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This qualitative longitudinal study examines how six in-service science teachers’ perceptions of student uncertainty evolved across two-year practice-based professional development (P-BPD). Using a teacher uncertainty perceptions rubric, we analyzed interview data across five stages to trace changes in five dimensions: roles, types, sources, comfort level, and desirability. Findings revealed the most consistent growth in roles and comfort level, with five teachers reaching the highest level. Desirability also improved as teachers integrated key factors like relevance and complexity into instruction. However, recognizing the intertwined relationship between conceptual and epistemic uncertainty and identifying co-occurring sources proved more challenging. These results underscore the value of authentic inquiry experiences and iterative reflection in supporting teachers to embrace uncertainty as a pedagogical resource.