Huxley came from the distinguished Huxley family. His brother was the writer Aldous Huxley, and his half-brother a fellow biologist and Nobel laureate, Andrew Huxley; his father was writer and editor Leonard Huxley; and his paternal grandfather was Thomas Henry Huxley, a friend and supporter of Charles Darwin and proponent of evolution. His maternal grandfather was the academic Tom Arnold, his great-uncle was poet Matthew Arnold and his great-grandfather was Thomas Arnold of Rugby School.  Huxley was born on 22 June 1887, at the London house of his aunt, the novelist Mary Augusta Ward, while his father was attending the jubilee celebrations of Queen Victoria. Huxley grew up at the family home in Surrey, England, where he showed an early interest in nature, as he was given lessons by his grandfather, Thomas Henry Huxley. When he heard his grandfather talking at dinner about the lack of parental care in fish, Julian piped up with "What about the stickleback, Gran'pater?" Also, according to Julian himself, his grandfather took him to visit J. D. Hooker at Kew.  At the age of thirteen Huxley attended Eton College as a King's Scholar, and continued to develop scientific interests; his grandfather had influenced the school to build science laboratories much earlier. At Eton he developed an interest in ornithology, guided by science master W. D. "Piggy" Hill. "Piggy was a genius as a teacher... I have always been grateful to him." In 1905 Huxley won a scholarship in Zoology to Balliol College, Oxford.  In 1906, after a summer in Germany, Huxley took his place in Oxford, where he developed a particular interest in embryology and protozoa. In the autumn term of his final year, 1908, his mother died from cancer at only 46: a terrible blow for her husband, three sons, and eight-year-old daughter Margaret. That same year he won the Newdigate Prize for his poem "Holyrood". In 1909 he graduated with first class honours, and spent that July at the international gathering for the centenary of Darwin's birth, held at the University of Cambridge. Also, it was the fiftieth anniversary of the publication of the Origin of species.

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That same year he won the Newdigate Prize for his poem "Holyrood".