Scientific knowledge, including the critical evaluation and comprehension of empirical articles, is a key skill valued by most undergraduate institutions for students within the sciences. Students often find it difficult to not only summarize empirical journal articles, but moreover to successfully grasp the quality and rigor of investigation behind the source. In this paper, we use instructional scaffolds (reading worksheets, RWs, with tutorials) to aid students in being able to comprehend, and ultimately transfer, the skills necessary in critically evaluating primary sources of research. We assess students' learning of these skills on a multiple-choice assessment of Journal Article Comprehension (JAC). Students in experimental classes, who received instructional scaffolds, improved on the JAC post-test compared with students in control classes. This result shows that students are acquiring fundamental research skills such as understanding the components of research articles. We also showed that improvement on the JAC post-test for the experimental class extended to a written summary test. This result suggests that students in the experimental group are developing discipline-specific science process skills that allow them to apply JAC skills to a near-transfer task of writing a summary.