We investigate how students connect explanations and arguments from evidence about plant growth and metabolism--two key practices described by the "Next Generation Science Standards". This study reports analyses of interviews with 22 middle and high school students postinstruction, focusing on how their sense-making strategies led them to interpret--or misinterpret--scientific explanations and arguments from evidence. The principles of conservation of matter and energy can provide a framework for making sense of phenomena, but our results show that some students reasoned about plant growth as an action enabled by water, air, sunlight, and soil rather than a process of matter and energy transformation. These students reinterpreted the hypotheses and results of standard investigations of plant growth, such as van Helmont's experiment, to match their own understanding of how plants grow. Only the more advanced students consistently interpreted mass changes in plants or soil as evidence of movement of matter. We also observed that a higher degree of scaffolding during some of the interview questions allowed mid-level students to improve their responses. We describe our progress and challenges developing teaching materials with scaffolding to improve students' understanding of plant growth and metabolism.