John was formerly Principal Marine Adviser at Scottish Natural Heritage. He holds honorary professorships at both the University of St Andrews and Heriot-Watt University. He is chairman of the Independent Research Advisory Panel for the Dornoch Environmental Enhancement Project (DEEP), a collaborative project between Glenmorangie, Heriot-Watt University and the Marine Conservation Society to reintroduce native oysters (Ostrea edulis) to the Dornoch Firth. He is also the chairman of the Orkney Independent Marine Advisory Group (OIMAG) established by Orkney Islands Council Harbour Authority to provide advice on the implications of various major infrastructure developments around Orkney.
He is Editor-in-Chief of the journal Aquatic Conservation: Marine and Freshwater Ecosystems and has edited a number of major reports on various aspects of the implications of climate change on the marine environment including ocean warming and ocean deoxygenation. His current range of research interests include investigations into the decline of harbour seals around Scotland, the use of genetics to establish the scale of connectivity between the network of Marine Protected Areas in Scotland and the implications of climate change, and the extent and distribution of blue carbon resources in Scotland together with the measures required to better protect and enhance these in the future.