"synthetic biology" entries

The biocoding revolution

The potential for synthetic biology and biotechnology is vast; we all have an opportunity to create the future together.

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. Read more…

Comment: 1

Announcing BioCoder

An O'Reilly newsletter covering the biology revolution and connecting the many people working in DIY bio.

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. Read more…

Comments: 3
Four short links: 11 October 2013

Four short links: 11 October 2013

DNA Coding, Quartz2D Shell, Hardware Sadness, and Manycore OS

  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.

Podcast: expanding our experience of interfaces and interaction

A chat with Amanda Parkes, Ivan Poupyrev, and Hayes Raffle.

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)

Read more…


Genetically modified foods: asking the right questions

Problems with GM foods lie not in genetics, but in the structure of industrial farming.

Monarch 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.

Read more…

Comments: 20

Podcast: emerging technology and the coming disruption in design

Design's role in genomics and synthetic biology, robots taking our jobs, and scientists growing burgers in labs.

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:

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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.

Comments: 4

George Church and the potential of synthetic biology

A review of George Church's book Regenesis: How Synthetic Biology will Reinvent Nature and Ourselves

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. Read more…

Comments: 7

Biohacking: The next great wave of innovation

The hacker culture that launched the computing revolution is now taking root in the bio space.

Genspace 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. Read more…

Comments: 9
Four short links: 19 March 2012

Four short links: 19 March 2012

The Quantified Professor, Bus Monitor, Arduino Confessor, and Ethics of Deceit

  1. Examining His Own Body (Science Now) — Stanford prof. has sequenced his DNA and is now getting massively Quantified Self on his metabolism, infections, etc. This caught my eye: George Church, who has pioneered DNA sequencing technology and runs the Personal Genome Project* at Harvard Medical School in Boston that enrolls people willing to share genomic and medical information similar to what’s presented in the Cell report, says some might critique Snyder’s self-exam as merely anecdotal. “But one response is that it is the perfect counterpoint to correlative studies which lump together thousands of cases versus controls with relatively much less attention to individual idiosyncrasies,” Church says. “I think that N=1 causal analyses will be increasingly important.”
  2. Bus Arrival Monitor (John Graham-Cumming) — hacked a toy doubledecker bus with LED display feeding bus arrival info from the Transport for London API via a modded Linksys WRT router.
  3. Arduino Tool That Connects Each Board to Its Own Source (Ideo) — If you create something with Arduino and put it out into the world, there is no well-established link to the source. If you personally made the device, the source can get lost over time. If you didn’t create it, you could have a tough time tracking the source down. You have the physical device, why can’t it tell you where it’s code lives? I made a tool for Arduino called “Upload-And-Retrieve-Source” that for the most part solves this problem. (via Chris Spurgeon)
  4. Mike Daisey is a Liar and So Am I — I linked to the original This American Life story, so now I’m linking to the best commentary on their retraction of the story. This is an excellent piece on the ubiquity and ethics of Daiseyesque means-justifies-the-end for-a-good-cause deceit.