Biotechnology

Scenes from the Open Science Summit

Ronald Bailey's first dispatch from the conference that aims to launch Enlightenment 2.0

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Berkeley, California—The inaugural Open Science Summit kicked off Thursday afternoon at the University of California, Berkeley's International House. Some 200 participants have gathered to "update the social contract for science." The summit's chief organizer, a young intellectual entrepreneur named Joseph P. Jackson III, says his aim is to jumpstart Enlightenment 2.0. Let's hope he succeeds, because the first panel of presenters made it clear that Enlightenment 1.0 is mired in a bureaucracy run by careerist professionals.  

Before the formal presentations began, the summit opened with a kind of free-forum forum where participants stood up to ask panel members questions. The first question from the floor was: What is "open science" anyway? My personal favorite definition was enunciated at the outset by quirky Cambridge University chemist Peter Murray-Rust: "The 'open' bit means that it is available to anyone in the world to do whatever they like without any restrictions." Statistician and Yale Law postdoctoral asssociate Victoria Stodden described the open science movement as an amalgam of folks who want open access to the peer-reviewed scientific literature; open access to all scientific data; and to improve the efficiency of how science is done, largely by enhancing cooperation between researchers. Surprisingly, none of the initial answers addressed one the more interesting motivating themes behind the conference: how the falling costs of enabling technologies are empowering citizen scientists to participate fully in the scientific enterprise, liberating science from the stifling bonds of the government-academic-corporate research complex.

The negative effect of those bonds was highlighted when University of Manchester computer scientist and research social networking guru Carole Goble noted that openness is being stymied in part because many young pre-tenure researchers are afraid to share their results before publication. They fear that sharing will allow their rivals to "steal" their results and that scientific journal editors will refuse to publish anything that has already been aired in public. Murray-Rust admitted that this is a problem which he hoped would be solved in the next 10 years.

From the floor, a young mathematician (unidentified) then ridiculed the fields of biology and chemistry for being backward fuddy-duddies with regard to publication and scientific priority. She pointed out that the norm among mathematicians and physicists is that as soon as they produce something reasonable, they put it up on the arXive preprint server. Everyone can then see that you've published it and that you got there first. Peer review, such as it is, happens when you get around to sending your results to the journals. One life scientist from the floor pointed out that genomic research has already fostered a similar culture where researchers make their data public.

Another issue raised was sharing negative and inconclusive results. Among other things, the failure to publish negative and inconclusive results skews statistical analyses that aim to determine the effectiveness of drugs or the alleged toxicity of chemicals. In addition, making negative or inconclusive results public would considerably speed up scientific research by sparing researchers from traveling down previously explored dead ends. Some panelists noted that several journals have tried this in the past and failed, due in part to the fact that researchers barely have enough time to put together and publish their successful results. Australian National University chemist Cameron Neylon responded that software developments will soon make these excuses untenable because it will be possible to standardize and upload the results of failed experiments onto the Internet where others can find them. Neylon also argued that researchers should want both more positive results and more rubbish published because then someone can build a Google for science. So instead of filtering information on a pre-publication basis, filter it once it's out there.

The free-form forum was followed by a number of brief, formal, TED-like presentations. To give readers an idea of what is on offer at the Open Science Summit, let's look at a selection from Thursday night's presentations. One of the fiercer presenters was statistician Victoria Stodden. She argues for framing the open science movement in terms of two principles: reproducibility and knowledge sharing. She actually views this as a return to the traditional scientific method of complete disclosure. According to Stodden, computation in research is now pervasive and many scientists fail or even refuse to release the computer code they use to determine their reported results. Without this code, outside investigators cannot reproduce the reported results. Although she didn't say it, this means that outsiders are being forced to take reported results on faith. Stodden noted that the "Climategate" scandal erupted, in part, because a clique of researchers refused to share their data and computer models with skeptical outsiders. This very week, three cancer treatment trials were halted because outside statisticians could not reproduce the results of Duke University scientists. Fortunately, as Stodden pointed out, this situation may be changing since funders like the National Science Foundation are requiring grantees to enact data release plans and journals are also setting up requirements that researchers share their code and data at the time of publication.  

Morgan Langille, a young University of California, Davis genomics researcher, unveiled his BioTorrents file sharing service which enables researchers to find and speedily download vast data files. It was a bit surprising that it has taken biologists this long to figure out how to leverage this technology. Kudos to Langille. Next up was Jason Hoyt, a geneticist and research director at Mendeley, which offers a software system that aims to break through the scientific silos that confine and often obscure relevant results from researchers. Ultimately, Mendely wants to build the world's largest academic database. In the 18 months since it went online, Mendeley has 450,000 users and has aggregated the metadata from 29 million papers. Hoyt noted that Thomson Reuters took 50 years to aggregate 50 million scientific papers.

Neuroscientist Martha Bagnall noted that a lot of valuable criticism of new published work takes place among colleagues in laboratories that never gets aired in public. She observed that lots of journals now allow commenting, but there is a big ironic problem—while peer review is anonymous, commenting at journals is not. Anonymity is important because researchers fear reprisal from criticized colleagues when their own papers or grant proposals come up for review. So to capture the lab's informal criticism and make it publicly available, she and her colleagues have created The Third Reviewer website. The site lists journal research by discipline, complete with abstracts, and lets anonymous commenters have at it without fear of reprisal. It also gives authors an opportunity to defend their research. Third Reviewer is now expanding to other disciplines.

In one of the more exciting presentations, young scientists D.J. Strouse and Casey Stark unveiled their Colab open source science site at the summit. They argue that open science is more than open publishing. Strouse and Stark complained that the state of scientific publication is static and keeping up with the latest results is much like "playing ping pong under a strobe light." In Colab, researchers can dynamically collaborate by describing a problem, figuring it out together, and publishing their results on the site, where those results can be continuously improved in public. Since the entire process is open, a researcher's idea is time-stamped so that everyone knows who gets credit for scientific priority. However, if a researcher still fears being scooped, she can make her research problem private and invite specific collaborators to work on it, only publishing once they are done.

On the subject of empowering citizen scientists, a number of young entrepreneurs discussed their efforts to build cheap biotech research equipment. Josh Perfetto talked about the Open PCR (polymerase chain reaction) project which aims to build a PCR thermocycler that will cost under $400. PCR thermocyclers are used to amplify DNA samples for analysis. Using the Kickstarter microfinance platform, Perfetto and his colleagues raised more than $12,000 for their project and have now completed a desktop prototype they plan to offer later this year. Similarly, University of Michigan stem cell biology Ph.D. student James Peyser and colleagues have created the Otyp project, which aims to get real biotech experiments—e.g., putting genes for green fluorescence into E. coli bacteria—into high school classrooms. Also using the Kickstarter financing platform, Otyp is developing affordable open source hardware, wetware, and software to achieve this goal.

The final presenter of the evening was Todd Kuiken from the Woodrow Wilson Center in Washington, D.C. Kuiken heads up the Center's DIYBiosafety project. Its aim is to create a culture of research safety among DIY biotechnologists. Apparently, some people are nervous about do-it-yourselfers genetically manipulating bacteria, plants, and animals in their garages and kitchens. Go figure.

Further dispatches from the conference will detail presentations on open peer review, distributed decentralized amateur science, alternative research funding methods, and more.

Ronald Bailey is Reason's science correspondent. His book Liberation Biology: The Scientific and Moral Case for the Biotech Revolution is now available from Prometheus Books.

NEXT: This Whole Congress Is Out of Order!

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  1. Among other things, they hope to untether scientific research from the stranglehold of the government-academic-corporate research complex and empower citizen scientists.

    I found the Friday Funny!

    1. Of course you can do your own research, citizen! Just make sure you have your IRB and/or IACUC approvals in place, all your MSDS are complete, and all your safety and waste disposal protocols are in place and approved.

      1. At least with the MSDS’s you just need to take them out of the package (or these days print them from the suppliers web page) when the Scary Stuff ™ comes by UPS and put them in your big binder…

        I can manage that…

        1. And when was the last time someone actually came to your lab to check that every material/reagent had an MSDS in the big binder …

          1. My university gets periodic visits from the state, where they pull a sample and check them. Last time, most of our deficiencies were actually in the Art building. Turns out that there are lots of hazardous materials in painting, ceramics, and sculpture studios. You may also be surprised to learn that most art faculty do not know or care about MSDS, required storage/disposal procedures, etc.

          2. No idea.

            We get periodic inspections, of course, and I’ve seen them pick up the folder, open it, close it and put it down…

            However, when we had an unknown material leaking in the flammables cabinet last year, I was glad that we had fifteen year old MSDS’s…and pissed that we had fifteen year old specialized solvents that know could even think of a use for.

            1. s/know/no one/

              What the hell is up with me. I’ve been really bad for the last few weeks.

              1. Did you get a whiff or two of those fifteen-year-old solvents?

  2. Among other things, they hope to untether scientific research from the stranglehold of the government-academic-corporate research complex and empower citizen scientists.

    Yep. I’ll just save up my quarters and in no time at all, I’ll have enough money to build my own large hadron collider.

    And after that, I’m going to start saving for my own 10 meter telescope with adaptive optics.

    1. Big science is going to be the province of big money, sure.

      But I see a colloquium or two every year where someone describes cutting edge work they’re doing on US$5000-25000. Which isn’t spur of the moment for most of us, but is well inside the range that ordinary people throw at their hobbies.

      Often this is going on around the edges of a much bigger and more expensive effort, but even now there is good science that can be done on the cheep.

      The cutting edge keeps moving on, but the gear keeps getting more powerful and affordable and materials keep getting cheaper and/or substitutes become available.

    2. This.

      So much this.

      This is silly.

      Reason needs to stop posting silly things.

  3. On the subject of empowering citizen scientists, a number of young entrepreneurs discussed their efforts to build cheap biotech research equipment.

    Will they be selling those through the Discovery stores? I think I know what to give my kid for Christmas…

  4. What the hell is up with the “update the social contract for science.” ?

    I research for one primary reason, and that is a base curiosity and a desire to know what’s actually going on. It’s utterly selfish I assure you.

    Open science is a good thing because it allows more eyes and minds to assess various results, but this social contract crap is just the same set of bullshit rationalizations in a different setting

    1. You must have met someone whose career derailed at a young age because he became obsessed with the method, not the result. You know, he had to write a computer program, and spent 100x the required time to get it just working in rewriting and rewriting it so that it was as bull’s-ass tight and as slick as a mosquito proboscis fresh from the puncture, not a single wasted unsigned char?

      That guy failed his prelim and dropped out, became a Web-site maintainer for a bank by day, raving crypto-anarchist and SCE jouster by night.

      But did you ever wonder what ever happened to people whose OCD derailed them at a later stage in their careers? Now you know!

      1. You just described me perfectly: career derailed at thesis writing stage due to attempt to make everything better. Tons of ideas, relatively intelligent, even productive. Looking at feasibility of DIY biotech.

  5. However, if a researcher still fears being scooped, she [sic] can make her research problem private and invite specific collaborators to work on it, only publishing once they are done.

    Oh, is she a friend of yours, Ron? Or are you using politically correct pronouns now?

    1. OMG OM! It’s misogynists like you who have kept the woman down all throughout herstory!

      1. No, sorry that was me. She seemed to enjoy it, though.

      2. Re: Fiscal Meth,

        OMG OM! It’s misogynists like you who have kept the woman down all throughout herstory!

        No need to throw a hersy fit…

  6. Some 200 participants have gathered to “update the social contract for science.”

    Hopefully they can get the 7 billion initials required per page (before the contract can be considered amended) in about 30 years . . . Uh, unless of course, this “social contract” thing is just pure rethorical bullshit.

    1. It’ll be released under GPLv4, which means you can talk to anyone you please, so long as you both exchange identical digitally-signed copies of a 3.8 Gb FLAC recording of Richard Stallman describing, line by line, which bits of the Linux kernel Linus Torvalds stole from him.

  7. The final presenter of the evening was Todd Kuiken from the Woodrow Wilson Center in Washington, D.C. Kuiken heads up the Center’s DIYBiosafety project. Its aim is to create a culture of research safety among DIY biotechnologists. Apparently, some people are nervous about do-it-yourselfers genetically manipulating bacteria, plants, and animals in their garages and kitchens. Go figure.

    Its other aim is to re-segregate the army and navy, bamboozle the people into going to war, place a few thousand dissidents in jail, supress the press, and . . .

    Oh, you mean, they don’t really live up to their name? Oh. That’s nice!

    1. Heh! You beat me to the comment on the irony of a site like Reason lauding such an eponymic disaster.

      As my roommate would put it:

      “Smart-ass Derby!!! You lose!!”

  8. However, if a [climate] researcher still fears being scooped reaching the wrong result, she [sic] can make her research problem private and invite specific collaborators to work on it, only publishing once they are done massaging the data and the model to reach the right result.

    Sorry, couldn’t help myself.

  9. What’s a failed experiment?

    They’re not trying to gin up a particular result are they?

    1. Michelson?Morley?

      1. Re: Theocrat,

        A failed experiment is when arrogant humans try to change man into the image they dreamed. For instance, Tony wants Paradise to return to Earth and by golly if whoever stands in the way of that dream will be sent to the gulag. Chad dreams of people giving 33% (at least) of what they “took” from “society”, “back” to “society.”

        And so on…

        Michelson-Morley was NOT a failed experiment, in that it showed once and for all that the “ether” hypothesis was pure bullshit. Knowing that something is not so is just as important than knowing something is so.

        1. But they were trying to provide insights in the aether. If they were modern they have buried the results or faced loosing their grants.

          1. Granted, they could have even written hundreds of e-mails disparaging their anti-aether opponents… Good thing they were not East Anglia “scientists.”

            1. Good thing, too, that there was no “consensus” in 1890 that Newton knew what the fuck he was talking about and that the idea of time passing differently for different observers was something only an embittered Patent Office clerk with no serious credentials would try to slip by Peer Review.

              1. Ignoring the “embittered” comment, did you have a point?

              2. Newton did know what he was talking about

                who are you lol

        2. Michelson himself was never totally convinced. He reran the experiment a bunch of times over the ensuing 20 years or so, even after everyone else had accepted the result. He just couldn’t quite completely believe it.

  10. It would be great if Bill Gates and Warren Buffet would support pure science research.

  11. “liberating science from the stifling bonds of the government-academic-corporate research complex.”

    so that part-time workers will show us the way.

    1. Not to mention the stifling bonds of classical arithmetic and the so-called Second Law of Thermodynamics.

      I don’t know how many times those fucks at the NSF have brusquely dismissed my proposal to spend $50 million investigating a clever perpetual motion machine my dog told to me in a dream. They’d rather just throw it down the rathole of cancer research and the Higgs boson, I guess.

      Short-sighted fools. What good will it do us to cure cancer if the little white spiders get us, as they surely will if we do not all turn around three times every hour, pressing left little fingertips to the bridge of the nose precisely 2cm below the browline? I can see one of the little white bastards right now, actually. Get it off me. Get it off get it off get it off.

  12. Great, we can do for science what the Internet has done for journalism. One serious person for every 1,000 crackpots.

    1. We call that a “kiloTony” (symbol kT).

      1. “GOOOOOOOOOOOOOOAAAAAAAAAAAAL!”

  13. I look forward to your updates from this conference. I believe the framework science exists in today is failed by such a closed system, it is chilling advances. Plus more open data means more accountability, also as citizen interested in the science I always enjoy reading scientific research.

    1. Science is under siege by both corporate and government interference, you can’t blame it if it tries to protect itself. But science rigorously depends on openness and accountability, and its competitiveness ensures it. I’m not sure what you think is being hidden.

      1. I think you misunderstood what I was trying to say. The closedness I was talking about was no just to the outside, but among the scientists in established systems. Secondly, I was not really thinking anything was hidden to the public, but inaccessible to the public. In the current infrastructure of academia and science papers are published in expensive peer reviewed journals, I think this reduces access to information and reduces the input in science. The accountability I was talking about was not on a systematic level, but accountability on individual scientists. I’m not a global warming denier if thats what you are getting at.

        1. As mentioned you can find preprints at:

          http://arxiv.org/

          Science can always strive to get better to make information more accessible. The world wide web was created out of the need for scientists to share information.

          As for expensive journals, only university libraries can really afford those things. They can be made available for online access, but they charge a ridiculous amount to view a paper. Is it the cost of server space? Can Google help out: don’t they have Google books? It’s not like scientists don’t want their papers inaccessible.

          1. ArXiv was originally a particle physics thing and it is still used much more by people in that and closely related disciplines. So it is only a partial solution.

            As for the cost of journals, even using volunteer labor for the review, they have to employ people and use expensive machines. The money has to come from somewhere and they can’t exactly make it up in advertising (well, Physics Today sells some), so that have to get it from somewhere. There are efforts to get some free or very low cost journals going on the web. Time will tell how well they work.

      2. Re: Tony,

        Science is under siege by both corporate and government interference,

        “Under siege” by corporations? As in “they don’t pony up”? Or what are you hinting at, Tony?

        Government interferences are well documented, Lysenko being the most often cited, but “corporate interference”?

        1. OM are you suggesting that corporations that sell things like, oh, say tobacco products haven’t tried to influence science reporting related to their products? Petro companies have a long history of funding junk science, not to mention supporting a vast propaganda campaign. You as a victim of that campaign won’t believe me, of course.

  14. “openness is being stymied in part because many young pre-tenure researchers are afraid to share their results before publication”
    Does Open Science require you make all your data available before publication?

    Once the paper is published it should be common practice to make all the data open to the public, so that the experiment can be reproduced. Some scientists argue that would require
    them to write computer code with loads of comments but that is BS, that would only make the code easier to follow. Some may be embarrassed to release their code because it is poorly written, but heck anyone who does data analysis does some programming without CS expertise that could be better written but that doesnt mean the science is wrong. If you dont want to release the code then give enough details as to what you did with the data to allow others to roughly reproduce the same results.

    1. blubi|7.31.10 @ 7:04PM|#
      “openness is being stymied in part because many young pre-tenure researchers are afraid to share their results before publication”

      Seems that one of the problems is “tenure”.
      If you are angling for an iron rice bowl, the incentives would make you chary of releasing *anything*.
      If you can get fired, you have a tendency to offer what you found yesterday.


  15. Recent online exchanges with researchers in climate science has tended to reveal an attitude prevailing in some quarters to the effect that the computer code devised by these individuals for the interpretation of their data is proprietary, and that they need not share the “nuts and bolts” workings of these tools with anyone.

    Intellectual property rights arguments are offered.

    My personal take on this contention is laden with contempt. It is akin to a student refusing to show the teacher his calculations, desiring only to put down the answer upon which he has arrived.

    Has anybody commenting in this thread any sort of thoughts to offer on this “proprietary” refusal to open up the code behind the vaunted computer models which are devised to analyze observational data and thereby arrive at the conclusions – and policy recommendations – by which science is manifest in the actions of civil government these days?

    Given that trillions of dollars (and the lives of millions of real human beings) are at stake, the reluctance of researchers to allow genuine transparency in their work seems perfidious and dangerous as all hell.

    1. Well if the research is publicly funded, as much work is, it should be public.
      If it?s private and the claim/experiment cannot be reproduced because the scientist refuses to provide sufficient data, then I can?t see why the scientific community should take them seriously, as in Phil Jones? infamous statement:
      “Why should I make the data available to you when your aim is to try and find something wrong with it?”

      1. The problem is that although the research is public, the methods may have been developed privately. For example, if you use an Excel spreadsheet, should Microsoft be compelled to give you the source code for Excel, for your calculations to be taken seriously?

        1. You don?t need the source code of Excel, just the data files. If you?re using proprietary software, provide the input & output data and if applicable, any data files.

          1. I think most researchers who work with computers get their data from the people who took the experimental measurements, which is usually published data. Data output is what the paper is all about, and there should be graphs and stuff in the paper.

            I think what’s not provided is the code used to generate the output data from the input data.

            Anyways, I agree with you that at the very least input and output data must be provided.

            And they really should provide the code that turns the input data into the output data. However, is it better to force people to provide the code, perhaps causing people to be reluctant to publish, or not force them and perhaps they made a mistake in coding which no one can catch?

            1. If its proprietary they cant release it, but I dont think that?s important. If it?s say a statistical program it should be able to reproduce the results with another program.
              The important thing is that there be enough info on data and methods used to reproduce the results.

  16. The last thing we need are a bunch of common citizens making bold scientific claims without bothering to consider something known in the field as “control experiments”. I’m all for opening up science, but let’s not pretend like this will directly involve the public at large.

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