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February 06 2014

Academic biology and its discontents

When we started BioCoder, we assumed that we were addressing the DIYbio community: interested amateur hobbyists and experimenters without much formal background in biology, who were learning and working in independent hackerspaces.

A couple of conversations have made me question that assumption — not that DIYbio exists; it’s clearly a healthy and growing movement, with new labs and hackerspaces starting in most major cities. But there’s another group mixed in with the amateurs, with a distinctly different set of capabilities and goals. DIYbio doesn’t mean exactly what we thought it did.

That group is what I broadly call “disaffected grad students and postdocs.” They’ve got training, loads of it. But they’ve spent the last few years working in a laboratory under a faculty member, furthering that faculty member’s agenda. They have their own ideas and their own research projects, but they can’t work on them within the context of academic biology. They’re funded by a grant, and the grant will only pay for certain things. And, as Anthony Di Franco points out in “Superseding Institutions in Science and Medicine” (in the current issue of BioCoder), grants are primarily given to people who already know what they’re going to find, and that is not how you get truly innovative and creative research.

So, grad students and postdocs are increasingly turning to the DIYbio scene to do work that makes a difference. Some are working within established labs like Genspace or BioCurious; others are building garage labs or kitchen labs of their own; and still others are working in more advanced biohacker facilities such as Berkeley BioLabs or Bio, Tech, & Beyond. These organizations offer mentoring, advice on fundraising, marketing, and other business issues. Their goal is to make it easier for professional biologists to get a startup off the ground. They aren’t all that different from other tech incubators, just with lab benches and centrifuges. QB3, the California Institute for Quantitative Biosciences, even offers a “Startup in a Box” kit for entrepreneurs in biology.

What’s important about the “disaffected postdoc” phenomenon is that it answers one of the biggest questions about the coming revolution in biotech. Sure, a student can make glowing E. coli. That’s the “hello world” of synthetic biology. Making a glowing plant is a lot harder, and still requires PhD-level expertise. That’s changing, as we understand what it means for synthetic biology to become an engineering discipline. We have a catalog of standard biological parts, we have tools for designing DNA, and we can outsource the actual DNA synthesis. It has gotten much easier to do innovative work, and we expect it to get even easier. But the bar to real innovation is still set very high, and it will be some time before we see many bioscience startups founded by enthusiastic amateurs.

Grad students and postdocs who are leaving academia have already gotten over that bar. They’re a critical missing piece to the puzzle: they have the knowledge and creativity necessary to drive biological innovation in the near term. And some of their innovation will be spent developing the tools that will open up biology to a much wider range of participants.

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.

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.

October 16 2013

Announcing BioCoder

We’re pleased to announce BioCoder, a newsletter on the rapidly expanding field of biology. We’re focusing on DIY bio and synthetic biology, but we’re open to anything that’s interesting.

Why biology? Why now? Biology is currently going through a revolution as radical as the personal computer revolution. Up until the mid-70s, computing was dominated by large, extremely expensive machines that were installed in special rooms and operated by people wearing white lab coats. Programming was the domain of professionals. That changed radically with the advent of microprocessors, the homebrew computer club, and the first generation of personal computers. I put the beginning of the shift in 1975, when a friend of mine built a computer in his dorm room. But whenever it started, the phase transition was thorough and radical. We’ve built a new economy around computing: we’ve seen several startups become gigantic enterprises, and we’ve seen several giants collapse because they couldn’t compete with the more nimble startups.

We’re seeing the same patterns in biology today. You can build homebrew lab equipment for a fraction of the price of commercial equipment; we’re seeing amateurs do meaningful research and experimentation; and we’re seeing new tools that radically drop the cost of experimentation. We’re also seeing new startups that have the potential for changing the economy as radically as the advent of inexpensive computing.

BioCoder is the newsletter of the biology revolution. Its goal is to connect the many people working in DIY bio, from postdocs who feel limited by the constraints of professional funding to high school students just starting to explore. We’ll be doing virtual tours of DIY labs and biology hackerspaces, bring you up to date on important projects such as the 3D BioPrinter and the Glowing Plant, and give you ideas for new experiments and useful tools. We’d like it to be a forum where you can ask questions, ranging from “is anyone working on this?” to “how do I build a gene gun?”

We don’t know when the biology revolution will come to fruition, any more than the hackers of the mid-70s could envision the web, Google, or the iPhone. But we know that something big is happening, and we want to be a part of it. We believe that you’ll want to be a part of it, too. That’s why we’re publishing BioCoder.

October 11 2013

Four short links: 11 October 2013

  1. Programming Synthetic DNA (Science Daily) — eventually enabling the reification of bugs.
  2. Schwartza shell for Quartz 2D with Python.
  3. The Slow Winter — best writing about the failure of Moore’s Law and the misery of being in hardware. Ever.
  4. Akarosan open source, GPL-licensed operating system for manycore architectures. Our goal is to provide support for parallel and high-performance applications and to scale to a large number of cores.

October 07 2013

Podcast: expanding our experience of interfaces and interaction

At our Sci Foo Camp this past summer, Jon Bruner, Jim Stogdill, Roger Magoulas, and I were joined by guests Amanda Parkes, a professor in the Department of Architecture at Columbia University, and CTO at algae biofuels company Bodega Algae and fashion technology company Skinteractive Studio; Ivan Poupyrev, principle research scientist at Disney Research, who leads an interaction research team; and Hayes Raffle, an interaction designer at Google [X] working on Project Glass. Our discussion covered a wide range of topics, from scalable sensors to tactile design to synthetic biology to haptic design to why technology isn’t a threat but rather is essential for human survival.

Here are some highlights from our discussion:

  • The Botanicus Interacticus project from Disney research and the Touché sensor technology.
  • Poupyrev explains the concept behind the Touché sensor is that we need to figure out how to make the entire world interactive, developing a single sensor that can be scalable to any situation — finding a universal solution that can adapt to multiple uses. That’s what Touché is, Poupyrev says: “a sensing technology that can dynamically adapt to multiple objects and can sense interaction with water, with everyday objects, with tables, with surfaces, the human body, plants, cats, birds, whatever you want.” (2:50 mark)
  • The ultimate goals of Google Glass and Touché, Raffle says, are similar in that they’re both trying to make computers disappear — Disney is putting the computation into the world so that it’s indistinguishable from objects around us, Glass aims to bring technology closer to you so that it almost fades into the background when you’re using it. (4:17 mark)
  • In a similar vein, Parkes is interested in bringing the interactivity of our surroundings — such as the overwhelming visual pollution in Times Square — back to a more natural, softer state — and is there any hope for the Times Square redesign? (5:56 mark)
  • Parkes’ discussion of her work prompted a nod from Stogdill to Design in Nature, by Adrian Bejan and J. Peder Zane.
  • We also discussed how the expansion in our experience of interfaces and interaction is enhancing our possibilities to be entertained as well as enhancing beauty, aesthetics and pleasure (9:15 mark); Poupyrev stressed as well that it’s the technology that makes humans who we are — technology isn’t a threat; it’s the most important thing for human survival. (13:28 mark)

Additional points of note include a discussion of Google Glass in the wild (14:19 mark); biocouture (19:15 mark); Parkes’ recent experiment: feeding organic conductive ink to slime mold to see if it’ll produce conductive circuit traces — can we can grow our own circuit boards? (17:50 mark). Also, research into haptic technology that creates tactile sensations in free air (23:58 mark) — have a look:

September 10 2013

Genetically modified foods: asking the right questions

Monarch ButterflyMonarch Butterfly

Monarch butterfly, photo by Mike Loukides

A while ago, I read an article in Mother Jones: GM Crops Are Killing Monarch Butterflies, After All. Given the current concerns about genetically modified foods, it was predictable — and wrong, in a way that’s important. If you read the article rather than the headline, you’ll find out what was really going on. Farmers planted Monsanto’s Roundup Ready corn and soybeans. These plants have been genetically modified so that they’re not damaged by the weed killer Roundup. Then the farmers doused their fields with heavy applications of Roundup, killing the milkweed on which Monarch caterpillars live. As a result: fewer butterflies.

But that’s really not what the headline said. The GM crops didn’t kill the butterflies — abuse of a herbicide did. It’s very important to distinguish between first order and second order effects. The milkweed would be just as dead if the farmers applied the Roundup directly to the milkweed. And, assuming that the farmers are trying to kill weeds other than milkweed (which only grows at the edges of the field), the caterpillars would survive if farmers applied Roundup more precisely, just to the crops they were trying to protect. Is it safe to eat corn that’s been genetically modified so that it’s Roundup resistant? I have no problem with the genetics; but you might think twice about eating corn that has been doused with a potent herbicide. Do you wash your food carefully? Good.

The article goes on to talk about corn that has been modified with the Bt gene, which causes it to produce its own insecticide. Bt insecticides are commonly used, frequently by organic farmers, to control caterpillars. With genetic modification, the corn plant produces the insecticide itself: it no longer needs to be applied externally. But the world is full of plants that produce their own insecticide; we call them “poisonous,” and we don’t eat them, though they’re just as natural as the plants we do eat. Milkweed is a prime example, as is tobacco (nicotine is a common insecticide). As a consequence of eating milkweed while they are caterpillars, Monarch butterflies are poisonous to birds, which have learned to avoid them. In the constantly shifting balances of evolution, insects are evolving resistance to Bt. The important question here, then, is whether Bt produced by modified corn and spread by pollen is safer for Monarch caterpillars than more intensive applications of Bt. The answer isn’t clear, though I’d be willing to go with the modified corn.

There is nothing new about genetically modified foods. Plants have genetically modified themselves for billions of years, and humans have grafted and cross-bred plants for thousands of years. I have no doubt that it would be possible to breed Roundup resistant corn the “traditional” way. It would take longer, but it can certainly be done, just as surely as we breed antibiotic-resistant bacteria by indiscriminate use of antibiotics. There’s nothing magical about what’s happening. We could probably do the same to create corn that makes its own pesticide. Genetic modification is faster and more precise than cross-breeding, but that’s really the only difference. Labelling GM foods is probably a good thing, but I’d be more interested in labelling all foods with the pesticides and herbicides that have been applied, by whatever means, genetic or otherwise.

Monarch CaterpillarsMonarch Caterpillars

Monarch caterpillars, photo by Mike Loukides

So, the story really isn’t about genetically modified organisms; it’s about industrial farming practices and second-order effects. (There’s an all-too-brief nod in that direction at the end of the article.) Second- and third-order effects are certainly important: they’re the consequences of our actions. But that’s different from blaming the GMOs themselves. As Thomas Pynchon wrote, “If they can get you asking the wrong questions, they don’t have to worry about the answers.” There is so much wrong with industrial farming practices that I suspect it’s even in Monsanto’s interest to focus attention on the genetics, rather than on the industry itself.

Synthetic biology is an extremely important technique that will affect our lives in ways as diverse as our food supply, lighting (the Glowing Plant), and medicine (can we create bacteria that live in a diabetic’s gut and deliver insulin as needed?). I am not so naive as to believe that all applications of synthetic biology are “good.” It’s easy to imagine unethical applications of biology: say, food that makes your slave labor energetic but docile and easily controlled. But that’s no different from any other technology. As Drew Endy said (and as I’ve quoted elsewhere), we need to keep synthetic biology weird and creative. It’s already in the hands of big corporations, but if all that comes from it is what big corporations want, we have failed. Likewise, if agribusiness can keep the public distracted with fears about Frankenveggies while ignoring the real issues in our food supply, we have lost.

We have to be aware of the biology we create and the consequences of that creation. Every action has consequences, and not all consequences are bad. Weed killer itself is not a bad thing (I’ve used a variety of Roundup to get rid of a Poison Ivy infestation), nor are GMOs. But I find it hard to imagine any circumstances under which the over-application of weed killer is a good thing. It’s clear and unfortunate that Roundup Ready corn creates the incentive to use weed killer indiscriminately, leading to abuse that the makers of that herbicide would like to encourage. But let’s understand where the problem lies: it’s not in genetics, but in the structure of industrial farming. If we don’t, we’re in danger of asking the wrong question. And then, the answer really doesn’t matter.

August 30 2013

Podcast: emerging technology and the coming disruption in design

On a recent trip to our company offices in Cambridge, MA, I was fortunate enough to sit down with Jonathan Follett, a principal at Involution Studios and an O’Reilly author, and Mary Treseler, editorial strategist at O’Reilly. Follett currently is working with experts around the country to produce a book on designing for emerging technology. In this podcast, Follett, Treseler, and I discuss the magnitude of the coming disruption in the design space. Some tidbits covered in our discussion include:

And speaking of that lab burger, here’s Sergey Brin explaining why he bankrolled it:

Subscribe to the O’Reilly Radar Podcast through iTunesSoundCloud, or directly through our podcast’s RSS feed.

April 26 2013

Glowing Plants

I just invested in BioCurious’ Glowing Plants project on Kickstarter. I don’t watch Kickstarter closely, but this is about as fast as I’ve ever seen a project get funded. It went live on Wednesday; in the afternoon, I was backer #170 (more or less), but could see the number of backers ticking upwards constantly as I watched. It was fully funded for $65,000 Thursday; and now sits at 1340 backers (more by the time you read this), with about $84,000 in funding. And there’s a new “stretch” goal: if they make $400,000, they will work on bigger plants, and attempt to create a glowing rose.

Glowing plants are a curiosity; I don’t take seriously the idea that trees will be an alternative to streetlights any time in the near future. But that’s not the point. What’s exciting is that an important and serious biology project can take place in a biohacking lab, rather than in a university or an industrial facility. It’s exciting that this project could potentially become a business; I’m sure there’s a boutique market for glowing roses and living nightlights, if not for biological street lighting. And it’s exciting that we can make new things out of biological parts.

In a conversation last year, Drew Endy said that he wanted synthetic biology to “stay weird,” and that if in ten years, all we had accomplished was create bacteria that made oil from cellulose, we will have failed. Glowing plants are weird. And beautiful. Take a look at their project, fund it, and be the first on your block to have a self-illuminating garden.

November 09 2012

George Church and the potential of synthetic biology

A few weeks ago, I explained why I thought biohacking was one of the most important new trends in technology. If I didn’t convince you, Derek Jacoby’s review (below) of George Church’s new book, Regenesis, will. Church is no stranger to big ideas: big ideas on the scale of sending humans to Mars. (The moon? That’s so done.) And unlike most people with big ideas, Church has an uncanny track record at making his ideas reality. Biohacking has been not so quietly gaining momentum for several years now. If there’s one book that can turn this movement into a full-blown revolution, this is it. — Mike Loukides

George Church and Ed Regis pull off an exciting and speculative romp through the field of synthetic biology and where it could take us in the not too distant future. If anyone with less eminence than Church were to have written this book then half this review would need to be spent defending the realism of the possibilities, but with his track record if he suggests it’s a possibility then it’s worth thinking about.

The possibilities are mind-blowing — breeding organisms immune to all viruses, recreating extinct species, creating humans immune to cancer. We’re entering an age where the limits to our capabilities to re-make the world around us are limited only by our imaginations and our good judgement. Regenesis addresses this as well, for instance proposing mechanisms to create synthetic organisms that are incapable of interacting with natural ones.

Although the book is aimed at a non-technical general audience, the science is explained in excellent detail and is well-referenced for further study.

As the book documents, we’re in the middle of an exponential increase in genomics capabilities that dwarfs even the pace of change in the computer industry. In such a rapidly changing field if you can imagine a plausible technical approach to a problem, no matter how difficult or cumbersome it may be, then soon it’s likely to become easy.

To give an example of an idea long discussed in science fiction, the book addresses re-creating extinct species. Surprisingly, there is already a successful example of this having occurred! The Pyrenean ibex, or bucardo, is a type of mountain goat that went extinct in 1999. But before the last ibex died, researchers scraped a few tissue cells from the ear of the last surviving ibex. They were able to induce the skin cells to become stem cells, and then in a process called interspecies nuclear transfer cloning they were able to fuse those stem cells with de-nucleated donor goat eggs, implant the eggs into domestic goats, and successfully birth a living ibex. By extension, the book examines the implications of reviving the wooly mammoth, or even neanderthals.

Similar detailed examples and discussions take the reader through the potentials of synthetic biology to transform fuel production, food production, waste processing, medicine, and even engineering of the human genome to produce Homo evolutis. Church’s background is in directed evolution — he invented many of the most powerful techniques to rapidly evolve portions of a genome to possess specified characteristics. To hear the inventor of such a powerful technology explore the ramifications of it is a real treat. Society will be exploring the issues raised in this book for many years — how to take advantage of the ability to re-engineer life while protecting against the risks that such a powerful technology must bring.

Refreshingly, in Church’s view protecting against those risks need not exclude amateurs and citizen scientists. Regenesis proposes a licensing scheme, but much more akin to a driver’s license than a formidable hurdle, and suggests a model where a combination of engineering techniques and basic shared procedures is sufficient to protect against any reasonable threats to safety while still ensuring the widest possible access to the technology.

Regenesis provides an accessible and engaging introduction to the revolutionary potentials of synthetic biology and should be of interest to both experts and a general science audience.


October 03 2012

Biohacking: The next great wave of innovation

Genspace and Biocurious logosGenspace and Biocurious logosI’ve been following synthetic biology for the past year or so, and we’re about to see some big changes. Synthetic bio seems to be now where the computer industry was in the late 1970s: still nascent, but about to explode. The hacker culture that drove the development of the personal computer, and that continues to drive technical progress, is forming anew among biohackers.

Computers certainly existed in the ’60s and ’70s, but they were rare, and operated by “professionals” rather than enthusiasts. But an important change took place in the mid-’70s: computing became the domain of amateurs and hobbyists. I read recently that the personal computer revolution started when Steve Wozniak built his own computer in 1975. That’s not quite true, though. Woz was certainly a key player, but he was also part of a club. More important, Silicon Valley’s Homebrew Computer Club wasn’t the only one. At roughly the same time, a friend of mine was building his own computer in a dorm room. And hundreds of people, scattered throughout the U.S. and the rest of the world, were doing the same thing. The revolution wasn’t the result of one person: it was the result of many, all moving in the same direction.

Biohacking has the same kind of momentum. It is breaking out of the confines of academia and research laboratories. There are two significant biohacking hackerspaces in the U.S., GenSpace in New York and BioCurious in California, and more are getting started. Making glowing bacteria (the biological equivalent of “Hello, World!”) is on the curriculum in high school AP bio classes. iGem is an annual competition to build “biological robots.” A grassroots biohacking community is developing, much as it did in computing. That community is transforming biology from a purely professional activity, requiring lab coats, expensive equipment, and other accoutrements, to something that hobbyists and artists can do.

As part of this transformation, the community is navigating the transition from extremely low-level tools to higher-level constructs that are easier to work with. When I first leaned to program on a PDP-8, you had to start the computer by loading a sequence of 13 binary numbers through switches on the front panel. Early microcomputers weren’t much better, but by the time of the first Apples, things had changed. DNA is similar to machine language (except it’s in base four, rather than binary), and in principle hacking DNA isn’t much different from hacking machine code. But synthetic biologists are currently working on the notion of “standard biological parts,” or genetic sequences that enable a cell to perform certain standardized tasks. Standardized parts will give practitioners the ability to work in a “higher level language.” In short, synthetic biology is going through the same transition in usability that computing saw in the ’70s and ’80s.

Alongside this increase in usability, we’re seeing a drop in price, just as in the computer market. Computers cost serious money in the early ’70s, but the price plummeted, in part because of hobbyists: seminal machines like the Apple II, the TRS-80, and the early Macintosh would never have existed if not to serve the needs of hobbyists. Right now, setting up a biology lab is expensive; but we’re seeing the price drop quickly, as biohackers figure out clever ways to make inexpensive tools, such as the DremelFuge, and learn how to scrounge for used equipment.

And we’re also seeing an explosion in entrepreneurial activity. Just as the Homebrew Computer Club and other garage hackers led to Apple and Microsoft, the biohacker culture is full of similarly ambitious startups, working out of hackerspaces. It’s entirely possible that the next great wave of entrepreneurs will be biologists, not programmers.

What are the goals of synthetic biology? There are plenty of problems, from the industrial to the medical, that need to be solved. Drew Endy told me how one of the first results from synthetic biology, the creation of soap that would be effective in cold water, reduced the energy requirements of the U.S. by 10%. The holy grail in biofuels is bacteria that can digest cellulose (essentially, the leaves and stems of any plant) and produce biodiesel. That seems achievable. Can we create bacteria that would live in a diabetic’s intestines and produce insulin? Certainly.

But industrial applications aren’t the most interesting problems waiting to be solved. Endy is concerned that, if synthetic bio is dominated by a corporate agenda, it will cease to be “weird,” and won’t ask the more interesting questions. One Synthetic Aesthetics project made cheeses from microbes that were cultured from the bodies of people in the synthetic biology community. Christian Bok has inserted poetry into a microbe’s DNA. These are the projects we’ll miss if the agenda of synthetic biology is defined by business interests. And these are, in many ways, the most important projects, the ones that will teach us more about how biology works, and the ones that will teach us more about our own creativity.

The last 40 years of computing have proven what a hacker culture can accomplish. We’re about to see that again, this time in biology. And, while we have no idea what the results will be, it’s safe to predict that the coming revolution in biology will radically change the way we live — at least as radically as the computer revolution. It’s going to be an interesting and exciting ride.


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