entire civilized world form a united front against the genuine enemies of civilization who are, with few exceptions, located in the Muslim world at the moment. I really think it is in some significant sense civilization against the Islamists.

We need to find some way of convincing hundreds of millions of Muslims that the Osama bin Ladens of the world are their enemies. We have to break this reflexive solidarity that many Muslims have simply because they're Muslims. This is really where my criticism is focused; this solidarity born of religious ideology is intrinsically divisive and causing conflict that would not otherwise occur.

So you agree with George Bush about the enemy?

We've elected a president who can't speak, who is animated by his own religious dogmas, who is beholden to genuine religious lunatics in our own culture, and who has been almost perfectly designed to alienate our allies and enrage our enemies. So it's a bad situation. And yet to compound the problem, his critics hate him with such fury that they manage to obscure how genuinely scary our enemies in the Muslim world are.

Unless liberals admit that there are tens of millions of people in the Muslim world who are far scarier than Dick Cheney, they're going to disqualify themselves as protectors of our society and of civilization. To keep harping on the fact that there were no weapons of mass destruction in Iraq is a dead end when it comes to dealing with the current reality, which is: we're in Iraq, Iraq now is a center of terrorism, and the fact that it wasn't before we got there is truly irrelevant at the moment. We all just have to get on the same page and realize who the enemy is.

Your books have sold well. Is atheism entering the mainstream?

The idea that 50 years from now we are still going to be a society in which half the people think Jesus is going to come back in their lifetime seems a recipe for disaster geopolitically. Given how our world is shrinking in terms of the scale of communication and the fact that religious provincialism is becoming quickly untenable, I don't think our view of religion can survive 50 more years of modernity. Or we won't survive our views of religion. Something's got to give.

Do you really believe that we will someday look upon our early 21st-century religious beliefs with the kind of horror with which we now look at slavery?

It's an apt analogy. Just look at the recent history of racism in America, the fact that we were lynching people based on a completely un-self-critical embrace of racist hatred. We had Southerners smugly defending their racism, resisting integration, killing blacks, and openly wishing they'd won the Civil War.

It seems to me the South still hasn't come to terms with how they were on the wrong side of that moral argument. But when you look back on our recent history of racism, it seems impossible that we could be racist in quite that way again, given popular culture. I think religion is up for the same transformation as racism. I also think nationalism is going to have to go in pretty short order.

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