"BioCoder" entries

The robotic worm

Does the way a brain is wired determine how we think and behave? Recent research points to a resounding yes.

Editor’s note: this is an excerpt from the latest edition of BioCoder; it is republished here with permission. Get your free copy of BioCoder Fall 2014 here.

CElegansNeurons

One of the age-old questions has been whether the way a brain is wired, negating other attributes such as intracellular systems biology, will give rise to how we think and how we behave. We are not at the point yet to answer that question regarding the human brain. However, by using the well-mapped connectome of the nematode Caenorhabditis elegans (C. elegans, shown above), we were able to answer this question as a resounding yes, at least for simpler animals. Using a simple robot (a Lego Mindstorms EV3) and connecting sensors on the robot to stimulate specific simulated sensory neurons in an artificial connectome, and condensing worm muscle excitation to move a left and right motor on the robot, we observed worm-like behaviors in the robot based purely on environmental factors. Read more…

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The future of food

We could soon have lab-grown hamburgers, not in the $300,000 range but in the $10 range — would you eat one?

Editor’s note: this is an excerpt from the latest edition of BioCoder; it is republished here with permission. Get your free copy of BioCoder Fall 2014 here.

“So I had an accident.”

That was the call I got from a scientist entrepreneur friend of mine, John Schloendorn, the CEO of Gene and Cell Technologies. He’d been working on potential regenerative medicine therapies and tinkering with bioreactors to grow human cell lines. He left the lab for the weekend, and then something went wrong with one of his bioreactors: something got stuck in it.

“So, I was wondering what happened with my bioreactor and how this big chunk of plastic had gotten in there and ruined my cytokine production run. I was pulling it out, and I thought it was was weird because it was floppy. I threw it in the garbage. A little later, after thinking about it, I realized it wasn’t plastic and pulled it out of the garbage.” Read more…

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Connecting the microcosmos and the macro world

Christina Agapakis explores the microbiological matrix that binds everything from pecorino to people.

human_cheese

Cheese from the Selfmade project.

This is part of our investigation into synthetic biology and bioengineering. For more, download the new BioCoder Fall 2014 issue here.

Good luck trying to jam Christina Agapakis into any kind of vocational box. Her CV cites disparate accomplishments as a scientist, writer, and artist — and teacher. Imparting highly technical information in a compelling, even revelatory way seems part of, well, her DNA. She can’t not do it. Moreover, her career arc represents a syncretic impulse that characterizes her general outlook on life.

“A friend is starting a group called Doctors without Disciplinary Borders, and I’m joining it,” says Agapakis. “It captures the spirit of my work pretty well.”

Agapakis is first and foremost a synthetic biologist and a microbiologist, but she’s not particularly happy with the way the synthetic biology narrative has played out. She thinks biocoding is inadequately explained by its practitioners and deeply misunderstood by the lay public, raising excessive expectations and misunderstandings about what synthetic biology can do. The discipline’s message would be better communicated, she believes, if metaphors grounded in biology rather than computers were employed. Read more…

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A glowing trend

Glowing plants disrupt the GMO narrative.

GlowingPlantProjectEditor’s note: this is an excerpt from the latest edition of BioCoder; it is republished here with permission. Get your free copy of BioCoder Fall 2014 here.

Unlike many of his generational peers, Glowing Plant chief scientific officer Kyle Taylor was never put off by genetically modified organism (GMO) crops. On the contrary: Kansas-born and bred, cutting-edge agriculture was as natural to him as the torrid summers and frigid winters of the southern plains.

“GMO corn first hit the market while I was still in high school,” says Taylor, “and I have to admit I was fascinated by it. It was Roundup resistant, meaning that it you could spray it with the most commonly used herbicide in commercial agriculture and it would remain unaffected. I found that really profound, a breakthrough.” Read more…

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Avoiding the tragedy of the anticommons

We're at the start of a revolution in biology, and it's time for a biological commons.

DNA_Extraction_in_Action_

Editor’s note: this post originally appeared in BioCoder Fall 2014; it is published here with permission. Download a free copy of the new issue here.

A few months ago, I singled out an article in BioCoder about the appearance of open source biology. In his white paper for the Bio-Commons, Rüdiger Trojok writes about a significantly more ambitious vision for open biology: a bio-commons that holds biological intellectual property in trust for the good of all. He also articulates the tragedy of the anticommons, the nightmarish opposite of a bio-commons in which progress is difficult or impossible because “ambiguous and competing intellectual property claims…deter sharing and weaken investment incentives.” Each individual piece of intellectual property is carefully groomed and preserved, but it’s impossible to combine the elements; it’s like a jigsaw puzzle, in which every piece is locked in a separate safe.

We’ve certainly seen the anticommons in computing. Patent trolls are a significant disincentive to innovation; regardless of how weak the patent claim may be, most start-ups just don’t have the money to defend. Could biotechnology head in this direction, too? In the U.S., the Supreme Court has ruled that human genes cannot be patented. But that ruling doesn’t apply to genes from other organisms, and arguably doesn’t apply to modifications of human genes. (I don’t know the status of genetic patents in other countries.) The patentability of biological “inventions” has the potential to make it more difficult to do cutting-edge research in areas like synthetic biology and pharmaceuticals (Trojok points specifically to antibiotics, where research is particularly stagnant). Read more…

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BioCoder strikes again

New issue: bioreactors and food production, modeling a worm's brain on a computer and letting it drive a robot, and more.

BioCoderCover_Page_01The fifth issue of BioCoder is here! We’ve made it into our second year: this revolution is in full swing.

Rather than talk about how great this issue is (though it is great), I’d like to ask a couple of questions. Post your answers in the comments; we won’t necessarily reply, but we will will read them and take them into account.

  • We are always interested in new content, and we’ll take a look at almost anything you send to BioCoder@oreilly.com. In particular, we’d like to get more content from the many biohacker labs, incubators, etc. We know there’s a lot of amazing experimentation out there. But we don’t know what it is; we only see the proverbial tip of the iceberg. What’s the best way to find out what’s going on?
  • While we’ve started BioCoder as a quarterly newsletter, that’s a format that already feels a bit stodgy. Would you be better served if BioCoder went web-native? Rather than publishing eight or 10 articles every three months, we’d publish three or four articles a month online. Would that be more useful? Or do you like things the way they are?

And yes, we do have a great issue, with articles about a low-cost MiniPCR, bioreactors and food production, and what happens when you model a worm’s brain on a computer and let it drive a robot. Plus, an interview with Kyle Taylor of the glowing plant project, the next installment in a series on lab safety, and much more. Read more…

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Looking for the next generation of biocoders

Natalie Kuldell on the hard work of bringing biocoding to the classroom.

Freshman_BiologySynthetic biology is poised to change everything from energy development to food production to medicine — but there’s a bottleneck looming. How fast things develop depends on the number of people developing things. Let’s face it: there aren’t that many biocoders. Not in the universities, not in industry, not in the DIY sector. Not enough to change the world, at any rate. We have to ramp up.

And that means we first must train teachers and define biocoding curricula. Not at the university level — try secondary, maybe even primary schools. That, of course, is a challenge. To get kids interested in synthetic biology, we have to do just that: get them interested. More to the point, get them jacked. Biocoding is incredibly exciting stuff, but that message isn’t getting across.

“Students think science and engineering is removed from daily life,” says Natalie Kuldell, an instructor of biological engineering at MIT. “We have to get them engaged, and connected to science and engineering — more specifically, bioengineering — in meaningful ways.”

Read more…

Comment: 1

Synthetic biology on the cusp

Oliver Medvedik on the grassroots future of biohacking and the problems with government overreach.

BioCoder image plants in dish with tweezersWhither thou goest, synthetic biology? First, let’s put aside the dystopian scenarios of nasty modified viruses escaping from the fermentor Junior has jury-rigged in his bedroom lab. Designing virulent microbes is well beyond the expertise and budgets of homegrown biocoders.

“Moreover, it’s extremely difficult to ‘improve’ on the lethality of nature,” says Oliver Medvedik, a visiting assistant professor at The Cooper Union for the Advancement of Science and Art and the assistant director of the Maurice Kanbar Center for Biomedical Engineering. “The pathogens that already exist are more legitimate cause for worry.” Read more…

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Designing real vegan cheese

Synthetic biology surely can get weirder — but this is a great start.

real_vegan_cheese_screenshot

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.

Read more…

Comments: 5

Open source biology

Joe Schloendorn is creating and distributing plasmids that can freely be reproduced — a huge breakthrough for DIY bio.

Photo by mira66 on Flickr, used under a Creative Commons license.

At O’Reilly, we’ve long been supporters of the open source movement — perhaps not with the religious fervor of some, but with a deep appreciation for how open source has transformed the computing industry over the last three decades.

We also have a deep appreciation for the dangers that closed source, restrictive licenses, patent trolling, and other technocratic evils pose to areas that are just opening up — biology, in particular. So it is with great interest that I read Open Source Biotech Consumables in the latest issue of BioCoder.

I’m not going to rehash the article; you should read it yourself. The basic argument is that some proteins used in research cost thousands of dollars per milligram. They’re easily reproducible (we’re talking DNA, after all), but frequently tied up with restrictive licenses. In addition, many of the vendors will only sell to research institutions and large corporations, not home labs or small community labs. So, Joe Schloendorn is creating and distributing plasmids that can freely be reproduced. That in itself is a huge breakthrough.

Read more…

Comments: 4