"BioCoder" entries
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.
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…
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…
Podcast: Personalizing hardware with data? Personalizing people with CRISPR?
Jim Stogdill, Jon Bruner, and Mike Loukides chat about personalizing all the things.
This week in our Radar podcast, Jon and I both had colds. You’ll be pleased to know that I edited out all the sneezes, coughs, and general upper respiratory mayhem, but unfortunately there is no Audacity filter for a voice that sounds like a frog caught in a mouse trap (mine). If that hasn’t dissuaded you from listening, we covered some things that were really interesting, at least to us.
Here are some links to things you’ll hear in this episode:
Are you a microphone geek? You’re welcome. Jon is a maximizer, I’m a satisfier. Mike remains indeterminate.
Blackberry’s salvation may reside in its QNX embedded systems division.
The Pennsylvania Railroad was an amazing technical organization in its heyday. Railroads were that time’s web, and Pennsylvania was its Google. It created a lot of the practices we still use today for testing and other technical disciplines. Also, I suppose if Atlas were to shrug today (shudder) John Galt would be a data center designer. Read more…
DIYbio and the hacking metaphor
Definitive answers require further testing
The following is from the second issue of BioCoder, the quarterly newsletter for synthetic biologists, DIY biologists, neurobiologists, and more. Download your free copy today.
Within DIYbio, one cannot escape the hacking metaphor. The metaphor is ubiquitous and, to a point, useful. The term connotes both productive play with an existing technology aimed at improvement and, at the same time, play with sinister undertones. In this sense, hacking captures the promise and pitfalls of the dual uses any mature technology might be put to, whether that technology is as dramatic as nuclear power/weapons or as mundane as a free/premium software license. But every metaphor has its limits. Pushed too far, metaphors break down, and instead of illuminating, they obscure. Which brings me to ask: how far can the hacking metaphor be pushed within DIYbio—at least the part of DIYbio falling in line with synthetic biology?
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 first two weeks of BioCoder
Our readers are the largest group of DIY biologists ever assembled.
We’ve been having a great time — more than 6,000 downloads, almost 13,000 visits to the landing page, and we don’t know how many people have shared it. Ryan Bethencourt observed that our readers are the largest group of DIY biologists that has ever been assembled. This is big — and we still don’t know how big.
Thanks for a great start! We’re looking forward to a second issue in mid-Jauary. And if you haven’t yet read the first issue of BioCoder, it’s time for you to check it out.
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…
Biotech’s Cambrian Era
Announcing BioCoder, an insider's review of DIY biotech
As I write this article, I’m reflecting on the long expanses of otherworldly playa I’ve just left, watching sandstorms pass in front of me while in altered mental states and contemplating the future of our beloved biotech industry.
I have, until recently been living a double life with one foot in the corporate biotech world and another deeply in the world of biohacking/radical science (working on DIY biolabs and equipment, longevity research, and ALS therapeutic development). I believe in the principles of citizen science and shared (or at least leaky) IP as a means of accelerating scientific progress, but I felt I needed to play my part in the “real” biotech industry. That changed three months ago when I realized that to create the innovation we want in biotech, we may have to burn the bridges that got us here and re-create it ourselves, with or without the dinosaur the current biotech industry has become.