When thousands of furious Muslims rallied in the streets of the West Bank, Pakistan, and Indonesia to protest Benedict XVI’s Regensburg address, many commentators spoke with pessimistic alarm about the “clash of civilizations” that had now become increasingly manifest. The reason for this peril, it was claimed, was religion of any kind. Thus, Sam Harris-a dreamer who hopes to achieve the wishful title of his book, The End of Faith , by atheist proselytizing-declared that the pontiff was “merely giving voice to his religious inanities,” which could “start a war with 1.4 billion Muslims who take their own inanities in deadly earnest.”

But in fact the pope was not pursuing a clash of civilizations. He actually had a quite different vision. “The true contrariety which characterizes the world of today is not that among diverse religious cultures,” he noted in a 2005 address, “but that between the radical emancipation of man from God, from the roots of life, on the one hand, and the great religious cultures on the other.” He also alluded to the commonalities of the “great religions,” which “have always known how to live one with the other.”

Of course, in the past two decades the violence perpetrated by the proponents of Islamism-an ideology distinct from Islam as a religion-has created serious doubts about the potential of Islam to live in harmony with others. The reaction to the pope’s comments-which, ironically, used violence to proclaim that Islam is not violent-only vindicated those doubts.

And yet, a month after the Regensburg speech, thirty-eight Muslim scholars and leaders around the world signed an “Open Letter to His Holiness Pope Benedict XVI,” which was a respectful and scholarly response to the issues he had raised about the Muslim faith. The letter clarified issues relating to violence and reason according to Islam and expressed an appreciation for the pope’s self-declared “total and profound respect for all Muslims.” The true Islamic goal, the leaders insisted, was to live together “in peace, mutual acceptance and respect.”

And, less than two months after that, there came a face-to-face meeting between the Vicar of Christ and the followers of Muhammad. At Istanbul’s Sultan Ahmet mosque, Benedict was hosted by Mustafa Cagrici, the mufti of Istanbul and one of the signatories of the open letter. After taking a tour of the seventeenth-century mosque, the pope stood beside the mufti with his face turned toward Mecca “in a moment of meditation.” Then he accepted the gift of a ceramic tile inscribed with the words “In the name of Allah, the Compassionate, the Merciful” in the form of a dove. Placing his hand on the tile, he said: “Thank you for this gift. Let us pray for brotherhood and for all humanity.” “Your Holiness,” the mufti replied with a smile, “please remember us.” What all this suggested is that the convictions of the Osama bin Ladens of the world, like those of the Sam Harrises, are wrong. Christianity and Islam can live together.

One needs only to look deeper into Turkey to see that. It is undeniable that the present-day Islamic world has a bad record of religious freedom. In extreme cases such as Saudi Arabia, faiths other than Islam are simply not allowed to exist. In other countries, Christians-and to a lesser degree Jews-have limitations on such rights as the right to proselytize. Last year, the Afghan convert to Christianity, Abdur Rahman, barely escaped the death penalty that traditional Islamic law decrees for apostasy.

The question is whether this intolerant attitude is an integral component of Islam as a religion or only a historical attitude that Islam has retained from premodern times. Many (including George Cardinal Pell, in his June/July 2006 article in First Things) think that intolerance is built into Islam, but there are reasons to disagree. The Qur’an decrees no sanction for apostasy and includes verses that recognize the rights of Christians and Jews to worship according to their own traditions. There are the “verses of the sword,” to be sure, but it is possible to argue that these verses refer only to those non-Muslims who have been belligerent toward Muslims in the first place. The Qur’an, in other words, makes a doctrine of just war and a live-and-let-live approach possible.

The more established interpretation, however, has not been so generous. The infusion of politics into religion since the early decades of Islam has skewed the tradition. Islamic jurists, the creators of sharia, not only introduced non-Qur’anic concepts such as the ban on apostasy but also developed the “method of abrogation” to bypass the peaceful verses and uphold the verses of the sword. They also adopted several laws from Sassanid Persia, which included the specifications for the second-class status of conquered Jews and Christians as dhimmis .

In premodern times, this was not shocking, and many Jews found it preferable to the attitude of medieval Christendom. The emergence in the West of such ideas as equal citizenship and religious freedom, however, changed the balance, making the Islamic world look backward. But it did take measures to improve itself. The Ottoman Turks, ruling much of the Islamic world, saw the need to reform the sharia according to modern political concepts. In two substantive reform edicts, first in 1839 and then in 1856, the dhimmi status was abolished, and Jews and Christians gained equal citizenship rights. Religious freedom was also guaranteed. “All forms of religion are and shall be freely professed in my dominions,” proclaimed the sultan in the Reform Edict of 1856. “No subject of my empire shall be hindered in the exercise of the religion that he professes.” The reforms also made apostasy possible, and half the members of the Ottoman Parliament of 1908 were non-Muslim. The crucial point is that the Ottoman Empire wasn’t abandoning Islam by reforming the sharia laws but modernizing from within the tradition. The Qur’anic verse “There is no compulsion in religion” was stressed by the Ottoman religious elite to justify the reforms.

The Ottoman Islamic modernization ended with the demise of the empire in the First World War. From its ruins, what we now call the Middle East arose-with a doomed legacy: All post-Ottoman states, except Turkey and Saudi Arabia, were colonized by European powers, a phenomenon that would soon breed anti-colonialism and anti-Westernism throughout the entire region. And the two exceptions went in totally opposite directions: The fanatic Wahhabi sect-which had been the bête noire of the Ottomans and their reforms-dominated Saudi Arabia, and Turkey became a secular republic.

The early Turkish Republic was influenced not only by the legacy of Ottoman reforms but more so by the French Enlightenment and its radically secularist worldview. Early Republican elites asserted that religion is an “obstacle to progress.” To deal with it, they incorporated laïcité , the French notion of secularism, which allowed no role whatsoever for faith in public life.

This stance drove Turkey into an acute version of the problem that Richard John Neuhaus identified in his book The Naked Public Square : The vacuum created by absent religion was filled by ersatz religion. In just a decade, Islam was replaced by a new public faith based on Turkishness and the cult of personality created around its hero, Mustafa Kemal Atatürk. “Let the Ka’aba be for the Arabs,” wrote poet Kemalettin Kamu, “for us, çankaya is enough.” That new shrine was Atatürk’s residence.

The cult of Mustafa Kemal continues in Turkey, along with the official illiberal secularism, both of which ensure not separation of mosque and state but the domination of the mosque by the state and the suppression of religious believers. Women wearing the Muslim headscarf, for example, are not allowed admission to any school or campus in the country. Unfortunately, the Muslim world has never experienced a secular government that grants religious freedom.

Nevertheless, republican Turkey is defined by both its fierce laïcité and by the surviving heritage of Ottoman Islam. The key figure of the latter has been the popular Turkish Islamic scholar Said Nursi (1878-1960), whose millions of followers constitute the Nur (“Light”) movement. In his thought, Nursi was closer to someone like C.S. Lewis than to Muslim contemporaries such as Hassan al-Banna, the founder of Egypt’s Muslim Brotherhood. His enemies were not Zionism or Western imperialism but materialist philosophy and communist ideology, and he saw the Christian West as an ally against both. In 1951, Nursi sent one of his books to the Vatican, along with a letter in which he called for an Islamo-Christian alliance against atheism. During the Korean War, which Turkey joined as an American ally, Nursi encouraged his followers to enlist in the army to fight against the communists.

Nursi’s followers have always steered away from Islamist political parties and opted for “conservative democracy.” Nursi’s line is represented today by Fethullah Gülen, the leader of the most populous and powerful Muslim community in Turkey. The Gülen movement has a media empire and hundreds of schools in which modern education is provided along with the development of moral character. Counted among Gülen’s good friends are such exceptional figures as the Chief Rabbi of Turkey and the Ecumenical Patriarch of Istanbul.

All of which brings us to the interesting fact that the main obstacle to Christian religious freedom in Turkey is not Islam but Turkish nationalism and laïcité . The problems of the Ecumenical Patriarchate are a good example. Until 1971, the patriarchate had a theological seminary on Halki, a small island near Istanbul. That year, Turkish authorities closed the seminary because of growing political tension with Greece. (Orthodox Christians, despite being Turkish citizens, are regarded by the nationalist establishment as the fifth column of this Hellenic neighbor.) The Halki seminary is still closed, and those who aggressively oppose its reopening are Turkey’s nationalists, not Muslims.

The same is true for the bizarre controversy over the title of the patriarchate. It has been calling itself “ecumenical” since the sixth century, and the Ottomans, who permitted it to exist, saw no problem with that ecclesiastic title. In the 1990s, however, the conspiracy theorist Aytunç Altindal, an ex-Marxist turned nationalist, invented a plot for the term: Ecumenical means “universal,” Altindal argued, so when Patriarch Bartholomew uses the word, he claims an authority that surpasses that of the Turkish Republic. Since then, Turkish nationalists have been obsessed with the title.

Secularists also fear that concessions given to Christians might be a precedent for Muslims. When an intra-Orthodox ecclesiastical-court meeting took place in Istanbul in 2005, at which the Ecumenical Patriarchate hosted the patriarchs of Jerusalem and Alexandria, the president of the Ankara chamber of commerce, a Kemalist named Sinan Aygün, called on the public prosecutors to sue the Orthodox Church. “In the secular republic of Turkey,” Aygun said, “we shouldn’t allow a Christian sharia court to take place.” As for the Halki seminary, secularist politician Onur öymen had warned, “If we allow that, we will have to allow Muslim schools, too.”

The Greek Orthodox and the Armenian churches, in fact, are the luckiest ones in Turkey. They, along with the Jews, are officially recognized by the Treaty of Lausanne, Turkey’s founding document, as minorities with certain rights. Other Christian denominations, such as Roman Catholics, Chaldeans, Syrian Catholics, Syrian Orthodox, and various Protestant groups, are not recognized by the state and so are not allowed to build any new churches or run institutions for the formation of the clergy.

When I interviewed Pastor Ihsan Ozbek, a Turkish convert to Christianity who chairs the Alliance of Protestant Churches of Turkey, he described the persecution that Turkish Protestants face, which includes police harassment and even torture: “While the situation is much better under the current AK Party government and its bid for the European Union,” Ozbek said, “attacks against Christians still continue.” He added that harassment to Christians comes from extreme nationalists, not from Muslims. The only civil-society initiative that demanded rights for Christians, Pastor Ozbek noted, came from Mazlum-Der (“Society of the Oppressed”), an Islamic human-rights group.

This is the Turkey that Pope Benedict has visited. He may have been able to build bridges with Muslim clerics and politicians, but the secularists were not impressed. Turkey’s die-hard Kemalist president, Ahmet Necdet Sezer, recently gave the annual Atatürk Award to a controversial historian famed for depicting Judaism, Christianity, and Islam as offshoots of ancient Sumerian sex cults. In his meeting with Sezer, the pope expressed his concerns about religious freedom-only to have Sezer reply: “There is religious freedom in Turkey. We are a secular Republic.” Next day, like a bad joke, he partially vetoed the new Foundations Law, which had been championed by the conservative AK Party government and would have given more freedom to religious institutions. This law, which would “allow religious foundations to extend their influence in society,” the president said, “is against the principles of the republic.”

On his return to Rome, Benedict XVI recounted his four days in Turkey. “I have returned,” he noted, “with a heart full of gratitude toward God and with sentiments of sincere affection and esteem for the people of the beloved Turkish nation.” And while talking about “this emblematic country in regard to the great challenge at hand today at the worldwide level,” he declared, “On the one hand, we must rediscover the reality of God and the public relevance of religious faith; on the other, we must ensure that the expression of this faith be free, exempt from fundamentalist distortions and capable of firmly repudiating every form of violence.”

That nicely summarizes the two concerns that will shape the future of Turkey-and of the Islamic world.

Mustafa Akyol is a journalist in Istanbul, Turkey.