Peter Sorger would like to see a model biological system that shows it all at a glance: molecular components, how the components work together, and how the system changes over time in the presence of activators or inhibitors.
He'd like to see something like a biology-based version of SPICE, an interactive simulation program created by electrical engineers and computer scientists at the University of California at Berkeley. SPICE analyzes electrical circuits with any configuration of resistors, capacitors, inductors, etc., in lots of conditions and scenarios.
Like a circuit board, a cell is a like a huge interconnected mess of wires, Sorger said. Instead of being engineered, its components and structures evolved over millennia.
Sorger, director of MIT's Computational and Systems Biology Initiative (CSBi), spoke about research and education in the new biology at the 2004 Symposium in Systems Biology, "From Bioinformatics to Biofabrication," held Jan. 8-9 in Wong Auditorium. The event was attended by researchers from academia and industry.
Someday, researchers may be able to analyze living systems the way SPICE analyzes circuit boards. This integration of biology and technology will be a powerful tool for developing new drugs and other uses, but it's going to take a lot more information and basic knowledge before it can be implemented.
A model in current molecular biology parlance is not really a model, Sorger pointed out, but more of an illustration that does not rely on a universal graphical language like the language of circuit boards. Because of the complexity of interactions at the levels of molecules, tissues, organism and populations, a wide spectrum of modeling methods will have to be applied to systems biology.
A molecular-genetic approach should provide a view of how the system works over time, instead of piling on ever-increasing lists of parts, Sorger said. "Knowing how an individual part works tells you a very limited amount about how they work together," he said.
Even with the plethora of existing biological data, Sorger contends that biology is data-poor in "systematically acquired sets of data. All the interesting data in what I work in seems to be missing," he said. "We need to be able to link unstructured data in a systematic way."
CSBi is a campus-wide education and research program that links biology, computer science and engineering in a multidisciplinary approach to the systematic analysis and computational modeling of complex biological phenomena.
Co-sponsored by the Industrial Liaison Program, the Cambridge-MIT Institute and the Singapore-MIT Alliance, the symposium featured speakers on systems, proteins and mechanisms; manipulating and measuring biological systems; systematic experiments and numerical models; and gene and protein networks.
In addition, the symposium featured a special session on "Research and Education in the New Biology," in which participants from MIT and other universities and institutions compared their approaches to systems biology. Pending approval, MIT will offer a new Ph.D. program in Computational and Systems Biology that integrates the Institute's programs in biology, engineering, mathematics and computer science. Graduates of the program will be prepared to develop new methods, make discoveries and establish new paradigms within academia and industry, where this new area is becoming increasingly important.
A version of this article appeared in MIT Tech Talk on January 14, 2004.