He was a member of the Parliament of Scotland for Whithorn from 1702 to 1707, and a Commissioner for the Union of Parliaments for the Whig Party: he sat in the first Parliament of Great Britain in 1707. He was appointed a Baron of the Exchequer for Scotland on the constitution of the Exchequer Court, 13 May 1708, a position he held for nearly half a century. With Baron Scrope, in 1726, he drew up an Historical View of the Forms and Powers of the Court of Exchequer in Scotland, which was printed at the expense of the Barons of Exchequer for private circulation. A leading supporter of the Act of Union 1707 with the Kingdom of England, Clerk wrote in his memoirs of Englishnovelist, journalist and secret agentDaniel Defoe that it was not known at the time that Defoe had been sent by Godolphin : "... to give a faithful account to him from time to time how everything past here. He was therefor a spy among us, but not known to be such, otherways the of Edin. had pull him to pieces".
Antiquarian leanings
Of his other treatises, Clerk wrote papers in the Philosophical Transactions: one an Account of the Stylus of the Ancients and their different sorts of Paper, printed in 1731, and the others On the effects of Thunder on Trees and Of a large Deer's Horns found in the heart of an Oak, printed in 1739. He was the author of a tract entitled Dissertatio de quibusdam Monumentis Romanis &c, written in 1730 but not published until 1750. For upwards of twenty years he also carried on a learned correspondence with Roger Gale, the English antiquary, which forms a portion of the Reliquiae Britannica of 1782.
Patron of the arts
Sir John Clerk was one of the friends and patrons of the poet Allan Ramsay who, during his latter years, spent much of his time at Penicuik House. His son, Sir James Clerk, erected at the family seat an obelisk to Ramsay's memory. Sir John was a patron to various other artists and architects, and even dabbled in architecture himself.
Musical talent
Clerk had a musical bent also, and while in Rome may have been tutored by the Baroque composer Arcangelo Corelli, but his own work has often been overlooked, primarily since the only record of his composition seems to be his own papers. One of his humorous songs was O merry may the maid be that marries the miller.
Family
Sir John succeeded his father in his title and estates in 1722. He unsuccessfully courted Susanna, daughter of Sir Archibald Kennedy of Culzean, Baronet and that correspondence is in the National Archives. She became the third wife of Alexander, 9th Earl of Eglinton. He married, firstly, on 23 February 1701, Lady Margaret, eldest daughter of Alexander Stewart, 3rd Earl of Galloway who died in childbirth on 26 December that year. Her son, John, survived, but died unmarried in 1722. Sir John married again, to Janet, daughter of Sir John Inglis of Cramond, by whom he had seven sons and six daughters. He died at Penicuik House on 4 October 1755.