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Burning Questions in Systems Biology

By John Russell

Feb. 12, 2007 | Sometime soon, I am planning to survey the readers of my Systems Biology Newsletter, one of Bio•IT World’s family of e-newsletters, on their attitudes and plans regarding systems biology (SB). In building the survey, I invited a few folks to suggest questions that might be included. Interestingly, their responses say quite a bit about the state of affairs in systems biology, and I’ve noted a few here.

Pieter Muntendam, CEO of BG Medicine, suggested SB still has definitional issues: “It is tough to say where we are with systems biology. SB still needs its defining moment, where a material finding will bring an important contribution to society and at the same time define what it is (and is not),” he says. “I think questions pertaining of what SB means (in their minds) might be of interest. There are probably many researchers who are trying to create a composite picture of multi-modality analytes, who do not consider this systems biology. SB has found limited adoption in major pharma, and the therapeutic area groups often view their SB/IB colleagues with some skepticism and claim they can do the same without the SB religion.”

Muntendam suggested further probing researcher SB perceptions and others trying to identify “the most important applications of systems biology; the most difficult part of systems biology (accurate measurement, integration, computation, measurement to biology, interpretation?); the most significant unmet need for the application of SB; [and the] biggest misunderstanding related to SB?”

I liked Optimata founder Zvia Agur’s suggestion: “I would be interested to know what the objectively measurable criteria are [that] drug developers suggest for evaluating the contribution of systems biology technologies to improving drug development along the critical path.”

Me too. Maybe a Bio•IT World reader in a position to know will take a stab at an answer, but my guess is that even among drug developers the criteria are often poorly defined and certainly vary from organization to organization.

Gustavo Stolovitzky, manager of functional genomics and systems biology, IBM Watson Research Center, suggested we ask: “Where does the hype of Sys Bio ends and the real science starts? Even for the best-intentioned scientist, the boundary can be blurred.” He also suggested trying to uncover what “is limiting the applications of biomarker discovery (such as microarray and MS) to diagnostics: Is it the noise in the technology? Is it variability in the population? Is it the FDA regulatory system?” Stolovitzky also wants to know what would make quantitative methods more appealing to researchers and what will convince biologists to accept quantitative modeling as a valid resource.

Ariadne Genomics president Ilya Mazo, perhaps sensing a new business opportunity, wondered “what people do right now when they need to compile the targeted databases for their area of interest. It seems that there is not much pathway/systems biology data available for plants and other non-mammalian organisms, human immunology/transplantology, even some human cancers.”

From Julie Bryant of GeneGo came these suggestions focused on more immediate SB uses and preparations to use SB:

•           Do you plan to deploy systems biology tools enterprise-wide through research, development and clinical?

•           Are you developing omics committees that can coordinate experiments to analyze multiple experimental data sets within the systems biology framework, including not only expression but [also] proteomics, metabolomics, HCS, siRNAi etc?

•           What immediate value are you seeing from systems biology concerning saving time and making findings that could not be immediately seen before?

•           Are chemists prepared and trained to utilize systems biology tools starting from compound structures?

•           How important is it to be able to edit pathways with your own proprietary knowledge?

•           How important is [it to you to have] a systems biology infrastructure ... that can hold all your experimental data as well as content, ontologies, proprietary information and databases?

Some of these suggestions will be incorporated into our survey, which we hope to get into the field early in the first quarter of ‘07. Please write to me with questions you think need asking or with answers to some of the questions already posed here.


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