Turkey took a lurch towards turmoil yesterday as the chief prosecutor outlined his case for banning the governing party and police detained two retired commanders, among others, in their pursuit of a group alleged to be plotting a coup.

For months, as this clash has been brewing, allies of Turkey hoped that it would fade away as an older generation of nationalist-minded generals gave way to younger, European-orientated politicians. It won’t. It now seems that the struggle for Turkey’s identity is going to get much worse, while its chances of a liberal, modern future dissolve.

Ever since Recep Tayyip Erdogan, the Prime Minister, and his Justice and Development Party (AK Party) were elected enthusiastically six years ago, the country’s old-guard defenders of its historic secularism have been uneasy. That is an entirely fair starting point. Turkey’s secularism, a fervent refusal to allow religion to shape the institutions of state, has been the heart of the republic founded by Mustafa Kemal Atatürk in 1923. It has underpinned the extraordinary position that Turkey has chosen for itself: as the only Islamic member of Nato; as the only Islamic friend of Israel; as a bridge, culturally and diplomatically, between Central Asia and Europe.

The Army has repeatedly intervened in Turkey’s history to protect that secularism. But this has clashed with its hopes of building a modern democracy. It has been coming to a head since 2002 when the people of Turkey overwhelmingly elected a government which, in the name of liberalism, set out to grant more licence for Islamic practices.

It is fair for the generals – and others – to have been suspicious of the AK Party initially. The party’s roots were in two overtly Islamic groups. Its intentions, on arriving in Government, were unknown. The 1979 Iranian revolution next door added to these worries.

Yet that is not how the AK Party has behaved in office (nor does its steady popularity appear to reflect any desire for it to turn Turkey into an Islamic state). The issue on which the Government began to clash with the courts was its move to overturn the ban on women wearing headscarves in universities. This might sound, to British ears for example, merely like one of the eye-catching cases where someone’s desire to wear religious dress clashed with the rules of their employer or school. But that would be to underplay the huge symbolic significance of the headscarf in Turkey, as the emblem of the religiously observant, and the long-standing principle that those who would not adapt their dress would not have access to university.

It is increasingly hard to square that kind of prohibition with a modern, liberal democracy of the kind that Turkey has been becoming. Nor is it fair to portray the AK Party’s desire to make that one change as the insertion of Islam into the state. Of course, no one would want to be relaxed about any kind of constitutional change that might lay the ground for more Islamic-tinged reforms. But it is unfair to imply that this is the party’s intention, given its six-year record that has been liberal, more respectful of human rights and interested in joining the European Union.

The courts have been erratic in their defence of the principle of secularism over the years. The decision by the chief prosecutor to accept the legal challenge of the opposition and to move ahead in seeking to ban the entire governing party – not simply to challenge the headscarf rule – is a disastrous one. It has taken Turkey towards a confrontation that will be hard to defuse, and almost certainly, farther from Europe.

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