LitClub

Social filtering of scientific information - a view beyond Twitter

This comment has received input from a number of FriendFeed users, as detailed in this thread, and was jointly blogged today by Björn Brembs (FriendFeed; blog post), Allyson Lister (FriendFeed; blog post) and Daniel Mietchen (FriendFeed; this blog post).



                                              "It's not information overload, it's filter failure." (Clay Shirky)

Bonetta (2009) gave an excellent introduction to the micro-blogging service Twitter and its uses and limitations for scientific communication. We believe that other social networking tools merit a similar introduction, especially those that provide more effective filtering of scientifically relevant information than Twitter. We find that FriendFeed (already mentioned in the first online comment on the article, by Jo Badge) shares all of the features of Twitter but few of its limitations and provides many additional features valuable for scientists. Bonetta quotes Jonathan Weissman, a Howard Hughes Medical Institute investigator at the University of California, San Francisco: “I could see something similar to Twitter might be useful as a way for a group of scientists to share information. To ask questions like ‘Does anyone have a good antibody?’ ‘How much does everyone pay for oligos?’ ‘Does anyone have experience with this technique?’” It is precisely for such and many more purposes that scientists use FriendFeed, which allows the collection of many kinds of contributions, not just short text messages.

Reinventing academic publishing online

Such is the title of a two-part publication by Brian Whitworth and Rob Friedman. It provides for a fascinating assessment of the state-of-the-art of Information Science over the last ten years, much of it generalizable to other fields. In the following, I will list some quotes from the papers — I will try to comment on them later as time permits: Part I

The corpus of science - a biophysical perspective


A month ago, Tim Jones posted the following video on his blog, featuring a montage of drawings people had made on the subject of what is important to them in science, along with their audio commentaries.

Once published, the post generated quite some interest in online communities of scientists, artists and others, and so he decided he would open up his experiment and invite others to follow, subject to a few rules. Some people have already submitted their contributions, which he has started putting together. This post is my attempt to join the party.

Herding effects in science

When I was notified recently that a new article on vocal learning had appeared in PLoS ONE, I took a brief look and found the study relevant but not interesting enough to actually read it now. However, I accidentally came across the phrase "Large-Scale Assessment of the Effect of Popularity on the Reliability of Research" - the title of a paper published the same day whose abstract and discussion actually got me interested, since they centred around the relationship between the popularity of research topics and the reliability of the corresponding results. This is related to the issues of (i) multiple testing, familiar to anyone working with statistics, and (ii) measuring research impact - a common subject here as well as on other blogs.

Science as a means of cross-cultural communication

Cell biologist Harold Varmus recently suggested, as previously announced here by David Weinreich, that science should play a much more prominent role in the way countries communicate with each other.

Research grant systems that encourage innovation

A recent paper entitled "Cost of the NSERC Science Grant Peer Review System Exceeds the Cost of Giving Every Qualified Researcher a Baseline Grant" suggests that there are opportunities to improve on currently prevailing research funding systems and gives concrete examples.

Abstract:

The energy use of the internet

In the light of limited global energy resources, we have to make up our mind on how to use them efficiently. An initial step in this process is to find out how much energy we currently spend on key elements of our global infrastructure, and how this may plausibly develop over the next few years to come.

One such attempt, relevant to online networks like WAYS, is being made in a recent paper by Jonathan G Koomey in Environmental Research Letters 3 (2008), entitled "Worldwide electricity used in data centers" (not Open Access).

Would be nice to link such considerations with those on the resource use by an individual scientist, as reported previously. Any takers?


Science and research blogging

"Advancing Science through Conversations: Bridging the Gap between Blogs and the Academy" - such is the title of an article recently published in the Open Access journal PLoS Biology.

In this article, blogging features prominently, and to add practical expericnce to academic discourse, one of the authors, Nicholas J. Anthis, has commented on the major ideas of the paper in his blog, as did John Dennehy (not involved in the paper) in his blog. Both also posted their blog entries to the platform researchblogging.org that aggregates blogs on the contents of peer-reviewed research papers.

Most of the blogs at researchblogging are in English but contributions in other languages are also possible.

Journal of Visualized experiments - a new way to teach biological subjects

This note is meant to make you aware of the Journal of Visualized Experiments - a peer reviewed online journal devoted to the publication of biological research in a freely accessible video format.

Reference knowledge structured by experts and the public?

(by Daniel Mietchen and Supten Sarbadhikari)

Introduction
Scientific research is the systematic dwelling at the frontiers of knowledge. Since these are scattered in space and time, successful dwellers require reliable reference works that assemble existing knowledge. Diderot and d'Alembert created their "Encyclopédie" to serve this purpose [1], and over the two and a half centuries since, many other encyclopedias have been produced following their scheme: Written by scholars, they charged users for access to the information they provided at update intervals on the scale of years. This resulted in credibility, the core currency of reference works, but (by today's standards) in limited dissemination and slow reactions to new knowledge. Web-based wikis, spearheaded by the Wikipedias, have extended knowledge accumulation to fields far beyond any traditional notions of expertise, provide their information at no cost to the user, and invite anybody to contribute (even anonymously) on a voluntary basis. This makes them popular and updateable on scales way below years but vulnerable to vandalism, thereby precluding credibility. Due to such problems, wikis had a slow start into the academic world but expert-only wikis like Scholarpedia [2] or the Encyclopedia of Earth [3] are gaining ground, and with the continued growth, diversification and global availability of the Internet, knowledge and the structuring thereof are becoming ever more dynamic and participatory [4]. Some key biology databases and communities are going wiki [5][6][7][8][9], as did OpenWetWare [10] - a place where lab notebooks are being kept in public. Besides, collaborative learning by structuring knowledge is a good preparation for later collaborative knowledge production in research teams. Collaborative, peer-to-peer learning principles thus develop in parallel and lead to more student-centred learning environments [11].

Citizendium (CZ)
Citizendium [12][13] is a web-based educational and reference platform that seeks to combine expert knowledge with public participation in a way that harvests the strengths of both worlds and avoids the major pitfalls of unilateral approaches. It allows anybody to contribute under their real names, provides all of its contents for free, and hosts two basic flavours of articles: As in Wikipedia [14], most content pages can be edited by any user but the information they contain will not be considered reliable. Credibility is lent to an article in a very traditional way, i.e. by means of approval by experts ("editors") upon fulfillment of a set of quality criteria like factual accuracy, balanced arguments, and readability by non-specialists. The approved articles then serve as a reliable introduction to a topic (much like in paper encyclopedias, just more up-to-date), and all the non-approved versions ("drafts") as an educational playground, with stubs actually being encouraged in the hope that they attract other contributors that improve them. Approved versions cannot be edited but work on an approved article can continue in the draft version which may eventually enter the approval process again.

This two-step (and potentially cyclic) approach is conceptually similar to Feynman’s thermal ratchet [15], the principle behind molecular motors [16][17]: Whereas Brownian motion can drive the paddle wheel randomly, the ratchet's movement will only follow if the pawl permits. If random motion can be translated into directed motion by means of appropriately structured molecular motors, the notion that reference works for human knowledge can be structured in a way that takes into account contributions by experts and the educated public may indeed be perceived as straightforward: given the incentive of presenting one's knowledge on a platform that regularly attracts putative employers or academic supervisors, the input provided by most registered users can be expected to average well above thermal noise, thereby facilitating the role of the pawl.

At CZ, the pawl's role (which requires energy) is being played by said editors - people whose life's work is to know things and who are willing to share the knowledge they have acquired during long years of dedication to their field. Consequently, CZ contributors are given credence for their work: The wiki allows to track individual contributions in a much more detailed way than any non-wiki system currently used in scholarly communication. This transparency of contributions to the structuring and expansion of global knowledge may well provide a fertile ground for the careers of knowledge workers and workers-to-be.

Education at CZ
Taking these educational considerations into practice, Citizendium, in collaboration with teachers and lecturers, has launched Eduzendium [18], a project that allows students to write their course assignments online on the Citizendium. Students work for course credits, and their teachers grade the finished work based on the quality of the article drafts produced from each student's input. But by writing their assignments under this scheme, students not only get to earn grade credits, they can see their work online and add to the global store of knowledge. By collaborating with the rapidly growing Citizendium community of expert and non-expert authors, they stand good chances that their essays eventually develop into a lasting encyclopedic article. Finally, perhaps best of all, students get to learn in a highly collaborative real-time way, and rumours have it that they might actually have fun doing so. Not surprisingly, educators who opted for Eduzendium noticed a higher degree of enthusiasm amongst their students. The educational potential of CZ is enhanced by the use of subpages which provide for an easy integration with other free educational materials like videos, e.g. the non-profit, K-12 educational video contest WatchKnow [19] or, at undergraduate level, the non-profit world lecture project (wlp)° [20].

Scholarly knowledge at CZ
CZ covers many fields, both academic and beyond, which are organized in workgroups whose main responsibility is to identifiy a set of core articles around which the field’s knowledge is structured, and to oversee the approval process (editorship in the sense discussed above is defined in terms of these workgroups).

As in traditional encyclopedias and Wikipedia, original research will not be allowed in the main namespace of CZ. Discussions are afloat for including original research into the subpages (e.g. as „signed articles“, similar to contributions to Scholarpedia) or other namespaces. Ways to take academic credit for contributions to CZ are also being discussed [21], whereas bot assistance for fact picking (as in [7]) can be made available on a case-by-case basis to facilitate data-intensive contributions.

Cross-disciplinary links are achieved in a variety of ways: First, several workgroups can collaborate on individual articles. Second, each article features a „related articles“ subpage where parent topics, subtopics and related topics are linked independent of their respective workgroups. Third, a coherent disambiguation strategy avoids page name disputes for articles on topics associated with different meanings in different fields, while allowing for a synopsis of what the different uses may have in common. Fourth, Citizendium organizes monthly Write-a-thons on broad topics to which anybody can contribute. Fifth, every user can nominate drafts as „Article of the Week“ or „New Draft of the Week“, and the winning entries are featured on the Welcome page, from where they usually receive lots of edits from specialists and non-specialists alike. Finally, as is typical for wikis, all contributions are immediately visible by anyone, and so the potential of frequent visits to the „recent changes“ page to initiate cross-disciplinary interactions should not be underestimated.

Activities in the biomedical fields have been especially visible: Biology is second to history in terms of number of articles (followed by health sciences), second to computers in terms of number of authors (followed by history) and fourth (after computers, engineering and health sciences) in number of editors (for details, see the CZ statistics [22].

"Biology" was the first article to be approved in Citizendium (on December 15, 2006, half a year after the launch of the project) [23]. The article Biology makes good use of subpages for related articles, bibliography, external links, gallery, videos and signed articles. This article's history also highlights how experts and non-experts work shoulder on shoulder, and that may be inspirational for others to join the bandwagon. A good opportunity for that will be "Biology Week" [24]- the first of a whole series of topic-dedicated weeks that will initially be held once a month (watch out for Health Sciences Week, Food Science Week, Agriculture Week and Anthropology Week).

How you can get involved
"Biology Week" is scheduled to be held during September 22 to September 28, 2008. For all biologists, this is a chance to start sharing their expertise by creating and improving biology articles, or to satisfy their curiosity by browsing (and contributing to) articles on other subjects. Others can lend their phrasing or illustration skills to make articles more attractive to non-specialist readers. Students, as explained above, can even get credits for that, and all the interested public can participate - it is an open wiki, after all.

References
1. Diderot, D.; D'Alembert, J. (1751). Encyclopédie ou dictionnaire raisonné des sciences, des arts et des métiers (Encyclopedia or systematic dictionary of the sciences, arts and crafts). Paris: Briasson, David, Le Breton, Durand. Online at http://artfl.uchicago.edu/cgi-bin/philologic31/getobject.pl?c.36:292.enc....
2. Main Page – Scholarpedia, http://www.scholarpedia.org/ . Retrieved on July 17, 2008.
3. Main Page - Encyclopedia of Earth, http://www.eoearth.org/ . Retrieved on July 17, 2008.
4. Butler, D. (2005). "Science in the web age: joint efforts". Nature 438 (7068): 548-9. http://dx.doi.org/10.1038/438548a.
5. Giles, J. (2007). "Key biology databases go wiki". Nature 445 (7129): 691. http://dx.doi.org/10.1038/445691a.
6. Mons, B.; Ashburner, M.; Chichester, C.; Van Mulligen, E.; Weeber, M.; Den Dunnen, J.; Van Ommen, G.J.; Musen, M.; Cockerill, M.; Hermjakob, H.; Others, (2008). "Calling on a million minds for community annotation in WikiProteins". Genome Biology 9 (5): R89. http://dx.doi.org/10.1186/gb-2008-9-5-r89.
7. Huss III, J.W.; Orozco, C.; Goodale, J.; Wu, C.; Batalov, S.; Vickers, T.J.; Valafar, F.; Su, A.I. (2008). "A Gene Wiki for Community Annotation of Gene Function". PLoS Biology 6 (7): e175. http://dx.doi.org/10.1371/journal.pbio.0060175.
8. Pico, A.R.; Kelder, T.; Iersel, M.; Hanspers, K.; Conklin, B.; Evelo, C. (2008). "WikiPathways: Pathway Editing for the People". PLoS Biology 6 (7): e184. http://dx.doi.org/10.1371/journal.pbio.0060184.
9. Biology-Online Dictionary, http://www.biology-online.org/dictionary/Main_Page . Retrieved on July 17, 2008.
10. Main Page – OpenWetWare, http://openwetware.org/wiki/Main_Page . Retrieved on July 17, 2008.
11. Boulos, M.N.; Maramba, I.; Wheeler, S. (2006). "Wikis, blogs and podcasts: a new generation of Web-based tools for virtual collaborative clinical practice and education". BMC Medical Education 6 (41): 1472-6920. http://dx.doi.org/10.1186/1472-6920-6-41.
12. Welcome to Citizendium - encyclopedia article – Citizendium, http://en.citizendium.org/wiki/Welcome_to_Citizendium . Retrieved on July 17, 2008.
13. Giles, J. (2006). "Wikipedia rival calls in the experts". Nature 443 (7111): 493. http://dx.doi.org/10.1038/443493a.
14. Wikipedia:Researching with Wikipedia - Wikipedia, the free encyclopedia, http://en.wikipedia.org/wiki/Wikipedia:Researching_with_Wikipedia#Citing... . Retrieved on July 17, 2008.
15. Feynman, R.P.; Leighton, R.B.; Sands, M. (1963). The Feynman Lectures on Physics, Vol. 1. Addison Wesley, Reading MA.
16. Oster, G. (2002). "Brownian ratchets: Darwin's motors". Nature 417 (6884): 25. http://dx.doi.org/10.1038/417025a.
17. Ait-Haddou, R.; Herzog, W. (2003). "Brownian ratchet models of molecular motors". Cell Biochemistry and Biophysics 38 (2): 191-213. http://dx.doi.org/10.1385/CBB:38:2:191.
18. Eduzendium - the collaborative learning environment, http://en.citizendium.org/wiki/Eduzendium . Retrieved on July 17, 2008.
19. WatchKnow, http://www.watchknow.org/ . Retrieved on July 17, 2008.
20. World Lecture Project, http://www.world-lecture-project.org/ . Retrieved on July 17, 2008.
21. How to cite Citizendium articles, http://en.citizendium.org/wiki/CZ:Proposals/Citing_CZ_article_by_authors . Retrieved on July 17, 2008.
22. Citizendium – Statistics, http://en.citizendium.org/wiki/CZ:Statistics . Retrieved on July 17, 2008.
23. Biology - encyclopedia article – Citizendium, http://en.citizendium.org/wiki/Biology . Retrieved on July 17, 2008.
24. Biology Week - encyclopedia article – Citizendium, http://en.citizendium.org/wiki/Biology_Week . Retrieved on July 17, 2008.

Acknowledgements:
We thank Chris Day, Larry Sanger and Anthony Sebastian for comments on earlier drafts of this blog.

"Using the impact factor alone to judge a journal is like using weight alone to judge a person's health."

The title of this post is a sentence taken from a report on citation statistics prepared by the
International Mathematical Union (IMU). Another such take-home message is "Research is too important to measure its value with only a single coarse tool." Given that citation statistics are heavily used in assessing research and researchers, young scientists might gain a lot from investing some time to familiarize themselves with this subject.

On the impact of research

Multiple approaches to measure the impact of research exist - the most common ones include citation metrics like the in-famous Journal Impact Factor or the relatively new Hirsch index, and the volume of research grants earned.

Open access book on Open Access

Found at http://openmed.nic.in/2789/ :

Open access to knowledge and information: scholarly literature and digital library initiatives – the South Asian scenario

Das, Anup Kumar (2008) Open access to knowledge and information: scholarly literature and digital library initiatives – the South Asian scenario. UNESCO, New Delhi, India. ISBN 9788189218218

Full text available as:
PDF - Requires Adobe Acrobat Reader or other PDF viewer.
12013 Kb
Abstract

The South Asia sub-region is now in the forefront of the Open Access movement within developing countries in the world, with India being the most prominent partner in terms of its successful Open Access and Digital Library initiatives. Institutional and policy frameworks in India also facilitate innovative solutions for increasing international visibility and accessibility of scholarly literature and documentary heritage in this country. This publication has its genesis in the recommendations and proceedings of UNESCO-supported international conferences and workshops including the 4th International Conference of Asian Digital Libraries (ICADL2001, Bangalore); the International Conferences on Digital Libraries (ICDL2004 & ICDL2006, New Delhi); and the International Workshop on Greenstone Digital Library Software (2006, Kozhikode), where many information professionals of this sub-region demonstrated their Digital Library and Open Access initiatives. This book describes successful digital library and open access initiatives in the South Asia sub-region that are available in the forms of open courseware, open access journals, metadata harvesting services, national-level open access repositories and institutional repositories. This book may be considered an authoritative Source-book on Open Access development in this sub-region.