- 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.”
- 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.
- 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)
- 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.
"synthetic biology" entries
Genetically modified foods: asking the right questions
Problems with GM foods lie not in genetics, but in the structure of industrial farming.
Monarch butterfly, photo by Mike Loukides
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.
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:
- Design’s increasing role in genomics and synthetic biology. (For more on the genomic/synthetic biology space, here’s a recent Wired video interview with Craig Venter.)
- Robots taking our jobs, and what we humans will do for work.
- Embedded sensor networks and connected environments — soon, we’ll never get lost in a building again.
- Cross-pollination of industries to inform and evolve our emerging connected environments, such as the cross-disciplinary nature of the Wyss Institute for Biologically Inspired Engineering at Harvard.
- Approaching political policy as a design problem — politicians could benefit from design theory and rapid prototyping techniques found in design and manufacturing fields.
- Scientists growing burgers in labs.
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.
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…
Biohacking: The next great wave of innovation
The hacker culture that launched the computing revolution is now taking root in the bio space.
I’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…
Four short links: 19 March 2012
The Quantified Professor, Bus Monitor, Arduino Confessor, and Ethics of Deceit
Four short links: 8 November 2011
Cell Operating System, Search Savvy, Smiling Sliders, and Recommendation Tools
- Attempts to Make a Cell Operating System (Science Daily) — finally we will be able to have the guaranteed quality of software and the safety of biological organisms.
- Why Kids Can’t Search (Clive Thompson) — kids need to be taught critical thinking skills about what they find on the web. Librarians are our national leaders in this fight; they’re the main ones trying to teach search skills to kids today.
- Smiley Slider — cute little way to get feedback. (via Jyri Tuulos)
- LensKit — an open source toolkit for building, researching, and studying recommender systems.
Four short links: 22 July 2011
Data Businesses, Multitouch Charting, 3D-Printing Glass, and Synthetic Biology
- Competitive Advantage Through Data — the applications and business models for erecting barriers around proprietary data assets. Sees data businesses in these four categories: contributory data sourcing, offering cleaner data, data generated from service you offer, and viz/ux. The author does not yet appear to be considering when open or communal data is better than proprietary data, and how to make those projects work. (via Michael Driscoll)
- Interactive Touch Charts — GPL v3 (and commercial) licensed Javascript charting library that features interactivity on touch devices: zoom, pan, and click. (via James Pearce)
- Solar Cutter, Solar 3D Printer — prototypes of solar powered maker devices. The cutter is a non-laser cutter that focuses the sun’s rays to a super-hot point. The printer makes glass from sand (!!!!). Not only is this cool, but sand is widespread and cheap.
- Synthetic Biology Open Language — a language for the description and the exchange of synthetic biological parts, devices, and systems. Another piece of the synthetic biology puzzle comes together. The parallel development of DIY manufacturing in the worlds of bits and basepairs is mindboggling. We live in exciting times. (via krs)
OSCON Preview: Interview with Eri Gentry on a biologist's coffeehouse
BioCurious is a Silicon Valley gathering place for biologists and
other people such as artists who are fascinated by biology. It serves
for learning, sharing, and an incubator for products and ideas.
OSCON Preview: Interview with Eri Gentry on a biologist’s coffeehouse
BioCurious is a Silicon Valley gathering place for biologists and
other people such as artists who are fascinated by biology. It serves
for learning, sharing, and an incubator for products and ideas.