Learning Physical Biology via Modeling and Simulation: A New Course and Textbook for Science and Engineering Undergraduates

Abstract

To a large extent, undergraduate physical-science curricula remain firmly rooted in pencil-and-paper calculation, despite the fact that most research is done with computers. To a large extent, undergraduate life-science curricula remain firmly rooted in descriptive approaches, despite the fact that much current research involves quantitative modeling. Not only does our pedagogy not reflect current reality; it also creates a spurious barrier between the fields, reinforcing the narrow silos that prevent students from connecting them. I'll describe an intermediate-level course on “Physical Models of Living Systems.” The course is a response to rapidly growing interest among undergraduates in a broad range of science and engineering majors. Students acquire several research skills that are often not addressed in traditional undergraduate courses:•Basic modeling skills•Probabilistic modeling skills•Data analysis methods•Computer programming using a general-purpose platform like MATLAB or Python•Pulling datasets from the Web for analysis•Data visualization•Dynamical systems, particularly feedback control.The combination of experimental data, modeling, and physical reasoning used in this course represents an entirely new mode of “how to learn” for most of the students. These basic skills are presented in the context of case studies from cell biology, including:•Virus dynamics•Bacterial genetics and evolution of drug resistance•Statistical inference•Superresolution microscopy•Synthetic biology•Naturally evolved cellular circuits.Outcomes include student reports of improved ability to gain research positions as undergraduates, and greater effectiveness in such positions, as well as students enrolling in more challenging later courses than they would otherwise have chosen. I'll show data based on a survey of students, in some cases several years after they took the course, documenting those outcomes, and connect to current ideas in education research.