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This study followed a social semiotic approach and focused on students’ agency in making sense of biological issues through their deployment of semiotic resources. It drew on thematic patterns theory and examined (1) how students develop their own scientific claims as shown in the patterns of semantic relations in their writing and (2) what factors may contribute to students’ thematic patterning. This study was situated in a biology classroom where Content and Language Integrated Learning pedagogy was employed to guide students’ learning of both subject knowledge and languaging of biology knowledge. The findings revealed the divergent emergence of learner conceptions and identified three influential factors: teachers’ pedagogical cut, students’ knowledge transfer, and the nature of scientific reasoning in biology.