"In the US, we see how, you know, fundamentalist Mormons are treated in the media. We're free to criticise," he says. "When a fundamentalist Mormon group, essentially a cult, in the US, comes under the glare of public scrutiny, no one is saying that multiculturalism dictates that we can't criticise their beliefs." He cites examples of young Mormon women forced into polygamous marriages and denied educations. "No one is under any illusions that they might be happier that way or that these ancient traditions are just as legitimate as their own, and who are we to judge?" he says. "You don't hear any of that. People just basically acknowledge that it's a hostage crisis. These women have been brainwashed and mistreated by these odious men who are living in just another age of the earth."

When it comes to covering Islamic fundamentalism, however, Harris contends that the US liberal view is all too ready to excuse the inexcusable. "Even the Charlie Hebdo massacre was not enough to convince many liberals that in the zero sum contest between freedom of speech and theocracy, all of our hopes rest upon freedom of speech winning," he says. "People get massacred for drawing cartoons and you had liberal commentators coming forward saying, 'Well, what were those cartoons exactly? Was there any implied racism in any of them?' "Immediately, they were willing to give away their freedoms with both hands. We have to admit we really are on a kind of knife edge where it could go either way in some respects." Harris' interaction with Islam runs considerably deeper than mere detached observation. He has recently completed a lengthy collaboration with British author and politician, Maajid Nawaz, a former radical Islamist who now heads a counter-extremism think-tank.

The result was a co-authored book, Islam and the Future of Tolerance. Working with the former Hizb ut-Tahrir member, he says, changed his idea of how to combat fundamentalism. "He's really impressed upon me the importance of the secular, of creating a secular trend within the Muslim world as opposed to looking for the moderates of the Muslim world," he says. "A moderate can be many different things. The people who pass for moderates in the Muslim world would often rank as fundamentalists if they were Christians, in terms of their actual social attitudes and level of conservatism. What Maajid has impressed on me is the importance of secularism, which is the commitment to keeping religion out of public policy and out of politics, whatever your religious commitments happen to be." Bearing this in mind, it seems particularly ironic that one of the American Left's greatest heroes, Noam Chomsky, earlier this year denounced Harris as a "religious fanatic who worships the state". Never one to turn down a spot of verbal biffo, Harris returned fire in a well-publicised email set-to with Chomsky over the moral dimensions of the September 11 attacks. The result was inconclusive, with Harris being the first to flinch, terminating the exchange because he felt it wasn't possible to conduct effective debate via email. He also says Chomsky's tone was "bordering on contempt".

Most commentators, however, felt Chomsky – 39 years Harris' senior and considerably more battle-scarred – carried the day. Writing his own match report, noted US radical philosopher Eugene Wolters described Harris as a man who "managed to artfully package trendy atheism with old-school Islamophobic bigotry". Indeed, it is the severity of his criticism of Islam that makes many of his audience uncomfortable. His work with Nawaz and his recognition of secular movements within the broad tapestry of the faith suggest he is not simply judging 23 per cent of the world's population by the violent actions of a tiny minority. However, his habit of drawing debating points from the more fundamentalist strands of Muslim thought makes him an awkward ally for older school atheists and agnostics for whom multicultural respect is a touchstone. Harris, though, is perhaps not in the business of winning converts. When it comes to criticising Islam – as distinct from Mormonism – he concedes that the picture is muddied by the history of colonialism and "qualms about current misadventures in the Muslim world". "You have other things that seem to confuse the matter but, no, we just have to talk very candidly about things like the rights of women," he says.

"You know, if you care that women have equal opportunity in this world then you have to admit that at a first pass forcing them to live in bags and beating them or killing them if they try to get out of those bags is not an ethical mode of living. And it doesn't matter if it's been going on for centuries, in a place like Afghanistan. It's just not acceptable." As he continues in this vein, two thoughts occur. The first is that his harsh attack on Afghani fundamentalism would probably find many sympathetic ears in the broader, progressive, modernist Muslim world. The second is that the real target of his ire is not actually Islam, but the liberal Left he sees as too wishy-washy to condemn its excesses. "The question is not whether or not you can criticise it," he says. "The question is whether there is anything you can do to help the situation. And it may well be that in certain situations there may not be something politically or economically or militarily that can be done to help the situation. But at the very least we have to stop lying about its propriety." Sam Harris is at the Melbourne Convention and Exhibition Centre on January 23 and State Theatre, Sydney, on January 24. Tickets through thinkinc.org.au