Sean Jacobs writes  about the origin of the idea:
At the end of 2011 we contemplated asking you, dear reader, who you think was the most influential African thinker alive. We abandoned the idea for a while because of our thing against lists (except our end of year lists, of course). I got the initial idea from the British blog, Left Foot Forward, which had run a contest to determine “the most influential leftwing thinker of the year 2010/11.”
He explains  how they came up with the list of candidates:
So here we are. To start things of, we came up with a list of candidates we canvassed internally. Not everyone will be happy with the list, but we tried thinking of a range of intellectuals representing different parts of the continent, not just from one country. As South African writer Zakes Mda recently tweeted: “Zimbabwe compares only with Nigeria in the per capita production of African intellectuals (scholars, writers, scientists, economists etc.)” In fact, an earlier draft of the List was heavily South African and Egyptian. (That draft was not supposed to be up and one reader responded in kind. It’s been corrected.)
We confess this list is subjective and that is why we have a second round where your suggestions will make up the choices.
Others wanted to know why we’re not including people on twitter: Our response is that we are not sure 140 characters make you “an intellectual.” A lot of stuff on twitter, including our own tweets, is half-baked and amounts to what Americans call “carnival barking” (in the service of traffic or attracting followers), so it is better to leave that alone.
The polls will be open until 5 March, 2012:
Once polls close, we will arrive at a shortlist of five. Then it gets interesting: We will have a second, separate round of voting based on your recommendations. That is while you vote in round one, we’ll compile a list of ten names from your suggestions in the comment section, on our facebook page and on Twitter. Candidates who are already on the first list, won’t be included on the second. A second vote/poll will proceed and we’ll announce the result. We will then combine the top five vote takers from the second list with the top five vote takers from the first list. There will then be a third and final round of voting based on the new combined list that will take one week. After that we will announce the overall winner.
The candidates are: Samir Amin , academic, activist (Senegal/Egypt), Jean  and John Comaroff , academics (South Africa/United States), Chinua Achebe , writer (Nigeria), Mahmood Mamdani , academic (Uganda), Mamdouh Habashi , academic, politician (Egypt), Kwame Anthony Appiah , academic, philosopher (Ghana/United States), Achille Mbembe , academic (Cameroon/South Africa), J M Coetzee , writer (South Africa/Australia), Issa Shivji , academic (Tanzania), Nawal el Saadawi , writer and activist (Egypt), Wole Soyinka , writer, activist (Nigeria) and Virginie Toure , activist (Cote d'Ivoire).
Africa is a Country is a group blog:
The media blog that is not about famine, Bono, or Barack Obama. For that, go to Newsweek. Frequent contributors are media expert Brett Davidson; academics Sean Jacobs (he started AIAC), Neelika Jayawardane, Kathryn Mathers, Marissa Moorman, Lily Saint, Melissa Levin and Dan Moshenberg; writer and health advocate Caitlin L. Chandler; filmmaker Dylan Valley; writer and academic Abdourahman Waberi; and graduate students Boima Tucker, Anni Lyngskaer, Sophia Azeb, Tom Devriendt, Loren Lynch, curator and filmmaker Basia Lewandowska Cummings, writer and journalist Elliot Ross, writer Orlando Reade; Hinda Talhaoui; and Mikko Kapanen.
Go here  to vote for the most influential African alive.