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NGSS calls for engaging students in science practices as they make sense of the natural world. However large database studies indicate negative relationships between students’ science practices and achievement. Using PISA 2015 US data and an observed variable structural equation, this study examined whether engaging in three spaces of science practices and teacher’s scaffolding activities predict students’ science achievement and if students’ independent practices of science mediate the relationship between teachers’ scaffolding activities and science achievement. The results showed that only one space of science practices, “explanation”, was positively related to students’ science achievement. In addition, results also indicated that certain positive mediation effects existed between teachers’ scaffolding activities with students’ science achievement through two spaces of science practices respectively.