Early Egypt election results show the Muslim Brotherhood is rolling (VIDEO)

With the first round of Egypt's long parliamentary election almost over (ballots are still being counted), it looks as if the Muslim Brotherhood is the big winner.

Turnout Monday was clearly very high – well above the 35 percent or so that typically voted in the rigged elections under Mubarak – and laid to rest concerns that the violent crackdown on protesters in Tahrir Square in the weeks leading up to the polls would convince many Egyptians to stay home.

Clearly the Egyptian public sees the stakes as high, and by and large they are convinced that their votes will be fairly counted. While there have been a lot of complaints about polling irregularities, they've largely centered on the Muslim Brotherhood's Freedom and Justice Party (FJP) campaigning too vigorously near polling places by handing out literature and showing confused voters on sample ballots where the "x" goes for the FJP. 

Issandr El Amrani thinks that when all the votes are counted that the FJP may end up taking 40 percent of the popular vote, which will make them by far the largest bloc. How many seats that will translate into precisely is hard to say. One-third of the seats are reserved for candidates who ran as individuals not officially affiliated with any party. Some of these will surely be FJP supporters that will caucus with the party. There are also quotas for candidates deemed to be "farmers" or "workers" that make seat allocation a more complicated question than a simple percentage of the vote.

Reuters quotes a FJP official as saying the party took about 40 percent of the votes for party lists in Cairo, and a leader of the secular Egyptian Bloc as saying the FJP could have taken as much as 50 percent of the votes in the capital city. To be sure, the second two rounds of voting, which will wrap up in January, could dramatically alter the picture. In 2005, when the Brotherhood's candidates did well in the first round of the parliamentary election, Mubarak's government ramped up its efforts to fix the final two rounds in order to stem the challenge. But with so many Egyptians hungry for a transition away from their authoritarian past, and willing to take to the streets to underscore that desire, the chances for blatant rigging are constrained. 

What does this mean? The assumption that the Brotherhood was the most organized and supported political force in Egyptian society seems to be true. While liberal parties spent much of the past six months squabbling amongst themselves over which names would be at the top of their tickets and holding the occasional campaign event in the sports and social clubs of Egypt's elite, the Brothers had an army of people out canvassing, knocking on doors, and spreading the word. On the day of the vote, they put a lot of resources into getting supporters to the polls. Meanwhile, reporters and activists in Cairo saw little in the way of that kind of political spadework from the Brotherhood's secular and liberal opponents.

As a question of formal authority, the Supreme Council for the Armed Forces (SCAF) will hold most of the cards when the new government sits. SCAF occupies Egypt's powerful presidency, and by existing rules will appoint the next government. But as a question of popular political legitimacy, the Brothers are going to have a strong hand. FJP Chairman Mohammed Morsi implied today that the party intends to use its popular mandate to pressure SCAF on government formation.

A writeup of remarks he made earlier today hosted at the Brotherhood's English-language website says Morsi insisted "the majority in the upcoming parliament will form the government, which will be a coalition government." It added that he "stressed that the Egyptian people are able to think and choose those who will represent them in parliament, and that there will be no division between Muslims and Christians, old and young, according to the rules of political action, which require non-discrimination among them."

In effect, he's insisting that the military cede control over the next government to the elected parliament.

The question of how willing the military really is to step aside, after almost 60 years of political dominance in Egypt, is the one looming over the whole transition. Marc Lynch and Steven Cook, both political scientists who specialize in the modern Middle East, argue in an Op-Ed today that the US needs to hold the SCAF's feet to the fire now on a proper transition.

"Egypt’s military rulers clearly believe that they have survived the political crisis, and have resisted calls for a more fundamental political change. The generals may prevail in the short term, as the numbers in Tahrir dwindle and Egyptians turn their attention back to the elections and political squabbles," they write.

"The Obama administration’s response should begin with a clear, public presidential statement specifying what transferring power to a civilian government means. This would not involve micromanaging Egyptian politics in a manner that risks a nationalist backlash in Egypt, but Washington should put the Egyptian military, which receives $1.3 billion annually from the United States, on notice that the officer’s efforts to carve out a post-transition political role for themselves is unacceptable."