Tech May 2013

The Hordes of Microbes Inside Your Body Are Your Friends

An interview with the synthetic biologist Christina Agapakis
Jonathon Rosen

As tools for engineering life’s building blocks have proliferated in recent years, our definition of human life has become more expansive. For example, we are learning that the vast ecosystems of microbes inside our bodies are as integral to our health as our own tissues, affecting everything from our immune systems to our brain chemistry. Meanwhile, the field of biology itself keeps expanding—see, for example, synthetic biology, the new subfield that uses the combined insights of molecular biology, engineering, and chemistry to construct biological parts and processes. The synthetic biologist Christina Agapakis, a postdoctoral researcher at UCLA, works at the intersection of these developments. She is also part of a cohort of scientists rethinking the role of biology in our culture.

Alexis Madrigal: People have big expectations for biology in the 21st century. Many say that biotech will be as big as information technology was in recent decades. Is that true?

Christina Agapakis: People want synthetic biology and biotechnology to be the next industrial revolution. Looking back, people have tended over time to imagine bodies functioning in ways that were analogous to the dominant technological paradigm of their day, whether that was steam engines or computers. I hope that soon biology will be the technology we judge things by. Maybe we’re going to see industry and computational stuff start to look more like biology, rather than biology looking more like industry and computation.

AM: Some synthetic biologists have pushed to bring an engineering mind-set to biology. People talk about creating standard DNA “parts,” called BioBricks. What are those?

CA: The idea behind BioBrick parts is that you can have a collection of pieces of DNA that have specific useful functions—off-the-shelf DNA parts. You are able to say, “Okay, I need a part that is fluorescent,” or “I need a part that will activate in response to this chemical.” Then you can mix and match: you put them both in a bacterium, and then you have fluorescence in response to some chemical—so we can have this kind of RadioShack.

AM: You’ve looked at how communities of bacteria work together in the human body and elsewhere. To what extent could we actively engineer our own microbial ecosystem in the future?

CA: We can influence it—we can change the diversity in our gut, and that can influence health. There’s the fecal-transplant example: Sometimes even antibiotics can’t clear up serious digestive infections, and you can’t repopulate the gut with enough good bacteria to get rid of the bad ones. But if you transplant the microbial community from a healthy gut into the person who has this infection, the healthy bacteria will push out the infectious bacteria. The challenge is, you can’t say “You need this many of this and this many of this, and it’s going to stay like that forever.” It’s more a matter of setting the right initial conditions.

AM: There seems to be a tension between the complexity of life, which only gets more intricate the closer you look, and the speed of improvement in the DNA-sequencing technologies that allow us to see that intricacy. The more we learn about the building blocks of life, the more we realize just how much we still don’t understand. Which will win out in the short term—the sense that we know more than ever, or the sense that life is even more mysterious than we’d grasped?

CA: It’s not really a matter of “winning.” Tools that read and write DNA help us understand that complexity, but they’re not enough. Sequencing is not going to tell you how genes are activated, how proteins interact with each other, how the cell interacts with its environment and with other cells. We’re seeing, in the explosion of other kinds of “-omes” [for example, genomes, proteomes, metabolomes], a complexity that will require more than DNA sequencing to decipher.

The price of DNA synthesis is falling, but the overall price of synthetic-biology projects isn’t going down at the same pace, because there is a lot more to the design, construction, and testing of synthetic systems. As Stanford’s Drew Endy likes to say, “Just because we can write DNA doesn’t mean we know what to say.” An artful biological design is an incredibly complex endeavor, not just because of the complexity inside the cell. We also have to think about how applications will be marketed, regulated, and patented; how they will interact with the environment; and many other things that we won’t learn from just the sequence—if at all.

This is the latest installment in a series of conversations about the future, moderated in alternate issues by James Fallows and Alexis Madrigal. For an extended transcript of this and other conversations, visit

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Alexis C. Madrigal

Alexis Madrigal is the deputy editor of He's the author of Powering the Dream: The History and Promise of Green Technology. More

The New York Observer has called Madrigal "for all intents and purposes, the perfect modern reporter." He co-founded Longshot magazine, a high-speed media experiment that garnered attention from The New York Times, The Wall Street Journal, and the BBC. While at, he built Wired Science into one of the most popular blogs in the world. The site was nominated for best magazine blog by the MPA and best science website in the 2009 Webby Awards. He also co-founded Haiti ReWired, a groundbreaking community dedicated to the discussion of technology, infrastructure, and the future of Haiti.

He's spoken at Stanford, CalTech, Berkeley, SXSW, E3, and the National Renewable Energy Laboratory, and his writing was anthologized in Best Technology Writing 2010 (Yale University Press).

Madrigal is a visiting scholar at the University of California at Berkeley's Office for the History of Science and Technology. Born in Mexico City, he grew up in the exurbs north of Portland, Oregon, and now lives in Oakland.

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