Coyne joined the Vatican Observatory as an astronomer in 1969 and became an assistant professor at the LPL in 1970. In 1976 he became a senior research fellow at the LPL and a lecturer in the UA Department of Astronomy. The following year he served as Director of the UA's
Catalina Observatory and as associate director of the LPL.
Pope John Paul I appointed him Director of the Vatican Observatory in 1978, and also associate director of the UA
Steward Observatory. During 1979-80 he served as acting director and Head of the UA Steward Observatory and the Astronomy Department. He spent five months of the year in Tucson as adjunct professor in the University of Arizona Astronomy Department. As Director of the Vatican Observatory he was a driving force in several new educational and research initiatives. He recruited young astronomers worldwide and established a program for non-resident adjunct appointments that allowed women to participate. Women accounted for almost half the participants in the biennial Vatican Observatory Summer School he established for astronomy graduate students. In the 1990s he organized conferences at the Observatory's headquarters in
Castel Gandolfo, including one titled "God's Action in the Universe" sponsored jointly with the Center for Theology and the Natural Sciences of
Berkeley, California. One of his successors said Coyne only asked his hires to do "good science" and that "He created a space where we were all free to pursue that science. He acted as a firewall between us and the vagaries of the Vatican. He made us welcome and he made our collaborators and visitors welcome." Coyne was a vocal proponent of the view that a scientific view of evolution in its classic form, including its random nature, is compatible with Catholic teaching. In August 2005, he sharply critiqued an op-ed column in which Cardinal
Christoph Schönborn appeared to question that position. He wrote that "If they respect the results of modern science, and indeed the best of modern biblical research, religious believers must move away from the notion of a dictator God or a designer God, a
Newtonian God who made the universe as a watch that ticks along regularly.” He proposed an alternative view of God's role as creator: "God in his infinite freedom continuously creates a world that reflects that freedom at all levels of the evolutionary process to greater and greater complexity. He is not continually intervening, but rather allows, participates, loves." In November 2005, he said that "Intelligent design isn't science even though it pretends to be. If you want to teach it in schools, intelligent design should be taught when religion or cultural history is taught, not science." From 2007 to 2011 Coyne directed the Vatican Observatory Foundation. ==Scientific research==