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January 29 2014

Cheese, art, and synthetic biology

We’ve published the second issue of BioCoder! In this interview excerpt from the new edition, Christina Agapakis talks with Katherine Liu about the intersection of art and science, and the changes in how we think about biotechnology. It’s one of many reasons we’re excited about this new issue. Download it, read it, and join the biotechnology revolution!

Katherine Liu: What can art and design teach us about biology and synthetic biology?

Christina Agapakis: That’s a great question. There are two different ways you can think about it: first as a way to reach different groups of people and have a different kind of conversation or debate around biotechnology. The second way that you could think about it is more interesting to me as a scientist because I think using art and design helps us ask different questions and think about problems and technological solutions in different ways. To make a good technology, we need to be aware of both the biological and the cultural issues involved, and I think the intersection of art and design with science and technology helps us see those connections better.

KL: What kinds of projects have you done by combining art and biology?

CA: I’m really interested in bacteria and bacterial communities, and how bacteria show us a different part of the world that we don’t normally see. So, a lot of the work I’ve been doing with art hasn’t necessarily been about synthetic biology directly, but instead about how we interact with bacteria on our bodies and in our environment, and how these relationships might change in the future as synthetic biology develops. For example, although it came out of Synthetic Aesthetics, which was about connecting synthetic biology with art and design, the cheese project isn’t really about the potential for genetic engineering to create synthetic biology technologies. Instead, we used cheese as a model for thinking about a much more basic form of biotechnology, how we can shape communities of bacteria to create these really fantastic and delicious products, and how our bodies and our food are these really fascinating ecosystems. Other projects I’ve been working on recently have been around more environmental issues. I’ve been isolating microbes from polluted water and from soils around California, using bacteria to understand how humans interact with the environment.

KL: How did you first get involved with biotechnology?

CA: I was really excited about biology in high school and then kind of obsessed with everything I learned about molecular biology and biochemistry in college. When I started working in a lab, I learned that a lot of basic biology experiments involve genetic engineering. To understand how genes work, people are moving genes around and understanding how things fit together, and I was excited to be learning those techniques and tools. But it wasn’t until graduate school when I first met my advisor, Pam Silver, that I heard about synthetic biology. She’s one of the leaders in the field, and she really inspired me to think about the things I had learned in my biology classes and in the lab, not just as a way to learn more about how cells work, but also as a way to do engineering and to build useful things. That was really exciting for me, and Pam is great. So that’s how I got into the field of synthetic biology!

KL: What kind of trends do you see coming up in biotechnology?

CA: I think the field is definitely maturing in some really interesting ways. In academia, we’re seeing a lot more complexity in the kinds of projects people are working on. A lot of the projects that have been talked about for a while but have been a lot of really hard work to build are starting to come online, in particular projects like the Church lab’s reprogrammed E. coli genome. I’m also really excited by what I see happening in terms of synthetic ecologies. You see more people working with communication between bacteria and engineering communities of bacteria to do things.

KL: What do you think the future of synthetic biology is going to look like?

CA: For me, I want to see it become more like biology — more messy, more like cheese making than like computer science. The analogies between computers and cells have been really interesting and have gotten people excited about synthetic biology’s potential, but I think what we’re going to see is a transformation: a new paradigm as we learn how complicated things are inside a cell and where those analogies break down. We’re going to be able to develop new ideas based around the ways that biology does things that are going to be more complex and more robust and able to adapt in interesting ways, and I think that’s going to shift the way that we think about biotechnology.

KL: I noticed that you’ve been an iGEM advisor. How can we bring biotechnology to younger students?

CA: I think iGEM in particular has been really excited about getting college-level and now high school students to think about biology as an engineering platform. In high school, I was on the robotics team, and there were a lot of engineering competitions. But that hasn’t really been there for biology yet, so iGEM is creating that same sort of idea of team-based projects around biology instead of around robots. It’s been great, and advising teams has been fun for me and really rewarding. I was an advisor for the Harvard team for a couple of years, and I’ve been working with students at UCLA — this is the first year UCLA competed in iGEM. There were a couple of students who were excited about starting a team and developing a project, and it was really fun and hard work to help them get this started. But it’s been great to see students learn by doing and learn about what is possible with those tools by jumping into the lab.

KL: What kinds of projects did the UCLA iGEM team work on?

CA: This year, the UCLA team was interested in phage, which are viruses that can kill bacteria, and they’re interested in that relationship and the specificity between phage and bacteria. They found a really cool system where one phage uses recombination to generate a lot of diversity in the way that it interacts with the bacteria, so there’s this natural system that the phage uses to accelerate evolution so it can interact with different things on the surface of the bacteria. They use that protein as a scaffold to do protein engineering, so they were looking at natural systems that created a lot of diversity and using those as a scaffold to generate diversity in vitro, in the lab to apply it to other cells.

KL: I think an issue that a lot of students who go into biology face is whether to go into academia or industry right out of school. Why did you choose academia?

CA: I wanted to learn forever — I was really excited about going to graduate school. I didn’t know a lot about biotechnology and I’d never heard of synthetic biology; I was just excited about biology and chemistry and how things worked. I wanted to figure out how those things worked, so that’s why I went into grad school right out of college. Now we see more and more that there’s an overlap between the applied technology-building side of industry and the knowledge-building side of academia. There’s a really interesting connection between making and knowing. In synthetic biology, that’s really clear — as we make things, we understand more about them, and there’s some really interesting crossovers happening between industry and academia, too.

KL: Do you have any advice for students who want to study what you do, especially areas combining biology and art?

CA: The advice that I give to students is always just to follow what you’re curious about, and read a lot. What I see a lot is students who are really curious and passionate about certain fields, but they actively stop themselves from learning more about it, from following this curiosity, because they think that it might not be useful or that it doesn’t fit with the idea of what a good student or a good scientist would be interested in. I was an instructor for an art and science summer program at UCLA for high school students, and many of the students came in with an idea of what counted as science and what counted as art, and what they were good at or not good at. They would say, “I’m good at physics, and I only want to do physics,” (or even worse, “I’m not good at math; I don’t want to do math and science”). But through the two weeks we were doing the program, they began to see the connections between what they were really excited about in physics or in art and other things, maybe in other fields of science or in fields of art and the humanities. So my advice is: don’t be limited by what you think you’re good at or what you’re supposed to be good at, because some of the most interesting things you can learn come from the connections that you can make from looking a little bit outside of the path that you’re on.

November 08 2013

Craig Venter on moving at the speed of light

Last week I had the privilege of speaking with J. Craig Venter at the Hillside Club in Berkeley, as part of the Bay Area Science Festival. Dr. Venter is a pioneer in biotech, from sequencing the Human Genome to creating a synthetic organism. It was an exciting moment for me, personally, as he thinks in terms of moonshots and succeeds often (through the failures).

Dr. Venter was in Berkeley as part of his tour to promote his new book, Life at the Speed of Light, which was inspired by Erwin Schroedinger’s question in 1943, “What is Life?” That question set Dr. Venter off on a life-long quest: first, to first take life apart and then rebuild it; to test his understanding of the machinery of life; and, ultimately, prove that he and humanity could rebuild life from scratch. The machinery of life still involves a lot of mystery, even for the simplest synthetic organisms. When when they were building the first synthetic organism, they focused on the minimum number of genes needed to create a viable life form. They found that they needed to include 50 genes with unknown functions. Without these genes, they couldn’t get the organism to “boot up.” They are clearly necessary, but why? What do they do? We still don’t know.

Venter also shared his thoughts on life on Mars. He thinks it is likely that life has existed on Mars, as Earth and Mars regularly exchange large amounts of particulate matter filled with bacteria. He’s planning a project to sequence Martian DNA (which he believes exists), with a plan to send the digital DNA sequence back to Earth for re-synthesis. His ultimate aim is to rebuild Martian bacteria on Earth for further study. Venter’s joy in exploring the domain of life rang through. With the rapidly decreasing costs of genetic sequencing and the tiny fraction of bacterial species that we have sequenced, anyone can now be an explorer. In every breath of air or every clump of dirt we grab, there are a multitude of new bacterial species waiting to be discovered.

At the end of Venter’s talk, I was able to ask him, “Where do you think the next moonshots in biotechnology will be?” His answer left me excited about the future. He said that the world’s population is rapidly rising; there are now seven billion people out there who desperately need access to medicine, food and energy. For humanity to live sustainability on this planet, we need revolutions in all of these areas, and those revolutions will be driven by new biotechnologies. His advice to any burgeoning scientist was that there is no area of human endeavor that will be left untouched by biotechnology, and all of these areas are fine areas to pursue.

As we’re all exploring, playing, biohacking DNA in front of computers, in labs, garages or at home, I look forward to the day when an innovation in biotechnology is just as likely to come from an industrial biotech lab in San Francisco as it is from the mind of a young biohacker in a home DIY Biolab. Venter left me with a sense of wonder and excitement for biotechnology and the future; I can’t wait to see what he sequences on Mars!

October 21 2013

The biocoding revolution

What is biocoding? For those of you who have been following the biotechnology industry, you’ll have heard of the rapid advances in genome sequencing. Our ability to read the language of life has advanced dramatically, but only recently have we been able to start writing the language of life at scale.

The first large-scale biocoding success was in 2010, when Craig Venter (one of my scientific heroes) wrote up the genome of an entirely synthetic organism, booted it up and created de novo life. Venter’s new book, Life at the Speed of Light, discusses the creation of the first synthetic life form. In his book and in video interviews, Venter talks about the importance of ensuring the accuracy of the DNA code they designed. One small deletion of a base (one of the four letters that make up the biological equivalent of 1s and 0s) resulted in a reading frame shift that left them with gibberish genomes, a mistake they were able to find and correct. One of the most amusing parts of Venter’s work was that they were able to encode sequences in the DNA to represent each letter of the English alphabet. Their watermark included the names of their collaborators, famous quotes, an explanation of the coding system used, and a URL for those who crack the code written in the DNA. Welcome to the future — and let me know if you crack the code!

Biocoding is just the beginning of the rise of the true biohackers. This is a community of several thousand people, with skill sets ranging from self-taught software hackers to biology postdocs who are impatient with the structure of traditional lab work. Biohackers want to tinker; do fun science; and, in the process, accelerate the pace of biotech innovation. There are plenty of differences between writing computer code and writing code in the building blocks of life, but the important thing is that it can be done and is being done now by citizen scientists working both from shared biohacker labs (like BiocuriousGenspace, and Counter Culture Labs) and at home (for example, Cathal Garvey, who works out of a spare bedroom in his mother’s home). Drew Endy’s short video about Engineering Biology gives a great overview of what we can accomplish when we start programming the genetic code. One of his projects is genetically encoded data storage — but it’s not just about replacing dry silicon with wet carbon; it’s about what can happen when you can do computing in an environment where you couldn’t possibly place silicon: inside a living cell.

Biotech is the wet nanotech we’ve been waiting for. It’s a little less logical and a lot buggier than we’d like, but we now have the tools to write DNA, insert this code into a cell, reboot the cell and make those cells produce custom-designed proteins and substances, and engineer biology. The potential for synthetic biology and biotechnology is vast. The biocoding era will be as transformative as the computer era, and we all have an opportunity to create the future together.

Biocoder is a new O’Reilly quarterly newsletter chronicling the rise of DIY bio, synthetic bio, biohackers, Grinders, and the new innovations being developed at the edges of the biotech industry. Check out Biocoder and download it for free.

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