We describe a third-year undergraduate course that focuses on multiscale modeling and protein folding and has as its primary goal the encouragement of students to integrate thinking across and beyond disciplinary boundaries. The ability to perform innovative and successful research work in STEM (science, technology, engineering, and mathematics) fields is often dependent on being aware of the multiple connections between the sciences, but how to develop such an integrated perspective is rarely taught in college classes. Designed for STEM majors, the course combines laboratory sessions and lectures, assessed through student journals and oral presentations. We report on some of the activities we developed for this course and on the associated outcomes. A syllabus, an assessment, and interview questions, as well as examples of student responses, are provided as supplementary materials. The course topics discussed in this article include an analogy between desiccated corn starch and basaltic columns, a discussion of the size of trees, diffusion at the microscopic and macroscopic levels, and computational aspects of protein folding. Teaching materials, including handouts, experimental methods, and MATLAB codes, as well as student journals, are available from the course website.