scifoo: Open Science

One of the themes at scifoo was “Open Science” or “Open Notebook Science” – the latter term coined by Jean-Claude Bradley. The idea that science is publicly recorded as it is done. The very first bottom-up session (i.e. Saturday morning) was run by J-CB and Bora Zivkovic of PLoS ONE. Here are two comments:

Corie Lok et al.Scifoo: day 1; open science

It’s late and so I’ll keep this short. I’ll write more detailed accounts of Scifoo soon, but here are some highlights so far.
My day today started off with a contentious talk about open science. It quickly veered off into a complaint session about how the slow publication process in biology and the fear of not being credited and of being scooped are hindering open science (putting prepublication info and data online). But the physicists in the room quickly got annoyed by the complaining (not exactly new complaints either) and so the discussion got back on track to focus on current efforts to put more data and discussion of prepublication research online (such as Jean-Claude Bradley’s open notebook efforts). The session set the stage for several other related ones later in the day. It also spawned one taking place tomorrow about the culture of fear among young scientists: fear of doing open science, at the risk of jeopardizing career prospects. I’ll definitely be at that one. For another perspective on this session, check out Anna’s post on it.

PMR: here’s Anna’s post:

Swimming in the Ocean

Saturday, 04 Aug 2007 – 22:46 GMT
Have you heard the expression “small fish in a big pond”? I have an updated version. How about, “plankton in an ocean”? That’s me. I am the plankton, spending the weekend with CEOs of major corporations, editors in-chief, a couple Nobel prize winners, people advancing science and media in ways I can hardly comprehend… and Martha Stewart. That, in a nutshell (or an ocean, as the case may be) is Science Foo Camp, where I am currently sitting with mouth hanging open and ears open wide.One of the major themes of this free-form gathering has been open access publishing. In a group discussion led by Bora Zivkovic of PLoS ONE, tempers flared (which made it even more fun than staring at science celebrities), and the many complications, pros and cons of open access were raised. Does the term “open access” refer to pre- or post-publication open access? Is it open, non-peer reviewed publication of articles or even complete lab notebooks, or access to reviewed, published articles free of charge? That aside, will open access publishing negatively affect the hiring potential of young faculty looking for tenure track positions or funding from organizations such as Wellcome Trust and the NIH?
What about intellectual property? How does one protect findings aired in a public forum? One attendee replied that you don’t, it doesn’t matter, it should all be free and open. As much as I personally admire this free love, Birkenstock/Woodstock approach to science and research, I do not believe it to be feasible at the moment. Science is run by money. In order to get money or funding, one must publish. The changes and minor revolutions in that need to occur in publishing before the concept of the science paper becomes obsolete are staggering. They are also occurring as we speak.
Back to gaping at people far smarter than me.

PMR: and comments to Anna (so far):


  • Bora Zivkovic said:
    Small fish? No way – I was very excited to get to meet you in person.
  • Anna Kushnir said:
    The pleasure was all mine. I am happy I got the chance to meet you!
  • Jean-Claude Bradley said:
    Concerning the question of intellectual property, I am guessing that you are referring to my comment. I was not saying that all research should be open and free – just that people who are interested in intellectual property protection should probably not do Open Notebook Science. And this is no different than in the traditional publication process. People who are interested in intellectual property should not publish manuscripts without filing a patent (at least a provisional US patent). This is an expensive route and completely unrealistic for most scientific research projects. Money is not the sole motivation of scientists. If that were the case who would study fields like archaeology and cosmology?I wish that we had more time to discuss these issues during the session.
  • Deepak Singh said:
    I think the IP issue didn’t get brought up enough, especially with the peer2patent and other IP types there. In many cases the flaws are not in intent, but in the system itself. That said, I think as a community, we know what the problems are. We should just focus on solutions rather than trying to go into what’s wrong in excruciating detail 🙂

PMR: and Duncan Hull

9.30am: open science 2.0: where we are, where we’re going

After breakfast at Googley’s, I head off to a session on Open Science 2.0. This session is game of two halves, the first half there is much talk of how publishing is a roadblock to many things we would like to achieve with science on the web. Peter Murray-Rust talks of “conservative chemistry”, where (un-named) publishers are the problem, not the solution and block the whole of the University of Cambridge for accessing content in unapproved ways (text-mining). Paul Sereno and Chemist Carl Djerassi discuss the importance of publications in getting jobs and tenure at Stanford. There is talk of the dangerous power of editors of journals, who ultimately decide careers that they are blind too. They don’t just accept papers when they publish, they make and break people’s livelihoods. Andrew Walkingshaw tells of a common perception amongst young scientists about the importance of the h-index and other publication metrics. Eric Lander points out that publication isn’t everything for young scientists, a lot of it comes down to letters of recommendation in job applications and this fact is often overlooked by young scientists. Pamela Silver talks of how the publish or perish mentality is slow like molasses, and sends many talented young scientists at Harvard running and screaming from academia into the arms of anywhere else that will have them, which is a great loss to science. We move on to Open Access, Tim Hubbard, head of informatics at Sanger tells how the Wellcome Trust insists any publications that arise from its funded research projects must be freely available within six months after publication. Jonathan Eisen talks of different types of open access, which is not just about reading papers for free, but reusing them for free too, as in Creative Commons. Somebody possibly Richard Jefferson, talks of a reputation engine called Carmleon? (not sure of spelling).
All of this makes young scientists risk averse and paranoid, which is bad. The only people who can take risks are established scientists, which is a shame. But the discussion takes a u-turn when Paul Ginsparg ( and Dave Carlson, point out we should be having fun not moaning about publishing. We didn’t all come here to whinge, we should be talking about the technology that will enable us to break the publishing roadblock and make science a better place to live, work and play. On this note, Bora Zivkovic tells of publication turnaround times at PLOS, which are now “9 weeks not 9 months”. This is great for young scientists, who often don’t have time to wait for the glacial turnaround times of many publishing companies. He asks what would cyber infrastructure look like in 2015? Jean-Claude Bradley, gives a demo of Usefulchem, see for example this experiment tools like blogs and wikis will play an important contribution in this area.


Science is becoming more open, but it will be a slow evolution not a rapid revolution. We’re heading in the right direction, some of the tools for doing it are beginning to work. PLOS asks people to be courageous and send their papers in, this can be a gamble, when scientists often favour the old favourites of Nature, Science and PNAS. This session was typical of scifoo, its a mashup of different ideas from very different people working in different areas. It doesn’t always summarise neatly, but thats life. A session on this came later on, called the Culture of Fear: led by Andrew Walkingshaw and Alex Palazzo.

PMR: The session didn’t go as planned – JCB had produced material to demonstrate and didn’t get to show it till near the end. The meeting got hijacked by the theme of Open Access and I helped in the hijack when I probably should have stayed quiet. It meant that we didn’t explore the bright future but reiterated the less inspiring present. But somehow that was the burden that a lot of people had brought with them. Scifoo doesn’t run  on predictable lines and one good thing was that Alex and Andrew were inspired to run a session (young scientists and the culture of fear) they hadn’t planned to when they came.
“Open Science” is a concept whose time has arrived. I prefer “open Notebook Science” because there is less chance of confusion with other terms which have nothing to do with the concept.  Under Open Research WP ha a stub which lists a few lists a few examples – add some more.

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