Eight-year medical programs aim to train physician-scientists capable of critically evaluating evidence and navigating complex ethical dilemmas. Medical Immunology, straddling multiple disciplines, can nurture these abilities. We hypothesized that a structured academic controversy (SAC), centered on a high-profile scientific dispute, could simultaneously reinforce conceptual understanding and foster higher-order thinking. A two-hour, debate-based seminar was conducted one week following the lectures on B-lymphocyte and antibody-mediated immunity. The case focused on the "Lieping Chen Nobel Prize controversy" concerning priority in the discovery of the PD-1/PD-L1 pathway. A pre-class micro-package—including an original article from Proceedings of the National Academy of Sciences of the United States of America, excerpts from the Nobel white paper, and a three-minute animation—was provided to prime students. In class, students were randomly assigned to pro or con teams and engaged in a 50-minute timed debate, followed by rebuttals after switching sides. Real-time scoring rubrics, a 6-item Likert scale (assessing critical thinking and ethical sensitivity), and 60-second post-class audio reflections provided multi-source evaluation data. The mean critical-thinking score rose from 3.2 to 4.1 (p<0.01), and the ethical-sensitivity score from 3.4 to 3.8 (p<0.05). A one-month transfer test showed that 83% of students accurately applied PD-1/PD-L1 concepts to novel immunological contexts, while 47% extended their critical inquiry to new targets (e.g., CD47, LAG-3). Qualitative analysis revealed an increased appreciation for collaborative credit and a decrease in ad hominem language. In conclusion, a single, tightly integrated 2-hour SAC debate significantly enhanced conceptual mastery, critical appraisal, and ethical reasoning without requiring additional curriculum time. This model can be scaled to other contentious scientific discoveries as a practical method for developing evidence-based and ethically-minded physician-scientists.