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Biweekly links for 06/15/2009

by Michael Nielsen on June 15, 2009
  • Fully homomorphic encryption
    • Very interesting paper about a cryptographic scheme that allows computation directly on the encoded data, without requiring decryption.
  • Torvalds on how to use git
    • Interesting discussion from Linus Torvalds on good git development practices.
  • Don’t Hide Your Research, Share It! (pdf)
    • Good article about Open WetWare.
  • State of the OWW | OpenWetWare Community
    • Drew Endy: “I would currently be hard pressed to make a successful argument that supporting and using OWW [Open WetWare] has made the research in my own laboratory significantly better, as judged by our traditionally published results. If anything, using OWW as it exists today has lead to increased frustration with the slow inanities to be found within the conventional research publication process, while simultaneously and naively reducing the pressure to publish more formally and enabling others outside the (v. small) OWW community to “borrow” results without giving credit. This said, I’m more invested in OWW than ever before, and am convinced that we are figuring out a new way to do research. We just have a lot of work to do in order to make the transition complete.”
  • The Way I Work: Matt Mullenweg | Printer-friendly version
    • Lots of thoughtful stuff from Matt Mullenweg, the creator of WordPress: “For WordPress, we’re trying to set up a community that will be around 10 to 30 years from now, that’s independent from the whims of the market. I feel like the nonelected benevolent dictator: It’s my responsibility to meet as many users as possible and direct the software project in a way that reflects their interests. Last year, I probably met 2,000 or 3,000 people who make their living from WordPress. We want to be like Google, eBay, Amazon — they all enable other people to make far more money than they capture. And that’s ultimately what we’re trying to do. We’re trying to create a movement.”
  • Blogs, papers, and the brave new digital world: Matt’s thoughts « Sauropod Vertebra Picture of the Week

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4 Comments
  1. A fine series of links.

    Doesn’t Drew Endy’s post (about the OpenWetWare movement) have an element of irony in it?

    Namely, many MIT students trained in an open (university) environment have ended up working within the (private-sector) enterprise Ginkgo BioWorks.

    In the context of an ongoing literature review of large-scale simulation mathematics, I am finding a similar trend. Namely, humanity’s most sophisticated algorithms for large-scale simulation (in finance, engineering, and biology too) are increasingly held in private hands.

    Not just the software is privately held … the simulation algorithms themselves are secret.

    This trend makes me uneasy, partly because it increases the power of faction, and partly because it is not clear (to me) what humanity’s shared knowledge base is evolving to become.

  2. John – I don’t know enough about Gingko Bioworks’ business model to be sure, but I think much (all?) of what they do is made open source, through the MIT Registry of Standard Biological parts. If true, then they are contributing back to the commons, in a fashion similar to (say) Red Hat; they’re an open source biology company. Anyone from GB reading who can confirm / explain?

  3. Comments from Bingko Bioworks would be great! And maybe someone from Synthetic Genomics/JCVI (or any other synthetic biology enterprise) can comment too?

    AFAICT, the key techniques for synthesizing organisms de novo are open/off-the-shelf. Good … this biological openness is necessary to the continued openness of the overall scientific enterprise.

    But what’s (increasingly?) *not* open/off-the-shelf in biology are the techniques (instruments/software/algorithms) for “debugging” the organisms synthesized … these debugging tools vary greatly among enterprises, and commonly they are closely held within each enterprise.

    Just to point out the obvious, effective “debugging” tools are similarly central to biological enterprises as they are to (say) software enterprises. Conversely, lack of access to effective debugging tools is an enterprise show-stopper—particularly for open enterprises.

    It’s surprisingly hard to find out much about these tools. However, one shining example of openness is the GNU/LINUX community, where debugging tools are similarly open (and similarly important) to the kernel/compiler tools.

  4. And as one more follow-up, Ginkgo BioWorks/News has a link to Tom Knight’s talk Life with Four Billion Atoms.

    The thrust of Prof. Knight’s talk is that the number of atoms in an organism now is of the same order as the number of logic gates on a VLSI/CPU.

    Now, in the VLSI world we have (open-source) compilers that allows us to program every logic gate, (open-source) emulators that allow us to predict the function of every logic gate, and (open-source) debuggers that allow us to inspect the state of every logic gate.

    Everyone is familiar with the synergy of combined design/simulation/inspection capabilities in VLSI — so familiar that it is easy to take for granted the power of this convergence of capability.

    Knight’s talk recognizes that this same convergence of capability is occurring in biology. Obviously, the inspection and simulation aspects are harder in biology — because molecules are quantum machines, the atomic-resolution sensing and dynamical simulation press against quantum limits. But these challenges are being met.

    The resulting convergence of sensing, simulation, and design techniques is arriving considerably faster than (IMHO) many people foresaw. At the 50th ENC, Peter Schulz (of Scripps) gave a talk on recent developments in synthetic biology/biochemistry that was absolutely eye-popping.

    A major challenge for universities is not to be left behind … it is mighty challenging to do research at this pace and at this scale, and yet still respect academic traditions of openness and commitment to teaching.

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