Knowles died on Thursday after a brief illness without revealing the answer to the question his readers have debated for decades -- did the novel's schoolboy hero, Gene Forrester, purposely cause the accident that crippled his best friend, Phineas?
"John used to say he would never answer that question," his brother-in-law Bob Maxwell told Friday's South Florida Sun-Sentinel. "He took that one with him."
The critically acclaimed novel, published in 1959, is one of the most widely read and studied novels in recent decades and sold as many as 500,000 copies a year. It was made into a movie starring Parker Stevenson in 1972.
"A Separate Peace" was inspired by Knowles' adolescent experiences at Phillips Exeter Academy, the New Hampshire prep school he graduated from in 1945.
Set in a New England prep school during the Second World War, the simply written novel explores themes of good and evil, friendship and envy. Gene causes his athletically gifted and seemingly perfect friend Phineas to fall out of a tree, suffering a leg injury that maims him for life.
"A Separate Peace is based on experiences that I had, but it is not literally true," Knowles told the Sun-Sentinel shortly after moving to Fort Lauderdale beach condo in 1987.
Knowles was born Sept. 16, 1926, in Fairmont, W. Va., and was sent at 15 to the prestigious Phillips Exeter Academy in New Hampshire, where he graduated in 1945. Exeter became the model for Devon, the school in "A Separate Peace."
After Exeter, Knowles qualified as a pilot in the U.S. Army Air Corps, then enrolled at Yale University before working as a reporter and drama critic at the Hartford Courant from 1950-52.
After touring Europe, he returned to New York in 1955, where he became an associate editor at the magazine "Holiday", a job he quit after "A Separate Peace" was published.
In the 1960s, he served as writer-in-residence at the University of North Carolina and at Princeton. Since moving to Fort Lauderdale 15 years ago, Knowles taught creative writing at Florida Atlantic University.
Encouraged by playwright and novelist Thornton Wilder to write about vivid events in his past, Knowles wrote "A Separate Peace," which made him rich and famous.
He wrote 11 other books but only two are still in print, "A Separate Peace" and its sequel, "Peace Breaks Out." He said he never minded that his reputation rested entirely on one book.
"How could I mind?" Knowles said in 1986. "It's paid the bills for 30 years. It has made my career possible. Unlike most writers, I don't have to do anything else to make a living. In addition, 'A Separate Peace' gave me an identity."
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