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Quo Vadis Systems Biology


By John Russell

Dec. 2006/Jan. 2007 | In keeping with the Outlook 2007 theme threaded through this issue I thought it would be worthwhile to ask a few prominent providers of systems biology (SB) technology where they thought the field — if it can be called that — was headed. Not surprisingly their answers varied, but just as predictably they mostly thought SB was taking firmer root in biopharma’s awareness.

You get some sense of SB’s growing traction elsewhere in the issue in the comments of David de Graaf, Pfizer’s director of systems biology (p. 18), and Manuel Peitsch, Novartis’s global head of systems biology (p. 24).

But amid the chorus of hope-for-the future came a cautionary note from Keith Elliston, co-founder and CEO of Genstruct. He believes the SB field is splitting and that the division is creating confusion:

“One school is pursuing the study of interacting networks of genes, proteins and metabolites at the level of cells, tissues and organs primarily using ‘omic-scale technologies, while the other is pursuing an ‘engineering’ approach to modeling systems using small amounts of highly detailed dynamic and kinetic data. These can largely be classified as “Hypothesis Generation” versus “Hypothesis Testing” approaches,” says Elliston.

“In the past, these have been seen as the same approach, but it is becoming quite clear that the community is diverging into these two distinct branches. Understanding the distinctions between these two approaches to systems biology has been confusing to the pharmaceutical industry and has had a chilling effect on the perception of ‘systems biology’ in the industry. For the field to grow, these distinctions need to become clearer to the industry, so that they can more effectively match the right approach to their specific problems.”

I’m not sure I buy that completely, but it’s interesting.  

Climbing Interest
Julie Bryant, VP of business development at GeneGo offered another interesting thought for the most important change in the SB community last year, “Probably the integration of a substantial number of labs and projects in a community around open source Cytoscape, led by the Leroy Hood’s Institute of Systems Biology. A number of different labs and projects can now cross-talk using BioPax protocols, share data, draw networks, write inter-compatible plug-ins etc.” 

Good point. It is easy to wonder how open source and standardization efforts will play out in SB.

Zvia Agur, chair and CSO of Optimata — an Israeli company we don’t hear enough about on this side of the Atlantic — thought the FDA’s Critical Path Initiative was stimulating more interest and activity than it is often given credit for. She singled out “opportunity 51” on the FDA’s CPI list — clinical trial simulation — as an area in which Optimata is having success and demand.

“When wedded with effective predictive markers, a biosimulation platform such as Optimata’s Virtual Patient (OVP), can serve as a theranostics tool and be used in patient stratification and in the matching of optimal drug or drug combination regimens to specific patient sub-populations,” Agur says.

Clearly interest in SB is climbing. One coarse measure is the number of systems biology citations in PubMed; it was 1166 on 12/6/06 up from 764 in the spring.

Some folks think the concept is being watered down. Researcher A. John Cornish-Bowden wrote “Putting the systems back into systems biology,” in Perspectives in Biology and Medicine, 2006, Autumn: “In recent years the term “systems biology” has become widespread in the biological literature, but most of the papers in which these words appear have surprisingly little to do with older notions of biological systems: they often seem to imply little more than reductionist biology applied on a large scale...”

You get the drift, and he’s not all that wrong. Systems biology will succeed or not based on results, and the evidence remains promising.

For a more expansive scan of SB technology providers’ 2007 plans, check out Bio-IT World’s survey of senior execs and write to me with your thoughts on the opportunities and challenges facing systems biology at john_russell@bio-itworld.com.

 

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