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A key aspect of using scientific models and other representations as cognitive learning tools is the reciprocal relationship between understanding the nature of models as representations, and understanding the specific concepts and phenomena that the model is intended to represent. However, challenges exist regarding how to describe and measure indicators of this reciprocity. We explored the ways in which 8th and 9th grade students utilized physical dynamic tabletop models towards developing sophisticated understandings of full scale Earth System processes. This approach allowed us to identify and describe evidence of the "bootstrapping" that occurs between understanding the model as a scientific representation, and understanding the science concepts of the represented entities, configurations, motions, and emergent phenomena in the real Earth System. We argue that this notion of bootstrapping is a productive means to conceptualize and support the development of students' epistemological understandings of both scientific models and the represented science concepts.