John Knowles Paine was born 9 January 1839 in Portland, Cumberland County, Maine, United States to Jacob Small Paine (1810-1856) and Rebecca Beebe Downes (c1808-1860) and died 25 April 1906 Cambridge, Middlesex County, Massachusetts, United States of unspecified causes. He married Mary Elizabeth Greeley (1836-1920) 7 September 1869 in Cambridge, Middlesex County, Massachusetts, United States.

In the 1850s Paine took lessons in organ and composition from Hermann Kotzschmar, completing his first composition, a string quartet, in 1855 at the age of 16.

On arrival in Europe Paine studied organ with Carl August Haupt and orchestration with Wilhelm Friedrich Wieprecht in Berlin.

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