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Training Systems Biologists


At the IBC “Implementing Systems Biology” meeting in Boston in late September, conference co-organizer Steve Naylor, who holds a dual appointment at Boston University School of Medicine and MIT, challenged the assembled audience of biologists, mathematicians, and businesspeople to decide whether it truly mattered whether the concept of systems biology did or did not have a specific definition as a discipline.

A fly on the wall would have heard two arguments: one, that to big pharma, identifying a new project as involving systems biology serves only as a tool for shaking the money tree; and two, that from an engineering perspective, creating a standard definition for systems biology would force researchers to be more specific about the kinds of experiments they can refer to as falling under systems biology.

But there’s another argument for why systems biology deserves a standard definition, and it involves education policy — at the funding agency level as well as at the individual universities. If it is important to teach students at the undergraduate and graduate level to specialize but still learn how to work in an interdisciplinary manner — as most advocates of systems biology agree — then it would behoove NIH and educational institutions to create degree programs that emphasize a common core curriculum. In this sense, it would be essential to define what systems biology means before trying to teach it.

Luckily, NIH and the Howard Hughes Medical Institute are already on the ball — at least in establishing a funding mechanism to support graduate training programs that integrate biomedical science with the physical sciences and engineering. In September, HHMI announced that it will award up to 10 three-year grants of as much as $1 million each to provide startup and supporting funds for interdisciplinary graduate programs, and the National Institute of Biomedical Imaging and Bioengineering will provide five additional years of support to the HHMI grantees through peer-reviewed institutional training grants.

Assuming the integration of biomedical and physical sciences with engineering qualifies as systems biology, what specifically would these programs teach graduate students?

Let me offer my suggestion as to what a systems biology department might teach: As a graduate student in systems biology, I would be expected to specialize in a particular biological system, but one general enough to apply to many different problems: the cell cycle, for example, or DNA replication. In addition, I would expect to acquire a strong grounding in advanced engineering mathematics, such as learning how to approximate solutions to analytic functions, and to gain experience working with and analyzing data from multiple high-throughput instrument platforms, including gene expression analysis, protein identification and characterization by mass spectrometry analysis, and SNP genotyping analysis.

In fact, it might make sense for the department to insist that earning a PhD require the grad student to develop new instrumentation — or at least a variation on an existing technology — that would produce complementary new types of data. Perhaps most importantly, I’d expect to learn bioinformatics skills, such as how to integrate and compare various datasets, and to master the most advanced software and programming languages for doing so.

Unfortunately, it’s apparent there are institutional barriers to adapting university programs for systems biology. At the IBC systems biology meeting, John Weinstein of NCI complained that funding agencies have a bias against non-hypothesis-driven research, which discourages the gathering of data potentially useful for modeling the behavior of biological systems. Other attendees lamented what they see as difficulty in gaining tenure when one’s research primarily involves developing new platform technologies — a potential obstacle for newly minted systems biology PhDs hoping to strike out on their own.

Progress in training a new generation of systems biologists won’t happen overnight, but with guidance and funding from NIH, HHMI, and other organizations, it should happen.

John S. MacNeil, a senior editor at Genome Technology, can be reached at [email protected] His Sense/Antisense column, which covers government research policy and regulatory issues, appears bi-monthly.

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