Corpus callosum: 1st edition of open science round-up

September 19, 2008

The idea for an open science round-up is not new. An open science carnival was suggested over at Plausible Accuracy and the carnival on scientific life, Praxis, has included quite a bit of open science. What I’ve produced here is not strictly a carnival, but a round-up of all sorts of material on the web focused on open science issues and themes (there is a little overlap with Praxis so feel free to ignore the redundant links).

For the most part, this round-up is concerned with writings, papers, and websites from the last couple weeks that have to do with open communication, open access, open data, open research, and the tools and policies that affect these endeavors. The hope is that by collecting these materials regularly we can make connections and communicate more easily on the subject. That is why, for now at least, I’ve called it Corpus Callosum.

Conferences, workshops, and meetings

To start, I think it’s exciting how many workshops and meetings there have been in the last one or two months. Not only has the content been fascinating, but there is also the feeling that momentum is gathering.

The meeting that arguably kicked off this latest flurry was the Policy and Technology for e-Science satellite meeting of the Euroscience Open Forum, which took a great step forward by creating a set of clear guidelines defining open science. Additional blog posts about the meeting are summarized over at Science Commons. The discussion continued a few weeks later at two unconferences, BioBarCamp (FF room) and SciFoo, with commentary at Science in the Open (biobarcamp, scifoo), Ouroboros, Public Rambling, and I was lost.

Soon after that was the Southampton Open Science workshop (FF room) initiated by Cameron Neylon at Science in the Open, with blog notes by Branwen Hide at Research Information Network on some of the tools that were discussed. JC-Bradley at UsefulChem summarizes his jaunt through various (open-ish) science meetings in the UK during this time and is accompanied by Cameron in an open science endurance event.

Most recently was Science in the 21st Century (FF room) in Toronto, which discussed the ways in which technology influences the practice and communication of science. Videos for the talks are archived at the Perimeter Institute (PIRSA). BackReaction summarizes the summary. Inspired by the meeting, WebGoddessCathy writes about reasons to share science. Uncertain Principles, normally unenthusiastic about Open Access, is pleasantly surprised by John Willinsky’s talk about making OA accessible to the public readership; a number of other topics also inspired blog posts, including discussions of “Journals of stuff I like” and open notebook software. If you missed the meeting, you can catch up by tackling this daunting reading list compiled at Confessions of a Science Librarian.

At the same time as Science in the 21st Century was the Access to Knowledge (A2K3) meeting in Geneva. Victoria Stodden, a research fellow at the Stanford Law School, won the Kaltura prize (open source and collaboration themes) for her paper, “Enabling reproducible research” (warning: PDF). Dr. Stodden also posts about a talk given by Tim Hubbard on open science.

Now it seems there is a bit of a lull as people catch their breath and regroup. One of the next meetings is the Open Science workshop at the Pacific Symposium on Biocomputing in January 2009. Speakers are confirmed and the organizers are (well, Cameron is) drafting a 5-page introduction that will be published in the conference proceedings (send feedback if you’d like!).

How and why to be open

So there’s all this talk about open science – what does this mean, who is doing it, and how do we start? Well, the principles for open science from Science Commons is a good guideline, and a paper published in PLoS Medicine earlier this month from Piwowar et al provides recommendations for leadership. Research Remix follows up on these recommendations by posting a letter to her department suggesting a BHAG (Big Hairy Ambitious Goal) for openness, and highlighting the US National Center for Research Resources strategic plan to facilitate information sharing among biomedical researchers. Dave de Roure gives his take on guidelines for the new e-science at the Digital Curation blog. And John Wilbanks implores us, regarding code at least, to “ship it or share it“.

In terms of policy and funding, Peter Lee writes about the movement towards the privatizing patent regulation and the “biomedical research commons”, while the Positive Tech Journal considers the possibility of crowdsourcing funding for science.

Sometimes it’s easy to get caught up in the furor and lose sight of why we become open in the first place. Cameron reminisces about the serendipity leading to his own decision to make his research open, Chris Patil is inspired enough by BioBarCamp and SciFoo to make a public promise to go open, and coffee research goes open inspired by talks at Science Blogging 2008. Cameron, JC-Bradley, Peter M-R and Egon Willighagen get together to do a real-time open science hackfest, and at some point during all this, Cameron and JC-Bradley sit down with Nature for an interview on their thoughts on open science (Cameron’s clarifications here).

But the devil is in the details. Science in the Open muses on the distinction between recording and presenting experiments in open notebooks, and Bench Press shares tips and experiences from making the transition to electronic online notebooks, with the strong advice: “whatever you can make electronic, make it so.”

Tools for open science

These days it seems like every week brings another dozen new “web 2.0” and “science 2.0” tools. Some of the latest to create buzz are Mendeley, yet another system for managing and sharing research papers (both online and downloadable desktop versions available), SciVee postercasts which combine interactive poster viewing with a short video clip of the author presenting the work, OpenScience.org writes about Exhibit, which helps you put your data online, and Laboratree makes their official launch and press release. And BBGM notes, FriendFeed continues its success as a homebase for many life scientists on the web.

A couple websites that may be of interest are SpreadingScience, which focuses on educating people and scientists about science 2.0, and the World Association for Young Scientists (WAYS) website for facilitating global access to science and collaboration. WAYS has some interesting blog posts, including this interview with Wikipedia co-founder Larry Sanger, who has founded what could be considered a more transparent and reliable version of Wikipedia, Citizendium – anyone can contribute, but they must use real names and “experts” (Ph.D. holders) can approve the contributions. Citizendium also partners with universities around the world to offer academic credit for high-quality entries in a program called Eduzendium.

Wikis have been around for a while but they have only recently started being used for science. This approach makes sense given that the small number of curators responsible for maintaining traditional knowledgebases is clearly insufficient for the amount of data now being produced; rather, take advantage of the vast communities of scientists (i.e. experts) by allowing any of them to contribute their individual knowledge.

This crowdsourcing strategy towards annotation has met with only limited success however, as this Nature News article on “wikiomics” discusses. The problem is always: how do you get scientists to contribute? There are at least two facets to this problem – contributing to a wiki requires time (though arguably not that much), and there are no incentives to contributing. Ouroboros writes about open access annotation, and, specifically, Gene Wiki (PLoS paper), a Wikipedia portal which hopes to ameliorate the barrier to contribution by pre-populating the wiki with “stubs”. Mememoir takes another angle through its WikiGenes knowledgebase (Nature Genetics paper) by providing clear authorship attribution, tracking, and peer review.

Wikis aren’t alone in sometimes having a barrier to adoption/contribution. So-called web 2.0 and science 2.0 tools like the ones mentioned above often face resistance from the majority of scientists, not to mention stiff competition. The SpreadingScience blog writes about the 5 step process for a person (or organization) to adopt innovation and Expression Patterns gives her thoughts on how to get scientists to adopt web 2.0 technologies. A New York Times article wonders how many web services one person can use. And stepping back even further, Peter Suber Gavin Baker blogs about, this liveblog post on Joho on a talk by James Boyle on the nature of openness.

Other developments

The US government DOE goes a little more open with increased access to scientific information in the release of science.gov 5.0. At the same time, Open Access is threatened in Congress. A Blog Around The Clock urges you to call your congressman to bury this specific anti-Open Access bill, the Fair Copyright in Research Works Act.

In the news, Phylogenomics comments on an MSNBC article called “The Era of Scientific Secrecy Nears its End” and points out an interview with Open Access reporter Amy Harmon at the New York Times.

For some fun, Open Economics goes to town on some agricultural data, revealing some interesting historical trends, and Grand Text Auto begins an experiment in open peer-review, as author Noah Wardrip-Fruin names a blog readership as the ideal reviewers for his forthcoming book.

Closing thoughts

With that, I’ll wrap up this round-up. I’m not sure what will happen with future issues yet – if someone wants to volunteer to host the next one, please do! – but it would be great to keep it going.

To close, I’ll share a quote from a talk I heard yesterday that seemed very appropriate given the recent attention towards structuring the until now very broad and scattered open science discussion. The talk was actually about vocal learning in songbirds and presented findings showing that canaries have innate rules guiding their song behavior but that they have tremendous range and versatility in the sounds they can learn and produce, leading to remarkable creativity. Towards the end, the speaker paused for a moment to say,

“I feel that there is some deep social message here… Something like, if you want to have great creativity and innovation you must give complete freedom, but if you want to reap the benefits you must provide a framework.”

Just so.

Acknowledgments



Many thanks go to Chris Patil for the encouragement, to Neil Saunders for his RSS experiment, to Daniel Mietchen who brought WAYS to my attention, and to the many people on FriendFeed who make it simply the best place to get the latest news and posts about open science. I was refreshing it and finding new items to include here all the way up until I pressed “publish”.