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Jim Harbaugh has taken the NFL by storm.
When Jim Harbaugh left Stanford to test his abilities in the NFL, he took with him the public perception that Stanford could be a top team.
It's hard to argue that this shouldn't have been the case, look at the job that Harbaugh has done with the 49ers. They're 5-1 in their first six games, and they keep finding ways to win football games.
That being said, Stanford is still a formidable team among the college ranks. Andrew Luck is arguably the best quarterback this country has produced in a decade. He simply doesn't make mistakes.
At the end of last year, Stanford was the best college football team in the country. They would have annihilated Oregon, Auburn or anyone else they played. That is simply a fact.
But the BCS doesn't care about that. Big names are what carry weight in the BCS and without Harbaugh, Stanford only has Andrew Luck. One quarterback can get you places, but it won't help you much in the BCS.