Blueprinting Biology

New Ideas / by Joe Kloc /

Scientists develop a visual language for mapping biological systems that they hope will become “the circuit diagrams of biology.”

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SBGN’s potential to become a true standard may meet other roadblocks, however. “It is hard to tell if the language will be adopted,” says Ross King, a computer scientist at Aberystwyth University who develops robotic scientists that design and perform biological experiments. “It depends on many things. Will the journals insist on it as part of the submission process? If you could persuade the journals, then it may actually become a standard.”

The team has already begun reaching out to journal publishers and online databases where information about biological systems is stored. They are targeting future scientists as well, appealing to high school textbook manufacturers with the hope that the next generation of biologists will be brought up speaking the new language.

Advancements in systems biology will have a strong impact on the synthetic biology industry, which takes an engineering approach to designing and assembling biological systems that do not occur naturally in the world and redesigning existing ones. This industry has been expanding rapidly over the past 10 years but it remains relatively small-scale. SBGN’s developers hope that their language will become “the circuit diagrams of biology,” meaning that with standardized maps of biological pathways, the industry will be able to operate on a larger scale than ever before.

The implications could be huge. The electronics industry is worth hundreds of billions of dollars, but had the International Electrotechnical Commission not developed a standard notation for electronic circuits in 1906, it’s unlikely the industry could have grown to such prominence.

The researchers stuck closely to the circuit diagram analogy when they designed and promoted SBGN, hoping that it would propel synthetic biology in the 21st century just as the circuit diagram propelled electronics in the 20th. But some, like Ben Fry, director of Seed Visualization and its research arm, the Phyllotaxis Lab, warn that, when trying to design a language that will advance our understanding of something as complex as a biological system, adhering so closely to any sort of analogy—be it with circuit diagrams or traffic signs—can be unnecessarily limiting.

“It seems odd that they took such a lo-fi approach,” Fry says. Circuit diagrams were developed at a time when engineers had to draw out diagrams on drafting tables. Nowadays, computers do so much of the work that not allowing design elements like color could unnecessarily limits the dimensionality of information encoded in the diagrams. If this really is to be the language of future biological research, maybe considering how compatible it is with fax machines isn’t so important.

There are times when it’s important to have a standard language that can be written by hand. Science cannot—and should not—happen only in front of a computer. As Le Novère explains, “When you’re at a conference and you meet a peer, what you end up doing after 15 minutes is writing down a network on a napkin.”

Any language scientists adopt will undoubtedly evolve in step with the new technologies and ideas of younger generations, and this process will take time. (After all, it took decades of traffic accidents and committee meetings for the stop sign to develop from a small black-and-white marker in Michigan in 1915 into the design we know today.) In order for this sort of evolution to take place, scientists must be in agreement that standardization is needed—something that SBGN has the potential to facilitate.

King sees the efforts of the SBGN team as indicative of a larger trend within biology. “There is a movement right now to increasingly formalize biological knowledge,” he says. “Experiments are getting so complicated and there are many things being done and recorded that we want to reuse it in efficient ways.”

Appropriately, the growth of systems biology has required scientists to step outside the traditional bounds of their research to reconsider how they communicate with one another. It remains to be seen whether or not SBGN will become the standard language for biology, but it seems clear that the efforts of its developers were not in vain. Their work represents a significant advancement in our understanding of how to articulate, formalize, and present the complex biological ideas that emerge from the unprecedented amounts of data researchers produce—and then must confront—today.

Originally published September 28, 2009

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