Biology is undergoing a crisis whereby technical innovations designed to overcome the difficulties encountered in explaining complex biological phenomena have not delivered the expected results. To overcome this problem, mainstream biomedical researchers favor adopting new technological wonders without considering that what hinders their research could be due to their philosophical stance, theoretical frame, or looking into the wrong level of biological organization. We address the conceptual problems underlying the scientific crisis by examining the philosophical stances that have illuminated biological thought for the last 200 years and their evolution into the conceptual frames now known as reductionism and organicism. We also analyze how these stances seek to establish causality. The reductionist fixation on bottom-up causation is based on physicalism, a stance that does not allow for emergent phenomena. Organicism, by contrast, allows for emergence and asserts that biological entities are defined by the relation between what they are and what they do; thus, they generate novel qualities and structures. Also, only organisms experience illness and health. Organicism recognizes the role of agency and normativity in determining biological phenomena. Based on these premises, we favor adopting organicism to resolve the current crisis in the biomedical sciences.