LONDON – Say what you like about the U.S. State Department’s mastery of foreign affairs, its annual report on human rights practice remains a beacon of precise, honest and clear thinking. Published two weeks’ ago it rightly chided China for going backwards after years of progress. And here in Turkey its sharp critique has been well covered in the press, giving the country a chance to see itself in the round.

Despite phenomenal progress in improving the parameters of free speech and beginning to confront the legitimate demands of the Kurds, Alevites and other minorities in recent years, Turkey still has not faced up to its two big outstanding historical questions – what has it done with all its Jews and Christians? – a very big question since Istanbul was the seat for centuries of the Byzantine Church and the Ottoman Empire was the principle place of refuge for the Jews after they were driven out of Christian Spain in the fifteenth century. And when will it have an honest discussion about the disappearance of the Christian Armenians, which some say was an act of genocide?

If we’ re all going to be forced to make the clash of civilizations the principle item on the geo-political agenda, as the Bush administration’s new National Security Strategy statement appears to suggest, then those who oppose such polarisation need to face up to why this modern, liberal Muslim state par excellence has not come to terms with its terrible past. Ironically, this law-abiding state, the creation of the pro-European, Westernising, Attatürk, has a worse record on these matters than its predecessor, the Ottoman Empire.

It is rarely acknowledged in the West that Islam, and in particular the Ottomans, has a much better historical record than Christianity in its tolerance of the other religions of “The People of the Book”.

For 700 years Jerusalem was under Muslim rule. The churches were open. The Jews were given funds to rebuild their synagogues. Likewise, from the fifteenth century on, when the majority of Arabs lived under Ottoman rule, Christians and Jews were recognised and protected.

Historically, there has never been a sustained, continuous, clash between these great civilizations. Undoubtedly there have been particular clashes and until the fall of the Ottoman Empire the Muslim world won most of them. Yet in victory the Muslims invariably showed greater magnanimity and tolerance than the Christian powers when they triumphed. So why is it that the dying Ottoman Empire and modern Turkey have such a poor record?

Some Turks would say in their defence it is because, since the Great War of 1914-18 and the break up of the Ottoman Empire by the victorious British and French, the West has inflicted one grevious blow after another on the Muslim world. This has pushed Turkey – and much of the Muslim world in this region – into an uncharacteristic degree of defensiveness and intolerance.

Caroline Finkel, the author of the big new study on the Ottomans much praised by Turkey’s most famous novelist, Orhan Pamuk, who was recently prosecuted for speaking in favour of honesty about the Armenians, argues that maybe it can’t be legitimately termed “genocide” when 80,000 Armenians have continued to live unmolested all these years since in Istanbul. Nevertheless, as she told me in her home in Istanbul, “terrible massacres did take place on both sides. That’s not in doubt. But the devil is in the detail. No ‘smoking gun’ has been found in the Ottoman archives”, although she adds that some documents could have been lost “perfectly innocently or removed”.

Finkel, whilst unsparing of the savagery of Ottoman forces in killing off so many Armenians, reminds her audience that more Muslim Turks than Armenians were killed in the war and that the fifth column activities of the Armenians made inevitable their relocation to Syria and Iraq, well away from the Ottoman-Russian front line.

An open reckoning of the evidence by an independent panel of distinguished historians should now be commissioned by the EU and paid for by the Turkish government. The longer the Armenian issue is left to stew, manipulated by the ignorant, the more damage to the EU digestive tract, as the EU entry negotiatians proceed, it is going to cause. Likewise, a separate inquiry into what happened to the Jewish and Christian minorities needs to be undertaken and why even today the continued existence of a major Orthodox seminary near Istanbul remains under threat.

The past weighs too heavily upon modern Turkey, even though its media and intellectuals can be very forthright about these issues. The Turkish government still needs to open up. Denial is no substitute for the whole truth. And if Turkey truly wants to enter the EU it must get on with it, sooner rather than later.