"DIY biology" entries

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…

Four short links: 25 February 2013

Four short links: 25 February 2013

Living Poetry, Distributed Systems, Hardware Incubator, and Young Lady's Illustrated Primer

  1. Xenotext — Sci Foo Camper Christian Bök is closer to his goal of “living poetry”: A short stanza enciphered into a string of DNA and injected into an “unkillable” bacterium, Bök’s poem is designed to trigger the micro-organism to create a corresponding protein that, when decoded, is a verse created by the organism. In other words, the harmless bacterium, Deinococcus radiodurans (known as an extremophile because of its ability to survive freezing, scorching, or the vacuum of outer space), will be a poetic bug.
  2. Notes on Distributed Systems for Young Bloods — why distributed systems are different. Coordination is very hard. Avoid coordinating machines wherever possible. This is often described as “horizontal scalability”. The real trick of horizontal scalability is independence – being able to get data to machines such that communication and consensus between those machines is kept to a minimum. Every time two machines have to agree on something, the service is harder to implement. Information has an upper limit to the speed it can travel, and networked communication is flakier than you think, and your idea of what constitutes consensus is probably wrong.
  3. Lemnos Labs — hardware incubator in SF. (via Jim Stogdill)
  4. OLPC Built the Young Lady’s Illustrated Primer — Neil Stephenson imagined it, OLPC built it. Science fiction is a hugely powerful focusing device for creativity and imagination. (via Matt Jones)
Four short links: 21 June 2012

Four short links: 21 June 2012

Randomized Trials for Policy, Crowdfunding Equity, Safe DIYBio, and Easy Unique Experiences

  1. Test, Learn, Adapt (PDF) — UK Cabinet Office paper on randomised trials for public policy. Ben Goldacre cowrote.
  2. UK EscapeTheCity Raises GBP600k in Crowd Equity — took just eight days, using the Crowdcube platform for equity-based crowd investment.
  3. DIY Bio SOPs — CC-licensed set of standard operating procedures for a bio lab. These are the SOPs that I provided to the Irish EPA as part of my “Consent Conditions” for “Contained Use of Class 1 Genetically Modified Microorganisms”. (via Alison Marigold)
  4. Shuffling Cards — shuffle a deck of cards until it’s randomised. That order of cards probably hasn’t ever been seen before in the history of mankind.
Four short links: 14 June 2010

Four short links: 14 June 2010

Open Data, Open PCR, Open Sara Winge, and Open Source Big Graph Mining

  1. Learning from Libraries: the Literacy Challenge of Open Data (David Eaves) — a powerful continuation of the theme from my Rethinking Open Data post. David observes that dumping data over the fence isn’t enough, we must help citizens engage. We have a model for that help, in the form of libraries: We didn’t build libraries for an already literate citizenry. We built libraries to help citizens become literate. Today we build open data portals not because we have a data or public policy literate citizenry, we build them so that citizens may become literate in data, visualization, coding and public policy.
  2. OpenPCR on KickstarterIn 1983, Kary Mullis first developed PCR, for which he later received a Nobel Prize. But the tool is still expensive, even though the technology is almost 30 years old. If computing grew at the same pace, we would all still be paying $2,000+ for a 1 MHz Apple II computer. Innovation in biotech needs a kick start!
  3. Wingeing It — profile of O’Reilly’s wonderful Sara Winge by the ever fabulous Quinn Norton.
  4. PEGASUS — petascale graph mining toolkit from CMU. See their most recent publication. (via univerself on Delicious)
Four short links: 10 November 2009

Four short links: 10 November 2009

DIY Diagnostic Chips, Genetics on $5k a Genome, Cellphones as Diagnostic Microscopes, AR-Equipped Mechanics Do It Heads-Up

  1. A children’s toy inspires a cheap, easy production method for high-tech diagnostic chips — microfluidic chips (with tiny liquid-filled channels) can cost $100k and more. Michelle Khine used the Shrinky Dinks childrens’ toy to make her own. “I thought if I could print out the [designs] at a certain resolution and then make them shrink, I could make channels the right size for micro­fluidics,” she says. (via BoingBoing)
  2. Complete Genomics publishes in Science on low-cost sequencing of 3 human genomes (press release) — The consumables cost for these three genomes sequenced on the proof-of-principle genomic DNA nanoarrays ranged from $8,005 for 87x coverage to $1,726 for 45x coverage for the samples described in this report. Drive that cost down! There’s a gold rush in biological discovery at the moment as we pick the low-hanging fruit of gross correlations between genome and physiome, but the science to reveal the workings of cause and effect is still in its infancy. We’re in the position of the 18th century natural philosophers who were playing with static electricity, oxygen, anaesthetics, and so on but who lacked today’s deeper insights into physical and chemical structure that explain the effects they were able to obtain. More data at this stage means more low-hanging fruit can be plucked, but the real power comes when we understand “how” and not just “what”. (via BoingBoing)
  3. Far From a Lab? Turn a Cellphone into a Microscope (NY Times) — for some tests, you can use a camphone instead of a microscope. In one prototype, a slide holding a finger prick of blood can be inserted over the phone’s camera sensor. The sensor detects the slide’s contents and sends the information wirelessly to a hospital or regional health center. For instance, the phones can detect the asymmetric shape of diseased blood cells or other abnormal cells, or note an increase of white blood cells, a sign of infection, he said.
  4. Augmented reality helps Marine mechanics carry out repair work (MIT TR) — A user wears a head-worn display, and the AR system provides assistance by showing 3-D arrows that point to a relevant component, text instructions, floating labels and warnings, and animated, 3-D models of the appropriate tools. An Android-powered G1 smart phone attached to the mechanic’s wrist provides touchscreen controls for cueing up the next sequence of instructions. […] The mechanics using the AR system located and started repair tasks 56 percent faster, on average, than when wearing the untracked headset, and 47 percent faster than when using just a stationary computer screen.

Etech Session Liveblogging: Real Hackers Program DNA (Ginkgo Bioworks)

GB is "Making the process of engineering biology easier." Synth bio is the idea that biology is a technology to engineer novel systems- say drugs, biofuels, other sexy sexy projects. This is to be a flavor of what engineering biology is all about. We will be installing a program into E coli to make it turn red, glow in the…