My research addresses philosophical questions about scientific inquiry and methodology, and looks closely at actual scientific practice. I focus on experimental and computational methods in sciences that deal with complex systems, in particular the life sciences. I have pursued these interests in a variety of projects spanning the philosophy of biology, philosophy of science, history of science, and bioethics, concentrating especially on experimental microbial systems and areas of inquiry that challenge our ideas about life and its simplest forms.
Philosophy of scientific experimentation
My dissertation is about the methodology and epistemology of scientific experimentation, and the relationship between experiment and simulation. I focus on examples from experimental evolution: the propagation of organisms, usually microbes, in a controlled laboratory setting to study evolution in real time. Experimental evolution offers a revealing lens through which to examine these issues, because it challenges the boundaries philosophers of science have traditionally drawn (i) between hypothesis-testing and exploration, and (ii) between experiment, observation, modeling, and simulation. In the first part of the dissertation I develop an account of how experimental evolution combines, and blurs the lines between, hypothesis testing and open-ended exploration. The broader implication is that we should not think of the conceptual landscape of experimental inquiry, and its relationship with scientific theories, as clearly divided into (or exhausted by) these two kinds of experiment. The second part of the dissertation addresses the relationship between experiment and simulation. The belief that experiments have epistemic privilege over simulations is common among philosophers and historians of science, and scientists themselves. I argue against that view. Focusing on the experiment/simulation distinction, per se, as a guide to judgments about epistemic value muddies the waters of a more important issue: evaluating how (any) scientific objects of study successfully inform us about our targets of inquiry in the natural world. I develop a preliminary account of the context-sensitive role that the experiment/simulation distinction should play in thinking through that larger question.
I am also interested in surprising or confounding results—the role they play in scientific inquiry, and the different kinds of sources of surprise that can be found in scientific objects of study, like experimental systems or computer models. People often think that simulations cannot surprise us the way experiments can. I am currently working on a paper in which I assess various versions of this claim, argue that it is false as a generalization across science, discuss limited contexts in which it is true, and in the process develop an account of the role and value of surprise in scientific inquiry.
- "Experiments, simulations, and epistemic privilege." Philosophy of Science, in press.
- "Surprise." In preparation.
- "Time travel, sex, and pushing boundaries: Why philosophers should pay more attention to experimental evolution." In preparation
Explanation and methodology in research on the origin of life and astrobiology
Another thread of my research examines the methodology and implications of attempts to find and characterize anomalous life forms, or challenge the basic biochemical constraints on life. In a recent paper I discuss the controversial 2010 discovery of bacteria that allegedly substituted arsenate for phosphate in their DNA. There is an important difference between challenging biochemical or physiological constraints, and investigating genuinely anomalous life forms. The so-called "arsenic bacteria" case, contrary to how it was portrayed in the scientific press and media, did not involve the kind of project that could, in principle, cause us to fundamentally revise our knowledge of life in the strong sense.
- "What could arsenic bacteria teach us about life?" Biology and Philosophy, 28(2), 205–218 (2013)
Ethical, legal and social issues in synthetic biology and biotechnology
From 2005–2008, as a member the PACE (Programmable Artificial Cell Evolution) research consortium funded by the European Union’s Future and Emerging Technologies Program, I researched ethical, legal, and social issues (ELSI) in bottom-up synthetic biology. This research area seeks to create minimal living or lifelike entities from nonliving materials. People have focused significant attention on ELSI in nanotechnology and top-down synthetic biology, or the modification of existing life forms to create new ones, famously exemplified by the work of J. Craig Venter. Bottom-up synthetic biology raises some of the same issues, but it is unlike top-down synthetic biology in a key sense: It operates at the transition from manipulating inert chemicals to manipulating lifelike or extremely minimal living systems. My research addresses the overlap and divergence from ELSI that arise in top-down synthetic biology, public communication of science, and applying precaution to policy decision making about new biotechnologies under extreme uncertainty.
The ethics of protocells: Moral and social implications of creating life in the laboratory (co-edited with M. Bedau). The MIT Press (2009)
Living technology: Five questions (co-edited with M. Bedau, P. Goldberg-Hansen, and S. Rasmussen). Automatic Press/VIP (2009)
"Social and ethical checkpoints for bottom-up synthetic biology, or protocells" (with M. Bedau, U. Tangen and B. Hantsche-Tangen). Systems and Synthetic Biology, 3, 65–75 (2009)
"The precautionary principle and its critics" (with M. Bedau). In Bedau & Parke (Eds.), The ethics of protocells (pp. 69–87). MIT Press (2009)
"Social and ethical issues concerning protocells" (with M. Bedau). In S. Rasmussen et al. (Eds.), Protocells: Bridging nonliving and living matter (pp. 641–654). The MIT Press (2008)
History of the life sciences
My research interests in the history of the life sciences are tied to my work on contemporary scientific study of microbes and the transition from nonliving to living matter. I am particularly interested in early modern natural philosophy, theories of spontaneous generation and the discovery of microscopic life forms. In a recent paper I examine the experimental methodology and theoretical commitments of Francesco Redi, the seventeenth-century Italian natural philosopher credited with initiating the end of belief in spontaneous generation.
- "Flies from meat and wasps from trees: Reevaluating Francesco Redi's spontaneous generation experiments." Studies in History and Philosophy of Biological and Biomedical Sciences, 45, 34–42 (2014)
When I am not doing philosophy, I am working in Paul Sniegowski's laboratory in the Biology Department, where I have been a member since 2010. I have worked on research projects studying the evolution of temperature sensitivity in experimental populations of E. coli with very high mutation rates, and investigating the specificity of dnaE911, an antimutator allele, by inserting it into different strains of E. coli. My current project is studying fitness evolution in populations with very high mutation rates after 2,500 generations of experimental evolution.
- "Dynamics of fitness evolution in populations with high and extremely high mutation rates" with C. Gentile and P. Sniegowski. In preparation.
- "General antimutators are rare in E. coli: Conditional antimutator effects of dnaE911." with C. Gentile and A. Shaver. In preparation.