- Programming Synthetic DNA (Science Daily) — eventually enabling the reification of bugs.
- Schwartz — a shell for Quartz 2D with Python.
- The Slow Winter — best writing about the failure of Moore’s Law and the misery of being in hardware. Ever.
- Akaros — an 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.
"synthetic biology" entries
Designing real vegan cheese
Synthetic biology surely can get weirder — but this is a great start.
I don’t think I will ever get tired of quoting Drew Endy’s “keep synthetic biology weird.” One of my favorite articles in the new issue of Biocoder is on the Real Vegan Cheese project.
If you’ve ever tried any of the various vegan cheese substitutes, they are (to put it kindly) awful. The missing ingredient in these products is the milk proteins, or caseins. And of course you can’t use real milk proteins in a vegan product.
But proteins are just organic compounds that are produced, in abundance, by any living cell. And synthetic biology is about engineering cell DNA to produce whatever proteins we want. That’s the central idea behind the Real Vegan Cheese project: can we design yeast to produce the caseins we need for cheese, without involving any animals? There’s no reason we can’t. Once we have the milk proteins, we can use traditional processes to make the cheese. No cows (or sheep, or goats) involved, just genetically modified yeast. And you never eat the yeast; they stay behind at the brewery.
Robots in the lab
Hacking lab equipment to make it programmable is a good first step toward lab automation.
An automated centrifuge at Modular Science — click here for instructions to hack one yourself.
In the new issue of BioCoder, Peter Sand writes about Hacking Lab Equipment. It’s well worth a read: it gives a number of hints about how standard equipment can be modified so that it can be controlled by a program. This is an important trend I’ve been watching on a number of levels, from fully robotic labs to much more modest proposals, like Sand’s, that extend programmability even to hacker spaces and home labs.
In talking to biologists, I’m surprised at how little automation there is in research labs. Automation in industrial labs, the sort that process thousands of blood and urine samples per hour, yes: that exists. But in research labs, undergrads, grad students, and post-docs spend countless hours moving microscopic amounts of liquid from one place to another. Why? It’s not science; it’s just moving stuff around. What a waste of mental energy and creativity.
Lab automation, though, isn’t just about replacing countless hours of tedium with opportunities for creative thought. I once talked to a system administrator who wrote a script for everything, even for only a simple one-liner. (Might have been @yesthattom, I don’t remember.) This practice is based on an important insight: writing a script documents exactly what you did. You don’t have to think about, “oh, did I add the f option on that rm -r / command?”; you can just look. If you need to do the same thing on another system, you can reproduce what you did exactly.
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.
Read more…
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…
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…
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.
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…
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: 11 October 2013
DNA Coding, Quartz2D Shell, Hardware Sadness, and Manycore OS
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)