My research in the recent past (2005–2015) is summarized on this page. My current research addresses three main topics, all part of a broader effort to develop a philosophy of microbiology. If a single simple research question could unify these three themes, it might be ‘How do microbes explain?’

1. Microbiota, microbiomes and causal explanations

This project looks at microbiota research and its molecular findings about associations between community composition and ecosystem states (e.g., human health and illness). My main aim is to understand how the field is shifting from finding patterns of association to establishing causal relationships. Can causal explanations be achieved from the top down (community-level explanations based on bioinformatic analyses and association studies)? Or are more traditional bottom-up approaches (component-level explanations based on experimental interventions) still the best way to establish causal claims? These are currently open questions that are deeply philosophical, as well as of considerable relevance to the scientific development of this field.

2. Microbial model systems

This strand of research looks at how microbes are used as model systems to generate evolutionary, ecological and physiological insight. There is a lot of historical research with microbial model systems that needs more detailed analysis, and a vast amount of new microbiological model-based research that has had little philosophical attention. My interests lie in understanding better how microrganismal systems work as models, especially when findings generated by these systems are generalized more broadly to large organisms, and what the relationship is between mathematical and microbial model systems of the same target phenomenon. I’ll be pulling these topics together in a book for Harvard University Press, due for completion in early 2018.

3. Microbes, metabolism, and macroevolution

In this part of my research, I focus on how microbial metabolism makes explanatory contributions to understanding macroevolutionary events. Metabolic explanations can provide new insights into macroevolution, including major evolutionary transitions. The same applies to evolution by secondary simplification from ‘primitively’ complex states. This is something many microbial lineages (plus some multicellular ones) have exhibited at a number of major junctures in evolution. Models targeting the interactions between simplification and complexification processes are only just developing, and offer new material for philosophy of macroevolution.