A principled framework is created for the development of learning progressions in science that can demonstrate how their use can transform the way researchers, educators and curriculum developers conceptualize important scientific constructs. Using the construct of transformation of matter, which requires understanding of both discrete learning goals and also the connections between them, a hypothetical learning progression is constructed for grades 5-12. Assessments are developed that link to the learning progression and require students to use cognitively challenging activities such as construction of models and scientific explanation to demonstrate their understanding of topics related to transformation of matter. The resultant set of assessment items can be used to place students along the transformation of matter learning progression, regardless of curriculum. The learning progression is empirically tested in grades 6-8 using mainly, but not exclusively, the chemistry units of the IQWST curriculum in a three year longitudinal study that measures the longitudinal progression of students and the cross-sectional development of teachers as they gain experience with the curriculum. The framework developed for creating the tools can inform the learning of other core ideas in science in emergent sciences that are inherently interdisciplinary. Also investigated is the relationship between student and teacher factors and different levels of students' developmental learning.