"synthetic biology" entries

Biology as the next hardware

Why DNA is on the horizon of the design world.

DNA by John Goode, on Flickr

I’ve spent the last couple of years arguing that the barriers between software and the physical world are falling. The barriers between software and the living world are next.

At our Solid Conference last May, Carl Bass, Autodesk’s CEO, described the coming of generative design. Massive computing power, along with frictionless translation between digital and physical through devices like 3D scanners and CNC machines, will radically change the way we design the world around us. Instead of prototyping five versions of a chair through trial and error, you can use a computer to prototype and test a billion versions in a few hours, then fabricate it immediately. That scenario isn’t far off, Bass suggested, and it arises from a fluid relationship between real and virtual.

Biology is headed down the same path: with tools on both the input and output sides getting easier to use, materials getting easier to make, and plenty of computation in the middle, it’ll become the next way to translate between physical and digital. (Excitement has built to the degree that Solid co-chair Joi Ito suggested we change the name of our conference to “Solid and Squishy.”)

I spoke with Andrew Hessel, a distinguished research scientist in Autodesk’s Bio/Nano/Programmable Matter Group, about the promise of synthetic biology (and why Autodesk is interested in it). Hessel says the next generation of synthetic biology will be brought about by a blend of physical and virtual systems that make experimental iteration faster and processes more reliable. Read more…

Comment

A commitment to biotech, in action

"I eat, breathe, live biotech,” says Ryan Bethencourt. “It’s really all I do at this point.”

Photo shows lab work. Ryan Bethencourt discusses his commitment to biotech.

This story is part of our ongoing exploration of synthetic biology and the DIYbio movement. Learn more by downloading a free edition of BioCoder.


Ryan Bethencourt seized his opportunity back in 2008. That made him an outlier: most people, after all, were seizing pink slips, not opportunities. But while the Great Recession wiped out billions in home equity and blew up companies by the score, it also freed up plenty of hard assets. In simple terms, you could buy a lot of expensive stuff for a song. And that’s just what Bethencourt and his pal, molecular biologist and fellow DIYbio enthusiast, John Schloendorn, did.

“The financial crisis resulted in the liquidation of a big chunk of the biotechnology sector,” says Bethencourt, a molecular geneticist-cum-biotech entrepreneur who was working as a business development director for a clinical research organization at the time. “So we bought up a lot of research-grade equipment. We felt we couldn’t afford to pass it up.” Read more…

Comment

The revolution in biology is here, now

Biological products have always seemed far off. BioFabricate showed that they're not.

Living_Hy-Fi_MoMA

Installation view of The Living’s Hy-Fi, the winning project of The Museum of Modern Art and MoMA PS1’s 2014 Young Architects Program. Photograph by Kris Graves.

The BioFabricate summit in New York rearranged my thinking. BioFabricate was about the intersection of manufacturing and biology: not just “we can make cool new microbes,” but using biology to manufacture products for the real world. Biological products have always seemed far off. But they’re not: the revolution in biology is clearly here now, just unevenly distributed.

The products discussed at BioFabricate aren’t what I thought they’d be. I’ve been asked plenty of times (and I’ve asked plenty of times), “what’s the killer product for synthetic biology?” BioFabricate convinced me that that’s the wrong question. We may never have some kind of biological iPod. That isn’t the right way to think.

What I saw, instead, was real products that you might never notice. Bricks made from sand that are held together by microbes designed to excrete the binder. Bricks and packing material made from fungus (mycelium)Plastic excreted by bacteria that consume waste methane from sewage plants. You wouldn’t know, or care, whether your plastic Lego blocks are made from petroleum or from bacteria, but there’s a huge ecological difference. You wouldn’t know, or care, what goes into the bricks used in the new school, but the construction boom in Dubai has made a desert city one of the world’s largest importers of sand. Wind-blown desert sand isn’t useful for industrial brickmaking, but the microbes have no problem making bricks from it. And you may not care whether packing materials are made of styrofoam or fungus, but I despise the bag of packing peanuts sitting in my basement waiting to be recycled. You can throw the fungal packing material into the garden, and it will decompose into fertilizer in a couple of days. Read more…

Comments: 3

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…

Comments: 10

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…

Comments: 4

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…

Comment

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…

Comment: 1

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…

Comments: 2

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