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This paper is interested in studying how the use of social annotations of readings matched with knowledge building activities leverage student learning. The affordances of social annotations are not sufficient to support inquiry and knowledge building on their own, but rather need be woven into pedagogical designs. This paper analyzes two graduate course designs in terms of constructed media, student artifacts and communication patterns, revealing routines of active (re)communication, autonomous discussion themes, affective contextualization and deep deliberation beyond the subjective interest of the instructor. We captured the individual and collective understanding that emerge from situating the documents within the social space of the community, thus giving students agency in shaping the knowledge production and practices of their learning community.