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This paper reports on a two-year effort to develop and use a cognitive process framework for critical thinking to evaluate the depth of students’ collaborative conversations and to inform the design of instructional scaffolds for student learning in science investigations. Results show that a cognitive framework for critical thinking processes can be used to evaluate the depth of critical thinking evident in students’ collaborative conversations as well as to inform design decisions that enhance the depth of students’ critical thinking processes during a middle school science investigation with digitized museum objects. Development of the cognitive framework is described and its application to three iterative classroom studies is discussed.