Crowd Computing with Bacteria: Balancing Phenotypic Diversity and Coordinated Behavior

Diversity among the individuals of a population can be advantageous in unpredictable situations because it diversifies the response of individuals to identical stimuli. Conversely, groups can engage in coordinated behaviors that provide important competitive advantages. The potential conflicts and synergies between diversity and cooperation have scarcely been examined in the context of cellular computation and collaborative decision-making. We are combining approaches from microbiology, physics, and applied mathematics to study the computational principles that enable even the simplest biological systems, such as bacteria, to engage in coordinated behavior while still exhibiting individuality. The team is examining the extent to which high-order computational abilities are achieved by harvesting rather than suppressing the functional diversity generated by molecular fluctuations. The project leverages recent breakthroughs in the labs of these Investigators that enable characterizing simultaneously the molecular mechanisms underlying computation at the single cell level, the behavior and performance of those same individuals, and the coordinating interactions among them.

Affiliated Investigators

Thierry Emonet, Ph.D.

Yale University

Thierry Emonet is Associate Professor of Molecular Cellular and Developmental Biology and of Physics at Yale University. He studies how bacteria sense and explore their environment, how flies smell, and how cells in bacterial colonies, in the immune system, and in developmental systems interact and make collective decision. Thierry graduated from ETH Zürich in 1992 with an MS in Physics. In 1998 he earned a PhD in Theoretical Astrophysics from the Instituto de Astrofísica de Canarias, Spain. In 1998 he was a postdoc at the National Center for Atmospheric Research in Boulder CO and from 1999-2002 he was a Research Associate at the Advanced Simulation and Computing Flash Center, Department of Astronomy and Astrophysics, The University of Chicago. In 2002 Thierry switched focus from studying dynamical systems in the universe to discovering how biological systems sense, compute and make decisions. From 2002-2006 Thierry worked as a Research Associate with Philippe Cluzel at the Institute for Biophysical Dynamics, The University of Chicago. He joined Yale University as an Assistant Professor in 2007 and was promoted to the rank of Associate Professor on term in January 2013 and to Tenured Associate Professor in January 2015.  Thierry has been the recipient of multiple awards including the Alfred P. Sloan Research Fellowship, Research Award on Complexity from the James Mc Donnell Foundation, Research award from the Whitehall Foundation, and Allen Distinguished Investigator from the Paul G. Allen Family Foundation. The Emonet lab is also funded by NSF and NIH.

Tom Shimizu, Ph.D.

FOM Institute for Atomic and Molecular Physics (AMOLF)

Tom Shimizu is Group Leader at the FOM Institute for Atomic and Molecular Physics (AMOLF). He studies the design principles underlying biological behavior by developing biophysical experiments and theoretical models that bridge dynamics at the scale of molecules, cells and the whole organism. He obtained his Ph.D. from the University of Cambridge in 2003, working with Dennis Bray on modeling cell signaling systems using statistical physics theories of magnetic spins. From 2003-2009 he was a postdoctoral fellow with Howard Berg at Harvard University, where he developed Förster resonance energy transfer (FRET) experiments to probe intracellular signaling in live bacteria, and a coarse-grained theory for bacterial chemotaxis signaling. In 2009, he joined the faculty of the FOM Institute for Atomic and Molecular Physics (AMOLF) as a Group Leader. Since 2013, he is a Tenured Group Leader at AMOLF, and since 2015 holds also a joint appointment at the Department of Physics and Astronomy, Vrij Universiteit Amsterdam. Tom is a recipient of multiple awards, including the NWO VIDI Award and the Allen Distinguished Investigator Award from the Paul G. Allen Family Foundation. The Shimizu lab is also supported by the Netherlands Organization of Scientific Research (NWO) and the Foundation for the Fundamental Research on Matter (FOM).

Steve Zucker, Ph.D.

Yale University

Steven W. Zucker is the David and Lucile Packard Professor at Yale University. He graduated from Carnegie Mellon University, obtained a Ph.D. at Drexel University, and did postdoctoral research in computer science with Azriel Rosenfeld at the University of Maryland. He joined McGill University in 1976, where he became professor of electrical engineering. From 1991 to 1996, he was also director of the program in Artificial Intelligence and Robotics at the Canadian Institute for Advanced Research. He moved to Yale in 1996, where he is currently professor of computer science and of biomedical engineering. He is also a member of the Interdepartmental Neuroscience Program and the Applied Mathematics Program, which he directed from 2003 to 2009. He was elected a fellow of the Canadian Institute for Advanced Research, a fellow of the Institute of Electrical and Electronics Engineers; a By-Fellow, Churchill College, Cambridge; and the Newton Institute for Mathematical Sciences. He was honored with the Siemens Award at the Institute of Electrical and Electronics Engineers Conference on Computer Vision and Pattern Recognition and was named an Allen Distinguished Investigator in 2013.

Zucker’s research is in computational neuroscience and computational biology. Seeking basic principles underlying information processing in the visual system, he pioneered the differential‐geometric view of early visual processing. At the network level, he introduced a game‐theoretic foundation for neural interaction, and is now focusing on how such networks could be learned. The goal is to reveal how activity‐dependent cortical plasticity could capture those high‐order statistical relationships in the natural world that are necessary to support complex, visually mediated behaviors. He remains fascinated by how mathematical ideas can inform seemingly unrelated problems, and is also working on a theory of vascular development in plants motivated by visual shape analysis and on collective behavior in bacteria motivated by game theory.