We identify three aspects of scientific thinking beyond the control-of-variables strategy that we claim are essential for students to master as a foundation for skilled scientific thinking. The first is strategic and involves the ability to coordinate effects of multiple causal influences on an outcome. The second is a mature understanding of the epistemological foundations of science, recognizing scientific knowledge as constructed by humans rather than simply discovered in the world. The third is the ability to engage in skilled argumentation in the scientific domain, with an appreciation of argumentation as entailing the coordination of theory and evidence. We present new empirical data with respect to the first two of these competencies, supporting the claim that they are not well developed by early adolescence and warrant attention and provision of effective kinds of scaffolding. © 2008 Elsevier Inc. All rights reserved.