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This paper reports on research in which students used agent-based computer models to learn about complex systems and climate change. The intervention in this study involved a set of problem-based learning activities used as part of a productive failure (PF) learning design. The experimental group used a hybrid approach that combined PF with analogical encoding theory, whereas the comparison group used a PF only treatment. Both groups made significant learning gains by the posttest and the complexity and climate change ideas, however, the experimental group performed at a significantly higher level on a posttest transfer problem that required the application of complexity ideas. Implications and directions for future research are discussed.