Being able to make claims about what students know and can do in science involves gathering systematic evidence of students' knowledge and abilities. This paper describes an assessment system designed to elicit information from students at many placements along developmental trajectories and demonstrates how this system was used to gather principled evidence of how students reason about food web and food chain disturbances. Specifically, this assessment system was designed to gather information about students' intermediary or middle knowledge on a pathway toward more sophisticated understanding. Findings indicate that in association with a curricular intervention, student gains were significant. However, despite overall gains, some students still struggled to explain what might happen during a disturbance to an ecosystem. In addition, this paper discusses the importance of having a cognitive framework to guide task design and interpretation of evidence. This framework allowed for the gathering of detailed information, which provided insights into the intricacies of how students reason about scientific scenarios. In particular, this assessment system allowed for the illustration of multiple types of middle knowledge that students may possess, indicating that there are multiple "messy middles" students may move through as they develop the ability to reason about complex scientific situations. (Contains 6 tables and 1 figure.)