Announcing BioCoder issue 3

We’re excited about the third issue of BioCoder, O’Reilly’s newsletter about the revolution in biology and biotechnology. In the first article of our new issue, Ryan Bethencourt asks the question “What does Biotechnology Want?” Playing with Kevin Kelly’s ideas about how technological development drives human development, Bethencourt asks about the directions in which biotechnology is driving us. We’re looking for a new future with significant advances in agriculture, food, health, environmental protection, and more.

That future will be ours — if we choose to make it. Bethencourt’s argument (and Kelly’s) is that we can’t not choose to make it. Yes, there are plenty of obstacles: the limits to our understanding of biology and genetics, the inadequate tools we have for doing research, the research institutions themselves, and even fear of the future. We’ll overcome these obstacles; indeed, if Bethencourt is right, and biology is our destiny, we have no choice but to overcome these obstacles. The only question is whether you’re part of the revolution or not.
Read more…

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Four short links: 15 April 2014

Four short links: 15 April 2014

Open Access, Lego Scanner, Humans Return, and Designing Security into IoT

  1. Funders Punish Open Access Dodgers (Nature) — US’s NIH and UK’s Wellcome Trust are withholding funding from academics who haven’t released their data despite it being a condition of past funding. It’s open access’s grab twist and pull move.
  2. Digitize Books with Mindstorms and Raspberry Pi — Lego to turn the page, Pi to take photo.
  3. Humans Steal Jobs from Robots at Toyota (Bloomberg) — Toyota’s next step forward is counter-intuitive in an age of automation: Humans are taking the place of machines in plants across Japan so workers can develop new skills and figure out ways to improve production lines and the car-building process.
  4. Implementer’s Guide to Security for Internet of Things, Devices and Beyond (PDF) — This white paper outlines a set of practical and pragmatic security considerations for organisations designing, developing and, testing Internet of Things (IoT) devices and solutions. The purpose of this white paper is to provide practical advice for consideration as part of the product development lifecycle.
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Four short links: 14 April 2014

Four short links: 14 April 2014

dategrep, Agile Signoff, Feedback Speed, and Modern Dev

  1. dategrepprint lines matching ranges of dates. Genius!
  2. Business Case Guidance in Agile Projects ( — how the UK govt signs off on Agile projects, which normally governments have no clue over how to handle properly.
  3. Hyper Growth Done Right“While I was at Oracle, it took a month before a new engineer would get any code in,” Agarwal says. “It sent this implicit message that it’s okay to take a month to write some code.” First time I’d heard this wise point articulated: slow feedback loops send the message that progress can be slow.
  4. Docker + Github + Jenkins — clever integration of the three tools to get repeatable continuous integration. The modern dev environment has workflow built on git, VMs, and glue.
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Distributed science

In the future, we will solve biological problems by running experiments in parallel.


Participants at #ScienceHack 2014, Synbiota’s Open Distributed Genetic Engineering event. Photo by Madison Matthews, courtesy of Synbiota.

In my post on biohacking and bioterrorism, I briefly mentioned the possibility of vaccines and other treatments developed outside of institutional research. That may be far-fetched, and I certainly hope we’re never in a situation where DIY treatments are the only ones available. But it is worth looking at how biologists outside of medical institutions are transforming research.

Perhaps the most ambitious project right now is Synbiota’s #ScienceHack. They are organizing a large number of volunteer groups to experiment with techniques to produce the compound Violacein. Violacein is potentially useful as an anti-cancer and anti-dysentery drug, but currently costs $356,000 per gram to produce. This price makes research (to say nothing of therapeutic use) impossible. However, it’s possible that bacteria can be genetically engineered to produce Violacein much more efficiently and cheaply. That’s what the #ScienceHack experiment is about: the groups will be trying to design DNA that can be inserted into E. coli bacteria to make it produce Violacein at a fraction of the cost. Read more…

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Security and the Internet of stuff in your life

The IoT isn't just a new attack surface to get into your enterprise — it's giving the Internet eyes and arms.

Your computer is important. It has access to your Amazon account, probably your bank, your tax returns, and maybe even your medical records. It’s scary when it gets pwnd, and it gets pwned regularly because it’s essentially impossible to fully secure a general purpose computing device. But the good news is that, at least for now, your computer can’t climb up the stairs and bludgeon you to death in your sleep. The things it manipulates are important to you, but they are (mostly) contained in the abstract virtual realm of money and likes.

The Internet of Things is different. We are embarking on an era where the things we own will be as vulnerable as our PCs, but now they interact with the real world via sensors and actuators. They have eyes and arms, and some of them in the not-too-distant future really will be able to climb the stairs and punch you in the face.

This piece from the New York Times has been getting some attention because it highlights how smart things represent an increased attack surface for infiltration. It views smart devices as springboards into an enterprise rather than the object of the attack, and that will certainly be true in many cases. Read more…

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Leading by example: two stories

When health care institutions are charging outrageous prices, we need to stand up and say, "That's insane."

I was struck recently by two stories in the New York Times. The first, “Bishops Follow Pope’s Example: Opulence Is Out,” tells how bishop after bishop, either inspired by the Pope’s example or afraid of being shamed for not doing so, is moving out of his expensive, newly renovated residence and emulating Pope Francis’ emphasis on living simply. “Francis has very definitely sent out a signal, and the signal is that bishops should live like the people they pastor, and they shouldn’t be in palaces.”

I contrast this in my mind with the “do as I say, but not as I do” style of leadership shown by the US Congress on health care, where the message of “bending the cost curve on health care,” and limits on “Cadillac plans” was for everyone else. Congress’ own gold-plated plan remained in place, despite posturing to pretend that members of Congress were in the same boat as everyone else.

But when the leaders themselves don’t lead, sometimes individuals stand up to be counted. Read more…

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