At this point in time, working with W. David Sharp, Shanks examined some puzzles concerning counterfactual interpretations of quantum mechanics.
He has argued that animal experimentation provided a crucial driving force behind the method of analysis and synthesis that would come to play a central role in the emergence of the physico-chemical sciences in the 17th and 18th centuries.
Physics would ultimately come to have profound implications for physiology, and these matters are explored by Shanks in his work on the writings of the great 19th century French physiologist, Claude Bernard.
Shanks was a staunch defender of evolutionary biology and a vehement opponent of creationism (and its recent incarnation in the form of intelligent design theology).
[1] Shanks is an advocate of methodological naturalism and has argued against drawing supernatural conclusions on the basis of either biological complexity or puzzles in cosmology concerning the fine-tuned universe.
In addition to evolution, Shanks emphasised the role played by self-organization in a purely naturalistic account of biological and cosmological phenomena.
It is now generally recognised[citation needed] that the implications evolutionary biology for medicine must be taken into account if modern medical inquiry is to be placed on a sound theoretical foundation.
Shanks claims that a prediction problem exists due to the fact that humans and their nonhuman models have taken divergent evolutionary trajectories, and are thus not qualitatively identical systems (once compensation has been made for purely quantitative differences in body weight, for example).