He was raised as a Quaker and, before moving to the South, worked on the Underground Railroad with his uncle.
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Johnson returned to teaching to become a professor and co-chancellor (1870) of the University of Nashville with former Confederate General Edmund Kirby Smith.
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Among the members of his class were several future Civil War generals: Paul Octave Hebert (1/CSA), William Tecumseh Sherman (6/USA), John P. McCown (10/CSA), George Henry Thomas (12/USA), Richard S. Ewell (13/CSA), James Green Martin (14/CSA), George W. Getty (15/USA), William Hays (18/USA), Bushrod Johnson (23/CSA), William Steele (31/CSA), and Thomas Jordan (41/CSA).