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Waugh’s main research interests are oriented toward understanding dynamics and transport in the atmosphere and oceans. Research in the atmosphere focuses on stratospheric and upper tropospheric dynamics/transport. Improved understanding of, and ability to model, fluid motions in these regions is important for understanding the distribution of trace constituents, such as ozone, and for assessing the impact of human activities on the atmospheric environment. In recent years he has also become interested in the transport in oceans and lakes, and the uptake of anthropogenic carbon.