What makes a high-quality biomarker experiment? The success of personalized medicine hinges on the answer to this question. Unfortunately, as many commentators have now emphasized, the quality of most biomarker experiments to date has been quite low. Although the technical side of this problem has received considerable attention, the philosophical issues remain largely unexplored. In this paper, I argue that understanding what constitutes a high-quality biomarker experiment requires some fundamental shifts in how we think about the epistemology, ontology, and methodology of clinical translation.