This book investigates potential neo-Darwinian fallacies, specifically regarding a priori assumptions, that may have led to weak scientific methodology and praxis. It was proposed that five concepts must be true for neo-Darwinism to be true. These are gradualism, the tree of life hypothesis, the evidence of microevolutionary change accounting for macroevolutionary change, time and chance, and methodological naturalism. Prima facie, these concepts have tremendous explanatory power. Yet, with an attempt to carefully examine these concepts, all five seem to be assumed a priori so as to dictate the outcome of neo-Darwinism rather than letting the evidence speak for itself. The evidence left by the Cambrian explosion, genomic potential, genetic entropy, irreducible complexity, genetic limits, cyclical change, probability theory, the epistemology of information, and the law of causality seems to pose a dilemma for neo-Darwinian assumptions.