Two atheists - John Gray and Alain de Botton - and two agnostics - Nassim Nicholas Taleb and I - meet for dinner at a Greek restaurant in Bayswater, London. The talk is genial, friendly and then, suddenly, intense when neo-atheism comes up. Three of us, including both atheists, have suffered abuse at the hands of this cult. Only Taleb seems to have escaped unscathed and this, we conclude, must be because he can do maths and people are afraid of maths.

De Botton is the most recent and, consequently, the most shocked victim. He has just produced a book, Religion for Atheists: a Non-Believer's Guide to the Uses of Religion, mildly suggesting that atheists like himself have much to learn from religion and that, in fact, religion is too important to be left to believers. He has also proposed an atheists' temple, a place where non-believers can partake of the consolations of silence and meditation.

This has been enough to bring the full force of a neo-atheist fatwa crashing down on his head. The temple idea in particular made them reach for their best books of curses.

“I am rolling my eyes so hard that it hurts," wrote the American biologist and neo-atheist blogger P Z Myers. "You may take a moment to retch. I hope you have buckets handy." Myers has a vivid but limited prose palette.

There have been threats of violence. De Botton has been told he will be beaten up and his guts taken out of him. One email simply said, "You have betrayed Atheism. Go over to the other side and die."

De Botton finds it bewildering, the unexpected appearance in the culture of a tyrannical sect, content to whip up a mob mentality. "To say something along the lines of 'I'm an atheist; I think religions are not all bad' has become a dramatically peculiar thing to say and if you do say it on the internet you will get savage messages calling you a fascist, an idiot or a fool. This is a very odd moment in our culture. Why has this happened?"

First, a definition. By "neo-atheism", I mean a tripartite belief system founded on the conviction that science provides the only road to truth and that all religions are deluded, irrational and destructive.

Atheism is just one-third of this exotic ideological cocktail. Secularism, the political wing of the movement, is another third. Neo-atheists often assume that the two are the same thing; in fact, atheism is a metaphysical position and secularism is a view of how society should be organised. So a Christian can easily be a secularist - indeed, even Christ was being one when he said, "Render unto Caesar" - and an atheist can be anti-secularist if he happens to believe that religious views should be taken into account. But, in some muddled way, the two ideas have been combined by the cultists.

The third leg of neo-atheism is Darwinism, the AK-47 of neo-atheist shock troops. Alone among scientists, and perhaps because of the enormous influence of Richard Dawkins, Darwin has been embraced as the final conclusive proof not only that God does not exist but also that religion as a whole is a uniquely dangerous threat to scientific rationality.

“There is this strange supposition," says the American philosopher Jerry Fodor, "that if you're a Darwinian you have to be an atheist. In my case, I'm an anti-Darwinian and I'm an atheist. But people are so incoherent on these issues that it's hard for me to figure out what is driving them."

The neo-atheist cause has been gathering strength for roughly two decades and recently exploded into very public view. Sayeeda Warsi, co-chairman of the Conservative Party, was in the headlines for making a speech at the Vatican warning of the dangers of secular fundamentalism, which aims to prevent religions from having a public voice or role. Warsi, a Muslim, subdivides propagators of this anti-religious impulse into two categories. First, there are the well-meaning liberal elite, who want to suppress religion in order not to cause offence to anybody. Second, there is the "perverse kind of secular" believer, who wants to "wipe religion from the public sphere" on principle.

“Why," she asks me, "are the followers of reason so unreasonable?"

As Warsi was on her way to catch her flight to Rome she heard Dawkins, the supreme prophet of neo-atheism, on Radio 4's Today programme. He was attempting to celebrate a survey that proved, at least to his satisfaction, that supposedly Christian Britain was a fraud. People who said they were Christians did not go to church and knew little of the faith. Giles Fraser, a priest of the Church of England, then challenged Dawkins to give the full title of Darwin's Origin of Species. Falling into confusion, he failed. Fraser's point was that Dawkins was therefore, by his own criterion, not a Darwinian. Becoming even more confused, Dawkins exclaimed in his response: "Oh, God!"

“Immediately he was out of control, he said, 'Oh, God!'" Warsi recalls, "so even the most self-confessed secular fundamentalist at this moment of need needed to turn to the Almighty. It kind of defeats his own argument that only people who go to church have a faith."

De Botton finds Dawkins a psychologically troubling figure.

“He has taken a very strange position. He's unusual, in that he came from an elite British Anglican family with all its privileges and then he had this extraordinary career, and now he stands at the head of what can really be called a cult . . . I think what happened was that he has been frightened by the militancy of religious people he has met on his travels and it has driven him to the other side.

“It smacks of a sort of psychological collapse in him, a collapse in those resources of maturity that would keep someone on an even keel. There is what psychoanalysts would call a deep rigidity in him."

I ask Fraser what he thinks are the roots of this ideological rigidity among the neo-atheists. “It coincides with post-9/11," he says. "The enemy is Islam for them. That was true about [Christopher] Hitchens in an obvious way and Dawkins said something like 'it was the most evil religion in the world'.

“With Hitchens, it was bound up with liberal interventionism. It is also clearly an Americanisation. It has come over from their culture wars . . . People are pissed off with Dawkins because there is a feeling that we don't do that over here."

For me, the events of 9/11 were certainly a catalyst, the new ingredient that turned the already bubbling mix of anti-religious feeling into an explosive concoction. Coming from a scientific family, I had accepted the common-sense orthodoxy that religion and science were two separate but complementary and non-conflicting entities, or what the great evolutionary biologist Stephen Jay Gould called "non-overlapping magisteria" (NOMA). I first became aware of my own complacency in this regard when I interviewed Stephen Hawking just before the publication of A Brief History of Time (1988). He had become - it was his then wife who told me this - vehemently anti-religious. And in my presence he was contemptuously anti-philosophical.

There had always been an anti-religious strain in science, a strain that had been present since Galileo and which, indeed, had grown stronger after Darwin. In the postwar period, both Francis Crick and James Watson conceded that one of their main motivations in unravelling the molecular structure of DNA was to undermine religion. It was strengthened even further in the popular imagination when Dawkins expounded the outlines of the neo-Darwinian synthesis in his fine book The Selfish Gene (1976). In the 1990s it became routine to hear scientists - notably in this country Peter Atkins and Lewis Wolpert - pouring scorn on the claims of philosophy and religion. They were, for entirely non-scientific reasons, in a triumph­ant mood. The sales of A Brief History of Time had sent publishing advances for popular science books soaring, and the more astounding the claims, the better the money.

While observing this, I became aware that the ground had shifted beneath my own cosy orthodoxy. Scientistic thinkers were no longer prepared to accept NOMA, the separate, complementary, non-conflicting realms. In the early 1990s I was engaged in a debate with Dawkins at the World Economic Forum in Davos. He said, to much applause, that the existence of God was a scientific issue. If, in effect, God could not live up to the standards of scientific proof, then He must be declared dead. There were no longer two magisteria, but just one, before which we must all bow.

After the September 2001 attacks, all the dams of reticence burst and neo-atheism became a full-blooded ideology, informed by books such as Dawkins's The God Delusion, Sam Harris's The End of Faith, Daniel Dennett's Breaking the Spell and Christoper Hitchens's God Is Not Great.

These authors became known as the Four Horsemen of the New Atheism. It was no accident that their books appeared not just after the 9/11 attacks, but also at a time of neo-Darwinian triumphalism. The Human Genome Project, combined with the popularisation of the latest Darwinian thinking, was presented as an announcement that science had cracked the problem of human life. Furthermore, the rise of evolutionary psychology - an analysis of human behaviour based on the tracing of evolved traits - seemed to suggest that the human mind, too, would soon succumb to the logic of neo-atheism.

It was in the midst of this that Fodor and the cognitive scientist Massimo Piattelli-Palmarini published What Darwin Got Wrong, a highly sophisticated analysis of Darwinian thought which concluded that the theory of natural selection could not be stated coherently. All hell broke loose. Such was the abuse that Fodor vowed never to read a blog again. Myers the provocateur announced that he had no intention of reading the book but spent 3,000 words trashing it anyway, a remarkably frank statement of intellectual tyranny.

Fodor now chuckles at the memory. "I said we should write back saying we had no intention of reading his review but we thought it was all wrong anyway."

For him, evolutionary psychology plays a large part in this mindset with its loathing of religion. "I think the story is that we are supposed to

understand why there is religion on Darwinian grounds without having to raise the question as to whether it's true. But these are just fabricated stories. If you found something with two heads and a horn in the middle you could cook up some story from evolution saying it was just dandy to have two heads with a horn in the middle. It's just sloppy thinking."

Ultimately, the problem with militant neo-atheism is that it represents a profound category error. Explaining religion - or, indeed, the human experience - in scientific terms is futile. "It would be as bizarre as to launch a scientific investigation into the truth of Anna Karenina or love," de Botton says. "It's a symptom of the misplaced confidence of science . . . It's a kind of category error. It's a fatally wrong question and the more you ask it, the more you come up with bizarre and odd answers."

The project is also curiously pointless. A couple of years ago I hired a car at Los Angeles Airport. The radio was tuned to a religious station. Too terrified to attempt simultaneously to change the channel and drive on the I-405, the scariest road in the world, in a strange car, I heard to my astonishment that Christopher Hitchens was the next guest on a Christian chat show.

In his finest fruity tones and deploying $100 words, Hitchens took the poor presenter apart. Then he was asked if this would be a better world if we disposed of all religions. "No," he replied. I almost crashed the car.

The answer demonstrates the futility of the neo-atheist project. Religion is not going to go away. It is a natural and legitimate response to the human condition, to human consciousness and to human ignorance. One of the most striking things revealed by the progress of science has been the revelation of how little we know and how easily what we do know can be overthrown. Furthermore, as Hitchens in effect acknowledged and as the neo-atheists demonstrate by their ideological rigidity and savagery, absence of religion does not guarantee that the demonic side of our natures will be eliminated. People should have learned this from the catastrophic failed atheist project of communism, but too many didn't.

Happily, the backlash against neo-atheism has begun, inspired by the cult's own intolerance. In the Christmas issue of this magazine, Dawkins interviewed Hitchens. Halfway through, Dawkins asked: "Do you ever worry that if we win and, so to speak, destroy Christianity, that vacuum would be filled by Islam?" At dinner at the restaurant in Bayswater we all laughed at this, but our laughter was uneasy. The history of attempts to destroy religion is littered with the corpses of believers and unbelievers alike. There are many roads to truth, but cultish intolerance is not one of them.

bryanappleyard.com.

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