Born in 1853 in Fairmont Springs, Pennsylvania, Haynes grew up in the state's anthracite coal region, witnessing the back-breaking work and poverty of the coal mining community. At the age of ten, he and his family moved to Philadelphia, where he eventually opened a medical practice after graduating from the University of Pennsylvania with an M. D. and a Ph.D. In 1882 he married Dora Fellows, a family friend from central Pennsylvania, who worked with John in the medical office and in his later reform endeavors. For health reasons, most of the Haynes family moved in 1887 to Los Angeles, where John became one of the city's busiest physicians.
It was in the City of Angels that Haynes embarked on his reform career. At the age of forty-four in 1897, he helped to organize a local chapter of the Union Reform League. Founded by William Dwight Porter Bliss, the League's long-range goal was Christian socialism, but in the meantime it settled for immediate reforms: woman suffrage, direct legislation, public ownership of utilities, civil service, graduated taxes, and other objectives of Progressive-era crusaders. This non-revolutionary program appealed to Haynes, who once confessed to a friend that he was an opportunist "willing to accept a quarter of a loaf if I cannot get a half and a half if I cannot get a whole."
In the next four decades Haynes became the major reform figure in Los Angeles and one of the most important in California. In local politics he served on numerous city charter revision committees, including the freeholders board which created the 1924 charter that guides the city today. He was instrumental in placing direct legislation in the Los Angeles city charter in 1902, making the city the first American municipality to embrace the recall of public officers. Haynes served on the city's civil service commission for a dozen years, was appointed to a number of other city and county positions, and became the city's leading force for public ownership in the 1920s and 30s in his capacity as a member of the Board of Water and Power Commissioners. A dominant influence in Los Angeles politics, he helped to guide the city's urban progressive movement from the early 1900s through the beginning of the New Deal.
At the state level, Dr. Haynes was involved in many Progressive era issues. Contributing heavily to the cause of state insurgents (both actively and financially), he became an advisor to three governors, a key strategist in state progressive politics, and was appointed to a half-dozen state commissions, including the University of California Board of Regents. For over three decades he was by far the dominant force in the inclusion of direct legislation in the California constitution, and in the protection of the initiative, referendum, and recall amendments from attacks by legislators and interest groups. In the 1920s he also was a major figure in the statewide campaign for public control of water and power resources, and assisted Dora Haynes in her 1911 campaign to win woman suffrage in the Golden State.
Beyond state and local issues, Haynes supported a number of other causes. Since 1911 he campaigned for federal laws to protect America's coal miners and other workers. From 1905 he contributed to the Socialist movement (both nationally and locally), and to national organizations promoting "half-way" measures such as public ownership and direct legislation. In the 1920s he became Southern California's leading advocate of protective legislation for Native Americans throughout the nation. Haynes was actively involved in all of these and other movements at the local, state, and national levels at the time he died in 1937.