Mercer was born 16 January 1726 at Pitsligo manse, near Rosehearty in Aberdeenshire, Scotland to Ann Monro and the Reverend William Mercer, a minister in the Church of Scotland. At 15, he began studying medicine at the University of Aberdeen’s Marischal College, and subsequently graduated as a physician in 1744. He was assistant surgeon in the army of Bonnie Prince Charlie in 1745, and was present at the Battle of Culloden when Charles’ army was defeated on 16 April 1746, and many survivors were hunted down and killed. As a fugitive in his homeland in 1747, Mercer fled Scotland after months in hiding. He bought his way onto a ship and moved to America, settling near what is now Mercersburg, Pennsylvania, and practiced medicine for eight years.
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