Biologists depend on visual representations, and their use of diagrams has drawn the attention of philosophers, historians, and sociologists interested in understanding how these images are involved in biological reasoning. These studies, however, proceed from identification of diagrams on the basis of their spare visual appearance, and do not draw on a foundational theory of the nature of diagrams as representations. This approach has limited the extent to which we under- stand how these diagrams are involved in biological reasoning. In (...) this paper, I characterize three different kinds of figures among those previously identified as diagrams. The features that make these figures distinctive as representational types, furthermore, illuminate the ways in which they are involved in biological reasoning. (shrink)

1. The Naturalistic Turn in Philosophy of Science 2. The Framework of Mechanistic Explanation: Parts, Operations, and Organization 3. Representing and Reasoning About Mechanisms 4. Mental Mechanisms: Mechanisms that Process Information 5. Discovering Mental Mechanisms 6 . Summary.

The philosophical doctrine of methodological naturalism holds that, for any study of the world to qualify as "scientific," it cannot refer to God's creative activity (or any sort of divine activity). The methods of science, it is claimed, "give us no purchase" on theological propositions--even if the latter are true--and theology therefore cannot influence scientific explanation or theory justification. Thus, science is said to be religiously neutral, if only because science and religion are, by their very natures, epistemically distinct. However, (...) the actual practice and content of science challenge this claim. In many areas, science is anything but religiously neutral; moreover, the standard arguments for methodological naturalism suffer from various grave shortcomings. [This is the first part of a two-part article.]. (shrink)