Analysis of results from research in cognitive science and discipline-based education in recent years suggests that student thinking and learning can be better understood and investigated by adopting a systemic perspective that recognizes the complex and dynamic interactions taking place within and across multiple interconnected and interdependent levels that shape student reasoning in academic settings, including individual and classroom levels. In this first article, we review and discuss the results from research that have helped us better understand the complex system dynamics that characterize thinking and learning at the individual student level. The second article in the set [Talanquer et al. "J. Chem. Educ." 10.1021/acs.jchemed.3c00839] addresses issues at the classroom level. In both papers, we use our analysis to foreground major research insights gained in recent years and to summarize their implications for chemistry education.