Students in the sciences learn to engage with primary research articles as a fundamental part of their discipline, essential to both writing and research. These sources are difficult to navigate, leading students to use (and misuse) these sources in a variety of complex ways. As instructors and researchers, we are aware of these challenges, but less aware of why they happen. Here, I analyze surveys, student papers and reflections to understand how students perceive primary research articles across science majors at one institution, as well as their challenges in citing these sources. Together, these results suggest that students gradually develop an understanding of a primary source as a model of the scientific process. To teach source use in the sciences and develop thresholds concepts, there must be an iterative approach that combines instruction and research from writing, STEM education, and information literacy.