The crisis in science education and the need for in-novative computer-based learning environments has prompted us to develop a multi-agent system, Betty’s Brain that implements the learning by teaching paradigm. The design and implementation of the system based on cognitive science and education research in constructivist, inquiry-based learning, involves an intelligent software agent, Betty, that students teach using concept map repre-sentations with a visual interface. Betty is intelli-gent not because she learns on her own, but because she can apply qualitative-reasoning techniques to answer questions that are directly related to what she has been taught. The results of an extensive study in a fifth grade classroom of a Nashville pub-lic school has demonstrated impressive results in terms of improved motivation and learning gains. Reflection on the results has prompted us to de-velop a new version of this system that focuses on formative assessment and the teaching of self-regulated strategies to improve students’ learning, and promote better understanding and transfer.