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The ongoing protests in the Middle East have opened up new possibilities for real change and reform throughout the region, but the protests obviously aren't going to solve long-standing security threats emanating from the region anytime soon. Terrorism, proliferation, state failure, and regional tensions such as the Arab-Israeli conflict remain major threats, and dealing with these problems may become even more complicated as the region moves through what is shaping up to be a major transformation in the balance of power.

The Obama administration will need to multitask as it responds to fast-moving events in multiple countries and works to help these societies deal with overwhelming political, economic, social, and demographic problems. In addition to the new uprisings, the administration will need to continue dealing with the other major challenges that existed long before the uprisings-the Arab-Israeli conflict, Iran's nuclear program, Iraq's reintegration into the Middle East, and ongoing threats from terrorist groups based in the region.

The ousters of leaders in Egypt and Tunisia in just a few weeks time demonstrate just how fragile the old order of "stability" imposed by leaders lacking popular legitimacy is. In the past week, the violent repression by Libya and Bahrain shows what some leaders are ready to do to cling to power. This struggle for political change will likely to take years to unfold, and the Obama administration has thus far struck the right balance in developing its responses, particularly in Egypt. But navigating the events in the Middle East in the next few months will consume considerable more time and attention on the Obama administration's crowded national security agenda.

State failure and civil war. The first immediate threat the United States needs to guard against is the collapse of any of these states into brutal repression, internal chaos, and even civil war. The past few days in Libya have offered some hints of how ugly the situation could get. The Middle East is not immune to protracted internal conflicts and insurgencies. Iraq suffered from a vicious civil war for years last decade even with a large presence of U.S. troops, Algeria saw internal conflict through much of the 1990s, and Lebanon had a 15-year civil war starting in 1975. Each of these conflicts claimed upward of 100,000 lives.

In Egypt, the United States played an important role behind the scenes encouraging the security forces to not fire on the protestors-it had leverage based on decades of close ties with Egypt's security agencies. In places like Libya, America has considerably less influence on its own and will need to work more closely with other countries like Italy that may have more sway. In encouraging stability, however, the United States should not fall into the trap of simply backing authoritarian leaders who have ruled without popular support for decades.

Continued threats from terrorist groups. Terrorist groups such as Al Qaeda on the Arabian Peninsula, or AQAP, and other groups that have conducted attacks in the region present a second immediate threat. Last year, White House counterterrorism advisor John Brennan called AQAP a bigger threat than Al Qaeda remnants in Pakistan, echoing CIA assessments from earlier last year. Overall, the popular uprisings have mostly shown Al Qaeda's growing irrelevance to the political, economic, and social problems facing the region. But terrorist groups could seek to exploit continued disorder to sow chaos. Earlier this month, a senior Hamas commander escaped an Egyptian prison and made his way back to the Gaza Strip to a hero's welcome-just one of several reported escapes. Another wave of terrorist attacks in the middle of the region's struggle for political reform could potentially fuel internal conflicts or ignite a broader conflict in the region like the 2006 war between Israel and Hezbollah in Lebanon.

The Obama administration should continue to strike the right balance in encouraging pragmatic political and economic reforms in each countries as the historic uprisings across the Middle East continue. The old order is not sustainable-it failed to deal with the crushing economic and social problems in many of these countries. But as this process of reform takes shape in places such as Tunisia and Egypt, the United States needs to take steps to safeguard its security interests in the region. This means continuing counterterrorism cooperation with security services and militaries in the region, just as it is encouraging those agencies to step back from politics and accept more civilian democratic oversight and checks and balances, as I wrote in this paper on Middle East reform. This process will take a long time to unfold-we are likely looking at a period of several years of uncertainty and change in the Middle East.

The Obama administration also needs to keep its eye on its broader goals as it addresses these historic changes in the region-including resolving the Arab-Israeli conflict and dealing with Iran's nuclear weapons program. The Obama administration has defined a two-state solution to the Arab-Israeli conflict as a core U.S. national security interest, and administration officials have said that they would "incorporate" comprehensive peace proposals such as the Arab Peace Initiative into its policy. The uprisings in the Middle East will obviously complicate short-term efforts to resolve the Arab-Israeli conflict. But in the long run, resolving the conflict will help countries in the region dedicate their resources and attention to dealing with the growing economic and social problems that motivated the protestors.

The clock still ticks on the unresolved Iranian nuclear program, although the Obama administration has worked to isolate the Iranian regime through a multifaceted diplomatic and military strategy. One challenge emerging in the Gulf region with the recent protests is the possibility that certain countries such as Bahrain that are seen as central pillars of containment of Iran are weakened by the legitimacy crisis their rulers face. U.S. policymakers may face some tough questions about whether it is wise to sell weapons systems to countries with shaky governments.

All of this adds up to 2011 shaping up to be a more complicated year for the Obama administration in the Middle East, and one with no easy answers and quite likely a great deal of uncertainty in the months ahead. The uncertainty in the Middle East has contributed to the recent run-up in global oil prices, and high energy prices could risk undermining the economic recovery at home and abroad.

Given what's at stake, the Obama administration needs to outline its long-term vision for the region, including a Middle East in which governments are more responsive to the needs of its citizens, internal conflicts and conflicts between states are minimized and resolved, and the region is much more integrated with the rest of the world than it was at the start of this century. These are lofty goalsand the process for change, which will take a long time, must be driven from inside the region. But the United States can play a key leadership role in helping this troubled region of the world address decades-long problems.