Kenan Malik's pages from New Humanist, May/June 2009"Can Europe be the same with different people in it?" asks the writer Christopher Caldwell in his controversial new book, Reflections on the Revolution in Europe. It is a question that has been asked with increasing urgency in recent years as the issue of immigration, and in particular of Islamic immigration, has taken centre stage. And it is one that liberals have found increasingly difficult to answer.

At the heart of this question lies the dilemma of how Western societies should respond to the influx of peoples with different traditions, backgrounds and beliefs. What should be the boundaries of tolerance in such societies? Should immigrants be made to assimilate to Western customs and norms or is integration a two-way street? Such questions have bedevilled politicians and policy-makers for the past half century. They have also tied liberals in knots.

There have developed two broad responses to the quandaries of pluralism. Multiculturalists argue that diverse societies can only function fairly if respect is shown towards all peoples, cultures and viewpoints. "The liberal is in theory committed to equal respect for persons," the political philosopher Bhikhu Parekh argues. "Since human beings are culturally embedded, respect for them entails respect for their cultures and ways of life." Social justice, in other words, requires not just that individuals are treated as political equals, but also that their cultural beliefs are given equal recognition and respect.

Others have responded to the challenges of a plural society by drawing upon the so-called "clash of civilisations" thesis. The phrase was coined by the historian Bernard Lewis in a 1990 essay on "The Roots of Muslim Rage". It was subsequently popularised by the American political scientist Samuel Huntington. The conflicts that had convulsed Europe over the past centuries, Huntington wrote, from the wars of religion between Protestants and Catholics to the Cold War, were all "conflicts within Western civilisation". The "battle lines of the future", on the other hand, would be between civilisations. And the most deep-set of these would be between the Christian West and the Islamic East, which would be "far more fundamental" than any war unleashed by "differences among political ideologies and political regimes". The West would need vigorously to defend its values and beliefs against Islamic assault.

It is an argument that has gained an increasing hearing in liberal circles, particularly in the wake of 9/11. The West, the American writer and atheist polemicist Sam Harris argues, is at war not with terrorism, nor even with Islamic terrorism, but with "Islam itself", with "the vision of life that is prescribed to all Muslims in the Koran". The distinction between moderate and fundamentalist Muslims is irrelevant because "most Muslims appear to be 'fundamentalist' in the Western sense of the word." "Is Islam compatible with a civil society?" asks Harris. "Is it possible to believe what you must believe to be a good Muslim, to have military and economic power, and to not pose an unconscionable threat to the civil societies of others? I believe that the answer to this question is no."

What is striking about these two approaches is how much they have in common. It is true that there is little love lost between multiculturalists and proponents of the clash of civilisations thesis. The former accuse the latter of pandering to racism and Islamophobia, while the latter talk of the former as appeasing Islamism. Beneath the hostility, however, the two sides share basic assumptions about the nature of culture, identity and difference. For at the heart of both arguments is a confusion between peoples and values. Multiculturalists claim that the presence in a society of a diversity of peoples limits the possibility of common values. Clash of civilisations warriors insist that such values are impossible within an ethnically diverse society. Neither is right.

The origins of both these responses can be seen in the Rushdie affair of 20 years ago. The worldwide protests against The Satanic Verses, the book-burnings and riots that accompanied them, and in particular Ayatollah Khomeini's fatwa of February 1989, which forced Rushdie into hiding for a decade, proved to be a watershed in the relationship between Muslim communities and Western societies. It was through the Rushdie affair that many of the issues that now dominate political debate - multiculturalism, free speech, radical Islam, terrorism - first came to the surface. It was also through the Rushdie affair that thinking about these issues began to change.

For multiculturalists the Rushdie affair demonstrated the necessity of accommodating to cultural and religious sentiments. The philosopher Shabbir Akhtar became a spokesman for the Bradford Council of Mosques at the height of the controversy over The Satanic Verses. "Self-censorship," he suggested, "is a meaningful demand in a world of varied and passionately held convictions. What Rushdie publishes about Islam is not just his business. It is everyone's - not least every Muslim's - business."

Many Western liberals came to agree. Whatever may be right in principle, they argued, in practice one must mollify religious and cultural sensibilities because such sensibilities are so deeply felt. "If people are to occupy the same political space without conflict," the sociologist Tariq Modood suggests, "they mutually have to limit the extent to which they subject each other's fundamental beliefs to criticism."

Other commentators, shocked by the sight of British Muslims threatening a British author and publicly burning his book, responded to the Rushdie affair by questioning whether a modern, Western, liberal democracy could safely accommodate Muslims. The Bible, the novelist, feminist and secularist Fay Weldon wrote in her 1989 pamphlet Sacred Cows, provides "food for thought" out of which "you can build a decent society". The Qur'an offers "food for no thought. It is not a poem on which a society can be safely or sensibly based."

As we have travelled from fatwa to jihad, so this idea of something inherently nasty lurking in the Qur'an has acquired greater purchase. "Islam is not just a religion," the right-wing Canadian journalist Mark Steyn tells us. "There's a global jihad lurking within this religion," which is "a bloodthirsty faith in which whatever's your bag violence-wise can almost certainly be justified."

Immigration has come to be seen as a Trojan Horse for the clash of civilisations. Once we abandon colonial guilt, Christopher Caldwell writes, and with it the belief that "Western Europeans are rapacious and exploitative by nature and that Africans, Asians and other would-be immigrants are inevitably their victims, then the fundamental difference between colonisation and labour migration ceases to be obvious." Muslim immigration "is not enhancing or validating European culture; it is supplanting it. Europe is not welcoming its newest residents but making way for them."

Multiculturalists and the clash of civilisations warriors have different views about the nature of Islam. Both, however, look upon Muslims as a distinct population, homogenous in its outlook, defined almost solely by its faith, and whose difference must dictate the way that wider society deals with it. In viewing cultural differences in this fashion, both sides have been led to betray basic liberal principles.

Multicultural policies have helped erode freedom of speech and undermine the most progressive movements within minority communities. Elected politicians have abandoned their responsibility for engaging directly with minority communities, subcontracting that responsibility instead to so-called community leaders. In the process they have allowed the most conservative elements to promote themselves as the true representatives of their communities.

Twenty years ago, Rushdie's critics no more spoke for the Muslim community than Rushdie himself did. Both represented different strands of opinion within Muslim communities. Rushdie gave voice to a radical, secular sentiment that in the 1980s was deeply entrenched. Rushdie's critics spoke for some of the most reactionary strands. Their campaign against The Satanic Verses was not to protect the Muslim communities from unconscionable attack from anti-Muslim bigots but to protect their own privileged position within those communities from political attack from radical critics, to assert their right to be the true voice of Islam by denying legitimacy to such critics.

As Shabbir Akhtar put it in his book Be Careful with Muhammad! "Islamic doctrine wisely discourages inappropriate kinds of curiosity; and orthodoxy encourages 'safe' thoughts." He himself refused "to countenance any subtlety of mind or will that might undermine Islam." People like Akhtar succeeded in their mission at least in part because secular liberals embraced them as the "authentic" voice of the Muslim community. In accepting that people "have to limit the extent to which they subject each other's fundamental beliefs to criticism", multicultural censors have helped undermine progressive movements within minority communities and legitimise reactionary tendencies.

The clash of civilisations argument is often presented as a critique of multiculturalism and a defence of Enlightenment values. September 11, Martin Amis has written, was "a day of de-Enlightenment" - a theocratic assault on liberal democratic traditions and on a secular, rationalist culture. Re-Enlightening the world requires us to engage in a civilisational war. Yet, in the writings of thinkers like Amis and Harris, the Enlightenment often seems less like a set of values through which to create a progressive politics than a myth by which to define the West. As much as multiculturalism, the clash of civilisations thesis has signalled an abandonment by liberals of basic liberal values.

"One of the main claims of Enlightenment philosophy," the writer Ian Buruma observes in Murder in Amsterdam, his meditation on the significance of the killing of Dutch film-maker Theo van Gogh by a Moroccan Islamist, "is that its ideas based on reason are by definition universal. But the Enlightenment has a particular appeal to some . . . because its values are not just universal, but more importantly 'ours', that is European, Western values."

So, Sam Harris has suggested, Islam is such an alien force that different rules must apply to the way that Muslims are treated. He makes a liberal case for torture, arguing that "if we are willing to drop bombs or even risk that pistol rounds might go astray, we should be willing to torture a certain class of criminal suspects and military prisoners." Since most terrorists are Muslims, there is, he argues, a need for ethnic profiling and discriminatory policing. And he believes that "some propositions are so dangerous that it may even be ethical to kill people for believing them." Harris has even written that "the people who speak most sensibly about the threat that Islam poses to Europe are actually fascists."

Martin Amis told The Times' Ginny Dougary about "a definite urge ... to say that the Muslim community will have to suffer until it gets its house in order. What sort of suffering? Not let them travel. Deportation - further down the road. Curtailing of freedoms. Strip-searching people who look like they're from the Middle East or from Pakistan ... Discriminatory stuff, until it hurts the whole community and they start getting tough with their children."

Once the Enlightenment becomes a weapon in the clash of civilisations rather than in the battle to define the values and attitudes necessary to advance political rights and social justice, once it becomes a measure as much of tribal attachment as of progressive politics, then everything from torture to collective punishment becomes permissible, and the pursuit of Enlightenment itself becomes a source of de-Enlightenment. Multiculturalists and clash of civilisations warriors both start with the question: "Can Europe be the same with different people in it?" They give different answers. But the question itself is the problem. It assumes that minority communities are homogenous wholes whose members will forever be attached to the cultures, faiths, beliefs and values of their forebears. Being born to European parents is not a passport to Enlightenment beliefs. So why should we imagine that having Bangladeshi or Moroccan ancestry makes one automatically believe in Sharia? In confusing peoples and values both sides betray a lack of faith in their own abilities to win people of different backgrounds to a common set of Enlightened values.

"For are they not conjoined opposites, these two, each man the Other's shadow?" asks Salman Rushdie in The Satanic Verses about his two anti-heroes, Saladin Chamcha and Gibreel Farishta. One might ask the same question about the multiculturalist argument and the clash of civilisations thesis. These two responses to fatwa and jihad appear as conjoined opposites, each as the other's shadow, each betraying fundamental liberal principles.

One abandons the basic Enlightenment idea of universal values, suggesting instead that we should accept that every society is a collection of disparate communities and that social harmony requires greater censorship and less freedom. The other turns belief in the Enlightenment into a tribal affair: Enlightenment values are good because they are ours, and we should militantly defend our values and lifestyles, even to the extent of denying such values and lifestyles to others. Or, as Rushdie says about Saladin and Gibreel, "One seeking to transform into the foreignness he admires, the other seeking contemptuously to transform." Twenty years on from the Rushdie affair it is time to challenge both the Saladin Chamchas and the Gibreel Farishtas of contemporary liberalism.

Kenan Malik's From Fatwa to Jihad is published by Atlantic