The widespread misperception of science as a deliverer of irrefutable facts, rather than a deliberative process, is undermining public trust in science. Science education therefore needs to better support students' understanding of the central role that disputes play in the scientific process. Successfully incorporating scientific disputes into science education is, however, challenging. The aim of this paper is to identify course components and design features that develop undergraduate students' abilities to write a logically coherent argument that is supported by evidence. First, we assessed student essays from a course that had gone through a major revision aimed at strengthening students' reasoning skills. When comparing pre- and post-revision essays, we found substantial, and significant, improvements across the assessment criteria. We then elicited oral and written feedback from instructors who taught the course pre- and post-revision. We identified several changes that instructors felt most impacted students' reasoning skills, most importantly: streamlining of learning outcomes and course content emphasizing argumentation skills; stronger scaffolding and better utilized peer review; and more detailed rubrics that specifically reference learning outcomes and course content. The study illustrates the power of iterative course revisions that incorporate findings from published research and instructors' reflections on teaching practices as a way to strengthen student learning.