Open Notebook Science is the practice of making the entire record of a research project publicly available online, along with all raw and processed data, and any associated material, as the data is generated. Jean-Claude Bradley, an Associate Professor in the Department of Chemistry at Drexel University, is a leader in the Open Science movement, particularly of its branch, Open Notebook Science. I was very pleased to have the opportunity to interview Jean-Claude last week and find out more about Open Notebook Science and what it means for the future of scientific research on the web.

The Interview

Before I give you a chance to talk, Jean-Claude, I want to tell you how I heard of you. Walter Jessen and I started Next Generation Science to explore science 2.0 and the impact of Web 2.0 on science. Walter introduced me to the Science 2.0 room at FriendFeed. I was immediately drawn to the comments that you and Michael Nielsen were making there about the terminology and nomenclatural matters surrounding open science and allied movements. They were clear and cogent – very helpful to those of us just starting to grasp the implications of Science 2.0 for science and medicine and for society at large. I hadn’t heard of either of you before but have since learned you are both leaders in the field. Could you discuss the different approaches you and Michael take given your different disciplines?

The main distinction between Michael’s and my discipline is that I am an experimental organic chemist and he is a theoretical physicist. Michael has written extensively about the future of science and open science and I think that it is useful to bring different perspectives to bear on the issues of Open Science.

Let’s now discuss the matters of nomenclature and definitions. Could you define for us the following terms and tell us why each mode of scientific communication is important and for which audiences: Open Notebook, research blog, science blog. Are there other terms that you would propose for other modes?

To my knowledge the only term in that list that was explicitly created with a definition is Open Notebook Science, the practice of making the entire primary record of a research project publicly available online as it is recorded:

http://en.wikipedia.org/wiki/Open_notebook_science
http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html
http://usefulchem.blogspot.com/2009/02/open-notebook-science-reproducibility.html

I had initially used the term “Open Source Science” but that term had already been used to describe Open Source Science Software. People still use the term Open Source Science or Open Source Drug Development to mean increased sharing of scientific data but it is unclear to what extent there is an expectation to share and with whom.

Based on the widespread success of http://researchblogging.org/ I would tend to associate the term “research blogging” with writing about peer-reviewed papers that have already been published.

The term “science blog” is very generic but I think it most often gets used to describe blogs popularizing science – for example discussing creationism vs evolution.

The term “Open Science” is also a very generic umbrella term. “Open Access” refers to traditional journal articles made available to the public for free – although there is a heated discussion going on now about whether or not that term implies unlimited re-use.

How does an Open Notebook differ from a wiki? Is it because an Open Notebook could include entries by only one researcher whereas a wiki is invariably a group endeavor?

Our Open Notebooks are actually on a wiki. See here:

http://usefulchem.wikispaces.com/All+Reactions
http://onschallenge.wikispaces.com/list+of+experiments

One of the reasons for using a wiki is to collaborate but another very useful feature is that it keeps track of every version of a page.

I have been looking over your very interesting blog, Useful Chemistry. First question on that: why no Twitter button?

I don’t have a Twitter account. My only exposure is spillover from Twitter to FriendFeed, which I use extensively.

You say on Useful Chemistry, “The Open Notebook can be thought of like insurance. We don’t want to have to use it – but if there is a problem we have to ability to trace the chain of provenance all the way to the source.” Can you elaborate on that?

A common misunderstanding about ONS is that we expect people to read it like a magazine. That would not make sense except for very close collaborators or supervisors perhaps. Its main use comes about when someone finds a discrepancy in a dataset. At that point one can investigate the source of the problem by digging right down into a very specific part of the notebook and raw data collection to try to spot the source of the error. Often just knowing that the researcher did not measure or control for a certain parameter might be enough to lose confidence in the data point. They can then decide to look at other similar measurements or even carry out the measurement again if necessary. In a traditional journal article, there is no way to investigate discrepancies in this way, except perhaps to contact the author and hope for a detailed response.

You also say, “Now we’re getting into some interesting territory. It is now so simple to refer to the solubility data of the ONS challenge that people who don’t know the first thing about wikis, blogs or coding can start to participate in the use of ONS measurements.” Please explain.

There are a lot of great ideas that don’t catch on because their implementation is just a little too difficult to use. The success of blogs and wikis is related to how much easier it is to post information compared to having to learn HTML. With this URL mechanism that Andy Lang has created, if I want to send you the solubility information for vanillin in a range of solvents I can just send you this link:

http://oru.edu/cccda/sl/solubility/allsolvents.php?solute=vanillin

To change the link you just put the common name of another compound at the end. That is much easier than looking up each reference and sending documents or links to each number. Also that link is dynamic – as data points get added and corrected in the ONSchallenge, the link will always point to the most updated information.

You had an interesting post about the recent launch of The ChemSpider Journal of Chemistry. You say, “Not only does it boast the option of an open peer-review in addition to Open Access, but it takes us tantalizing closer to the promise of Web 3.0: the semantic web.” How so and so what? Tell us about open peer review. Are we entering a bifurcated world where science is done in two spheres – by those scientists who stick to the hallowed halls of Elsevier, Springer and Wiley and incredibly expensive journals that only a few libraries can afford and those scientists who are engaging in up to the minute, fruitful scientific exchanges on blogs and other open fora?

The idea of the “semantic web” is that machines can deal with concepts instead of just text. What ChemSpider is doing here is marking up the plain text in a way that it identifies what is a molecule, what is an organism, a named reaction, etc. Going forward this will make it easier for machines to process chemistry articles. For example you might say find me documents where an aromatic aldehyde is associated with a mammal. There is no good way of doing that unless the search engines knows that a cat is a mammal and that benzaldehyde is an aromatic aldehyde. We’re not there yet but that where we’re headed.

As for Open Peer Review, I think we’ll see more traditional publishers experiment with ideas like this. Certainly Nature has been very active in trying out similar approaches. To some extent there might be a bifurcation in terms of where researchers spend most of their energy – but any relevant toll access articles do get cited on blogs and FriendFeed. And there are some examples of citing blog posts or wikis from peer-reviewed journals. I think that will continue.

Is there a visibility problem for those early career scientists who engage in Open Notebook Science? For example, how would a headhunter for a pharmaceutical company or a major research university learn about an Open Notebook that reveals that a young scientist is a genius? Would hiring committees know where to look for such evidence of future eminence? Would they turn to tools like ResearchScorecard to see who is getting the grants? How do you incentivize Open Notebook Science for young researchers and which disciplines are most suited to it? Just chemistry?

Having an Open Notebook or even just participating more in Open Science can only make your work more visible. Scientists should still publish in traditional journals.

To some extent we have incentivized ONS by making available small prizes for students to participate. Beyond that I think that just experiencing more interaction with the community is incentive enough. I certainly don’t want to convert anyone.

Is there a directory anywhere on the Web of Open Notebook projects? Calling young search engineers – is there a market niche here?

There is a collection here: http://en.wikipedia.org/wiki/Open_Notebook_Science

Can you point to any seminal, world-changing discoveries that have come out of Open Notebook Science? Or any careers that have been made because of participation in such projects?

Well “world-changing” is a tall order. In our ONS solubility work the goal is to allow chemists to predict the solubility of organic compounds in non-aqueous solvents – either because the measurements have been made or we have reliable models. That could change the way chemists plan their reactions and how they purify products. Time will tell.

Please tell us about the Submeta Open Notebook Science Award. What do you hope will come of it?

The Sumeta ONS Awards are $500 cash prizes for students who have contributed to measuring solubilities in non-aqueous solvents and have reported their work in an Open Notebook. Once a month a panel of judges decides the next winner. There are 10 prizes in total and 3 have been awarded so far. See preceding answer for what we hope to accomplish. Details are available here:
http://onschallenge.wikispaces.com/submetaawards08

Is Open Notebook Science out of the question for the clinical trials realm given the restrictions of confidentiality and the tight regulatory regime it functions under? Are regulatory frameworks an insurmountable obstacle to Open Notebook Science? And are pharmaceutical companies open to it given intellectual property and patent concerns? Are research universities reluctant to support Open Notebook Science for fear of losing funding from such companies? And doesn’t this all create nightmares for scientific editors and librarians? How is all of this information to be tracked? In standard scientific journals eventually or in open access journals that will grow out of the Open Notebook Science movement?

Yes I think anytime you have human subjects ONS is out of the question. Certainly where there are intellectual property concerns it will be difficult to carry out ONS. But companies could perhaps pool resources for some aspects of science. For example, could phamaceutical companies benefit from openly sharing some solubility data without disclosing their drug targets?

As for losing funding or collaborators, of course you can’t unilaterally change the terms of a research agreement in mid course. You need to think about ONS at the start of a project. Also some funders actually make you donate your patents to the public on work done with their money. See the PRF for example: Every patent, United States or foreign, that shall be taken out by or on behalf of the recipient or by or on behalf of any individual or institution acting at the direction of or on behalf of the recipient in carrying out such research shall be immediately dedicated to the public, royalty free. (from http://portal.acs.org/portal/fileFetch/C/CTP_006296/pdf/CTP_006296.pdf).

Journals will track ONS resources the same way they currently handle any web based information sources. When you write a paper and you use information from a lab notebook page you cite it. See http://usefulchem.blogspot.com/2008/11/from-ons-to-peer-review-our-jove.html.

You use the phrase, ” … chain of provenance.” Do you see Open Notebook Science as better than traditional methods vis-à-vis documentation and the prevention of scientific misconduct given the transparency of the whole Open Notebook process? Will this have the concomitant benefit of engendering public support for science?

I do think that scientific misconduct is a lot harder with an Open Notebook. It is also harder for innocent mistakes to make it through and remain undetected in the community. But that should not be used as a reason to make ONS mandatory – researchers have a right to pursue and protect their IP if they choose.

Do you use ResearchBlogging.org?

Not yet. But it looks like a very successful project!

Let’s say I am a young chemist. I come to you and say, “I love science and want to make it my career. But I have to allocate my time most productively in order to advance science and to get tenure. How can I best do this in the era of Science 2.0? Isn’t it just too risky to spend time blogging and in wikis and in open science endeavors when ultimately I will be judged by a tenure review committee that lives in utter ignorance about these things or deeply distrusts them? What’s a young person to do?”

My recommendation is that you start with a small project – say 5-10% of your total research effort and make that ONS. That way you will benefit from collaborating with other open scientists and still make a safe option for the bulk of your research. In the future it may become safer to be open just to remain visible.

Who are your personal heroes either in technology, chemistry or in any other realm?

If you’re asking about people who inspire me on a daily basis it would be my closest collaborators: Andrew Lang, Antony Williams, Rajarshi Guha and Cameron Neylon. Watching people make things happen in the open, especially on joint projects, is very encouraging. It continually reminds me of the point behind openness.

Thank you for your time.