lessons from software for synthetic biology

The Architecture of Participation:Lessons from software for the

biohacking communityTim O’Reilly

SynbioBetaNovember 3, 2015

@timoreilly#SynBioBeta@timoreilly#SynBioBeta

“History doesn’t repeat itself, but it sure does rhyme.”

Mark Twain

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It Begins With Generosity

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John von Neumann

Don Estridge

Tim Berners-Lee


The Same Is True in Bio

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Jim KentCraig Venter Drew EndyTom Knight


A lot of people think freedom is a matter of license

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Despite having a proprietary license, and being owned by one company, Unix was developed collaboratively by small teams of independent developers.

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What do these things have in common?

Unix/LinuxThe internetThe world wide webWikipedia

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Small Pieces Loosely JoinedEnabled by:

• Common, well-understood data formats• A communications protocol• A variety of tools for accessing and representing the

data

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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.”

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“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.”

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Linus Torvalds

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The Robustness Principle“Be conservative in what

you send, be liberal in what you accept from others.”

RFC 761

Jon Postel


But that began to changeGoogle didn’t change the architecture of the web, but it did change the architecture of how it was controlled.

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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!

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Don Estridge “Freed” the PC

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Don Estridge


What happened?

In a world of commodity hardware, control over software APIs gave proprietary advantage.

The hacker became the despot.

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Bill Gates

(Control by API)

Desktop ApplicationStack

Proprietary Software

Hardware Lock InBy a Single-Source Supplier

System Assembled fromStandardized

Commodity Components

Free and Open Source Software

Cheap Commodity PCs

Intel Inside

ProprietarySoftware As a Service

Subsystem-Level Lock In

Integration of CommodityComponents

Internet ApplicationStack

Apache

"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 ChristensenAuthor of The Innovator's Solution

In Harvard Business Review, February 2004


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.

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“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.”

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Losing the way of life, men rely on goodness;Losing goodness, they rely on laws.

- Lao Tzu

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The way of life = The architecture of the system

Goodness = “Don’t be evil”

Laws = “We need a free gene license”

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Small Pieces Loosely JoinedEnabled by:

• Common, well-understood data formats• A communications protocol• A variety of tools for accessing and representing the

data

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Who sets the gauge rules the worldSixty per cent of the world's railways use 4 ft 8 1⁄2 inch standard gauge, developed by George Stephenson in 1822.

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http://www.warwickshirerailways.com/lms/lnwrns305.htm

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You standardize railroads by building tracks

“The strategy is delivery!”

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UK GDS Director Mike Bracken

lessons from software for synthetic biology

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