When President Obama stepped into the State Department on May 19 to deliver his long-awaited speech on the Middle East, he did so amid fears that the Arab Spring was devolving into a Summer of Discontent. Egypt was sagging under a weakening economy and escalating crime; NATO's efforts in Libya were stuck in neutral; the Syrian government was boasting that its rebellion was over. Sectarian tensions were roiling Bahrain and Syria, and a wave of church burnings in Cairo had spawned a week of deadly violence between Muslims and Christians.

In his speech, Obama confronted these religious struggles head-on. "In a region that was the birthplace of three world religions, intolerance can lead only to suffering and stagnation," he said. "For this season of change to succeed, Coptic Christians must have the right to worship freely in Cairo, just as Shia must never have their mosques destroyed in Bahrain."

Beyond their political implications, the religious dimensions of the Middle East uprisings have always been central, particularly to the West. Ever since 9/11, the West and Islam have been locked in a chilly standoff. The relationship was captured by Harvard professor Samuel Huntington's lightning-rod phrase "the Clash of Civilizations." Huntington's thesis, which was roundly trashed when it was published as an article in 1993 but became a best seller in book form following Sept. 11, was that Islam taught Muslims to be hostile to freedom, pluralism and individualism.