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Lessons from Software for Synthetic Biology

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In my November 4, 2015 keynote at the SynBioBeta conference, I talk about lessons from open source software and the internet that should shape our thinking about the bio revolution. Licenses are only part of the open source story. The architecture of interoperability may matter even more.

In my November 4, 2015 keynote at the SynBioBeta conference, I talk about lessons from open source software and the internet that should shape our thinking about the bio revolution. Licenses are only part of the open source story. The architecture of interoperability may matter even more.

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Lessons from Software for Synthetic Biology

  1. The Architecture of Participation: Lessons from software for the biohacking community Tim O’Reilly SynbioBeta November 3, 2015
  2. @timoreilly #SynBioBeta@timoreilly #SynBioBeta “History doesn’t repeat itself, but it sure does rhyme.” Mark Twain 2
  3. @timoreilly #SynBioBeta@timoreilly #SynBioBeta It Begins With Generosity 3 John von Neumann Don Estridge Tim Berners-Lee
  4. @timoreilly #SynBioBeta@timoreilly #SynBioBeta The Same Is True in Bio 4 Jim KentCraig Venter Drew EndyTom Knight
  5. @timoreilly #SynBioBeta@timoreilly #SynBioBeta A lot of people think freedom is a matter of license 5
  6. @timoreilly #SynBioBeta@timoreilly #SynBioBeta Despite having a proprietary license, and being owned by one company, Unix was developed collaboratively by small teams of independent developers. 6
  7. @timoreilly #SynBioBeta@timoreilly #SynBioBeta What do these things have in common? Unix/Linux The internet The world wide web Wikipedia 7
  8. @timoreilly #SynBioBeta@timoreilly #SynBioBeta Small Pieces Loosely Joined Enabled by: • Common, well-understood data formats • A communications protocol • A variety of tools for accessing and representing the data 8
  9. @timoreilly #SynBioBeta@timoreilly #SynBioBeta I think it has more to do with architecture “The book is perhaps most valuable for its exposition of the Unix philosophy of small cooperating tools with standardized inputs and outputs, a philosophy that also shaped the end-to-end philosophy of the Internet. It is this philosophy, and the architecture based on it, that has allowed open source projects to be assembled into larger systems such as Linux, without explicit coordination between developers.” 9
  10. @timoreilly #SynBioBeta@timoreilly #SynBioBeta “I couldn’t have built a new kernel for Windows even if I had access to the source code. The architecture just didn’t support it.” 10 Linus Torvalds
  11. @timoreilly #SynBioBeta@timoreilly #SynBioBeta The Robustness Principle “Be conservative in what you send, be liberal in what you accept from others.” RFC 761 Jon Postel
  12. @timoreilly #SynBioBeta@timoreilly #SynBioBeta But that began to change Google didn’t change the architecture of the web, but it did change the architecture of how it was controlled. 12
  13. @timoreilly #SynBioBeta@timoreilly #SynBioBeta What I learned from Nutch: Even if you have the source code for a Google-like search engine, you don’t have Google. The game had changed! 13
  14. @timoreilly #SynBioBeta@timoreilly #SynBioBeta Don Estridge “Freed” the PC 14 Don Estridge
  15. @timoreilly #SynBioBeta@timoreilly #SynBioBeta What happened? In a world of commodity hardware, control over software APIs gave proprietary advantage. The hacker became the despot. 15 Bill Gates
  16. (Control by API) Desktop Application Stack Proprietary Software Hardware Lock In By a Single-Source Supplier System Assembled from Standardized Commodity Components
  17. Free and Open Source Software Cheap Commodity PCs Intel Inside
  18. Proprietary Software As a Service Subsystem-Level Lock In Integration of Commodity Components Internet Application Stack Apache
  19. "The Law of Conservation of Attractive Profits" "When attractive profits disappear at one stage in the value chain because a product becomes modular and commoditized, the opportunity to earn attractive profits with proprietary products will usually emerge at an adjacent stage." -- Clayton Christensen Author of The Innovator's Solution In Harvard Business Review, February 2004
  20. @timoreilly #SynBioBeta@timoreilly #SynBioBeta More open licenses are necessary, but they are rarely sufficient. We must fight restrictive licenses and other forms of IP, but replacing them with open licenses isn’t the answer. 22
  21. @timoreilly #SynBioBeta@timoreilly #SynBioBeta 24
  22. @timoreilly #SynBioBeta@timoreilly #SynBioBeta “Everyone applauds when Google goes after Microsoft’s Office monopoly, seeing it simply as “turnabout’s fair play,” (and a distant underdog to boot), but when they start to go after web non-profits like Wikipedia, you see where the ineluctable logic leads. As Google’s growth slows, as inevitably it will, it will need to consume more and more of the web ecosystem, trading against its former suppliers, rather than distributing attention to them. We already take for granted that common searches, such as for weather or stock prices, are satisfied directly on the search screen. Where does that process stop? “Ultimately, I think we see this pattern in the economic development of every innovation. When a new technology is introduced, there’s a lot of green-field opportunity, and so much value is being created that there’s no need to capture it all. But as the technology matures, the winners need to capture more of the total value being created. They gradually crowd out suppliers as well as competitors.” 25
  23. @timoreilly #SynBioBeta@timoreilly #SynBioBeta Losing the way of life, men rely on goodness; Losing goodness, they rely on laws. - Lao Tzu 26
  24. @timoreilly #SynBioBeta@timoreilly #SynBioBeta The way of life = The architecture of the system Goodness = “Don’t be evil” Laws = “We need a free gene license” 27
  25. @timoreilly #SynBioBeta@timoreilly #SynBioBeta Small Pieces Loosely Joined Enabled by: • Common, well-understood data formats • A communications protocol • A variety of tools for accessing and representing the data 29
  26. @timoreilly #SynBioBeta@timoreilly #SynBioBeta Who sets the gauge rules the world Sixty per cent of the world's railways use 4 ft 8 1⁄2 inch standard gauge, developed by George Stephenson in 1822. 30 http://www.warwickshirerailways.com/lms/lnwrns305.htm
  27. @timoreilly #SynBioBeta You standardize railroads by building tracks “The strategy is delivery!” 31 @timoreilly #SynBioBeta UK GDS Director Mike Bracken

Notizen

  • I was disappointed to discover that this great quote attributed to Mark Twain is actually a modern fabrication. But the sentiment is completely true.
  • When I look at the history of the computer industry, I see a recurring pattern. A huge Cambrian explosion of innovation happens when someone makes their breakthrough work available to the world for others to build on. The fundamental architecture of modern computing, developed by John von Neumann and team at the Institute for Advanced Study at Princeton during and after WWII, was put into the public domain, and led to the first wave of computing, led by IBM. Then, Don Estridge, the head of IBM’s PC division, put the specifications for the PC out for everyone to copy, letting folks like Michael Dell start his company from a university dorm room. And more recently, Tim Berners Lee kicked off the web revolution by putting his work into the public domain.
  • We see this same pattern in biology. Back when Craig Venter and the Human Genome Project were racing to be the first to sequence an entire human genome, Venter was hoping to patent the work, but Jim Kent’s gene assembler helped the public project to keep the human genome in the public domain. And of course, Tom Knight and Drew Endy have worked tirelessly to build an open source culture and community around synthetic biology.
  • But all too many people still think that the freedoms of open source software come from licenses. They are a necessary part of the story, but not sufficient.
  • And the history of what became Linux teaches us that free software licenses came after, not before, the fundamental innovations that grew into Linux. Despite having a proprietary license, and being owned by one company, Unix was developed collaboratively by small teams of independent developers. Much of the fundamental software of Unix and the internet was developed at universities. The ATT license was just open enough for sharing to happen. When ATT tried to clamp down, the Berkeley Unix project continued, and many of the utilities they’d built were copied and added into Linux, which was just then emerging.
  • So what do these things have in common? Unix/Linux. The Internet. The world wide web. Wikipedia.
  • They all have an architecture of “small pieces loosely joined”, enabled by Common, well-understood data formats, A communications protocol, A variety of tools for accessing and representing the data
  • In the Wikipedia entry for the book The Unix Programming Environment, I wrote: “The book is perhaps most valuable for its exposition of the Unix philosophy of small cooperating tools with standardized inputs and outputs, a philosophy that also shaped the end-to-end philosophy of the Internet. It is this philosophy, and the architecture based on it, that has allowed open source projects to be assembled into larger systems such as Linux, without explicit coordination between developers.”
  • And when we were putting together our 1998 book Open Sources, which consisted of interviews with various free software and open source leaders, Linux Torvalds remarked “I couldn’t have built a new kernel for Windows even if I had access to the source code. The architecture just didn’t support it.”
  • One of the key tenets of the early internet design was something called “The Robustness Principle.” The idea was that the internet would be robust if people followed what really amounts to the Golden Rule applied to networks. “Be conservative...”

    This needs to be true of biotech as well.
  • But that began to change. Google didn’t change the architecture of the web, but it did change the architecture of how it was controlled.
  • I was on the board of Nutch, a non-profit formed by Doug Cutting, the original architect of Hadoop. The idea was to build an open source search engine, but Doug soon realized that Nutch could never reach the scale of Google, because it was no longer just a matter of software and algorithms, but of data and operations at scale.
  • Similarly, Don Estridge “freed the PC”
  • but Bill Gates realized that there was a new lock-in via software.
  • Back in 2003, I gave a talk called “The Open Source Paradigm Shift” where I started by talking about the architecture of the PC industry, which looked something like this.
  • With their mindset shaped by the desktop application stack, open source developers imagined the pattern replaying itself like this. They accept intel inside, and loved the cheap commodity PCs, but they imagined proprietary software being replaced by free and open source applications at the top of the stack. Red Hat or maybe SuSe would displace Microsoft, MySql would displace Oracle, and so on.
  • But instead, we got a world that looks like this. This is my slide from 2003 - obviously, some of the companies highlighted in the graph would be different today.
  • Clayton Christensen described this pattern perfectly in a 2004 Harvard Business Review article. He called it “The law of conservation of attractive profits.” “"When attractive profits disappear at one stage in the value chain because a product becomes modular and commoditized, the opportunity to earn attractive profits with proprietary products will usually emerge at an adjacent stage."
  • That’s why well-meaning initiatives like the open source seed initiative, which are modeled on the free software foundation, may be missing the point.
  • Much as I love 23&me and what they are doing, when I see a headline like this, it really worries me. Because a future in which one company controls too much data is not a future that will keep the innovation engine going.
  • You see the real risk is that, whatever their good intentions, companies with a monopoly position eventually tend to exploit it. In 2007, I wrote an article about lessons from Wall Street for the future of the Internet.
  • In that article, I wrote: ““Everyone applauds when Google goes after Microsoft’s Office monopoly, seeing it simply as “turnabout’s fair play,” (and a distant underdog to boot), but when they start to go after web non-profits like Wikipedia, you see where the ineluctable logic leads. As Google’s growth slows, as inevitably it will, it will need to consume more and more of the web ecosystem, trading against its former suppliers, rather than distributing attention to them. We already take for granted that common searches, such as for weather or stock prices, are satisfied directly on the search screen. Where does that process stop?

    “Ultimately, I think we see this pattern in the economic development of every innovation. When a new technology is introduced, there’s a lot of green-field opportunity, and so much value is being created that there’s no need to capture it all. But as the technology matures, the winners need to capture more of the total value being created. They gradually crowd out suppliers as well as competitors.”
  • The answer lies in architecture. I saw an article recently called “the Internet of DNA” - and that is the right answer. How do we create an architecture for synthetic biological and genetic data that makes sharing of data the norm, that builds applications on a common shared substrate?
  • That is how can we build an architecture of “small pieces loosely joined”, enabled by Common, well-understood data formats, A communications protocol, A variety of tools for accessing and representing the data
  • The lesson I want to leave you with is this: a lesson from British history and the design of real world platforms. Most of the world uses a standard gauge of railroad track originally developed by George Stephenson in 1822. It was a foundational tool for the British Empire, and was eventually copied by other nations around the world.
  • In a very different context, Mike Bracken, the founder of the UK’s Government Digital Service, put it in one line: “The strategy is delivery.”

    Build a system with the architecture of interoperability that you want, and insist on that interoperability.
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