"BioCoder" entries

Design for disruption

A look at the need for design thinking in the IoT, advanced robotics, 3D printing, and synthetic biology.

Editor’s note: This is an excerpt from our recent book Designing for Emerging Technologies, a collection of works by several authors, curated and edited by Jon Follett. This excerpt is included in our curated collection of chapters from the O’Reilly Design library. Download a free copy of the Experience Design ebook here.

Let’s look briefly at the disruptive potential of each of these emerging technologies: the IoT, advanced robotics, 3D printing, and synthetic biology — and the need for design thinking in their formations.

The IoT, connected environment, and wearable technology


Download a free copy of the Experience Design ebook here.

The IoT is a popular shorthand that describes the many objects that are outfitted with sensors and communicating machine-to-machine. These objects make up our brave, new connected world. The types and numbers of these devices are growing by the day, to a possible 50 billion objects by 2020, according to the Cisco report, The Internet of Things: How the Next Evolution of the Internet Is Changing Everything (PDF).

Inexpensive sensors providing waves of data can help us gain new insight into the places in which we live, work, and play, as well as the capabilities to influence our surroundings — passively and actively — and have our surroundings influence us. We can imagine the possibilities of a hyper-connected world in which hospitals, factories, roads, airways, offices, retail stores, and public buildings are tied together by a web of data.

In a similar fashion, when we wear these sensors on our bodies, they can become our tools for self-monitoring. Combine this capability with information delivery via Bluetooth or other communication methods and display it via flexible screens, and we have the cornerstones of a wearable technology revolution that is the natural partner and possible inheritor of our current smartphone obsession. If we consider that the systems, software, and even the objects themselves will require design input on multiple levels, we can begin to see the tremendous opportunity resident in the IoT and wearables. Read more…

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…

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…

The revolution in biology is here, now

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


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…

A programming language for biology

Antha is a high-level, open source language for specifying biological workflows.

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


The OT.One liquid handling robot, photo courtesy of OpenTrons.

In a couple of recent posts, I’ve written about the need for a high-level programming language for biology. Now we have one. Antha is a high-level, open source language for specifying biological workflows (i.e., describing experiments). It’s available on Github.

A programming language for scientific experiments is important for many reasons. Most simply, a scientist in training spends many, many hours of time learning how to do lab work. That sounds impressive, but it really means moving very small amounts of liquid from one place to another. Thousands of times a day, thousands of days in preparation for a career. It’s boring, dull, and necessary work, and something that can be automated. Biologists should spend most of their time thinking about biology, designing experiments, and analyzing results — not handling liquids. Read more…

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.


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…

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…

Connecting the microcosmos and the macro world

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


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…

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…

Avoiding the tragedy of the anticommons

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


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…