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What Manjoo fails to account for -- and therefore removes much of his objections -- is the claim that the 2000 election was also flawed. (And the 2002 election, by implication, as well, though that was not a presidential year.) His first point, about counties voting differently on state-wide elections than presidential elections, is dismissed on this point. He further doesn't account for the fact that after the 200 elections predicted an Al Gore win based on exit polling, the pollsters tightened up their polling methods for the 2002 and 2004 elections. Exit polling isn't the election, but Manjoo fails to counter Kennedy's observation that the Democrats surveyed were more likely to be reticent than the Republicans.
Robert Heinlein predicted that a religious, rightwing extremist named Nehemiah Scudder would win the 2012 election and there would be no elections after that, resulting in the Second American Revolution. He was only 12 years off.