What is the source of the conflict between science and religion? Is theism rational for a scientist? Naturalism has become the dominant belief system in Western culture, permeating society on levels both obvious and subtle. Naturalistic philosophy has strong underpinnings in 19th century scientific discoveries but why is naturalism perceived as scientifically objective and defensible, whereas theism is perceived as emotional and without evidential support? It is the thesis of this presentation that, in contrast to popular perception, naturalism is to a great extent faith-based and that naturalists bring to bear many arguments that are philosophical, rather than scientific, in nature. This proposition will be explored by examining the statements of theistic and naturalistic scientists and philosophers, particularly in the area of ideas concerning origins. Complexity will be discussed with respect to origin of life theories to underscore that random genesis and development of biological systems defies all reasonable probability. Moreover, we will examine criticisms of irreducible complexity to evaluate whether they sufficiently address the concern of probability and plausibility. Finally, reasons for individual bias towards naturalism or theism will be discussed by considering the life experiences of several individuals, including Sigmund Freud and C.S. Lewis.