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He was appointed Instructor (later Assistant Professor) of Astrophysics at Imperial College and worked there until his death. He was an expert in spectroscopy, being one of the first to determine that the temperature of sunspots was cooler than that of surrounding regions.
"Associate of the Royal College of Science. Assistant Professor of Physics (Astrophysics Department) Imperial College and Technology, South Kensington. Distinguished for his contributions to Astronomical Physics by spectroscopic observations of eclipses, solar pre-eminences, and sunspots, and by experimental researches bearing on their interpretation. Associated in observations of total eclipses of the sun with Sir Norman Lockyer in 1893, 1896, 1898, 1900, and (with Prof Callendar) in 1905. "
In 1896, Edward Charles Pickering published observations of previously unknown lines in the spectra of the star ζ-Puppis, which he attributed to hydrogen. Fowler managed to reproduce these lines experimentally from a hydrogen-helium mixture in 1912, and agreed with Pickering's interpretation that they were previously unknown features in the spectrum of hydrogen. These lines became known as the Pickering–Fowler series and turned out to be of great significance in understanding the nature of the atom.Niels Bohr included a theoretical examination of these lines in his 'trilogy' on atomic structure and concluded that they had been wrongly attributed to hydrogen, arguing instead that they arose from ionised helium, He+. Fowler was initially skeptical but was ultimately convinced that Bohr was correct, and by 1915 "spectroscopists had transferred [the Pickering–Fowler series] definitively [from hydrogen] to helium." Bohr's theoretical work on the series had demonstrated the need for "a re-examination of problems that seemed already to have been solved within classical theories" and provided important confirmation for his atomic theory.