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Open Notebook Science: Exploring a model of emergent scientific practice


Kalpana Shankar
Assistant Professor, School of Informatics
Indiana University
shankark@indiana.edu


Posted 15 May 2008 by Kalpana Shankar

This is a proposal for an internal grant submission at my university. I'm an information/social scientist who studies scientific work and recordkeeping/data management, and am particularly interested in emergent digital technologies and their implications for data sharing/use/reuse. I would appreciate feedback from the community on sites to explore, researchers willing to be interviewed/have their work observed, and other comments.
I have obtained human subjects clearance through the IRB at my university, and intend to pursue this project regardless of funding. I have not yet interviewed any researchers for this project, but am only in the background stage of my data gathering.

More broadly, I would be interested in the community's thoughts on the implications of open science for policymaking, teaching science, and intellectual property issues.

A minor rant: I had submitted this to Nature Precedings and was first told that it couldn't be accepted because I hadn't mentioned IRB and because I didn't create a cover page. Ok, I did both: and then got rejected because they no longer take proposals.


Introduction


Contemporary science is being influenced by competing impulses that permeate the daily work practices of scientists and the institutions in which they work. One impulse is the need to share research results, data, and tools to promote greater impact of research, leverage scarce resources, conduct longitudinal studies, apply new analytical tools to existing data sets, and to verify and refine the results of other researchers. However, competition for those same scarce resources often demands greater and greater protection for intellectual property. In the scientific publication area, these competing forces have engendered national and even international discussions and argument. Since published results are foundational for scientific progress, proponents of open access argue, publishing research results in open access journals creates wider dissemination of results for other researchers and provides greater value to the public, which funds most resaerch in the United States. Advocacy groups for greater taxpayer access to scientific research, librarians, and even national governments and the United Nations have supported this approach to the dissemination of results. Commercial publishers and other critics of open access have argued that there is little evidence of its merits. They contend that most people can get the literature they need, that open access would place undue burdens on researchers in some fields, and would not be economically viable.

More recently, this discussion has trickled down to the primary scientific data itself. Although the United States government directly or indirectly sponsors a significant portion of basic scientific research, few research data are publicly accessible. Thus, the practice of science often comes into conflict with its often-expressed ideals of openness, shared data, intellectually rigor, and verifiability. Again, advocacy groups and other stakeholders contend that open access to data promotes greater use of research data, not just by scientists, but also by health care providers, individuals, and nonprofit organizations. However, contemporary science and its commercialization have been built upon the protection of data and records as forms of intellectual property that are closely held by the scientific community. The conflict of these competing paradigms is precipitating a scientific crisis.

However, there is resistance to such closure. Science is highly networked, globally dispersed, and dependent upon expensive (often publicly funded) and large-scale information technologies. These technologies are also enabling and encouraging resistance against the predominant paradigm. One such emergent model of scientific research is Open Notebook Science (ONS) in which all data and research is made publicly available from the outset of research. As one researcher defines it, “By [Open Notebook Science] I mean that there is a URL to a laboratory notebook that is freely available and indexed on common search engines. It does not necessarily have to look like a paper notebook but it is essential that all of the information available to the researchers to make their conclusions is equally available to the rest of the world. Basically, no insider information” (http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html). This is different than open access science discussed in the introduction, which emphasizes access to the published journals through institutional repositories and other mechanisms, but is built upon a similar spirit of sharing.


Significance


Although Open Notebook Science is not yet widespread for numerous reasons, it presents an intriguing new approach to scientific research with implications for data sharing, the development of institutional repositories, e-science and e-social science, cyberinfrastructure use, and national/international policy on data in science. Studying it from the perspectives it offers for collaboration, access, and ease of data management will be important to understanding current bottlenecks in access to data, verifiability, and the development and use of data repositories, topics of great interest to the National Science Foundation and the National Institutes of Health. However, extensive foundational work needs to be done to explore its uses, challenges, and its community of users.

Research Design


For this preliminary study, I will focus on two active open science and semi-open notebook portals: Myexperiment.org, a general scientific workflow collaborative environment; and Openwetware.org, an collaborative semi-open science environment for biologists and biological engineering. I will also find other researchers who may not be using portals such as these, but are still using the open notebook science model. I intend to use listservs to recruit volunteers. I have already approached Professor Jean-Claude Bradley at Drexel University, a key proponent for Open Notebook Science, about working with him on this project. Other respondents will be recruited as the research takes shape.

The first phase of the project will involve will involve online research. Because this is a foundational exploration of the phenomenon, it suggests a qualitative approach to research that focuses on text, interviews, and documents. I will use “virtual ethnography” to participate and observe then analyze online listservs devoted to the subject of Open Notebook Science. I propose to examine the following questions:

• What kinds of problems lend themselves to open notebook science?
• Why do people stop using open notebook science?
• What differentiates the tools that are currently available?
• What kinds of barriers and incentives exist to using this research approach?
• What privacy and security implications exist when researchers wish to use ONS for human studies?

Building on this work, I will conduct phone interviews with professional scientists and science students who are involved in open notebook science. Interviews will help answer the following questions:
• How do scientists who use this approach differentiate themselves and their work from other scientific practices?
• What is the role of open notebook science in the development of professional
and personal identity, socialization to the profession, and group identity?
• What challenges and advantages arise in using open notebook science?

To understand how this model of science intersects with bench science and daily work practice, it is necessary to combine virtual ethnography with in situ (place-based) ethnography. Therefore, the third piece of this project will require in-person site visits to the physical laboratories of participating scientists to conduct observations and interviews in person.

For the online portion of the project, I have obtained human subjects clearance through the IRB at my university, and intend to pursue this project regardless of funding. No subjects have been recruited yet. When they are, they will be shown a study sheet that will inform them of their rights.

Anticipated research outcomes include publications and conference presentations as well as formative data for larger grant proposals to agencies. More importantly, I anticipate lessons learned from this project on how and when ONS is used, its potential for creating and fostering research and teaching, and furthering access to data for the public will be essential if we are to develop better digital data repositories and policies for equitable and useful data storage and access.


References


Bradley, Jean-Claude, Owens, Kevin, and Williams, Antony (2008). Chemistry crowdsourcing and Open Notebook Science. Nature Precedings: doi:10.1038/npre.2008.1505.1: Posted 10 Jan 2008.
Coles, Simon J. and Lyon, Elizabeth J. (2008) eCrystals Federation: open repositories for global open science. In, DRIVER II Summit meeting, Gottingen, Germany, 16-17 Jan 2008. Southampton, UK. Advance: http://eprints.soton.ac.uk/50067/
Hooker B. (2006). The future of science is open, part 2: Open Science. Available: http://3quarksdaily.blogs.com/3quarksdaily/2006/11/the_future_of_s.html.
Murray, Sally, Choi, Stephen, Hoey, John, Kendall, Claire, Maskalyk James, Palepu, Anita. (2008). Open science, open access and open source software at Open Medicine. 2(1).
Neylon, Cameron. (2007). Open Notebook Science: perspectives from a newbie. Nature Precedings : doi:10.1038/npre.2007.1130.1 : Posted 26 Sep 2007.
Piwowar HA, Day RS, Fridsma DB. (2007). Sharing detailed research data is associated with increased citation rate. PLoS ONE 2007;2(3):e308.
Rio Framework for Open Science. (2008). Available: http://wiki.icommons.org/index.php/The_Rio_Framework_for_Open_Science