During the Victorian period science shifted from being practiced in a theistic context to a naturalistic context. This book examines the foundations of that change. It is generally thought that this transformation was due to the methodological superiority of naturalistic science. However, this book shows that most of the methodological values underlying scientific practice were virtually identical between the theists and the naturalists. Each camp agreed on the importance of the uniformity of natural laws, the use of hypothesis and theory, the moral value of science, and intellectual freedom. This was despite the claims by both groups that those fundamentals were intrinsic to their worldview, and completely incompatible with that of their opponents. The victory of the scientific naturalists came from deliberate strategies executed over a generation to gain control of the institutions of scientific education, and to re-imagine the history of their discipline. Rather than a sudden revolution, the similarity between theistic and naturalistic science allowed for a relatively smooth transition from the old guard to the new in terms of practice. This book explores this shift through a parallel study of two major scientific figures of the century: James Clerk Maxwell, a devout Christian physicist, and Thomas Henry Huxley, the iconoclast biologist who coined the word agnostic. Both were deeply engaged in the methodological, institutional, and political issues that were crucial to the theistic-naturalistic transformation. This re-examination of the ascendance of scientific naturalism is used to help understand controversies over science and religion in modern America (particularly regarding “Intelligent Design”).