Expressing Scientific Insight

I was interviewed about Open Source Science recently for Linux Insider. The interview — Open Source Science: A Revolution From Within — was published this morning. I plugged the Life Scientists Room on FriendFeed but, unfortunately, it didn’t make the cut for publication. In fact, there were a number of questions/answeres left out of the final article, so I’ve posted the entire interview below.

The Interview

What is your exact title? Where are you based?

I’m a Bioinformatician and Cancer Biologist at Cincinnati Children’s Hospital in Cincinnati, Ohio. I use functional and comparative genomics to study peripheral nerve tumor disorders: Neurofibromatosis type 1 (NF1), Neurofibromatosis type 2 (NF2) and Schwannomatosis.

I’m also the founder, editor and head writer for two online publications:

Highlight HEALTH reports on advances in biomedical research and how they affect you. We write for patients and healthcare consumers, provide credible and reliable health information, and advocate health literacy for improving self-management in health.

Next Generation Science discusses tools and ideas for the future of technology and science. We write reviews and interviews on emerging technologies and tomorrow’s science for scientists, researchers, informaticians and technologists.

How would you define open source science?

Open Source Science is a collaborative and transparent approach to science. To me, it means four things:

1. Open Source: the use of open and freely accessible software tools for scientific research and collaboration.
2. Open Notebook: transparency in experimental design and data management.
3. Open Data: public accessibility of scientific data, which allows for distribution, reuse and derived works.
4. Open Access: public access to scholarly literature.

How did you get involved in open source science? Why is it important to you?

I saw the advantages of Open Source Science early in my career as a scientist. During my undergraduate and graduate studies, the inability to access scientific publications or databases due to the lack of Open Access was extremely frustrating. At that time, all the high impact journals weren’t publicly available (indeed, most high impact journals still aren’t Open Access today).

On the low rungs of the academic ladder journal publications essentially validate your career as a scientist – the expression often used is “publish or perish”. Scientific reputation is measured by the number and impact of citations, and scholarly publications are linked to a successful job search, research funding and tenure.

You can see the conflict: on one hand, I wanted to publish my research in a journal other researchers could easily access, but on the other hand I wanted to publish in the best journal possible, which wasn’t Open Access. And although I had some voice about where to publish, senior scientists made the final decision.

Thankfully, over the years I’ve had a several papers published in Open Access journals. I think for many researchers, lack of Open Access is one of the first issues they discover in traditional “closed science”.

More recently, I struggle with the lack of Open Data. Earlier this summer, we had a cancer journal submission rejected because a reviewer felt that one of the two integrated studies in the manuscript didn’t have a large enough sample population. However, it was the only publicly available data set that included both benign and malignant samples, which were necessary for the comparisons made in the study. I think it’s a good example of how scientific progress can be delayed by the lack of Open Data.

Today, I communicate with other researchers on Twitter (my account: wjjessen) and FriendFeed (my account: wjjessen) almost as much as I talk to researchers at my own institution. Much of the conversation is focused on interesting articles or useful URLs, and it demonstrates how valuable freely accessible tools on the Web can be for broadening scientific awareness.

As my career continues to grow, I’m positioning myself to adopt other aspects of Open Source Science. And I think that’s how many of us get involved, by struggling with the issues as junior researchers and recognizing that we can do something about those issues as we become more senior.

What are some examples of open source science in action?

The Polymath Project is a great example of Open Source Science. The goal of the project was to use blogs and wikis to collaboratively work on an unsolved problem in mathematics. In less than two months, it was announced that the Polymath participants had worked out an elementary proof, and a manuscript describing the proof is currently being written. The project demonstrated that many people could work together to solve difficult mathematical problems.

Reference: Timothy Gowers and Michael Nielsen, Massively collaborative mathematics, Nature, October 14, 2009.

Another example is the Life Scientists Room on FriendFeed. Online collaborations are being made there between researchers around the world. Indeed, a paper was recently published in which only three of the eight authors have actually met. This illustrates how the networked world of the Web can be used to advance science.

Reference: Huss et al., The Gene Wiki: community intelligence applied to human gene annotation, Nucleic Acids Research, September 15, 2009.

The Public Library of Science (PLoS) is a great example of Open Access. With a grant in 2003, it started two Open Access journals. Today, there are seven PLoS journals and all are publically accessible. Each PLoS journal provides a suite of metrics for every article, including measures of online usage, citations from the scholarly literature, social bookmarks, blog coverage, and the Comments, Notes and ‘Star’ ratings. Its most recent journal, PLoS One, has experienced substantial growth since it was launched in 2006; it’s already the largest Open Access journal in the world and is projected to become the third largest journal in the world by the end of the year.

Nature Precedings is another great example of Open Access; it is a permanent, citable archive for pre-publication research and preliminary findings. Pre-publication of research was unheard of a decade ago. Nature Precedings allows researchers to communicate their thoughts and observations, solicit feedback and date stamp their ideas.

What are the benefits of open source science?

There are many benefits to Open Source Science: speed, efficiency, quality, increased communication, worldwide participation, accelerated progress towards understanding and eradicating disease.

What are possible drawbacks of open source science? How would you address these drawbacks? Who are some of the major detractors or critics?

I don’t think there are drawbacks to Open Source Science. We live in a networked society; on the Web, it’s easier to find just about anything than it is to do science. If anything, the problem with Open Source Science is that the Web doesn’t yet provide support for networked scientific research; it’s great for documents, but terrible for data. But I think that’s slowly changing, thanks in large part to Science Commons, a project to apply the philosophies and activities of Creative Commons in the realm of science.

I believe that the major detractors of open source science are the publishers, because their business model is based on people paying for access, and older researchers accustomed to “closed science” that haven’t embraced the potential of a networked science culture.

What is in the future for open source science? How is it evolving?

Technologies are coming with will enable the Web, not just for documents, but also for data. The Shared Names Project is working on a format to assign universal resource identifiers as names for publicly available biomedical information records and establish a community managed shared infrastructure for providing durable access to documentation about those names. John Wilbanks, Executive Director of Science Commons, talked about the project in a talk he gave earlier this month on Open Source Science.

Could you give me the name(s) and contact info for any other scientists involved in opens source projects who might be good to interview?

Absolutely. These guys are on the front lines of Open Source Science:

• Jon Wilbanks
• Steve Koch
• Cameron Neylon
• Michael Nielsen
• Jean-Claude Bradley