The use of science classroom discourse analysis as a way to gain a better understanding of various student cognitive outcomes has a rich history in Science Education in general and Physics Education Research (PER) in particular. When students talk to each other in a collaborative peer instruction environment, such as in the CLASP classes (Collaborative Learning and Sense-making in Physics) at UC Davis, they get to practice and enhance their reasoning and sense-making skills, develop collaborative approaches to problem solving, and participate in co-construction of knowledge and shared thinking. To better understand these important cognitive processes, an analysis tool for monitoring, assessing and categorizing the peer talk arising in this environment is needed as a first step in teasing out evidence for these processes inherent in such talk. In order to meaningfully contribute to the extensive body of knowledge that currently exists, deeper, more insightful answers to the question of what happens linguistically when students struggle to "make sense" and how students use language to mediate these important cognitive outcomes is needed. To this end, a new tool for interpreting particularly qualitative linguistic data is needed, and the first part of the dissertation expounds on the development of a discourse analysis tool that has as its underpinnings a framework for coding borrowed extensively from Systemic Functional Linguistics Theory (SFL). The second part of this dissertation illustrates multiple ways in which the tool is used and how it can be utilized to address many current research questions. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://bibliotheek.ehb.be:2222/en-US/products/dissertations/individuals.shtml.]