The NSF-funded Earth and Space Science Partnership at Penn State has been designing, conducting and assessing research into student learning of plate tectonics and solar system astronomy (two critical ideas for deep domain understanding) for five years. Over 530 student interviews from middle grades, high school and college have been videotaped, coded and analyzed to develop learning progressions; we focus here on plate tectonics. Partner teachers in Philadelphia and State College middle schools have employed instructional modules developed on the basis of this research, and videos of over 20 instructional days linked to pre-/post-instructional interviews document the impact of new content and pedagogical approaches on student learning. The plate tectonics team also developed an 8-question on-line assessment of student comprehension that has been nationally validated through analysis of over 1000 responses. Our work reveals important gaps in student understanding which we attribute to an instructional approach that emphasizes observations (both modern and historical) in the development of the plate tectonic paradigm, while deferring the mechanistic understanding to higher instructional levels that often are not available to students. As students strive to integrate the observations, many of which involve terminology rather than processes – layers of the earth, rocks and minerals, magnetic stripes on the sea floor – they construct self-consistent models of earth processes that are inevitably non-normative. In addition, pre-college instruction that emphasizes biological processes conveys the message that all energy on earth comes from the sun, resulting in a frequent student (and teacher) conception that volcanoes are most commonly found at the equator because the sunlight is strongest and most consistent there. Unfortunately, subsequent addition of new information does not result in the replacement and realignment of non-normative ideas but instead leads to models that are increasingly complex ways of reconciling disjointed material in support of these early-formed conceptual models.