The northern states invested large amounts in infrastructure and education, the southern states didn't. Unfortunately, the ideology that the rural life/slavery society had spawned and that rejects government infrastructure and education investments persisted through the civil war and right up to the present day, and so the vast majority of the south never caught up.
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now in all honesty, i did not take a hard look, I just know i was checking Universities in the Northeast recently.

it sure seems like Christian Religions and really rich people did a very nice job of setting up a bunch of Universities. Not a single Ivy covered socialist created place in the lot

I musta missed the really good schools.