Computer-assisted instruction (CAI) has been shown to enhance rote memory skills and improve higher order critical thinking skills. The challenge now is to identify what aspects of CAI improve which specific higher-order skills. This study focuses on the effectiveness of using CAI to teach logarithmic graphing and dimensional analysis. Two groups of ninth graders participated in a one-class period laboratory. Experiment 1 compared a fully automated computer laboratory to an equivalent paper-and-pencil exercise. Experiment 2 compared the same automated computer laboratory in Experiment 1 with a revised, less automated computer version. Both the paper-and-pencil exercise and the less automated computer exercise required students to perform basic mathematical calculations. The results from a post-test revealed that very few students were able to master the complex task of dimensional analysis, but students who took the paper-based and revised, less automated version scored higher overall. These results imply that students required to perform basic calculations had a better understanding of the lab as a whole. These results suggest that until students master basic skills, they do not have the cognitive resources to concentrate on higher-order concepts. This is supported by cognitive load theory.