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This longitudinal study investigates how secondary students’ understanding of scientific inquiry develops over time using the Views About Scientific Inquiry (VASI) framework. Tracking 416 students from Grades 9 to 12, the study reveals diverse, non-linear growth patterns across inquiry dimensions, with U-shaped trajectories indicating temporary conceptual regressions followed by integration. Growth cluster analysis identifies distinct developmental pathways, while network analysis shows increasing coherence and clustering among inquiry dimensions. Findings highlight the dynamic, individualized nature of epistemic development and emphasize the importance of tailored, developmentally informed instruction. This research positions VASI as a powerful diagnostic tool for capturing cognitive processes and offers insights into designing effective science education interventions aligned with students’ evolving scientific reasoning.