Since its inception in the 1960s, the scientific research of Buddhist-based meditation practices have grown exponentially with hundreds of new studies every year in the past decade. Some researchers are using Buddhist teachings, such as not-self, as an explanation for the causal mechanism of meditation’s effectiveness, for conditions such as stress, anxiety, and depression. However, there has been little response from Buddhist studies scholars to these proposed mechanisms in the growing discourse surrounding the engagement of ‘Buddhism’ and ‘Science.’ I argue that the mechanistic causal explanations of meditation offered by researchers provide an incomplete understanding of meditative practices. I focus on two articles, by David Vago and his co-authors, that have been cited over nine hundred and three hundred times. I make explicit internal criticisms of their work from their peers in neuroscience, and offer external criticisms of their understanding of the cognitive aspects of meditation by using an extended, enactive, embodied, embedded, and affective (4EA) model of cognition. I also use Chinese Huayan Buddhist mereology and causation to provide a corrective for a more holistic understanding. The constructive aspect of my project combines 4EA cognition with Huayan mereology and causation in order to propose new directions of research on how meditative practices may lead to a changing sense of self that does not privilege neurobiological mechanisms. Instead, I argue a fruitful understanding of change in ethical behavior is a changing sense of self using support from a consummate meditator in the Japanese Zen Buddhist context: Dōgen and his text Shoakumakusa. Contemporary research looking for mechanistic causation focuses on the physical body, specifically the brain, without considering how the mind is involved in meditative practices. The group of researchers I focus on reduce the senses of self to localized parts of the brain. In contrast, according to Mahayana Buddhist terminology, Huayan offers a nondualistic understanding of the self that does not privilege the brain. Rather, Huayan characterizes the self as a mind-body complex and meditation is understood to involve the whole of the person. My critique notes how the methodology used in these studies focuses too much on the localized, explicit, and foreground, but not enough on the whole, implicit, and background processes in meditative practices. Bringing in Huayan also offers a constructive aspect to this engagement of Buddhist studies and neuroscience as there are implications of its mereology for a more complete understanding of not just meditation, but also of neuroplasticity. To be clear, the corrective is only meant for the direction of research that focuses on neural-mechanistic explanations of meditation. Surely, there is value in scientific research on meditative practices. However, that emphasis on neural mechanisms gives a misleading impression of being able to fully explain meditative practices. I argue that a more fruitful direction of engagement between Buddhist traditions and scientific research is the small but growing amount of experiments conducted on how meditative practices lead to ethical change. This direction provides a more complete characterization of how meditative practices changes the senses of self. / Religion