There are some small urban high schools that have high levels of student engagement in science. However, much of the science education research and student teacher placement in urban areas is done in large, somewhat dysfunctional schools. Those who have created these effective environments for science show that it is only in the "whole school context" in which these effective science classrooms exist and the "matrix" of interactions organized by the teachers "outside" the science classroom that leads to this success. The theory and research behind the success of this "matrix" of interactions that differentiates these effective classrooms from traditional inner city science classrooms is presented. Implications for science teacher educators are also presented.