The destruction of a synagogue in Damascus is the latest manifestation of a fundamental, and troubling, shift going on in the Middle East. The Jobar Synagogue, thought to be 2,000 years old, was looted and burned to the ground. Both the government and the Islamist-dominated rebels are denying they were behind it, but either way the incident appears to have been a deliberate act. It’s not the first time historical sites have been damaged in the suicidal violence of the Syrian civil war, nor the first time that minorities have been targetted.

Unfortunately this kind of random act against that which is dissonant amid the whole is a sign of the times. Since the Iraq war in 2003, communities have been “polarising” and clearing out elements that don’t fit, in acts reminiscent of the 1947-9 war that saw the state of Israel established in Palestine and the ethnic cleansing witnessed at the collapse of the Ottoman Empire. Shi’ite districts of Baghdad became more Shi’ite and Sunni districts become more Sunni in a bloody, domestic exchange of populations that left Baghdad a segregated city and Iraq a divided nation. Iraq’s Christian community has been decimated, as hundreds of thousands (among others) fled the violence inflicted on them by al-Qa’ida Islamists who themselves are warring the Shi’ite Islamists who have taken control of government.

Fear bred by events like the disastrous Iraqi adventure, as well as broader ideological shifts in recent decades, have led individuals in numerous locales around the region to think of themselves more as members of discrete ethnic or sectarian groups within the nation-states in which they live. This is one reason why many Sunnis have rallied around the ruling family in Bahrain and why many Copts in Egypt remained mistrustful of the Muslim Brotherhood during the years of Mubarak’s persecution of the group.

Brotherhood rule is viewed by Copts as every bit as bad as they feared (thought it could surely be worse), with the state unwilling to check Salafi violence against them, or incapable of that, while the fear of Brotherhood rule in Syria has been enough to keep a significant number among the “minority” groups – in fact some 40 percent of the population – on the government’s side.

The irony here is that so far the Brotherhood, with the likely help of its regional backer Qatar, has presented itself convincingly to influential Western powers as the moderate middle ground that can hold the radicals in check, in Egypt, Syria, Tunisia and elsewhere. The secular Left and Arab nationalists, the argument goes, are too weak before the juggernaut of political Islam in general – a trend that dates to Nasserist Egypt’s loss to Israel in 1967 – to occupy the political centre alone.

Of course, U.S. officials have objected that they are simply going by the results of the ballot box and only favour what publics have chosen in fair votes. But the imperfections of Egypt’s post-Mubarak electoral experience so far have been glaringly obvious and Washington’s acquiescence in the machinations to place the Brotherhood in pole position among the Syrian opposition, the first among equals, has been equally clear.

Homogeneity is the name of the game in the new Middle East unfolding before our eyes and it could entail untold suffering for hundreds of thousands if not millions of people in the ensuing years, as it has already. Rather than see this as a dislocation provoked by one historical event such as the Arab Spring or the Iraq invasion, however, it should probably be analysed as part of a wider process of messy, unfinished nation-state formation – the creation of distinct political-economic units that the West can deal with.

Acutely aware of what European nationalism did to Palestine, Edward Said once lamented the end of the Ottoman millet system under which confessional communities managed their own legal and judicial affairs; he suggested half-jokingly that some form of political and social organization along those lines would be better suited for the Levant at least.  Yet the changes that may be in store for what has been called the ‘Arab state system’ could be just as major, if Iraq and Syria were reconfigured along Sunni-Shi’ite sectarian lines, for example (see how al-Qa’ida is thinking and remember the infamous 2002 RAND presentation). It wouldn’t be surprising if policy mandarins are once again dusting out old maps to see what lines could be redrawn in the sand.