Scientific inquiry (experimentation and investigation to test hypotheses) is the basis for discovery and theory building in the natural sciences. Learning from the process of scientific inquiry requires loosening our grasp on prior conceptions and constant revision of our mental models based on new experimental results. We posit that learners will require multiple iterations through a 'reflective prediction cycle' in order to identify, reconcile and revise their misconceptions. Amending the traditional scientific method for experimentation with system model building will help learners to articulate their mental models, make better predictions, and reflect more effectively. Working to reconcile the gaps and inconsistencies within their mental models, systems models, predictions and results, will provide the learners with a powerful, explicit representation of their misconceptions and a means to repair them. Although learners in this project will be firmly seated in scientific concepts relating to plant biology, advanced life support and space colonization, conceptual change within the cycle of modeling, prediction, experimentation, and reflection should be investigated across domains.