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Scientific literacy encompasses students’ ability to evaluate connections between evidence and models, a crucial aspect for addressing socially relevant scientific issues. However, the exploration of contradictory associations has been limited thus far. This mixed methods study aims to examine this association across various Earth science topics and explore how students explain contradictions between evidence and models. Through descriptive and correlational analysis and path modeling, findings reveal that link type significantly predicts evaluation scores for two of the three topics. Qualitative content analysis uncovers common categories of contradictions in written responses. This research contributes to a deeper understanding of students’ scientific reasoning and enhances our ability to foster scientific literacy in addressing societal challenges.