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John Henry Cooke was born in Weymouth on 29 November 1862, and received his education at St Vincent de Paule Roman Catholic School, Liverpool, and St Mary's Training College of Catholic Teachers, Hammersmith, London. In 1887 he travelled to Malta to take up a post of teacher of English at the Valletta Lyceum. Cooke lived in Malta for seven years, founding an editing the journal 'The Mediterranean Naturalist' after becoming interested in the natural history of the island. He also made significant contributions to the understanding of the geology of Malta, publishing papers on the Tertiary Rocks and Pleistocene deposits of the island, and collecting fossils (which he donated or sold to various European museums).
Cooke was forced to leave Malta in 1894 due to his wife's poor health, but he still produced papers on the geology of Malta on his return to England for the next few years. He became an Inspector in the Science and Art Department of the South Kensington Museum, but when that department closed he was appointed Inspector of Schools in Shropshire and Wolverhampton.
Cooke was commissioned as a Lieutenant in the 3rd (Volunteer) Battalion, The Gloucestershire Regiment in July 1901, transferring to the 1st (Volunteer) Battalion, King's Shropshire Light Infantry (later 4th Battalion, King's Shropshire Light Infantry) in October the same year. He rose to the rank of Captain.
After his retirement from military service and until his death on 7 December 1933, Cooke continued to investigate and write about the prehistory of his local area.