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Plants gradually drew Balfour away from patients and in 1840 he carried the divorce so far as to establish himself as a teacher of Botany in the Extra-mural Medical School in Edinburgh—that exemplar of free-trade in teaching—from which so many of the famous occupants of Chairs in the University have entered its portals. But only in 1842, when Sir William Hooker moved to Kew and a vacancy was then caused in the Glasgow Chair of Botany to which Balfour was elected, was he able to give up medical practice entirely.
In Glasgow the first years of Balfour's botanical career were spent, but they were few. On the death of Graham he returned to Edinburgh as Professor of Medicine and Botany and Keeper of the Royal Botanic Garden—the electors passing over Joseph Dalton Hooker also a candidate. In the sphere of these offices the rest of his active life was passed until his retirement in 1879. He came to the University of Edinburgh at a time when the reputation of its medical school was upheld by a remarkable band of teachers in the Medical Faculty—Allen Thomson, Alison, Christison, Goodsir, Gregory, Jameson, Simpson, Syme—and when the struggle of the University after a revised constitution was approaching the climax reached in 1858, when with other Scottish Universities Edinburgh obtained autonomy, and science was enfranchised. Of this Faculty he became Dean, and held office until close upon the time when he became Emeritus. In all the discussions and controversies, destructive and constructive, that attached to so weighty a crisis, Balfour's influence and outlook for science were used with effect, and no less influential were his action and advice in subsequent years when the specific question of medical reform was raised, as it so often was.
Absorbing administrative work of this kind, to which were soon added the duties of a Secretary of the Royal Society of Edinburgh—(and he remained in the Secretariat to the end of his active life)—as well as those of an editor of the Edinburgh New Philosophical Journal—(afterwards merged in the Annals and Magazine of Natural History)—of Secretary of the Royal Caledonian Horticultural Society and of other offices, made inroad alike upon time and energy of a man who had also the