Pope Benedict XVI’s return to his old university at Regensburg in Germany for a speech entitled Faith, Reason and the University: Memories and Reflections was not the most obvious trigger for a new front in the clash of civilisations. The Pope began with a mild joke at the expense of his own religion, recalling that critics used to ask why the university had two departments devoted to God when He did not even exist. Then he strayed into controversial territory.

Arguments about whether religion is based on rationality are not quite on the level of how many angels it is possible to get on the head of a pin, but they are manna from heaven for students of theology. That was Pope Benedict’s audience and that was where he expected his remarks to stay. But these are unusual times, and his decision to quote the Byzantine emperor Manuel II Palaeologus’s views on Islam guaranteed that his speech rang out beyond the ivory tower.

The emperor’s words, taken at face value, certainly look explosive. “Show me just what Muhammad brought that was new, and there you will find things only evil and inhuman, such as his command to spread by the sword the faith he preached,” he said. The point was to illustrate the fundamental contradiction between religion and holy war. The same contradiction, as any Muslim interested in debating the issue could point out, applies to Christianity. Violent conversion to any religious faith, or for that matter violent oppression of religious opponents, goes against God’s nature.

The reaction this weekend shows that many Muslims and their leaders are not interested in this kind of debate. Pervez Musharraf, the Pakistan president, has accused Benedict of trying to associate Islam with terror. Churches have been firebombed in the West Bank. Indian Muslims burnt effigies of the Pope. In Iraq, Shi’ite and Sunni political parties and clerics, at each others’ throats most of the time, united in attacking his speech. Angela Merkel, the German chancellor, has to her credit defended his words, insisting they were misunderstood.

The Pope’s important trip to Turkey in November will go ahead, Turkish officials said. But its aim, building bridges between faiths, looks even more of a challenge. Salih Kapusuz, deputy leader of the country’s ruling Islamic party, accused Benedict of either “pitiful ignorance” or a “deliberate distortion of truths”. Not only was the Pope trying to revive the mentality of the Crusades: “He is going down in history in the same category as leaders such as Hitler and Mussolini.”

This is, in some ways, a re-run of the hoo-ha among some Muslims over the publication in a Danish newspaper of cartoons depicting Muhammad. In the frenzy that followed, with bloody riots and demonstrations in Afghanistan, Pakistan, Syria, Libya, Indonesia and India, about 140 people were killed and hundreds were injured. The cartoons were implicated in religious riots in Nigeria in which 200 people — Muslims and Christians — died. Denmark was targeted, its embassies attacked and its businesses boycotted.

The clash of civilisations is not between Christianity and Islam, it is between nations that encourage religious diversity and those which practise religious intolerance. It is between those who favour open debate and those who think free speech is anathema. The Pope may or may not have known what a hornets’ nest he was stirring up. Even if he did, there was nothing inappropriate, within context, in what he said.

The Vatican has said he is very sorry his speech caused such offence to Muslims. That is fine but it should not go further than that. He should certainly not be pushed into withdrawing his remarks. As in the case of the Danish cartoons, Muslim zealots are trying to impose their restrictions of free expression on the West. Mindful as we should be of religious sensitivities, that cannot be allowed to happen.