In 1800, he ran for U.S. Senator from New York but was defeated by Federalist Gouverneur Morris.
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The previous commissioners Gouverneur Morris, Stephen Van Rensselaer, William North, Thomas Eddy, State Senator DeWitt Clinton, Surveyor General Simeon DeWitt and Congressman Peter B. Porter were re-appointed; and Ex-Chancellor Robert R. Livingston and Robert Fulton, who were running a steamboat service between New York City and Albany, were added to the Commission.
Madam De Stael, a French author, at one time invested in the town lands, on the advice of her friend Gouverneur Morris, while it was still part of Pierrepont.
Gouverneur Morris had been elected in 1800 to complete the term (1797-1803) after Philip Schuyler (1797-98), John Sloss Hobart (1798), William North (1798) and James Watson (1798-1800) had occupied the seat.
In Miracle at Philadelphia, Catherine Drinker Bowen called Johnson "the perfect man to preside over these four masters of argument and political strategy i.e. fellow committee members Alexander Hamilton, Gouverneur Morris, James Madison, and Rufus King...His presence on the committee must have been reassuring; the doctor's quiet manner disarmed." (Bowen, p. 235 of the 1986 edition)