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Previous studies show the process of biological decomposition is a difficult ecological phenomenon for elementary/middle school students to understand (Leach, 1996; Cetin, 2007; Author, 2012). In this paper, we report a design-based research study (Cobb, diSessa, Lehrer & Schauble, 2003) in which we investigate the structure and form of first-grade students’ knowledge, as well as the development of reasoning about biological decomposition, as they engaged in a year-long modeling-based unit on soil decomposition. The study reported here is part of multi-year longitudinal study (in progress) on the development of elementary students’ biological knowledge. This curriculum is grounded in the “science as practice” perspective (Lehrer & Schauble, 2006), in which concepts, tools and practices of science are considered deeply intertwined.