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John Cornwell struggled with his faith for two decades before finally returning to Christianity. Here he explains why Richard Dawkins, and all those who believe religion is the root of all evil, completely fail to understand what it means to believe

It is a year since Richard Dawkins' The God Delusion prompted a torrent of adulation and anguished riposte. The crucial issue he raised is not so much that religious believers can morph into violent extremists (which they patently can), but what is to be done about it. Dawkins thinks that religion is irrational, because it means accepting truths without logic and evidence; and dangerous, because such systematic irrationality can lead to extreme acts of violence. So hideously irrational and dangerous is the disease of faith, he claims, that faith instruction to the young is worse than paedophile abuse. Dawkins wants to rid the world of religion.

What are the prospects for wiping religion off the face of the earth? Stalin attempted, in vain, to eliminate religionists by working them to death or hanging them. Hitler starved and gassed them. Dawkins wants to eliminate belief with a dollop of science. While his book has no doubt offered encouragement to convinced atheists, there is scant evidence that he is discouraging even the lukewarm believers, let alone enthusiasts. Yet if it is unrealistic to rid the world of religion, surely there is a third, well-tried way, which is to tame religion of its excesses by encouraging believers to respect, and to coexist with, all those they regard as dissidents and heretics, as well as agnostics and atheists. The fact that religionists already do this in vast numbers, in many parts of the world, notably most of Europe and North America, brings us to what I see as not so much a flaw as a vacuum in Dawkins' thinking: he simply does not get the point of pluralist societies under secular auspices. Nor does he credit believers with the capacity to be pluralists and democrats, even though members of the great world religions have contributed to the formation and preservation of pluralism, and resistance to its opposite - totalitarianism - in the modern period. Dawkins' failure to accept that religious believers are capable of respect, a healthy measure of doubt and latitude of imagination, needs examination. But first, here's a believer who had doubt and imagination in abundance.
Not long before his death in 1991, I was sent by a newspaper to Antibes in the south of France to quiz Graham Greene about his religious beliefs. His faith, on the surface, seemed to be a mix of superstition, guilt and scepticism, spiced with Catholic orthodoxy. He thought it only natural to hope for an afterlife, but heaven sounded boring and hell implausible "because God is supposed to be infinitely merciful". And he admitted to uttering a prayer whenever his plane came in to land. He said he had met John Paul II, whom he thought an unpleasant dogmatist, in his dreams: "Instead of dispensing communion wafers he was giving out ornate Italian chocolates."

So which central doctrine, I asked Greene, enabled him to describe himself as a Christian? He said that he started writing fiction while working as a reporter on a provincial newspaper. So he felt he had an intuition, "as good as any Glaswegian chief sub-editor", to distinguish between fact and fiction. When he read the story in John's gospel of the two disciples racing each other to the empty tomb after Christ's body had disappeared, he felt that it was "authentic reportage". It was this, he went on, that "enabled me to doubt my doubt about the resurrection". Doubt my doubt! What is more, he saw the resurrection less as a literal historical fact and more as a powerful symbolic notion that could be reinterpreted from age to age. It was clear that Greene's resistance to dogma, whatever its origins, underpinned his attitude towards politics as well as religion. He was as scathing of the atheistic persecution of religion in Mexico in the 1930s as he was criticial of Franco's campaign, under Catholic auspices, in the Spanish civil war.

As someone who had wavered between agnosticism and atheism for two decades, before having returned queasily to Christianity, I empathised with Greene's faith as "doubt of doubt" as opposed to faith as certitude. Faith is a journey without arrival, complicated by false turns, breakdowns, dead ends and wheel-changes. Faith, like love, is seldom entirely constant; nor is it irrevocable. While frequently assailed by doubt, faith is open to provisional, symbolic interpretations (most Christians outside the American bible belt do not take the book of Genesis literally). Those who pursue a religious vocation are not spared vicissitudes of faith and doubt, any more than card-carrying atheists. Mother Teresa, the Albanian nun who worked for the poor in Calcutta, left letters in which she spoke of her doubts right up to her death: "Where is my faith?" she once wrote to a confidant. "Even deep down ... there is nothing but emptiness and darkness. If there be a God - please forgive me." By the same token, Professor AJ Ayer, the most ardent atheist of his day, proclaimed that he believed in an afterlife following a near-death experience in 1988 when he was clinically dead for four minutes. After a few days, and an outcry from the atheists' society, of which he was the president, he partially recanted: "What I should have said is that my experiences have weakened, not my belief that there is no life after death, but my attitude towards that belief." Doubt of doubt.

And yet, Dawkins is as reluctant as any evangelical fundamentalist to recognise the importance of an element of doubt, or doubt of doubt, in religious faith, or to accept that much of the content of religious faith is metaphorical, poetic and symbolic rather than factual in a scientific sense. He is convinced that faith is in all circumstances absolute, seamless, literal. This implausible understanding of what it means to believe gives his case against religion its sensationalist, emotive edge; by the same token it robs his solution - what do we do about extremism? - of any feasibility.

Dawkins nourishes a disturbing contempt for religious believers. Here are some of the descriptions he applies to them: "malevolent ... vicious, sadomasochistic and repellent ... dodgy, perniciously delusional ... sanctimoniously hypocritical ... cockeyed ... " At the heart of his book, he makes a distinction between what he calls "mild religion" and "extreme religion". But both, he maintains, are equally capable of prompting acts of extremism, such as suicide bombing, in religion's name. "The take-home message," he writes, "is that we should blame religion itself, not religious extremism - as if there were some kind of terrible perversion of real, decent religion." Then he asserts: "I do everything in my power to warn people against faith itself, not just against so-called 'extremist' faith. The teachings of 'moderate' religion, though not extremist in themselves, are an open invitation to extremism."

Through the excited syntax he is declaring that if you go to church, synagogue, mosque or temple only once a year, you are just as liable to perpetrate fanatical deeds on the basis of faith as an al-Qaida terrorist. Faith, mild or extreme, is a mental state, Dawkins argues, that involves an open invitation to hatred and violence.

While religious belief may be sufficient to explain some extreme acts, it does not explain all extreme acts. Fundamentalism is as likely to be found in the qualitative conclusions of science as in religion. Under Hitler, it was the science-based ideology of racial hygiene that led to the first concentration camps - based on the recommendation that certain groups were in need of quarantine. Stalin's ideology saw the implementation of socio-biological principles based on Lamarck - the inheritance of acquired characteristics - legitimising strategies of enforced collectivisation of agricultural labour, and ruinous systems of agricultural production. Biologists who refused to believe in the inheritance of acquired characteristics landed in jail. It is not religion alone and of itself that leads to fundamentalism and its social consequences, but an insistence from any ideological source that only one set of convictions should prevail.

The oppression and violence that invariably attends fundamentalism and totalitarianism, whatever its origins, are precisely the result of a withdrawal of respect for the nay-sayers, dissidents and heretics. The Catholic church was patently capable of oppression of heretics in countries where Catholicism had a monopoly, right up to the papacy of John XXIII. It was Pope John who in 1960 insisted, even in the case of Soviet communism, that "one should respect the person even if one does not respect his or her convictions". The very last decision of the reforming Second Vatican Council, which Pope John initiated in 1962, approved a crucial and unprecedented document on religious freedom, insisting on the basic human right of all to hold values and beliefs of their own choosing. One is perfectly entitled to proclaim: "Well, better late than never!" But it shows that even the most dogmatic of the world's religions, if encouraged, can discover a latent propensity towards pluralism in the ideal of non-judgmental universal love.

Dawkins claims, however, that religious believers deserve neither respect nor rights in any circumstances. One of his constant explanations for the spread and lethal nature of religion is based on the idea of cultural traits transmitted by what he calls "memes", items of information that behave like viruses. He writes of those "afflicted with the mental virus of faith, and its accompanying gang of secondary infections". The idea of religious believers as disease carriers is not trivial, for it suggests a contrast between the disease and the theoretically healthy body of society, along with the necessity for antidotes.

Religious memes, he writes, go around together from brain to brain in mutually compatible gangs: "These gangs will come to constitute a package, which may be sufficiently stable to deserve a collective name such as Roman Catholicism ... it doesn't much matter whether we analogise the whole package to a single virus." The shocking aspect of this notion is its depersonalisation, reinforced in an alarming chapter which claims that Jews, and indeed Jesus Christ, did not teach love thy neighbour as thyself and that the 10 commandments - including thou shalt not kill - applied only within the Jewish group.

Dawkins parallels his viral analogies, moreover, with sinister medical analogies. "In the history of the spread of faith," he writes, "you will find little else but epidemiology and causal epidemiology at that." He refers to believers as "faith sufferers", and to himself and like-minded associates as "we doctors". Much as I am convinced that Dawkins deplores the ideology of nazism, the precedents of such medical analogies, applied to certain religious and racial groups, have hardly been innocuous in the history of the 20th century.

Nazi ideology subscribed from the very outset to the idea of the German people as a type of anatomy subject to bacilli. It harped on the introduction of undesirable extraneous influences on the healthy societal body, the Volkskorper, behaving like pathogens; analogies of cures, surgery and purging naturally followed. As early as 1925 Hitler lamented the fact that the state did not have the means to "master the disease" that was penetrating the "bloodstream of our people unhindered". Such ideas, bogus as they were pernicious, referred to the leadership as "healers". By the mid-1930s the ideological bio-political content of nazism merged with Nazi medical science. The Nazi plenipotentiary Dr Gerhard Wagner wrote of the volkisch body being in need of "cleansing", while the language of "immunity" and "radical therapy" became routine.

Dawkins' recourse to the analogies of disease and medicine is, of course, entirely well meant, and I know him to be a man of the most liberal sympathies, but has he considered the far-reaching consequences of similar metaphors employed by far less well-meaning figures? It was only to be expected that a bold thesis that condemned religion en masse would have profound socio-political implications. Dawkins is a brilliant natural historian, whose science books I have celebrated in a string of reviews. The God Delusion has been criticised for trespassing clumsily in the realms of theology; but my own objections are more in the ambit of socio-politics. Put bluntly, The God Delusion is liable to persuade religious fundamentalists that a pluralist secular society is every bit as hostile to the practice of faith as they ever thought it to be. By urging the elimination of religion in the name of all that civil society holds dear, Dawkins is inviting fundamentalists to be even more fundamentalist. His book, then, is a counsel of despair as well as an incitement to the very thing he deplores and seeks to remedy.

· John Cornwell is director of the Science and Human Dimension Project at Jesus College, Cambridge. His book Darwin's Angel: An Angelic Riposte to the God Delusion is published in hardback by Profile on September 6, priced £9.99.