Interdisciplinary Theoretical Biology Team

Finding order in complexity

For decades, molecular biology has been primarily the domain of experimentalists—building a deeper understanding of living systems through direct observation and manipulation. Paradoxically, however, the remarkable success of experimentalists has created an unprecedented need for theoreticians who can make sense of the resulting mountains of data. “We have experienced an inflation of molecular-scale information, including gene regulatory networks and interactions between proteins,” says Atsushi Mochizuki, head of the Interdisciplinary Theoretical Biology Team at iTHES. “It is almost impossible to understand the properties of whole biological systems without using theoretical or computational methods.”

Mochizuki’s contributions to the field include ‘linkage logic’, a theory that helps scientists to simplify the highly complex dynamics of the cell, based on an understanding of the functional relationships between subsets of interacting biomolecules—for example, knowing that gene A turns gene B on but turns gene C off1,2. At iTHES, Mochizuki hopes to benefit from the expertise of scientists from fields with a well-established mathematical and theoretical background. “Early work by theoretical physicists helped determine the direction of modern particle physics,” he says. “We may be able to establish such basic theories in biology, and participation by theoreticians from physics or chemistry will give us the power to accomplish this aim.” As an example, he cites renormalization-group methods, which are commonly used by physicists to achieve ‘coarse-graining’: minimizing the number of elements in a model system without excessively compromising the model’s accuracy.

Mochizuki is already working closely with Tetsuo Hatsuda, iTHES Director and head of the Interdisciplinary Fundamental Physics Team. Hatsuda’s group is helping to address questions related to the distribution of hormones responsible for plant growth and the physical principles underlying the way that chromosomes condense prior to cell division. In parallel, Mochizuki and colleagues are applying their expertise in the dynamics of networks to help Hatsuda explore the process by which heavy elements form in outer space.

Although opportunities for such collaborations have existed in the past, Mochizuki sees iTHES as a powerful incubator for productively bringing together like-minded theoreticians from different fields. “Over the last five years, the number of theoretical researchers at RIKEN in physics, chemistry and biology has increased, but we studied the theoretical sciences independently even though our mathematical techniques might be related,” he says. “iTHES was founded to break these barriers, so that we can share discussions and try to exchange methods between different fields of sciences.”

Theoretical Biology

Research papers

  1. Mochizuki, A., Fiedler, B., Kurosawa, G. & Saito, D. Dynamics and control at feedback vertex sets. II: A faithful monitor to determine the diversity of molecular activities in regulatory networks. Journal of Theoretical Biology 335, 130–146 (2013).

http://dx.doi.org/10.1016/j.jtbi.2013.06.009

  1. Fiedler, B., Mochizuki, A., Kurosawa, G. & Saito, D. Dynamics and control at feedback vertex sets. I: Informative and determining nodes in regulatory networks. Journal of Dynamics and Differential Equations 25, 563–604 (2013).

http://dx.doi.org/10.1007/s10884-013-9312-7

Credit: © alanphillips/iStock

Caption: Physical principles can help to explain biological phenomena, such as the way that chromosomes (shown in dark blue) condense prior to cell division.