- Reboot Britain Video Archive — video from the talks at Reboot Britain are online. The event also produced a essay set (PDF), CC-licensed. (via Paul Reynolds)
- Revealing Errors — Benjamin Mako Hill blog using computer errors as starting points for understanding how computers control the world around us. (via Dan Meyer)
- New Microbe Strain Makes More Electricity, Faster — University of Amherst researchers made current-generating bacteria work harder to live, and in five months had a strain that made an 8x larger current.
- Netflix Culture — readable slide deck which talks about the Netflix company culture. It’s hard to read it and not nod in full agreement. (via joshua on Delicious)
The O’Reilly Hardware Podcast: The merging worlds of software, hardware, and biology.
Subscribe to the O’Reilly Hardware Podcast for insight and analysis about the Internet of Things and the worlds of hardware, software, and manufacturing.
In this new episode of the Hardware Podcast—which features our first discussion focusing specifically on synthetic biology—David Cranor and I talk with Charles Fracchia, an IBM Fellow at the MIT Media Lab and founder of the synthetic biology company BioBright.
- The blurring of the lines between biology, software development, hardware engineering, and electrical engineering
- BioBright’s efforts to create hardware and software tools to reinvent the way biology is done in a lab
- The most prominent market forces in biology today (especially healthcare)
- How experiments conducted using Arduino or Raspberry Pi devices are impacting synthetic biology
- Pembient’s synthetic rhino horns
Solid's long view includes biology as part of the creator's toolkit.
Tim O’Reilly subjected himself to an engaging Ask Me Anything session on Reddit earlier this week. The focus of the exchange was the Internet of Things, in anticipation of our Solid conference taking place next month.
We’re always listening for faint signals from our community about what they’re getting interested in, and one area that’s stood out to us is biology, which is becoming easier to experiment with at home, as a hobbyist, and through hackerspaces like Biocurious and Genspace. You’ll find a few threads on biology at Solid this year, but we’ve tagged it to be a little more central at Solid 2015. Beyond the hobbyist and health-related applications, we see synthetic biology as another way to translate between virtual and physical, like 3D printers and stereoscopic cameras.
Here’s an exchange from Tuesday’s Reddit thread that sums it up nicely.
What prompted the start of BioCoder? Are people really doing biotech in their garages in the same way that many computer hardware and software innovations happened?
How scientists become scientists, whether science is still advancing at Newton's pace, and the future of neuroscience and bioengineering.
At Sci Foo Camp last weekend, we enjoyed sitting down with several thoughtful scientists and thinkers-about-science to record a few podcast episodes. Here we speak with Tom Daniel, a professor of biology, computer science, and neurobiology at the University of Washington, and Ben Lillie, co-founder of The Story Collider and a Stanford-trained physicist. First topic: what brings people to science, and how we compare to our icons. Along the way, we mention Hans Bethe, Isaac Newton’s epitaph, and John McPhee’s trip across Interstate 80.
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.
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…
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…
Rebooting Britain, Revealing Errors, Reproducing Generators, Netflix Culture
UI Library, 3rd Party Wave Server, Mobile Phones + Parasites, Single API to Cloud Providers
- CNMAT Resource Library — The CNMAT Resource Library is our fast growing collection of materials, sensors, gestural controllers, interface devices, tools, demos, prototypes and products – all organized and annotated to support the design of physical interaction systems, “new lutherie” and art installations. (via egoodman on Delicious)
- PyGoWave Server — first third-party Google Wave server, based on Django.
- Mobile Phones Identify Parasites and Bacteria — UCB Researchers developed a cell phone microscope, or CellScope, that not only takes color images of malaria parasites, but of tuberculosis bacteria labeled with fluorescent markers.. The sensor network is built out, and the computers in our pockets surprise us with their uses. (via BoingBoing)
- libcloud — a unified interface to cloud providers, written in Python and open source. Covers EC2, EC2-EU, Slicehost, Rackspace, Linode, VPS.net, GoGrid, flexiscale, Eucalyptus. (via joshua on Delicious)
- Ignite OSCON — 56m of video from Ignite OSCON. They’re all great, but Dan Meyer remains the highlight for me.
- gheat — a maptile server in Python, delivering heatmaps to be superimposed on Google Maps. Handy for visualization fiends.
- CaDNAno — open source software for design of 3-dimensional DNA origami. One of George Church’s projects. I love the combination of math, biology, and whimsy in open-source giftwrap. (via timoreilly on Twitter)
- CommentPress — an open source theme for the WordPress blogging engine that allows readers to comment paragraph by paragraph in the margins of a text. Annotate, gloss, workshop, debate: with CommentPress you can do all of these things on a finer-grained level, turning a document into a conversation. It can be applied to a fixed document (paper/essay/book etc.) or to a running blog. I’m taking a greater interest in tools that channel and focus participation rather than simply providing “edit this page”. (via gov2.net.au’s issues paper)