The by-product theory of religion in the cognitive science of religion is problematic on both scientific and philosophical grounds. The by-product theory of religion argues that the explanation for religious beliefs can be reduced to a by-product of the unconscious processes of evolutionary cognitive adaptations. At the scientific level, the concept of emergence describes processes related to religious beliefs that are not causally reducible to cognitive adaptations. At the philosophical level, the by-product theory is often associated with certain metaphysical assumptions about the non-existence of supernatural beings, which is not warranted based on the empirical evidence alone. In general, evidence from the cognitive science of religion does not necessitate the elimination of theological explanations of religious beliefs and theology can act as a competing interpretative framework for the empirical findings at the levels of cognitive and evolutionary science.The by-product theory of religion in the cognitive science of religion (CSR) claims that religious beliefs and behaviors are ultimately reducible to a by-product of evolutionary cognitive adaptations. This view of religion is problematic on two counts. First, evidence from a wide range of sources in the cognitive neurosciences demonstrates that the by-product theory is unable to account for a number of important causal processes in the formation and function of religious beliefs. The by-product theory characterizes religious phenomena from a causally reductive perspective which assumes that causation is primarily bottom-up from part to whole. However, an emergent view of cognition provides a better account of the multiple causal factors involved in religious beliefs.Secondly, the by-product theory is often assumed to indicate that any theological explanation of religious belief is invalidated through the process of eliminative reduction. Thus, the real explanation for religious beliefs is at the level of cognitive and evolutionary science, not higher-level descriptions offered by religious studies or theology. However, the problem here lies in a lack of discrimination between scientific and metaphysical statements. Metaphysical