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Dr. Amy Koerber
English 5386: Written Discourse & Social Issues
October 11, 2006
Creating a Definition of "Open Chemistry" in Relation to Practice
Technical Communicators will play an important role in the future of scientific communication. As grant funding bodies and federal agencies like the National Institute of Health (NIH) require Open Access (OA) publishing as part of the dissemination process, scientists are moving beyond traditional scientific approaches (peer reviewed journals) by embracing practical and technological approaches of sharing discipline-specific information within, or at the conclusion of, the research process. The biomedical community, for example, has pioneered efforts for sharing information through sites like BioMed, which offers open access to peer reviewed journal articles without the sharing of primary or in-process data.
The chemistry community has not wholly adopted open access or the concepts of open data (the sharing of primary data). Historically, chemical information has been shared through the traditional peer review process, and, even then, the information is masked so that it can not be replicated easily by another lab. “Open Chemists” are working to change this system by sharing data via technology within the research process. While "open chemistry" does not operate in opposition to traditional approaches, it does offer an alternative to standard or accepted procedures. Those who embrace "open chemistry" hope to lead the future of shared information by respecting the current practices within the chemistry community. However, practicing "open chemistry" will impact patenting and tenure procedures.
In an effort to establish the legitimacy and benefits of open access science, open source science, and open data, the chemistry community, and the technical writers that serve as advocates, needs to develop and establish a working, yet solid, position statement and philosophy. However, since the philosophy of sharing is not the same as accepting or defining suitable ways to practice sharing, there needs to be a distinction between philosophy and practice. At present, there are several terms that refer to the same concept, and the differences are not expressed in conversations about the root philosophy of sharing data, but, rather, in the actual practice of when and how the data is shared using technology. In short, the chemists spend most of their time focusing on how to share data and not engaging in conversations about their joint mission. As a result, they are not able to advocate for their needs in the funding community.
There are three goals for this project. First, this paper will focus on the various existing definitions of “open chemistry” or “eChemistry” and will attempt to formulate a global understanding of the shared terminology in hopes of establishing a more unified core definition. It may be that all those invested in sharing information will adopt a core philosophical statement, but, in practice, may defend varying starting points. The second goal of this project is to help “open chemists” create and institute a position statement for “open chemistry” by offering a call to action for them to discuss and collaborate on the most effective methods to share information that remains free, accessible, and modifiable. If they fail to do this on their own, they will be subject to others creating and perpetuating a definition and purpose for them. For example, the American Chemical Society is rumored to not support these “open initiatives,” and, yet, no formal definitions exists for them to support or deny. Further, while the ACS seems to oppose Open Access Publishing, they do not appear to oppose sharing data though technology. Thus, the final goal of this paper will be to explore the ACS's position on collaborative data and to make the distinction between Open Access and Open Chemistry in terms of both philosophy and practice. Once this community establishes a working definition of what they are already doing, their collective power will aid them in receiving funding for labs and projects
While much needs to be written about "open chemistry" and "open science" throughout the academy, the concept of "Open Access" publication is not new. The OA movement is strong and well defined by Peter Suber; “Open-access (OA) literature is digital, online, free of charge, and free of most copyright and licensing restrictions” (Overview). In general, though, OA refers to the final product of research and not the process by which it is shared. Chemistry, a discipline rich in raw data, is a perfect candidate for sharing collaborative data within the research process. Technology offers cost effective methods to share data. Google searching, for example, allows for free and simple access to core data; this shared data produces faster results via the cheapest methods.
Open Source Science, Open Data, Open Standards, and Open Access Science generally refer to the same principle; it indicates the publication of data for free use and distribution via the web using wikis, blogs, chemical docking programs, or other RSS technology. Historically, this same data has only been available, in parts, through traditional peer review journals. ODOSOS is one acronym used to define "Open Data, Open Source, Open Standards" (Murray-Rust). However, there is legitimate discussion about what constitutes “Open Source” as compared to “Open Standards” and “Open Data.” Open Access, for example, refers to the publication of "final" data or articles, and is not, inherently, about the sharing of collaborative data although there is a place for that to exist within OA (BOAI). “Open Source Science” refers to the sharing of all data, including failed experiments, and is likened to “open source” code in computing. It includes both the process and the resulting data. As such, it communicates the "thinking behind the chemistry" - a practice not embraced by traditional methods (Bradley). “Open Data” is similar to Open Source Science in the philosophy of sharing, but differs because it does not include the publication of failed data or experiments, and shares, instead, successful processes and data. In short, "open data" refers to data "which we can attach a CC [Creative Commons] or similar license" (Murray-Rust). Finally, “Open Standards” refers to the sharing of the processes by which data is shared. Again, the core philosophy appears to be shared by “open chemists,” but, at present, all of these terms are confusing. While the differences are subtle, they do, in fact, exist. In defining the concept, it will be essential to explore the practice of chemistry as it relates to the existing and forming definitions.
I will argue that "open chemistry" is defined as the sharing of chemical data for free use, distribution, and modification. However, not all persons who believe in the philosophy of sharing agree on the process (when and how the information should be shared). The term "Open Data" is used most frequently by Peter Murray-Rust to describe the work he does to share information with other chemists; his pioneering efforts, along with Henry Rzepa, creating the Chemical Markup Language (CML) have great potential to change the process by which chemical information is shared within the community. Open Source Science is a phrase used most frequently by Jean-Claude Bradley and refers to the sharing all experimental data, including failed experiments, in open access formats (blogs, wikis, and other RSS technology). Open Standards generally refers to the process by which chemical information is shared; in the open chemistry community, there are several formats to share information. Among them, CML and InChi are just a tiny sample of the variety of out-put formats available. One of the problems in establishing a unifying process is that there are many more out-put formats and there is not one “standard” reader. This paper will not, directly, focus on this aspect of sharing data, as I am not qualified to analyze the benefits or weaknesses of any particular system.
The difficulty in creating a definition has been a result, likely, from a misunderstanding of the philosophical nature of Open Data and the Open Source technology tools used to share data and a confusion between Open Access publishing and shared data. The present focus of the rhetoric between these chemists has focused, almost exclusively, on the technologies by which the information is shared. There has not been a great discussion on defining the core concept or offering that core concept a unified name. This leads to confusion by those who do not understand that while “open chemistry” and “open source science” may share the same root philosophy, they are practiced in different ways. Outsiders may not realize that practicing chemists and collaboration sites share a core philosophy but function differently in the "open community." For example, Jean-Claude Bradley, an Organic Chemist from Drexel University, supplies all data from his lab including failed experiments that would, otherwise, not find placement in journals or repositories. In supplying failed experimental data, he hopes to prevent others from making similar mistakes (interview). His goal is to provide the "thinking behind the chemistry.” Peter Murray-Rust, a chemist from Cambridge, shares successful data through his Chemical Markup Language. Other organizations like Chemists without Borders and The Synaptic Leap function as collaboration sites to help chemists work together on similar projects. The Blue Obelisk is a site that provides a place for chemists to share and discuss ideas relevant to the technology of sharing data. Collaboration sites are useful, but they do not necessarily publish data. What is most striking about all of these groups is that they all agree about the principle of sharing with one another; the question to explore will be whether or not "when" is as important as "why."
Contributions to the Field of Technical Communication and Rhetoric and Further Opportunities for Study
Technical writers assigned to grant writing tasks for open chemists will need to fully understand and appreciate the current role of open chemistry and its future implications. The role of the technical communicator will change as new technology emerges. In chemistry, some may rely on technical communicators to help prepare and shape documentation. These chemists will need advocates to promote their work. Further, government agencies will rely on technical communicators to translate scientific principles into readily accessible terminology for the purposes of disseminating funds to research labs.
The research in this project will deal almost exclusively with open access primary materials. By examining blogs and wikis of the “open” community, I will be able to understand the current positions of key members. Since this project centers on the sharing of information via the web, I am examining only those materials that are freely accessible using web technology. I will be looking at the blogs of “open chemists” Peter Murray-Rust, Jean-Claude Bradley, Rich Apodaca, Geoff Hutchinson, Egon Willighagen, and Joerg Kurt Wegner. Further, I will examine Open Access wikis to document my research; specifically, I will examine The Blue Obelisk Wiki, The Blue Obelisk Mailing List Archive Wiki, the Useful Chemistry Wiki, and Peter Suber's Open Access Wiki.
In order to frame a discussion about the technical communicator's role in disseminating practical information about open chemistry, I will examine literature in the field of technical communication and rhetoric. In an effort to understand the process by which movements are defined, I will look at the scholarship of Charney, D. (2004), Dayton, D. (2002), Friese, J., Jung, U., Röhm, T., & Spettmann, R. (2006), and Harding, S. (2006). To examine how advocacy plays a role in defining and perpetuating movements, I will look at the scholarship of Edbauer, J. (2005), Eisenhardt, P. (2003)., Ergenzinger Jr, E., Cunningham, M., Webber, P., & Spruill, W. (2004), Fox, R. (2001), Kent, J. (2003), Lanclolt, F. (2004), Ornatowski, C. M., Bekins, L.K. (2004), Parsatharathy, S. (2003), Van Kammen, J. (2003), and Zavestoski, S., Brown, P., Linder, M., McCormick, S. and Mayer, B. (2002).
1. Gather Resources in field of Technical Communication and Rhetoric
2. Gather Resources in field of Chemistry (specifically blogs and wikis)
3. Examine statements of the American Chemical Society
4. Examine popular literature about "open" science as it applies to chemistry
5. Examine federal guidelines for chemists (NIH, NSF)
6. Establish contacts in chemistry community
7. Participate in ongoing discussions (Blue Obelisk)
A. All “primary research” (blogs, wikis, mailing lists, etc.) must be publicly accessible on the web.
B. Literature in TCR must discuss, at some level, medical, chemical, or drug development discourse
C. Blogs and wikis of chemists must deal with, in whole or part, "open" or collaborative efforts
D. Federal guidelines for grants and funding must address "open" or collaborative efforts
· August/September: Gather resources, establish contacts
· October 11: Submit proposal for approval
· October - November 15; Read and prepare notes on open access wiki; begin article
· November 15: Complete final outline for article
· November 30: Finish article; submit draft copies for assessment
· December: Submit final copy
The purpose of this project is to aid the “open” chemistry community by helping them shape and define their core philosophy with an understanding that the process may or may not be essential to the definition.
Formal Proposal for Research Paper
(150 points)—For this assignment, you will write a detailed proposal outlining your plans for the paper. Although there’s no length requirement for this document, I’d expect that a successful proposal for this assignment would be somewhere around 3 pages, single-spaced. Your proposal should include the following sections: Introduction, Background, Literature Review, Research Plan, Timeline, and Conclusion.
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