"synthetic biology" entries

Announcing BioCoder issue 3

Advances in biology and biotechnology are driving us in exciting new directions — be part of the revolution!

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.
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Biohacking and the problem of bioterrorism

Natural bioterrorism might be the bigger threat, and the value of citizens educated in biosciences can't be overstated.

You don’t get very far discussing synthetic biology and biohacking before someone asks about bioterrorism. So, let’s meet the monster head-on.

I won’t downplay the possibility of a bioterror attack. It’s already happened. The Anthrax-contaminated letters that were sent to political figures just after 9/11 were certainly an instance of bioterrorism. Fortunately (for everyone but the victims), they only resulted in five deaths, not thousands. Since then, there have been a few “copycat” crimes, though using a harmless white powder rather than Anthrax spores.

While I see bioterror in the future as a certainty, I don’t believe it will come from a hackerspace. The 2001 attacks are instructive: the spores were traced to a U.S. biodefense laboratory. Whether or not you believe Bruce Ivins, the lead suspect, was guilty, it’s clear that the Anthrax spores were developed by professionals and could not have been developed outside of a professional setting. That’s what I expect for future attacks: the biological materials, whether spores, viruses, or bacteria, will come from a research laboratory, produced with government funding. Whether they’re stolen from a U.S. lab or produced overseas: take your pick. They won’t come from the hackerspace down the street. Read more…

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Academic biology and its discontents

Disaffected grad students and postdocs increasingly turn to DIYbio to do work that makes a difference.

When we started BioCoder, we assumed that we were addressing the DIYbio community: interested amateur hobbyists and experimenters without much formal background in biology, who were learning and working in independent hackerspaces.

A couple of conversations have made me question that assumption — not that DIYbio exists; it’s clearly a healthy and growing movement, with new labs and hackerspaces starting in most major cities. But there’s another group mixed in with the amateurs, with a distinctly different set of capabilities and goals. DIYbio doesn’t mean exactly what we thought it did.

That group is what I broadly call “disaffected grad students and postdocs.” They’ve got training, loads of it. But they’ve spent the last few years working in a laboratory under a faculty member, furthering that faculty member’s agenda. They have their own ideas and their own research projects, but they can’t work on them within the context of academic biology. They’re funded by a grant, and the grant will only pay for certain things. And, as Anthony Di Franco points out in “Superseding Institutions in Science and Medicine” (in the current issue of BioCoder), grants are primarily given to people who already know what they’re going to find, and that is not how you get truly innovative and creative research. Read more…

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Cheese, art, and synthetic biology

Christina Agapakis discusses the intersection of art and science in the new edition of BioCoder.

We’ve published the second issue of BioCoder! In this interview excerpt from the new edition, Christina Agapakis talks with Katherine Liu about the intersection of art and science, and the changes in how we think about biotechnology. It’s one of many reasons we’re excited about this new issue. Download it, read it, and join the biotechnology revolution!

Katherine Liu: What can art and design teach us about biology and synthetic biology?

Christina Agapakis: That’s a great question. There are two different ways you can think about it: first as a way to reach different groups of people and have a different kind of conversation or debate around biotechnology. The second way that you could think about it is more interesting to me as a scientist because I think using art and design helps us ask different questions and think about problems and technological solutions in different ways. To make a good technology, we need to be aware of both the biological and the cultural issues involved, and I think the intersection of art and design with science and technology helps us see those connections better.

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The biocoding revolution

The potential for synthetic biology and biotechnology is vast; we all have an opportunity to create the future together.

What is biocoding? For those of you who have been following the biotechnology industry, you’ll have heard of the rapid advances in genome sequencing. Our ability to read the language of life has advanced dramatically, but only recently have we been able to start writing the language of life at scale.

The first large-scale biocoding success was in 2010, when Craig Venter (one of my scientific heroes) wrote up the genome of an entirely synthetic organism, booted it up and created de novo life. Venter’s new book, Life at the Speed of Light, discusses the creation of the first synthetic life form. In his book and in video interviews, Venter talks about the importance of ensuring the accuracy of the DNA code they designed. One small deletion of a base (one of the four letters that make up the biological equivalent of 1s and 0s) resulted in a reading frame shift that left them with gibberish genomes, a mistake they were able to find and correct. One of the most amusing parts of Venter’s work was that they were able to encode sequences in the DNA to represent each letter of the English alphabet. Their watermark included the names of their collaborators, famous quotes, an explanation of the coding system used, and a URL for those who crack the code written in the DNA. Welcome to the future — and let me know if you crack the code!

Biocoding is just the beginning of the rise of the true biohackers. This is a community of several thousand people, with skill sets ranging from self-taught software hackers to biology postdocs who are impatient with the structure of traditional lab work. Read more…

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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…

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Four short links: 11 October 2013

Four short links: 11 October 2013

DNA Coding, Quartz2D Shell, Hardware Sadness, and Manycore OS

  1. Programming Synthetic DNA (Science Daily) — eventually enabling the reification of bugs.
  2. Schwartza shell for Quartz 2D with Python.
  3. The Slow Winter — best writing about the failure of Moore’s Law and the misery of being in hardware. Ever.
  4. Akarosan open source, GPL-licensed operating system for manycore architectures. Our goal is to provide support for parallel and high-performance applications and to scale to a large number of cores.

Podcast: expanding our experience of interfaces and interaction

A chat with Amanda Parkes, Ivan Poupyrev, and Hayes Raffle.

At our Sci Foo Camp this past summer, Jon Bruner, Jim Stogdill, Roger Magoulas, and I were joined by guests Amanda Parkes, a professor in the Department of Architecture at Columbia University, and CTO at algae biofuels company Bodega Algae and fashion technology company Skinteractive Studio; Ivan Poupyrev, principle research scientist at Disney Research, who leads an interaction research team; and Hayes Raffle, an interaction designer at Google [X] working on Project Glass. Our discussion covered a wide range of topics, from scalable sensors to tactile design to synthetic biology to haptic design to why technology isn’t a threat but rather is essential for human survival.

Here are some highlights from our discussion:

  • The Botanicus Interacticus project from Disney research and the Touché sensor technology.
  • Poupyrev explains the concept behind the Touché sensor is that we need to figure out how to make the entire world interactive, developing a single sensor that can be scalable to any situation — finding a universal solution that can adapt to multiple uses. That’s what Touché is, Poupyrev says: “a sensing technology that can dynamically adapt to multiple objects and can sense interaction with water, with everyday objects, with tables, with surfaces, the human body, plants, cats, birds, whatever you want.” (2:50 mark)

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Genetically modified foods: asking the right questions

Problems with GM foods lie not in genetics, but in the structure of industrial farming.

Monarch Butterfly

Monarch butterfly, photo by Mike Loukides

A while ago, I read an article in Mother Jones: GM Crops Are Killing Monarch Butterflies, After All. Given the current concerns about genetically modified foods, it was predictable — and wrong, in a way that’s important. If you read the article rather than the headline, you’ll find out what was really going on. Farmers planted Monsanto’s Roundup Ready corn and soybeans. These plants have been genetically modified so that they’re not damaged by the weed killer Roundup. Then the farmers doused their fields with heavy applications of Roundup, killing the milkweed on which Monarch caterpillars live. As a result: fewer butterflies.

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.

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Comments: 20

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:

And speaking of that lab burger, here’s Sergey Brin explaining why he bankrolled it:

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