New Paradigms in Scientific Publishing

3-D Rendition of a Molecular Structure

3D Rendition of a Molecular Structure

It’s been several years since I experienced my first earthquake. I remember it clearly because I was fishing on a small pond in the Adirondack Mountains near my home. When it hit, the pond shook like a bowl of jelly and a low tectonic rumble ascended from the depths below.

I felt the same seismic tremor last week while working at the computer. This time it came with an online collection of digitally enhanced articles published by the Public Library of Science (PloS), under the title “Structural Biology and Human Health: Medically Relevant Proteins from the SGC”. Within each article, one finds scholarly text linked to 3D interactive visualizations of molecular structures. In essence, the reader is immersed in a rich virtual experience that lends insight into the researcher’s narrative – at least that’s the assumption.  

Text and Interactive Visualizations

YouTube Direkt

The interactive 3D structures provided in the PloS articles are enabled by an integration of data types and related annotations within individual files that are platform-independent. The integration is explained in an overview article, “A New Method for Publishing Three-Dimensional Content”.  This method provides for any number of visualization renditions (with animated transitions) that can be linked to the article’s text via hyperlinks. The 3D data include 2D attachments such as chemical data in spreadsheets and plots, and the documents can also be downloaded for viewing in 2D format. Please note that a free web plug-in is required to view the enhanced article versions.

Online, a reader can conjure and interact with a virtual 3D structure described in the document’s text. The effect is not only deeply engaging but may have real pedagogical value. In my recent posts on geospatial literacy and scientific visualization, I’ve highlighted the links between spatial reasoning, visual representations, and learner comprehension. We still have much to learn concerning interactions between human perception and 3D animations with regard to their impact on memory and insight. We also need to consider the relative value of complex vs. simplified visual models to communicate concepts about natural phenomenon. In what case(s) might one be more or less appropriate than another?

I believe it will be some time yet before we can address this and other related questions competently. Nonetheless, multi-media publications will likely benefit a wider cross-section of learning modalities than traditional text alone and, as a visual learner who likes to get his hands dirty, I find such multimedia publications appealing.  Interestingly, readers of the PloS articles are directed to cite  article versions that don’t contain the enhanced graphics. This owes to concerns that readers might draw unintended conclusions from their use of the interactive representations.

Open Access Journals

I should also point out that as an open access , peer reviewed journal, PloS makes these publications available to us for free.  For those less familiar, open access publications lend the author(s) and copyright holder(s) perpetual access to their work for use, display, and distribution of derivative materials. Such publications are archived in online repositories by established organizations that seek to enable open access. In the case of PloS, a Creative Commons Attribution License is also fixed to works they publish, enabling commercial reuse of the journal’s content.

Open access is a win-win situation for the academic community and the public at large.  While publishing fees may still be applied by open access journals, authors stand to maximize the research impact of their labors since this work isn’t hidden behind subscription barriers. In a 2006 study, PLoS Biology found that articles published as immediate open access in the Proceedings of the National Academy of Science (PNAS) were three times more likely to be cited than non-open access papers, and were also cited more than PNAS articles that were only self-archived. Similar studies confirm this trend (see OpCite and Norris et al. 2008).

Arguments for traditional publishing can be made on the basis of a journal’s popularity, reputation, and strength of it’s peer review process. As open access journals enter the mainstream, however,  publisher branding may become less important to scholars. In some cases, publishers may also turn to open access formats to supplement their journal portfolio. For example,  Nature Publishing Group recently released Nature Communications – a multidisciplinary online journal with an open access option.

Other Examples

As the tools and workflows for 3-D visualization are simplified and further integrated, we will have greater freedom to explore their use for classroom projects and student publications. I would point you to Biomolecules at Kenyon as an example of such learning- where interactive molecular tutorials have been created by students using Jmol and data from the Protein Data Bank of the Research Collaboratory for Structural Bioinformatics. It’s also worth mentioning that Cell Press and Elsevier are collaborating on the Article of the Future project, described as a media rich online publication. I will be interested to see if this work lives up to its title.

If you are working on projects that integrate scholastic writing and interactive graphics for the sciences (and other disciplines), please let me know. I’d love to learn more about your activities and welcome the opportunity to share it with others in the academic community. I will also be writing about open access publication and open science in future posts. Keep your eyes on the horizon.

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  1. [...] Techne » New Paradigms in Scientific Publishing25 Oct 2009 by Sean Connin  The integration is explained in an overview article, “A New Method for Publishing Three-Dimensional Content”. This method provides for any number of visualization renditions (with animated transitions) that can be linked to the … [...]

  2. Written by Techne » Open Access: No Longer Parlor Conversation
    on December 21, 2009 at 7:05 am

    [...] an earlier Techne post titled, ” New Paradigms in Scientific Publishing”, I outlined some of the benefits of OA electronic journals, such as the Public Library of Science [...]

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