>newground
When organic molecules, cells, and organisms interact, they give rise to limitless variation and ever more complex structures. “Systems level” biology—how groups of simple agents or cells or organisms come together to exhibit complex behaviors—is the basis of biocomplexity, the study of these phenomena. To understand how a biological system works, a multidisciplinary approach is necessary. Electricity, chemistry, biology, and physics all come together to make a heart beat.
The structures and functions of even the simplest biological phenomena are astoundingly intricate. Multiply these by the complex nature of a more advanced organism—humans, for instance—and we get an inkling of the tasks involved in unraveling the processes. The Indiana University Biocomplexity Institute, soon to be housed in the new multidisciplinary science building at IUB, will deepen our understanding of the web of life.
Why Study Biocomplexity?
According to Biophysics Professor James Glazier, director of the Biocomplexity Institute, “Almost everything in life has this characteristic of simple agents interacting in complex ways. It’s important at the cellular level, for example, how cells differentiate to become cancerous. It’s important in how the machines in our cells work, giving rise to how organs and muscles work. It’s important at the level of how they organize to become more complex organisms. This phenomenon of increasing complexity exhibits itself even in other systems, such as stock markets, traffic jams, economics, or the weather, for example. We apply the principles exhibited here to biological research.”
Further, the ongoing debates governing world policy affect everything from the environment to medical practice. Such critical decisions make Biocomplexity an essential undertaking if we are to understand our place in the world and guide developments in a knowledgeable and prudent manner.
Training
The Biocomplexity Institute will provide interdisciplinary training through multiple departments and institutions. Such training encompasses active participation in research, the involvement of students across different disciplines, and long-term residences in remote laboratories for specialized training and research. The training will also involve new courses shared among institutions and departments; distance-education technology allowing students at other locations to benefit from lectures; and student, postdoctoral, and faculty recruiting.
Indiana University already has a strong interdisciplinary biocomplexity research program, and IU is committed to expanding this program for five additional hires through the Commitment to Excellence. The Biocomplexity Institute is composed of physicists, computer scientists, chemists, biologists, and so on. Andrew Lumsdaine works in computer science. Three new faculty in physics—John Beggs, Sima Setayeshgar, and Rob de Ruyter begin this year, and Filippo Menczer has also joined IU with a joint appointment in Informatics and Computer Science. This overlap in interests adds depth and breadth to the interdisciplinary possibilities.
Finding Solutions
Andrew Lumsdaine researches large-scale scientific computing, and develops software applications including some for biocomplexity. “It's a natural area for us. The computations can span the scale from atoms through organisms. Computational experiments let us understand how behaviors at smaller scales give rise to characteristics at larger scales—for instance how molecules affect cells or how cells affect tissues and organisms. The power of IU's two supercomputing systems will let us create detailed computer models in this way and give us a higher fidelity, higher resolution ‘picture’ of what is going on.”
Sima Setayeshgar works on biologically motivated problems, from the cellular and microscopic—such as how bacteria sense and respond to gradients of food—to how healthy and unhealthy waves of electric potential propagate through heart tissue. Despite the sheer complexity of biological systems, the fact that nature solves many problems—such as measurement of external concentrations by bacteria or photons by the retina—in similar ways points to the existence of unifying principles in the web of life. “This notion makes our quest uniquely rewarding.”
Rob de Ruyter works on understanding the optimization principles underlying biological information processing. The signals collected by the sense organs, such as sound pressure on the ear drum or photons illuminating the retina, are noisy. It is the statistics of signal and noise together that determine how the signal should be processed in the best possible way. An interesting question is how close biological systems are to being optimal. His lab's research efforts, centered on the blowfly visual system, addresses neural coding and optimal processing with quantitative experimentation.
John Beggs grows brain cells, “a brain in a dish, that can live for about a month,” he says. “We eavesdrop on its activity, and look for patterns that this activity produces.” The tie-in with physics is that some of the math that describes the physics of condensed matter can also describe the electrical activity in a living neural network. “When you do basic research, you never know what the outcome might be. But figuring out how the brain works could well bring tangible benefits down the road in new approaches to Alzheimer’s, epilepsy, or blindness, for example. In other words, if we understand the system, we might know how to fix it when it goes wrong.”
Filippo Menczer uses his interdisciplinary approach to make web search engines more adaptive and scalable. He models and simulates complex systems with algorithms inspired by ecological systems to build and apply them to intelligent search agents. “Search environments are complex by nature, and we can take clues on how to approach them by stealing ideas from biological evolution and learning. Systems such as insect colonies and neural networks adapt to their environments. In a sense, we’re teaching search engines to ‘think’ in a similarly adaptive fashion.”
Why at Indiana University
IU has a strong tradition of successful Centers, and vibrant graduate programs in relevant departments. With the Lilly Genomics grant, and other aspects of the Life Sciences Initiative at IU, the university is well positioned to become a leader in the area. Further, it seems likely that Biocomplexity will bolster the state’s economy through the biotechnology and medical industries. “Besides Lilly, Dow, and Cook,” says Glazier, “there are possibilities for expansion, including the Pervasive Technology Laboratories, for example those headed by Geoffrey Fox and Andrew Lumsdaine. PTL is spinning off start up companies, and while it may take awhile, Indiana may well develop the infrastructure.”
The new $50 million Multidisciplinary Science Building at IUB will house the Biocomplexity Institute, a natural fit for the interdisciplinary programs planned for the MSB. “Having a physical home in the new MSB will be great,” says Glazier. “We need the space. We need modern labs.”
>Cary Boyce
Read more about biocomplexity and the new Multidisciplinary Sciences Building.