Writing plays an integral role in any disciplinary course setting. In the sciences, WAC and WID initiatives primarily focus on using writing to deepen student understanding of scientific concepts. Scholars, however, have paid less attention to how writing may facilitate an understanding of the link between concepts and their quantitative expressions and applications. This study, therefore, takes as its subject the use of writing to encourage metacognition. Using a speak-aloud protocol, we taped forty students completing math and science questions. Students would, in other words, talk through their approaches to answering math and science questions. Analysis of the transcripts revealed three distinct cognitive processes demonstrated by students. We discuss the characteristics of each cognitive process and suggest concrete approaches to encourage metacognition through writing in science classrooms. These suggestions are a result of both our analysis of the students' transcripts and our investigation into new approaches to encourage metacognition in the sciences. Our study adds to the general discussion of how writing might facilitate student transfer between scientific concepts and their quantitative applications.