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John Twombly was born in Rochester, New Hampshire on July 19, 1814. After working at various jobs and mostly educating himself, he graduated from Wesleyan University in 1843 and was ordained a Methodist minister. During the next thirty years Twombly was a pastor at various churches in Massachusetts, an overseer of Harvard College (1855-67), secretary of the New England Education Society (1857-71), director of the American Institute (1868-70), and superintendent of the Charlestown, Massachusetts public schools (1866-70).
The regents elected Twombly president of the University of Wisconsin on June 30, 1871, and he took office with the start of the school year in September. During most of his presidency Twombly had good relations with faculty and students and was an outspoken proponent of co-education. The latter issue brought him into conflict with the regents, however, as did their reluctance to give him much real executive authority.
In June of 1873 the regents asked Twombly to resign, but he refused. Over the next several months the conflict between Twombly and the regents intensified and the issue even was taken to the legislature. Finally, on January 21, 1874, Twombly resigned.
He returned to the ministry, and served as pastor at several churches in the northeast. He died on January 1, 1893, in Newton Lower Falls, Massachusetts.