October 18, 2008
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.
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) (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 of libraries, universities, and scholars requiring crucial publications for teaching, learning and research.
In February 2009 Jennifer McLennan, SPARC’s 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)  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).
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.”
Young, N.S,; Ioannidis, J.P.A; Al-Ubaydli, O. 2008. “Why Current Publication Practices May Distort Science.” PLoS Medicine. 5:10.
Indifference to faith has left Europe’s churches mostly empty. But debate over religion is more intense than its been in many decades. Religion is re-emerging as an issue because of Europe’s growing and restive Muslim populations and a fear that faith is reasserting itself in politics. That is adding up to momentum for a combative brand of atheism.
Colbert, Stephen. 2007. Unquisition. May 3.
Delacroix, Eugène. Jacob Fighting the Devil. Lutte de Jacob avec l’Ange. Eglise Saint Sulpice Detail. 2005.1
Hitchens, Christopher. 2007. God is Not Great: How Religion Poisons Everything. Twelve/Warner Books.
“Jacob Fighting the Devil.” chapter 32 of Genesis
Kinsley, Michael. 2007. “In God, Distrust.” Sunday Book Review. New York Times. May 13.
Lacroix, Alexandre, Truong, Nicolas. 2007. “Nicolas Sarkozy et Michel Onfray: Confidences entre Ennemis.” Philosophie Mag. No. 8. >> Philomag.com
Onfray, Michel. Atheist Manifesto: The Case Against Christianity, Judaism, and Islam.
Higgins, Andrew. 2007. “As religious strife grows, atheists seize pulpit.” Northwest Herald. >> nwherald.com. April 13.
Etzioni, Amitai. 2007a.”The West Needs a Spiritual Surge” >> Amitai Etzioni Notes. March 6, 2007.
Etzioni, Amitai. 2007b. “L’Occident aussi a besoin d’un renouveau spirituel.” Le Monde. 7 avril.
Flynn-Burhoe, Maureen. 2007. “Unquisition: Selling Nothingness.” >> Speechless. may 13.
December 30, 2006
“It’s just the way it is,” isn’t anymore. As I read the Nasar and Grubermanifold New Yorker article (2006) I was deeply moved by the life story of Gregory Perelman who can live on a $100 a month and who managed to wipe out an entire branch of pure mathematics in a few years by working alone, even isolated in the slow world. He is described as an idealist, an ascetic, a Russian Jew who lives with his mother in a gray neighbourhood of gray apartment buildings. But in this article he shines brilliantly. He may be part of the answer to my own puzzle, the ethical dilemma of being an academic in the 21st century.
Henri Poincaré created a True Knowledge Gap in mathematics, giving rise to an entire branch in his discipline when he slipped in an offhand question that became the legendary problem of the 20th century (Nasar and Grubermanifold 2006).
By the nineteen-sixties, topology had become one of the most productive areas of mathematics, and young topologists were launching regular attacks on the Poincaré. To the astonishment of most mathematicians, it turned out that manifolds of the fourth, fifth, and higher dimensions were more tractable than those of the third dimension. By 1982, Poincaré’s conjecture had been proved in all dimensions except the third. In 2000, the Clay Mathematics Institute, a private foundation that promotes mathematical research, named the Poincaré one of the seven most important outstanding problems in mathematics and offered a million dollars to anyone who could prove it.
In 1992 when Gregory Perelman (b. 1968) posted his solution to the problem on the Internet on a site used by mathematicians working with advanced concepts, he supplied enough information for the handful of minds capable of understanding to know that he had cracked it.
It took me a few days to feel I had understood enough of their article to appreciate it. I used my new Firefox add-on Gnosis.
Why then did this story continue to unfold on some very messy battle Fields? Politics, power and control. To understand more fully, I worked out some of the ideas at Tim’s and in an easy chair playing with pictures. I also had to map out a brief timeline and the biographies of the main characters: Perelman, Hamilton, Yau, Tian, Zhu, Cao, Ball and Thurston. I played with the concepts of Knowledge Collisions in the Battle Fields of Mathematics but this was not about knowledge collisions on a level playing field.
Poincaré’s bagel, coffee mug handle, soccer ball and noose knot were great for starters. The table itself was easily transformed into a topology of Battle Fields. Cigars and necks protruded on the topological landscape like stalagmites. I laid a silk cloth over it all so it could drape over the edge of the table. I left a space on the table edge for a dented fender. The True Gap gaped like a crevice in an otherwise relatively level playing field. The coffee mug with its insignia of Stephen Hawkings casts a long shadow and the handle represented the branch of mathematics called topology. Since we are looking at a cross section of topological field the branch that has disappeared over the edge represents a small sorrow 
I didn’t know where to put Gregory Perelman my new hero, so I put a spoon in the coffee mug which he of course had stirred up. Then I balanced a swing at the top of it giving him a higher vantage point from which he can quietly survey the field. He swings slowly back and forth without those below noticing. All they can see is the spoon and the bottom of his swing. I turned him into a pearl and remembered a quote, “Not every sea has pearls . . .”
My early experiences in academia were entirely positive. It was only when I was in my fifth year of graduate studies, my second in my PhD that I began to realize the hidden power and politics behind the scenes in the ivory towers as one professor after another sought to gain control over academic and/or grant capital at any cost. I caught myself transforming campus towers into Freudian phallic symbols as I watched with dismay my PhD slipping away from me. I was disgusted mainly with my own naïvity, my lack of campus street-smarts but by then it was too late. It seems my university students in their twenties had figured it out long before I did. No wonder we all make fun of Ph.D.s!
So here I am typing away in my living room office with my old PC perched on this great glass-topped Business Depot computer desk, reflecting Mount Tzuhalem with the fire crackling off to my left and our family sound asleep. I’m emptying my PC into a dozen or more free Web 2.0 sites.
I’m not a Perelman but he is my hero. If you can only learn to live on $100 a month, keep access to the Internet, connect one’s PC’s memory to the free Web 2.0 you can sit back in the slow world and quietly watch a lifetime of experience upload to this strange virtual space we call the Internet.
Perelman’s copyright took the risk of losing his intellectual capital. For some Yau and his students really did deserve the Fields Award he received from Ball.
But for me I would rather face the perils of a Perelman Risk, tie my intellectual capital to my Creative Commons stake and at least let people share some of the amazing experiences I was privileged to have before the Fawlty Towers crumbled around me.
 See the article on ClearForest. I had to select a chunk of the article at a time for Gnosis to do its magic but undeniable it makes digesting lengthy, complex articles less cumbersome. At the most elemental level it is similar to the Google generated highlighted key words in .pdf files found in response to a user’s Google search inquiry. Gnosis uses a number of colour codes to highlight a number of themes which I am just trying to work out now.
 Its a bit like the death of a meteorite in a fiery explosion would be to the person who had named and followed the passage of the meteorite for decades.
[I have even heard on academic hearsay which is as reliable as Frank I suppose, so I should not repeat this but . . . this is not a journal it is a blog . . . an archaeologist explained to his First Nations guide (who later whispered this to me) that he would not reveal their findings in the field since it would be so hotly contested by his colleagues in his branch it would consume his entire career to defend it. Academic hearsay. Fireworks, not a meteor. Take away 5 credibility, legitimacy points from this author immediately!]
For more reading on science on Web 2.0 see yanfeng.org
Swaminathan, Nikhil. 2006. peer_review_is_sooooo_old_school
Scientific American Blog. December 22, 2006.
Nasar, Sylvia , Grubermanifold, David. 2006.”Manifest Destiny.” The New Yorker: Fact. Annals of Mathematics. A legendary problem and the battle over who solved it. Issue of 2006-08-28; Posted 2006-08-21; accessed December 22, 2006.