Whatton was born in Loughborough and worked as an apprentice in Nottingham before qualifying MRCS in 1810. He served as an army surgeon in Portugal between 1811-13. In 1815 he was appointed resident surgeon at the Manchester work house, before setting up in private practice. Whatton was known as an antiquarian and wrote histories of Manchester Grammar School and Chetham's Hospital. He also wrote the biographical sections of Baines, History of Lancashire. Whatton was made FSA of London and Edinburgh and FRS. Whatton was also an early advocate of a university for Manchester. He administered unsuccessfully to William Huskisson following his accident at the opening of the Liverpool and Manchester Railway in 1830. In 1833, Whatton was elected to the honorary staff of MRI, beating Joseph Jordan for this post. He only served in this position for eighteen months, before dying suddenly in 1835.
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