Bringing an end to synthetic biology’s semantic debate

The O'Reilly Radar Podcast: Tim Gardner on the synthetic biology landscape, lab automation, and the problem of reproducibility.

Editor’s note: this podcast is part of our investigation into synthetic biology and bioengineering. For more on these topics, download a free copy of the new edition of BioCoder, our quarterly publication covering the biological revolution. Free downloads for all past editions are also available.

Tim Gardner, founder of Riffyn, has recently been working with the Synthetic Biology Working Group of the European Commission Scientific Committees to define synthetic biology, assess the risk assessment methodologies, and then describe research areas. I caught up with Gardner for this Radar Podcast episode to talk about the synthetic biology landscape and issues in research and experimentation that he’s addressing at Riffyn.

Defining synthetic biology

Among the areas of investigation discussed at the EU’s Synthetic Biology Working Group was defining synthetic biology. The official definition reads: “SynBio is the application of science, technology and engineering to facilitate and accelerate the design, manufacture and/or modification of genetic materials in living organisms.” Gardner talked about the significance of the definition:

“The operative part there is the ‘design, manufacture, modification of genetic materials in living organisms.’ Biotechnologies that don’t involve genetic manipulation would not be considered synthetic biology, and more or less anything else that is manipulating genetic materials in living organisms is included. That’s important because it gets rid of this semantic debate of, ‘this is synthetic biology, that’s synthetic biology, this isn’t, that’s not,’ that often crops up when you have, say, a protein engineer talking to someone else who is working on gene circuits, and someone will claim the protein engineer is not a synthetic biologist because they’re not working with parts libraries or modularity or whatnot, and the boundaries between the two are almost indistinguishable from a practical standpoint. We’ve wrapped it all together and said, ‘It basically advances in the capabilities of genetic engineering. That’s what synthetic biology is.'”

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Building and deploying large-scale machine learning pipelines

We need primitives; pipeline synthesis tools; and most importantly, error analysis and verification.

There are many algorithms with implementations that scale to large data sets (this list includes matrix factorization, SVM, logistic regression, LASSO, and many others). In fact, machine learning experts are fond of pointing out: if you can pose your problem as a simple optimization problem then you’re almost done.

Of course, in practice, most machine learning projects can’t be reduced to simple optimization problems. Data scientists have to manage and maintain complex data projects, and the analytic problems they need to tackle usually involve specialized machine learning pipelines. Decisions at one stage affect things that happen downstream, so interactions between parts of a pipeline are an area of active research.

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Some common machine learning pipelines. Source: Ben Recht, used with permission.

In his Strata+Hadoop World New York presentation, UC Berkeley Professor Ben Recht described new UC Berkeley AMPLab projects for building and managing large-scale machine learning pipelines. Given AMPLab’s ties to the Spark community, some of the ideas from their projects are starting to appear in Apache Spark. Read more…

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How to make a UX designer

Heather Wydeven talks about her entry into the field of UX and what helped her succeed as a new UX designer.

Where do new designers come from? In the case of Heather Wydeven, a UX designer at The Nerdery, she came to UX via theater and then graphic design. In a recent interview, Wydeven took the time to speak with me about her route to UX design, what it was like entering the UX field, what new designers should know, and how more experienced designers can help bring new designers into the fold.

After spending several years working in theater, Wydeven decided to channel her creative skills into a career in graphic design. She came to UX design without even realizing what UX was, but the root of her motivation was something that’s familiar to many UX designers: a recognition that things could be better and a desire to solve problems.

“While I was doing graphic design,” Wydeven said, “I started to become more curious about web design and UX design specifically, though at the time I didn’t know it was called ‘UX design.’ I was using websites and being frustrated about my experiences on those websites and thinking, ‘There’s got to be a way to make these better. This has got to be somebody’s job to design these websites better than they are now.’” Read more…

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The 3Ps of the blockchain: platforms, programs and protocols

There is a burgeoning landscape around the blockchain’s decentralized consensus protocol technologies.

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Although it may be early to baptize new buzz lingo like “Blockchain as a Service” (BaaS) or “Blockchain as a Platform” (BaaP), there is a burgeoning landscape of various implementations and activity in and around the blockchain’s decentralized consensus protocol technologies.

I’ve already covered the blockchain’s sweet spot as a development platform in “Understanding the blockchain,” so it is no surprise that its landscape will be made up of platforms, protocols, and (smart) programs.

Breaking-up the bitcoin-blockchain paradigm

In a perfect world, we would have a single blockchain and a single cryptocurrency. But that doesn’t seem to be in the cards, whether it is technically feasible or not. Although wide-scale adoption and a critical mass of users aren’t there yet, the market is signaling for a diversification of choices, some based on the bitcoin currency and its blockchain protocol, and others not. Read more…

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The Internet of Things is really about software

Our new report, "What is the Internet of Things," traces the IoT's transformations and impact.

The Internet of Things (IoT) is everywhere right now. It appeared on the cover of the Harvard Business Review in November, and observers saw it in practically every demo at CES.

One of the reasons that it’s ubiquitous is that it bears on practically everything. A few years ago, many companies might plausibly have argued that they weren’t affected by developments in software. If you dealt in physical goods, it was hard to see how software that existed strictly in the virtual realm might touch your business.

The Internet of Things changes that; the kinds of software intelligence that have already revolutionized industries like finance and advertising are about to revolutionize all the other industries.

Mike Loukides and I have traced out our idea of the Internet of Things and its impacts in a report, “What is the Internet of Things,” that’s available for free here.

As much as we all love the romance and gratification of hardware, the Internet of Things is really about software; the hardware just links the Internet to the rest of the world. If you think of the IoT as a newly developing area in software, it’s easy to draw out some characteristics of it that are analogous to things we’ve seen in web software over the last decade or so. Read more…

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What containers can do for you

Docker, Rocket, and big industry changes are making it a great time to seriously consider using containers.

Container Image: CC BY-SA 2.0 Photocapy https://www.flickr.com/photos/photocapy/252737232/in/photostream/

If you read any IT news these days it’s hard to miss a headline about “the container revolution.” Docker’s year-and-a-half-old engine had a monopoly on the buzz until CoreOS launched its own project, Rocket, in December.

The technology behind containers can seem esoteric, but the advantages of bringing containers to your organization are more compelling than ever. And containers’ inherent portability opens up exciting new opportunities for how organizations host their applications.

Containerization is having its moment and there’s never been a better time to check it out for yourself.

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