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This paper presents an analytical framework for tracing knowledge re-organization through self-generating explanations and representations. The analytical framework, inspired by the knowledge in pieces perspective (diSessa, 1993), is applied to one case study, to illustrate the type of insight the framework could provide. Data comes from observations on pairs of 4-8th grade students engaged in one to two hour sessions, generating representations to explain the phenomenon of the moon phases, and collaboratively elaborate their representations and explanations. The analysis traces the development of explanations of one pair of students as an indication of their developing understanding, and tracing the re-organization of knowledge pieces throughout the process.