Posts Tagged with “science”

Open Science — Incremental Advances

December 6th, 2006

A couple of days ago a colleague referred to the Open Science post a while back, and I realized I had meant to follow up. So here goes.

Given the issues with “open science” how might progress towards openness be made?

  1. It’s unlikely that those with a big financial stake in the current arrangements will change. This obviously includes the commercial ventures aiming for large returns on their investment. It probably also includes the major research and development institutions who may not be public companies but who are deeply involved in the current system. If you’re an academic institution and you’ve spent millions of dollars outfitting labs and have a set of people working and studying at your institution assuming the research and its results will be treated a certain way, it’s hard to make big changes. So even if one takes the position that these organizations should change (which I’m not necessarily advocating) I think it’s unlikely that leadership toward Open Science will come from here.
  2. It’s more realistic to expect change around the edges than at the very center of the system. Periodically I read about diseases that could probably be treated, but exist mostly in impoverished areas. So there’s very little economic reward for the necessary research, development and deployment. I could imagine organizations concerned with alleviating these diseases to be more inclined to find ways to collaborate, particularly if relevant patents have expired.
  3. There is usually a hierarchy of research organizations and universities; the “top tier” schools are more able to get research funds and to capitalize on the results of their work. But, there are massive numbers of very smart and very motivated people at other organizations. It may be that collaborative scientific techniques will develop at unanticipated places that aren’t well positioned in the current system.
  4. It may be that successful Open Science doesn’t start at the central, biggest problems. It may grow by solving pieces of problems. Free compilers existed before the complete GNU Linux operating system; the same incremental change may occur with Open Science. Sadly, many of the big problems are the health topics where people’s lives are at stake.
  5. The realm known as “Citizen Science” may well lead the way. Citizen Science is based on large numbers of people working together. Since those participants aren’t expected to have scientific training, there are a whole set of problems that can’t even be approached through this method. But we may be surprised at the areas where Citizen Science can move our understanding forward.

Open Source, Open Science

August 30th, 2006

At Sci Foo Brian Behlendorf and I hosted a session about how the lessons learned from the open source software experience might be applicable to scientific endeavors. The hope is that we can support the “open” movement in science as well. By “open” I mean a system where effort and resources are pooled and the result shared. This is in contrast to an increasing focus on what’s “my intellectual property, how can I best protect that intellectual property, use it to create a closed system and then extract the most value for me from that closed system.”

We ended up with a list of things that are different about the life sciences that make it difficult to transport open source software methods wholesale. These are listed below in no particular order. I use “science” here to cover the range of topics, although it feels a bit basic. The real value is in trying to figure out how to alleviate some of these problems. I haven’t tried to do that here; rather I’m trying to start a list of the various issues.

  1. A lot of scientific effort is expensive. It’s hard to work in many areas without being tied to an institution that provides the equipment, the labs and other necessary support. This greatly reduces an individual’s ability to break out of the standard way of doing things.
  2. A lot of scientific efforts require long periods of outlays before getting meaningful results — it’s harder to find incremental projects that can demonstrate value (whether economic or social) quickly.
  3. It’s much more difficult to “scratch one’s own itch.” Someone choosing to work in many scientific fields is unlikely to be solving his or her own immediate problem. The result may be years away, unknown, and not directly applicable to his or her own life. This is quite different from software development, where many people get involved to fix something that is bugging their daily experiences.
  4. There’s no accepted set of free and unencumbered tools and building block for the life sciences. This problem was raised by Richard Jefferson of, who notes that the technologies used to pursue the scientific process are encumbered by patents in such a way that the end result is hard (or impossible) to use and share freely. It’s as if a patent on a compiler (or all compilers) applied to any code that had been compiled. Richard’s pithy summation of this problem is: “there’s no LAMP stack.” (Thanks to Richard for permission to attribute this to him, which is required under the Chatham House Rule under which SciFoo operated.)
  5. There’s already a recognition system in place through the peer-reviewed journals. This mechanism has a variety of problems itself and may be due for change. But even so, there is an accepted review, recognition and advancement system for the sciences outside of collaboration.
  6. Collaboration often needs to occur between institutions rather than individuals. This makes it harder to get started than simply having a few people decide to try something.

Science Foo Recap

August 16th, 2006

This weekend I went to Science Foo Camp, also known as “Sci Foo.” This was an extension of the “Friends of O’Reilly” camping events (“Foo Camp”) that the O’Reilly publishing folks have held for the last couple of years.

Foo Camp is an invitation-only event at the O’Reilly facilities in California (and leter expanded elsewhere) where one literally camps out for the weekend (in cubes or by pitching a tent on the lawn or in the apple orchard). O’Reilly makes meeting rooms and meals available, and sets out a large grid showing meeting rooms on one access and time slots on the other. The event starts with an initial gathering where everyone introduces themselves. Tim O’Reilly’s rule is: you get to say your name, an organizational affiliation, and 3 words (literally, 3 words) to describe yourself. After this, the content and events of the weekend are up to the participants to decide. It’s a “conference” created by the participants on the fly. Naturally, a lot of the great stuff also happens outside of any particular session. Foo Camps have been focused in the software and technology space. Not entirely, but that’s been the focus.

Science Foo was different. Its focus was -– no surprise -– science. It was organized by O’Reilly and Nature magazine, and hosted by Google at Google’s Mountain View campus. The idea was to gather interesting people who didn’t necessarily know each other or work in the same field, but were open to cross-fertilization and new ideas. No camping this time, but a bunch of folks in the same hotel generating late night discussions.

As you might imagine, the combination of O’Reilly, Nature and Google assembled a fascinating set of scientists. This included biologists of all sorts, chemists, physicists, earth scientists, clinicians, historians, technologists, science fiction writers and a set of people interested in large data sets. The topics ranged from the physics of light to gene expression to citizen science to emergent evolution to the politicization of science to open science. Here’s what the Saturday schedule ended up looking like.

The O’Reilly folks also invited a few of us involved in open source projects. The idea was to bring some of what we’ve learned in opening software development to the efforts to make science more open and collaborative rather than focused only the fierce secrecy required to protect IP and publish first. It was great fun to go because today’s science is utterly boggling, it’s a joy to find groups of interesting people, and I would like to see some ways to promote more openness rather than intellectual property protection in science.

I noticed a set of things were different right away. First, I was surprised at how many people posted to the wiki before the conference started describing discussions they would like to lead. I had thought that since the format was new to many of the participants it might be slow getting started. But there were probably 50 ideas posted before anyone arrived in Mountain View. And when it came time to pick a slot on the schedule people were not shy either. Later I realized that many of the participants have made their career in writing and presenting their results and that they are very accustomed to making presentations and leading discussions.

Some other things that stood out:

  • Many people were unable to describe themselves in the allotted 3 words. A bunch of people managed to hypenate words into phrases and get them counted as 1 item (“data-visualization techniques” for example), and a bunch more needed complete sentences.
  • The average age was much higher, at least 10 years and maybe 15 years.
  • The number of people who came with presentations was high.
  • The rapid-fire, high interruption, bounce around the room discussion of Foo Camp was much more measured and deliberate here. Not necessarily less effective, just different.
  • The sense of people just starting to get to know each other was much stronger. At Foo Camp a bunch of people know each other already. This was less so at Sci Foo. It was the first one, and the people came from a very broad set of disciplines and much of the weekend was learning enough about other people for a discussion to emerge.

At the beginning most people went to the sessions. As time went on, and especially on Sunday, the open space was more and more filled with people who had come across an interesting idea and had settled down somewhere to keep discussing it. The sense of people creating conversations and connections was palpable on Sunday. It was as if Friday and Saturday set the stage, Saturday night a bunch of folks started to connect and by Sunday people were wildly open to new ideas, new people and new connections.

The closing session was surprisingly lively. Maybe I’m used to Foo Camp where a bunch of people are up most of the night and everyone is a zombie by Sunday afternoon. I don’t recall a closing session at Foo Camp; maybe I’ve just missed them all !!! But the Closing Session at Sci Foo was well-attended, lively, full of ideas and a good gathering in itself. One person wanted “real-time intelligence” on what’s happening in other sessions so he can constantly evaluate if he’s in the right place. (What’s the noise level in other sessions, can we tag people’s cell phone so we know who is in other sessions, etc.) Someone else replied “no thanks, the best part has been wandering into the wrong session. Or finding a session cancelled but talking with whoever showed up about other things.”

We had a few discussions about how the lessons of open source software might be useful in “open science” but this was just a beginning. I’ve got a bunch of ideas about this that I’ll try to get written down and posted shortly. Tim was clear that most of the people at Sci Foo won’t be at the next one (assuming there is a next one) – the goal is to mix people up so they can’t keep inviting the same folks back. But whether or not I’m there, I’d like to see the discussion of bringing (and retaining) openness and collaboration to scientific research bear fruit.

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