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Stewart was born in 1964 in East Kilbride, in Lanarkshire, to Sheena and Jack. He has two younger brothers, Graeme and Frazer. He attended Mount Cameron Primary and then Claremont High School from 1976 to 1982. In an interview with the Glasgow Herald, Stewart revealed that he initially struggled with geology: "I was a middling student, never really at the top of the class, nor at the bottom. Which I think is good, in a way. When you're out there at the top, it can be quite isolating."
Stewart was a child actor and holder of an Equity card. His first appearance on television came in 1978, in a BBC Scotland adaptation of John Buchan's 1922 novel Huntingtower. Amongst his contemporaries at the East Kilbride Rep Theatre was the actor John Hannah. Leaving acting behind, he studied geography and geology at Strathclyde University, graduating in 1986 with a first class honours Bachelor of Science degree. He obtained his doctorate, entitled "The evolution of neotectonic normal fault scarps in the Aegean Region" in 1990 at the University of Bristol on research into earthquakes in Greece and Turkey. In 1990 he began teaching geology at the West London Institute of Higher Education (WLIHE) in Osterley (occupying the Warden's flat with his wife for several years), and from 1995 at Brunel University due to its merger with WLIHE. After 12 years in London he moved back to Scotland to develop a new career as a science broadcaster. Nostalgic for Brunel, he said "And invariably, you move on to places that for all their benefits, seem surprisingly narrow, and more fallow, in comparison. In short, it was a remarkable place to be". He moved to the University of Plymouth in 2004, later becoming Professor of Geoscience Communication, a position he believes to be unique in the world.
Stewart returned to television as an expert academic for Helike - The Real Atlantis, a 2002 BBCHorizon film about the destruction of the Greek city of Helike by earthquake and tsunami in 373 BCE, newly rediscovered in 2001. This, he says, "gave me a hunger to get more geology on telly." He featured in another Horizon film, on earthquakes, in April 2003, before appearing as a team member in the fourth series of Rough Science (shown January/February 2004), a series where a group of scientists is challenged to solve tasks using only the resources of the local surroundings and a small set of supplies.
As well as teaching at Plymouth University, he is a patron of the English Riviera Geopark, a member of the Scientific Board of UNESCO's International Geological Programme and chair of its 'Hazards' theme, a vice-president of The Geographical Association and its primary Geography 'Champion', a member of the Steering Committee of the IUGS-Commission on Geoscience for Environmental Management Working Group on 'Communicating Environmental Geoscience', a member of the UK National Coordinating Centre for Public Engagement's Academic Action Research group, and a member of The Geological Society of London's external relations committee. He is a member of the board of directors at the Centre for Research into Earth Energy Systems, University of Durham.
Journeys from the Centre of the Earth (2004), six one-hour films charting how geology has shaped the history of the Mediterranean, shown in the United States on Discovery's Science Channel as Hot Rocks: Geology of Civilization. The series won the prestigious "Best Earth Science programme" award at the 2005 Jackson Hole Film Festival.
Earth: The Power of the Planet (2007), US title: Earth: The Biography, five one hour films (Volcano, Oceans, Atmosphere, Ice, Rare Earth) about the forces that have shaped the planet and made it what it is.Cerapachys iainstewarti, a species of Madagascar ant discovered during the filming of this series, was named after Stewart.
Ten Things You Didn't Know About... Volcanoes (2006), Tsunamis, Earthquakes, Avalanches, (2008).
The Climate Wars (2008), three one-hour films tracing the history of the science and politics of global warming.