The largely peaceful protests against President Hosni Mubarak in Egypt this week has raised the question that if Mubarak falls, will a radical Muslim extremist group take charge of the new parliament as happened in Iran in 1979 or Lebanon  in 2011?

Several in the blogosphere are quick to link the Muslim Brotherhood with terrorist groups like Hamas and al Qaeda.    But as my colleague Matt Berkman reminds me, not only has the Egyptian Muslim Brotherhood consistently condemned terror attacks from 9/11 to a recent bombing by militants in Palestine, but they claim not to be seeking a leadership role in government. Of course, this reluctance to lead may change. They are seeking to lead at least a coalition in parliament, if they are permitted to re-form. This rallies old suspicions that maybe Western governments have based policies to prop up dictators in the Middle East to prevent takeovers by Islamic radicals on false assumptions.

My first experience with the Muslim Brotherhood, the large, Egypt-based radical movement known in Arabic as “al Ikhwan”, was actually kind of frightening, and it led me to misunderstand what it represented.

While consulting for an aid agency in the Sanag region of Somalia in 2005, my colleagues and I found ourselves lodging with several Somali members of the Brotherhood in a very remote village. The men were very warm to me, an American. At the same time, they criticized my Somali-Canadian female colleagues for not acting more conservatively. The next morning, I went to say hello again, to learn more, but was warned not to.

This Somali MB splinter group which came from Dubai apparently had been organizing rallies in villages across the “un-governed” parts of Somalia, and some were inspiring youth to join the Islamic, terror-wielding rebel movement which would merge with al Shabab. The rally shook the village, and I got threatened. A week later, my team intersected with them again and had to keep cover in our compound after someone started shooting at the MB organizers for fear of losing another son to the war.

The thing is, that was Somalia. Not Egypt. Those men claiming to represent the Muslim Brotherhood were inspired by Egypt’s movement, so they used the same name. Maybe they went to their international conferences. But in the end, as with al Qaeda and al Shabab, many radicals who continue to be inspired by the core beliefs of the Muslim Brotherhood, continue to break with them, even arguing fiercely with them about how to bring those core beliefs to communities.

While Saad al-Husseini, one of MB’s leaders, may give a speech that sounds a bit harsh though Western lenses, he would probably take Osama bin Laden by the ear and kick him down stairs were he to have the chance. In a sense, the radical Muslim fringe that celebrates the MB while using violence are like the many Christian paramilitary groups that fought wars or bombed pubs to “protect” their faith allies in past decades.

The point is, we may see the MB leading a powerful coalition in the future Egypt if they are permitted by the authorities to re-form. They may even win a Prime Minister post eventually. They may question policy on Israel and the Gaza Strip, but they are unlikely to ally with Hamas as long as it bombs civilians. They may question Egypt’s reliance on aid from the United States, but may change their mind when they realize no one else can afford to keep Egypt’s security in tact. And it is very unlikely that al Qaeda or other terror groups will be welcomed in Egypt any time in the future.

Of course, nothing is certain in this time of tremendous change and the MB are not going to be allies of the U.S. anytime soon. Egypt is facing a painful time regardless of who comes in power, and after such dark days they deserve a true, stable, civil-society democracy.

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