Winner’s Curse Effect: Biomedical Research in the Deep Web
October 12, 2008
Economic principles applied to publication systems for biomedical research reveal a publication bias, a winner’s curse. Elite high-impact scholarly journals continue to raise artificial publication barriers by underusing open access, neglecting negative data and publishing unrepresentative results of repeated samplings of real world. Access to our communal knowledge and memory through archives is essential to the democratic process.
read more Young, Ioannidis, Al-Ubaydli (2008), | digg story
Currently publicly-funded peer-reviewed academic research published in exclusive journals largely informs public policies on biomedicine, the economy, environment, education, justice, housing, etc. These journals now make articles available on-line at exorbitant prices. Contributors to these journals earn tremendous academic capital crucial to professional advancement. Password protection and high costs prevent the public from accessing the most recent relevant and accurate research. The number of publicly accessible sites are growing as search engines dig deeper in the Deep Web and the open access movement grows among some academics and scientists [2, 3].
In this concise, fact-filled, informative article published by the Association of Research Libraries (ARL)[1] (2003-05-04) the authors described how even five years ago librarians were concerned by the mergers in scholarly publishing which reduced the number of players and by rising journal subscription rates that severely eroded the purchasing power[6] of libraries, universities, and scholars requiring crucial publications for teaching, learning and research.
In February 2009 Jennifer McLennan, SPARC’s[5] Director of Communications encouraged all supporters of public access to taxpayer-funded research – researchers, libraries, campus administrators, patient advocates, publishers, and others to oppose H.R. 801: the “Fair Copyright in Research Works Act which was re-introduced in February 11, 2009 by Chairman of the House Judiciary Committee (Rep. John Conyers, D-MI). This bill would reverse the National Institutes of Health (NIH) Public Access Policy and make it impossible for other federal agencies to put similar policies into place.”The bill goes further than prohibiting open access requirements, however, as the bill also prohibits government agencies from obtaining a license to publicly distribute, perform, or display such work by, for example, placing it on the Internet, and would repeal the longstanding ‘federal purpose’ doctrine, under which all federal agencies that fund the creation of a copyrighted work reserve the ‘royalty-free, nonexclusive right to reproduce, publish, or otherwise use the work’ for any federal purpose. The National Institutes of Health require NIH-funded research to be published in open-access repositories (Doctorwo 2009).” HR801 would benefit for-profit science publishers and increase challenges for making the Deep Web more accessible. See also Doctorwo, Cory. 2009-02-16. “Scientific publishers get a law introduced to end free publication of govt-funded research.”
In 2000 The Open Archives Initiative (OAI) [4] focused on increased access to scientific research (Van de Sompel & Lagoze, 2000). Since then it has reached deeper into the Deep Web with is OAI-Protocol for Metadata Harvesting (OAI-PMH). See Cole et al (2002).
Notes
1. In early 2002, Association of Research Libraries (ARL) Office of Scholarly Communication task force recommended that the Association promote “open access to quality information in support of learning and scholarship.” Society benefits from the open exchange of ideas. Access to information is essential in a democratic society. Public health, the economy, public policy all depend on access to and use of information, including copyrighted works.
2. UC-Berkeley Biologist Michael Eisen, Nobel Laureate Harold Varmus and Stanford biochemist Patrick Brown helped start the Public Library of Science, PLoS in 2000, a “nonprofit organization of scientists and physicians committed to making the world’s scientific and medical literature a freely available public resource” by encouraging scientists to insist on open-access publishing models rather than being forced to sign over their (often publicly-funded research) to expensive scientific journals. Wright (2004) cited Eisen, Varmus and Brown as examples of scientists who are making making some areas of the Deep Web more accessible to the public.
3. Alex Steffen (2003 [2008-09-04]) open source (OS) movement
4. The Open Archives Initiative (OAI) “develops and promotes interoperability standards that aim to facilitate the efficient dissemination of content. The OAI Metadata Harvesting Protocol allows third-party services to gather standardized metadata from distributed repositories and conduct searches against the assembled metadata to identify and ultimately retrieve documents. While many proponents of OAI advocate open access, i.e., the free availability of works on the Internet, the fundamental technological framework and standards of the OAI are independent of the both the type of content offered and the economic models surrounding that content (ARL).”
5. The Scholarly Publishing and Academic Resources Coalition, (SPARC) launched in June 1998, is an international alliance of academic and research libraries working to correct imbalances in the scholarly publishing system.
5. SciDev.Net (Science and Development Network) “is a not-for-profit organisation dedicated to providing reliable and authoritative information about science and technology for the developing world. Through our website www.scidev.net we give policymakers, researchers, the media and civil society information and a platform to explore how science and technology can reduce poverty, improve health and raise standards of living around the world. We also build developing countries’ capacity for communicating science and technology through our regional networks of committed individuals and organisations, practical guidance and specialist workshops.” SciDev.Net “originated from a project set up by news staff at the journal Nature (with financial assistance from the Wellcome Trust, United Kingdom) to report on the World Conference on Science, held in Budapest in 1999. This was warmly received, leading to discussions about creating a permanent website devoted to reporting on, and analysing the role of, science and technology in development. The initiative was endorsed at a meeting held at the Academy of Sciences for the Developing World (TWAS) in Trieste, Italy, in October 2000. Immediately following the Trieste meeting, the UK Department for International Development (DFID) agreed to finance a six-month planning stage, starting in November 2000. At the end of this planning stage, sufficient funding had been raised from international aid agencies and foundations for a full-time staff and an independent office in London. The SciDev.Net website was officially launched on 3 December 2001. The website has expanded continuously since its launch. We regularly add dossiers, spotlights, ‘quick guides’ and ‘news focuses’ on specific subjects, in addition to a growing amount of regular news coverage. An enhanced and redesigned version of the website was launched in January 2008. Regional networks were launched in Sub-Saharan Africa (2002), in Latin America (2003), in South Asia (2004) and in China (2005), each bringing together individuals and organisations that share our goals and objectives. There are plans for future networks in the Middle East and North Africa, West Africa and South-East Asia. SciDev.Net held its first workshop, in collaboration with the InterAcademy Panel, on science in the media in Tobago in February 2001. Since then we have collaborated with partners to deliver numerous specialist science communication workshops for journalists and other professional communicators across the world (SciDev.Net History).”
6. “Expenditures for serials by research libraries increased 210% between 1986-2001 while the CPI increased 62%. The typical library spent 3 times as much but purchased 5% fewer titles. Book purchases declined by 9% between 1986-2001 as libraries sought to sustain journals collections. Based on 1986 purchasing levels, the typical research library has foregone purchasing 90,000 monographs over the past 15 years. In the electronic environment, the model has changed from the purchase of physical copies to the licensing of access. In general, libraries do not own copies of electronic resources and must negotiate licenses (rather than depend on copyright law) to determine access and use. Large bundles of electronic journals offered by major commercial publishers will force smaller publishers out of business. Multiple-year licenses to large bundles of content that preclude cancellations will force libraries to cancel titles from smaller publishers to cover price increases of the bundles. This diminishes competition and increases the market control of the large publishers. Lack of corrective market forces has permitted large companies to reap high profits from publishing science journals. In 2001 Reed Elsevier’s STM division’s operating profit was 34% while its legal division’s operating profit was 20%, its business division’s 15%, and education 23%. Mergers and acquisitions increase prices and eliminate competition. Research has shown that mergers exacerbate the already significant price increases of journals owned by the merging companies. While there were 13 major STM (Science, Technology and Medicine) publishers in 1998, only seven remained by the end of 2002 (ARL 2003-05-04:2).”
Webliography and Bibliography
Cole, Timothy W.; Kaczmarek, Joanne; Marty, Paul F.; Prom, Christopher J.; Sandore, Beth; Shreeves, Sarah. 2002-04-18. “Now That We’ve Found the ‘Hidden Web,’ What Can We Do With It?” The Illinois Open Archives Initiative Metadata Harvesting Experience. Museums and the Web (MW) Conference. Archives and Museums Informatics. University of Illinois at Urbana-Champaign, USA. April 18-20.
Smith, Richard. 2008-10-07. “More evidence on why we need radical reform of science publishing.”
Steffen, Alex. 2008-09-04 [2003]. “The Open Source Movement.” WorldChanging Team.
Young, N.S,; Ioannidis, J.P.A; Al-Ubaydli, O. 2008. “Why Current Publication Practices May Distort Science.” PLoS Medicine. 5:10.
ARL. 2003-05-04. “Framing the Issue.” Association of Research Libraries (ARL).
“Every single mainstream outlet syndicates headlines and summaries rather than publishing full-text RSS feeds — even for paid subscribers. They often don’t credit or link to bloggers who break stories first. And don’t get me started on the nuisance of interruptions such as interstitial ads and video pre-rolls.”
Drawn deeper and deeper into that mesmerizing alternative virtual space called Web 2.0, caught in a cybernarcosis that hits me before I’ve even poured my second cup of morning coffee I now read all my news from my Customized Google New Reader fed by social-minded (not Socialist) .rss feeds producers. I’ve just placed three of the most recent .rss feeds by Steve Rubel at the top left where I begin, my daily news headlines, so to speak.
I learned about Micro Persuasion from Jonathan Yang’s (2006a) Rough Guide to Blogging which I found while browsing the stone and glass Cowichan Valley Regional Library’s print and paper stacks. Steve Rubel explores how social media is transforming marketing, media and public relations. See also Yang’s blog (2006b) which complements his recent Rough Guides publication.
While I’m still trying to figure out where I am since (this is obviosly not Kansas) I’m bumping into cyberspace inhabitants of this strange new world. Somehow I feel as though I am blurking unseen, like a voyeur, bordering on scopofilia. But there is so much information on them that I have this illusion that I can get very close to verstehen understanding. What is concealed and what is revealed here?
For now I am just grateful for the Rubies out there. I am going to start keeping track of them so I can remember months from now why I del.ico.used, Dugg, blogrolled, and finally .rssd them. (Blog lexicons really hurts the ears and conjures up some very ugly metaphors.) I think it is time for a poet laureat of the blog to whom innovators turn before creating new terms that will stick for all blog eternity.
One of the emerging concepts in cyberspace is the “deep internet” which came to mean that part of cyberspace that was exclusive, not social, pay-per-use or members-only and therefore in terms of acedemic capital, somehow more profound, valued, authentic, legitimate, timely and quotable. Academic journals are by far the worst offenders. Jstor (you-do-not-have-access) on my screen gives me a feeling similar to the blue screen of death. Main stream media seemed to be going in that direction but I am not so sure now. I can read full-text articles from the New York Times, the Boston Globe, Le Monde, Le Figaro, Toronto Star and Nunatsiak News (including their archives) with no cost to me. Some require registration which is free and painless. Which is good for I for one would not pay a dime to access information on the Internet. In a way it is like a purist’s experiment. If I can access it for free that so can those who have Internet access but have no capital at all for even a dime-per-factoid user-fee.
Thank you Jonathan Yang I will be harvesting detailed information from your timely publication over the next while. Thank you Steve Rubel for holding a virtual flash light for the net novices who are blindly groping through the dark.
Selected webliography and biblography
Yang, Jonathan. 2006a. The Rough Guide to Blogging. Rough Guides: London, UK & New York, New York. p. 188 www.roughguides.com
Yang, Jonathan. 2006b. Rough Guide to Blogging: The Blog Accessed December 4, 2006.
© NASA: Hubble Heritage Project
NGC 1999, a reflection nebula in the constellation Orion
This nebula in the constellation Orion is a reflection nebula which does not emit visible light on its own but is illuminated by a neighbouring recently born white star, V380 Orionis which is visible left of center. NGC 1999 became famous when the first Herbig-Haro object was discovered next to it. Herbig-Haro objects are now known to be jets of gas ejected from very young stars. V380 Orionis has a mass three times that of our sun and it twice as hot on its surface. This jet-black cloud near the centre is an example of a “Bok globule,” (after Bart Bok) a dense, cold light-eating cloud which might be where new stars are formed.(NASA 2006)
Hosted by NASA, National Aeronautics and Space Administration on their image of the day, November 21, 2006.
Space invasion with fireplace and PC (1998-1999)
November 2, 2006
Space invasion with fireplace and PC (1998-1999),
originally uploaded by ocean.flynn.
I began making my first web pages when Dave and I lived here on Lac Gauvreau, Chemin de la Baie Ste. Anne, Ste Cécile de Masham, Québec. I had already taken my first contemporary social theory courses with Rob Shields. From that time onwards he has been a valued mentor for my grad studies. I was working on the year long PhD seminar course with Professor Wallot at the University of Ottawa. This Canadian Studies PhD was a life-transforming experience. It was education as its best. The institution provided everything a grad student could need including access to a super coach and computer lab. As always Dave and I were squeezing as much as we could with bare bones technology. I was using our first digital camera and this flat bed scanner. My son Dan, who was studying at the Cite collegiale in Ottawa, taught me just enough .html coding so I wouldn’t make too much of a mess for him to clean up. He was a bit of a purist.
This acrylic painting was painted over the Christmas holidays in 1998-1999. I had already painted the tree outside our cabin by Lake Gauvreau. The next day the branches were so burdened with snow I had to repaint them entirely. I decided to let them invade the inner space of the cottage since their presence was so insistent.
The painting is 30″ x 22.5″ on Arches paper.
It was shown in March 1999 at an exhibition on Bank Street in Ottawa, ON and again in a gallery on Great George Street , Charlottetown, Prince Edward Island in the summer of 1999.
Space invasion with fireplace and PC was one of the first images on my Carleton University home page and on the collaborative, innovative virtual space called artengine. It is one of my favourite images and after our chaotic move out west I really don’t know where the actual physical painting is or the great high resolution digital images the professional photographer took of my work in May-June? of 1999.
One of the challenges for me is to find the kinds of sites that provide me with ideas I can build upon. For example, currently I am unable to simply use a search engine to find useful information on the concept of memory work. I have kept track of this concept over the years using my EndNote bibliographic database. My sister Sharon introduced me to EndNote c. 1992?, an authoring software for creating digital databases with a powerful cross-referencing ability. Thousands of useful entries later and numerous upgrades later I continue to thank you Sharon.
Technorati spider release
November 1, 2006
In my attempt to understand how Frimr reached its scores I found sites called blogjuice? which led me again to Technorati. I had visited their site before so this time I decided to register. I now have a Technorati Profile. I am now trying to use Technorati to refine searches for key concepts such as memory work, answerability, post-national, ethical topography of self.
I continue to find so many free, useful and fun internet services. Flickr is by far the most entertaining. For keeping track of bookmarks, which I call my webliographies, del.icio.us and swicki offer much more than I could ever have imagined. Swicki even does it with image collages of your individualized tag clouds. I have been learning how to interconnect my Flickr with WordPress and Blogspot. That is also amazing.
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I have decided to no longer keep an account with Frimr, a fictional site that offers to track how famous you are becoming on the Internet. I just could not figure out how to fill in their on-line form. Apparently my score jumped from 0 to 9999 and back down to 0 in a few weeks because of the way I entered my ‘feeds.’ I didn’t even know what a feed was until I tried being a frimeuse. (This term in French for boastful: ‘Link me, I’m famous’ ) Since I am in this for the pure pleasure as well as the teaching, learning and research I prefer not to work too hard to keep track of my score. |
del.icio.us | swicki | Technorati Profile | wordpress | Flickr | blogspot | photoblog | digg | gather | thinkfree | Picasaweb | Carleton homepage
Folksonomy II
October 29, 2006
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Using Adobe Photoshop I layered Friedrich’s (1818) Voyageur au-dessus de la mer de nuages (1818), a Google Earth generated image of Garibaldi Mountain region, British Columbia (49.51.20.64N – 122.57.18.09W elev 6026′ eye alt 13964) and my del.icio.us tag cloud as it emerges from the fog of my thinking. Tags are user-generated so the author chooses how to categorize each .url. Eventually a pattern emerges from this exercise in taxonomy from the ground up. As I visit other peoples’ blogs and del.icio.us webliographies, I learn better ways to categorize certain theories and/or theorists. Gradually I changes these tags, folksonomies or ethnoclassifications so that I can better connect with others making similar journeys. |
del.icio.us | swicki | wordpress | Flickr | blogspot | photoblog | digg | gather | thinkfree | |Picasaweb | Carleton homepage
Creative Commons: Light Flickring on Water
October 23, 2006
Creative Commons from my online Flickr album is composed of multiple layers. They include a .jpg of the Google Earth generated globe which is inverted, stretched and manipulated in 3 other layers, ripples from an M. C. Escher print and a stunning photo by a Professor Andrew Davidhazy from Rochester, NY. described on a few of the 80, 000+ references to him on Google as modest, talented, a great teacher and a ghost expert for photography. I have just licensed my work on line with the Creative Commons. Their icon lets people know that they can use your work for non-commercial reasons if they attribute it to you; they can make derivatives but they have to share-alike. Of course the challenge with Goggle Images is some of the most stellar images available are difficult to track down in terms of authorship because there are already so many derivatives. This was the case with this drop of water by this well-known professor who continues to do astounding work. I left a comment on his web blog but I re-entered it three times before I realized he had wisely included an administrator’s block for unedited entries. It may take him ages to even check his comments. When he does he will find to his annoyance in his busy life, that I’ve inadvertently left three. More than that I just emailed him instead of Flckr’s team re: emailing our Flickr photos to WordPress. He is going to put me on his ‘block permanently list.’
An Inuit friend reminded me that many Inuit of Canada view the world from a circumpolar point of view. In honour of my Inuit friends and students from time to time I view the earth through their lens. I positioned then froze the globe from a circumpolar point of view using a Google save screen option. So I have geotagged this to the north east of Baffin Island, perhaps somewhere near Pond Inlet. Hello to the family of Julia and Ernie! Their family photo in their traditional clothing taken when they visited you in Pond Inlet in 2005, is framed and hanging in our home on Vancouver Island.
Folksonomies as a Shape Shifting Topography of Self and the Other
October 20, 2006
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An Adobe Photshop image consisting of 5 layered images: my Del.icio.us cloud tag, title layer, google generated 3-D virtual space with branching rivers as metaphors for organically emerging rhizomic pathways, |
a miniaturized image of Vancouver, BC’s skyline, the del.icio.us tag cloud image (my first since I began to use this free social bookmarking tech tool) and an altered topographical map of a site where a meteor landed. This final layer was inverted so the meteoric collision with the planet became the sun in this delicious cloud.
‘Folksonomies’ is an organic emerging term in an organic emerging system. Is it perhaps an example of autopoiesis constituting and nurturing its own rhizomic organization? There are economic, political, social as well as ontological and axiological dimensions to the unfolding taxonomy of cyberspace. Tag clouds leave visible trails of a blogger’s inner life. Unlike solitary browsing through library stacks or flipping through pages of a book, internet searching and browsing leaves digital imprints that allow us to retrace where we were yesterday in terms of our understanding of a topic. Theoretically how well we understand a debate or discussion informs how discerning we are in our judgments. Our ethical topography changes as we travel and encounter Others whose ideas and/or values resonate or are in dissonance with our own. Encounters with the stranger, one whose experience differs greatly from our own in some way, provides us with an opportunity to re-evaluate previously held beliefs or assumptions. In welcoming the Stranger in friendship with a heightened degree of hospitality that includes a willingness to tolerate ambiguity temporarily, to briefly at least set aside prejudices, we open ourselves to the possibility of fresh insight that expands for both of us. It is only through the invention of unique terms such as folksonomies, or ethnoclassification or perhaps tag.clouds that I might filter through infinite numbers of blogs on taxonomy and find the like-minded individual who is concerned about the potential emergence of an inclusive taxonomy that somehow includes the more socially vulnerable not as objects of charity but as fully participating members in civil society.
Stumble it!
papergirls 