"biology" entries

Biology as I/O

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.

Question from rhops:

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?

Thanks.

Read more…

Comment

Podcast: what makes a scientist?

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.

We’ll post the rest of the series over the coming weeks. In the meantime, you can find more episodes of our podcast and subscribe on iTunes or SoundCloud.

Comments: 2

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: 5 August 2009

Four short links: 5 August 2009

Rebooting Britain, Revealing Errors, Reproducing Generators, Netflix Culture

  1. 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)
  2. Revealing Errors — Benjamin Mako Hill blog using computer errors as starting points for understanding how computers control the world around us. (via Dan Meyer)
  3. 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.
  4. 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)
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Four short links: 28 July 2009

Four short links: 28 July 2009

UI Library, 3rd Party Wave Server, Mobile Phones + Parasites, Single API to Cloud Providers

  1. CNMAT Resource LibraryThe 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)
  2. PyGoWave Server — first third-party Google Wave server, based on Django.
  3. 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)
  4. 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)
Comments: 2
Four short links: 27 July 2009

Four short links: 27 July 2009

  1. Ignite OSCON — 56m of video from Ignite OSCON. They’re all great, but Dan Meyer remains the highlight for me.
  2. gheat — a maptile server in Python, delivering heatmaps to be superimposed on Google Maps. Handy for visualization fiends.
  3. CaDNAnoopen 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)
  4. CommentPressan 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)
Comment: 1
Four short links: 15 July 2009

Four short links: 15 July 2009

A collection inspired by Science Foo Camp attendees

  1. Endogenous steroids and financial risk taking on a London trading floor (PNAS) — We found that a trader’s morning testosterone level predicts his day’s profitability. We also found that a trader’s cortisol rises with both the variance of his trading results and the volatility of the market. Our results suggest that higher testosterone may contribute to economic return, whereas cortisol is increased by risk. Our results point to a further possibility: testosterone and cortisol are known to have cognitive and behavioral effects, so if the acutely elevated steroids we observed were to persist or increase as volatility rises, they may shift risk preferences and even affect a trader’s ability to engage in rational choice.
  2. The Origin of Universal Scaling Laws in Biology — eye-opening paper that blew my mind. Highlight of Sci Foo was meeting the author and shaking his hand. Relates metabolic rate, size, heart rate, and lifespan by applying physics to biology.
  3. Ushahidi — open source software for managing disasters. The Ushahidi Engine is a platform that allows anyone to gather distributed data via SMS, email or web and visualize it on a map or timeline. Our goal is to create the simplest way of aggregating information from the public for use in crisis response.
  4. Dissecting the Canon: Visual Subject Co-Popularity Networks in Art ResearchIn this paper we analyze a classic da-
    taset of art research, which collects ancient art and architecture and their Western
    Renaissance documentation since 1947. [T]here is clearly a long tail of monument
    popularity.
Comment: 1
Four short links: 9 June 2009

Four short links: 9 June 2009

Biological Radio, Laggy Smart Grids, API Moneys, and Pubsub Server

  1. Drawing Inspiration From Nature To Build A Better Radio — based on the design of the cochlear, this MIT-built RF chip is faster than others out there, and consumes 1/100th the power. Biomimicry and UWB radio are on our radar.
  2. Why the Smart Grid Won’t Have the Innovations of the Internet Any Time SoonWhile it’s significant that utilities are starting to build out smart grid infrastructure, utilities are largely opting for networks that provide connections that are far from real time, and this could stifle the desired innovation. […] smart meter data that is pushed to Google’s PowerMeter energy tool has to make its way back to the utility before it can be sent to Google. That means that even for Google’s energy tool, there can be both a significant delay before information reaches consumers, and significant gaps in energy data details. These delays and gaps can undercut the premise of how smart meter technologies will empower consumers to make decisions about their energy use based on real-time costs. Smart grids (houses and devices able to take use of instantaneous pricing changes) have the potential to help us with our energy obesity problem, but the architecture must be right.
  3. API Value Creation, Not MonetizationOn the side of the unexpected but interesting outcomes, Kevin said they have seen a flurry of internally developed business applications. In the past many valuable, internal-facing projects were turned down because the programs had to meet strict top line to bottom line ratios. With the availability to data and services, many teams within the company now have access to things they didn’t in the past, and project costs have been minimized. Throughout the company, consumers of the API have been able to launch successful projects that have created additional revenue and have reduced the overall development costs for new projects. Some solid numbers and names to help convince businesses to offer APIs, though the battle is still much harder than it should be.
  4. Watercoolr — a pubsub server for your apps. A channel is a list of URLs to be notified whenever a message is posted to that channel. Clever little piece of infrastructure for web apps, embodying the Unix philosophy of small tools that each do one thing very well. (via straup on Delicious)
Comments: 6