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Frank R. Lillie was born in Toronto, Canada, on 27 June 1870. His mother was Emily Ann Rattray and his father was George Waddell Little, an accountant and co-owner of a wholesale drug company. While in high school Lillie took up interests in entomology and paleontology but went to the University of Toronto with the aim of studying ministry. He slowly became disillusioned with this career choice and decided to major in the natural sciences. It was during his senior year that he developed his lifelong interest in embryology.
From 1886 to 1889 Charles Otis Whitman was director of the Allis Lake Laboratory in Milwaukee, Wisconsin. The lab was established by Edward Phelps Allis, Jr. to provide a place for biological research separate from a university setting and a place where an independent scholar like Allis himself could work. Allis had hired Whitman as an instructor to establish the lab, direct it, and lead a research program there. The lab lasted for eight years, attracted several researchers, and the papers that came out of the lab included a focus on embryology.