Geosciences SEI investigated student learning difficulties in the geological and environmental sciences, particularly in light of "expert" vs. "novice" understanding and approaches to solving geologic problems. Much of our effort to date has focused on learning difficulties encountered in introductory physical geology and historical geology, and concepts bridging the two courses.
We've been compiling literature references to learning difficulties and documenting previously unreported difficulties (very much work in progress!) Some difficulties we've observed (briefly) and are investigating interventions to improve student learning are:
1) Density differences between Earth materials related to large-scale patterns and processes (i.e., plate tectonics, solidification of magma bodies, atmospheric and oceanic circulation)
2) Arrangement of continental and oceanic crust (ex., a common misconception appears to be that oceanic crust everywhere underlies continental crust; another is that there is always a plate boundary between oceanic and continental crust when they meet)
2) How we know the age of the Earth and earth materials
3) Radiometric half-life, and ratios
4) The rock cycle and rock-forming processes
5) Relative dating/ordering of events problems (which appears to involve several distinct conceptual difficulties)
6) Groundwater and petroleum reservoirs (where these are stored)
7) 2-D to 3-D; map to cross-sectional views
Libarkin, J.C., J.P. Kurdziel, and S.W. Anderson. 2007. College student conceptions of geologic time and the disconnect between ordering and scale. Journal of Geoscience Education 55(5):413-422.
Stokes, A., H. King, and J.C. Libarkin. 2007. Research in Science Education: Threshold Concepts. Journal of Geoscience Education 55(5):434-438.