Many people are not aware of the current literature regarding alternatives to methodological naturalism. This is not aimed at being a comprehensive list, but rather a starting point for further investigation on a number of different fronts.
A good starting place for thinking about Alternatives to Methodological Naturalism is to take a look at the videos of the sessions from previous AM-Nat conferences. You can find most of these sessions here.
AM-Nat organizers have been involved with a number of prior conferences dealing with methodological naturalism in a number of disciplines. These conferences include:
The Nature of Nature Conference.
This conference was held in 2000, and covered the nature of reality and how that affected our inquiry of it, focusing on biology, evolution, and cosmology. The proceedings can be found here.
The 2012 Conference on Engineering and Metaphysics.
This conference was similar in spirit to the Nature of Nature conference, but focused on the nature of reality as it applied to engineering disciplines, including architecture, reverse engineering, computer science, search, and other engineering specialties. The proceedings can be found here.
For and Against Method by Lakatos and Feyerabend. This book examines the role of methodology itself in science, and contains numerous helpful case studies about when methodology did and did not help out scientific inquiry.
Knowledge and Power by George Gilder. This book presents a non-materialist view of economics, and shows how materialist philosophies of nature obscure the really interesting parts of macro-economics.
The Mind and the Brain by Jeffrey Schwartz. This book presents a non-materialist view of psychology and shows how a non-materialist view of the mind can improve results in psychology.
Agents Under Fire: Materialism and the Rationality of Science by Angus Menuge. This book shows how materialism undercuts the foundations of science itself, and how a non-materialistic framework is required to understand science itself.
The Myth of Religious Neutrality by Roy Clouser. This book shows how different fundamental philosophical propositions work their way into scientific theories, with examples from a number of different disciplines.
The Emperor’s New Mind by Roger Penrose. This book discusses the non-algorithmic nature of conscious thought and the impact of that upon the sciences.
Minds, Machines and Gödel (Lucas).
Creativity, the Turing test, and the (better) Lovelace test (Bringsjord et al).
What Would Teleological Causation Be? (Hawthorne and Nolan).
Using Turing Oracles in Cognitive Models of Problem-Solving (Bartlett).
Toward Complexity Measures for Systems Involving Human Computation (Crouser et al).
Methodological Dualism and a Multi-Explanatory Framework in Psychology (Rakover).