Sam Harris, the American writer, neuroscientist and leading proponent of the new atheism, rarely invites indifference. The novelist Marilynne Robinson wrote recently that his "aspirations . . . contain much that is not laudable". The writer and commentator Andrew Sullivan once accused Harris of a "form of intolerance that reminds me of some of the worst aspects of fundamentalism". The columnist Theodore Dalrymple said of a passage from Harris's first book, The End of Faith, that it was "quite possibly the most disgraceful that I have read in a book by a man posing as a rationalist".

His supporters are no less voluble. The jacket of his latest book, The Moral Landscape: How Science Can Determine Human Values, carries gushing testimonials from Ian McEwan ("Reason has never had a more passionate advocate") and Richard Dawkins ("As for religion, and the preposterous idea that we need God to be good, nobody wields a sharper bayonet").

When I meet Harris - a dapper man of 43 who bears a decided resemblance to the actor Ben Stiller - at the office of his English publishers in London, the bayonet is out more or less straight away, even though he is suffering from jet lag after a flight from New York.

A few days before our meeting, the news had broken of the award to Sir Martin Rees, Astronomer Royal and former president of the Royal Society, of the £1m Templeton Prize. The prize, given annually by the John Templeton Foundation, rewards individuals who have made "exceptional contributions to affirming life's spiritual dimension" - or, as Harris puts it in The Moral Landscape, "split[ting] the difference between intellectual integrity and the fantasies of a prior age".

“Rees looks like a cagey and successful choice from the Templeton Foundation's point of view," Harris tells me. "He's certainly not who you'd expect to be shilling for the cause. He is on the record as being a non-believer, but is too politic for his own good, or for our common good. He thinks science shouldn't be in the business of criticising religion, and that scientists can do their job perfectly happily without ever engaging in a contest with religion - but I think that's fundamentally untrue."

Zero-sum game

That "religion and science are in a zero-sum conflict with respect to facts" is one of the central contentions of The End of Faith, the book with which Harris, then aged 36, made his name when it was first published in 2004. He was followed into print in 2006 by the philosopher Daniel Dennett (with Breaking the Spell: Religion as a Natural Phenomenon) and by Dawkins, who argued in his bestseller The God Delusion that religion is the enemy of science. Dawkins, like Harris, meant all religion - not just the fundamentalist, apocalyptic varieties whose adherents are indifferent to the fate of this world because they await imminent transposition to another.Dawkins, Dennett and Harris later made common cause with Christopher Hitchens, whose polemic God Is Not Great was published in 2007. That year, the quartet convened at Hitchens's apartment in Washington, DC for a discussion, conducted over cocktails, that was filmed and subsequently released as a DVD under the title The Four Horsemen.

As Harris observes in The Moral Landscape, somewhat ruefully, there is now a "large and growing literature" attacking "the so-called New Atheists" (a term coined in 2006 by Gary Wolf in an article for Wired magazine).

“It is often said that we caricature religion," he writes. "We do no such thing. We simply . . . take the specific claims of religion seriously." What Harris means is that the New Atheists treat religion - of the kind espoused by the mildest Anglican as much as the ravings of the most incendiary Islamist - as consisting of a set of purportedly factual claims about the nature of reality, the origins of the universe and so on, to which believers assent as they would to an ordinary empirical proposition about the weather or the colour of my trousers. If that is what religion is, then it conflicts with science by definition.

When I try to suggest that there might be more to religious faith than this description allows, Harris is emphatic. "Look at the New Testament," he says. "It makes a variety of claims that are by definition at odds with what we know to be scientifically plausible."

Yet there are many eminent scientists who also happen to be religious believers - John Polkinghorne, for instance, the mathematical physicist and Anglican priest who won the Templeton Prize in 2002, or Francis Collins, formerly director of the National Centre for Human Genome Research in the United States, who was appointed director of the National Institutes of Health by President Obama in 2009. Why, if atheism is the world-view that best accords with the scientific evidence, do so many intelligent people persist in faith?

For Harris, this can be explained only as a "failure of intellectual honesty". He is parti­cularly scathing about Collins. "There's something repugnant about the fact that he [is a believer] and one of the most prominent and influential representatives of science in the United States," he says. "And he's not some weak-tea Christian - he thinks the dead will walk again and will be remade out of new matter. And not only that, he doesn't keep those crazy convictions private. He publishes on the mutually reinforcing character of those two world-views [science and religion]."

However, it is not Christians such as Collins who are the most vociferous critics of Harris and the other New Atheists. The most powerful assaults have come from fellow atheists and secularists. Take the literary critic James Wood, who was brought up in an evangelical Christian household but is now an atheist. Wood has written of the "parochialism" of new atheism. Religion, for Harris and the others, he argues, "seems to mean either fundamentalist Islam or American evangelical Christianity". More "relaxed or progressive" forms of Christianity tend not to register - nor do Hinduism or Buddhism, both of which Harris flirted with in his early twenties after dropping out of an English degree at Stanford University, or Judaism, the faith into which he was born.

Harris swats away the criticism when I put it to him. "If you want to take that tack, at least do me the courtesy of acknowledging that at least 50 per cent of the American population is fundamentalist. This is not a fringe problem. And in the Muslim world it's the same.

“But if you want to talk about some far more relaxed, noncommittal, non-dogmatic form of Christianity or Islam, then let's talk about what it's committed to, because it's committed to some propositional claims. If it's committed to none, then we're just talking about someone who happens to like the Bible as literature, or who happens to like going to St Paul's because he likes the architecture." The problem with this response is that it does not address whether there is more to religion than beliefs about the world. The philosopher Philip Kitcher, an avowed secularist, thinks Harris is attached to something he calls the "belief model of religion", which he finds wanting.

“Besides beliefs," Kitcher wrote in a paper on "militant modern atheism" published last October, "there are emotions, aspirations, desires and actions . . . Those who merely believe, if there are any such people, are not full participants in the religious life." In other words, living in a moral community in which one engages in shared practices is as important to the religious person as believing in a set of dogmas about the metaphysics of transcendent entities.

Beyond belief

Harris does not dispute that religious concepts articulate a moral vision as well as purport to describe the world. But he wishes that scientists wouldn't leave morality to those of faith, and The Moral Landscape is devoted to explaining why they need not do so. "Secular scientists very commonly think that science has nothing to say about morality and human value, and so it's not science's job to tell people what constitutes a good life," he argues.

In the new book, Harris tries to give a scientific answer to the question of atheist morality. "Questions about values", he writes, "are really questions about the well-being of conscious creatures" - and well-being is something that is measurable, scientifically verifiable. The "science of human flourishing" that he lays out in the book is an updated version of utilitarianism, in which well-being replaces pleasure as the source of moral value. Crudely put, in the view that Harris defends, an action is right to the extent that it promotes well-being.

Judging the rightness of an action by its consequences in this way seems to lead Harris, however, to countenance practices that most of us would regard as morally repugnant - such as torture. His arguments about this in The End of Faith caused such controversy that he now maintains a page on his website devoted to the topic. He describes his position thus: "collateral damage is worse than torture across the board". If we bomb civilians, then why are we squeamish about waterboarding?

His opinions are shaped by what seems to him the biggest threat to western civilisation today: radical Islam. The irony is that, in this struggle, he finds himself on the same side as the Christian right. "It's inconvenient, certainly," Harris says laconically. "When I talk to Christians about Islam, they're running the same software. They know how it feels to be sure that the Book is the word of the Creator."

Jonathan Derbyshire is culture editor of the New Statesman