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Charles Darwin’s theory of evolution interacted with non-empirical factors including a range of theological concerns. The influence of these theological concerns is typically modeled as secondary to that of empirical evidence. In both Darwin’s thought and later development of the theory of evolution, theological concerns have been viewed as serving in a range of possible roles. However, the theological concerns have consistently been viewed as, ultimately, subservient to empirical science. In the end, science has the final say regarding the content and evaluation of the theory. Here, this paper demonstrates the failure of this model. Theological concerns do have primacy over the science. They motivate the development of evolutionary theory, and they control the interpretation of the empirical evidence and justification of the theory. It is more accurate to view evolution as a theological research program.