Archive for September, 2007

Clumsy solutions point the way to OA?

There’s a thought-provoking column, entitled: The best way to solve our biggest problem: Be clumsy, by Doug Saunders, in The Globe and Mail, September 22, 2007. Excerpt:

When governments face big, nasty problems, they hear contradictory stories from citizens: a) “We need to be forced to change our behaviour;” b) “We need to have regulations to keep things under control;” c) “We need to spend some money on an alternative;” d) “This isn’t a problem at all and you shouldn’t get in our way.” Most times, leaders will choose one of these stories and find a solution that fits it.

The Clumsies argue that our leaders mistakenly strive for elegance, which “means pursuing just one of these stories and, in the process, silencing the other voices.” More often than not, they say, better solutions can be found by giving each of the stories, however contradictory, a piece of policy.

The “Clumsies” are identified in the column as those whose manifesto is the book Clumsy Solutions for a Complex World, edited by Marco Verweij and Michael Thompson.

The focus of Doug Saunders’ column is on “the most pressing issue of our age – climate change“. He argues that “There are some fundamental paradoxes in the climate-change problem that make any single solution self-defeating“.

As is pointed out in the Bangalore Declaration [PDF]:

The resolution of many of the world’s problems, such as emerging infectious diseases, environmental disasters, HIV/AIDS or climate change, cannot be achieved without incorporation of the research from developing countries into the global knowledge pool.

Complex problems such as these require the cooperation of many people in the research and development process. OA provides a powerful framework for co-operation. (Excerpted from The Future of Science is Open, Part 1: Open Access, Bill Hooker, 3 Quarks Daily, October 30, 2006).

Might some paradoxes posed by the open access movement also defy any single solution?

An example is provided by a conflict between two recommendations in the European Research Advisory Board Final Report, Scientific Publication: Policy on Open Access, (EURAB 06.049), December 2006. The first recommendation is:

1. The publication policy should not compromise the freedom of scientists to publish wherever they feel is most appropriate.

The fourth recommendation is:

4. EURAB recommends that the Commission should consider mandating all researchers funded under FP7 to lodge their publications resulting from EC-funded research in an open access repository as soon as possible after publication, to be made openly accessible within 6 months at the latest.

These recommendations are also included in: EURAB’s Proposed OA Mandate: Strongest of the 20 Adopted and 5 Proposed So Far, Stevan Harnad, Open Access Archivangelism, January 15, 2007.

But, how to deal with journals, such as those of the American Association for Cancer Research (AACR), when its copyright policies do not permit OA within 6 months? (At the SHERPA/RoMEO website, search for information on copyright policies & self-archiving for the publisher American Association for Cancer Research).

If an author, following recommendation #1, chooses to publish in an AACR journal, and is not able to obtain a waiver of the AACR copyright policies (e.g. via mutual acceptance of an appropriate Author Addendum), then recommendation #4 (OA within 6 months) cannot be achieved without violation of this particular publisher’s copyright policy.

What to do? A solution (a somewhat “clumsy” one?) is to permit some violations of recommendation #4, but only via an acceptance of what Peter Suber has called the “dual deposit/release strategy“, and Stevan Harnad has called the “immediate deposit / optional access” strategy. (The latter ID/OA strategy has a focus on University-based Institutional Repositories). An excerpt from the ID/OA version of this strategy:

The deposit — of the author’s final, peer-reviewed draft of all journal articles, in the author’s own Institutional Repository (IR) — is required immediately upon acceptance for publication, with no delays or exceptions. But whether access to that deposit is immediately set to Open Access or provisionally set to Closed Access (with only the metadata, but not the full-text, accessible webwide) is left up to the author, with only a strong recommendation to set access as Open Access as soon as possible (immediately wherever possible, and otherwise preferably with a maximal embargo cap at 6 months).

Please note the word “preferably” in the final part of this excerpt. This permits an author to avoid violating copyright.

Another excerpt from the ID/OA version of this strategy:

[In the meanwhile, if there needs to be an embargo period, the IR software has a semi-automated EMAIL EPRINT REQUEST button that allows any would-be user to request (by entering their email address and clicking) and then allows any author to provide (by simply clicking on a URL that appears in the eprint request received by email) a single copy of the deposited draft, by email, on an individual basis …

Another somewhat “clumsy” strategy? (Perhaps, but it’s one that does provide a solution, by permitting recommendation #1 to prevail over recommendation #4, while still providing a means for individual readers to obtain access).

The CIHR Policy on Access to Research Outputs involves a conflict in principles somewhat analogous to the one outlined above (in relation to the 1st and 4th EURAB recommendations). The first of CIHR’s “guiding principles” is:

* Committing to academic freedom, and the right to publish;

The fifth “guiding principle” is:

* Effective diffusion of research results;

Stevan Harnad’s advocacy of an IR-deposition strategy for CIHR is provided in his blog post No Need for Canadian PubMed Central: CIHR Should Mandate IR Deposit, Stevan Harnad, Open Access Archivangelism, June 10, 2007.

See CIHR Policy on Access to Research Outputs for some additional comments about the policy.

My own view? The CIHR access policy and its implementation will evolve (and, in doing so, may utilize a variety of “clumsy” solutions).

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Better access to cancer care in Canada

A CIHR news release, dated 24 August 2007, is: Canada’s New Government Invests $10.1 Million for Better Access to Cancer Care from Prevention to Palliation.

Excerpts:

Canada’s New Government through the Canadian Institutes of Health Research (CIHR) in partnership with CancerCare Manitoba and Cancer Care Nova Scotia will provide the funding over the next five years to seven research teams.

“Evidence, based on solid scientific research, is key to informed health decision making. The 7 teams being funded today will provide exactly the kinds of evidence that cancer patients, policy makers and family doctors need to improve the quality of cancer care across Canada” stated Dr. Alan Bernstein, President of the Canadian Institutes of Health Research (CIHR).

“We are committed to working with provinces and healthcare experts to improve timely access to high quality health care, a top priority for CIHR and for all Canadians,” said Dr. Branton, Scientific Director of the CIHR Institute of Cancer Research. “These teams will advance knowledge in many areas that are of strategic importance to our health care system, and will ultimately allow for better access to cancer care for patients and their families.”

It seems self-evident the the “kinds of evidence that cancer patients, policy makers and family doctors need to improve the quality of cancer care across Canada” should be openly accessible, when the research that’s being described has been supported from public funds.

Note that 7 teams have been awarded funding. The leaders of these teams are listed below, together with information about their 5 previous publications that have been highest-ranked by Google Scholar.

1) Richard Doll (B.C. Cancer Agency): Of the first 5 articles that were co-authored by Richard Doll (not the Oxford epidemiologist Sir Richard Doll, now deceased), 3 were found to be freely accessible (60%). These 3 were published between 2001 and 2005.

2) Brenda Elias (University of Manitoba): Excluding contributions to books, all of the 5 highest-ranked articles or reports were found to be freely accessible (100%). These 5 were published between 1998 and 2006.

3) Eva Grunfeld (Dalhousie University / Cancer Care Nova Scotia): All 5 highest-ranked articles were found (one after an additional Google search) to be freely accessible (100%). These 5 were published between 2004 and 2006.

4) Alan Katz (University of Manitoba): Of the 5 highest-ranked publications, 3 were found to be freely accessible (60%). These 3 were published between 1998 and 2004.

5) William Mackillop (Queen’s University): Of the 5 highest-ranked articles, 3 were found to have at least one version that’s freely accessible (60%). These 3 were published between 1999 and 2000.

6) Devidas Menon (University of Alberta): No way was found to access any of the 5 highest-ranked articles (0%). However, an article in Health Affairs (2001) is freely accessible.

7) Scott Tyldesley (B.C. Cancer Agency): Of the 5 highest-ranked articles, one (published in 2005) was freely accessible, and 4 (published in 2003 and 2004) were accessible by patients in need of medical information, via Elsevier’s Patient Research Beta.

Excerpt from About Patient Research:

Elsevier has launched a beta pilot that supports patients and their family members looking for medical information; providing access to individual full text journal articles from selected Elsevier publications. The articles are delivered via email for a minimal handling fee of $4.95.

The pilot will help the individual journals assess the level of demand for medical information from the public and provide a public service to those in medical need. The journals testing this approach cover different medical fields and represent both publisher and society journals. These journals are testing this approach because they have content that is relevant to common medical conditions and are relatively straightforward to understand. …

Of the 35 articles, published previously by these 7 team leaders and highly-ranked by Google Scholar, 20 (about 60%) were found to be freely accessible.

Can this percentage (already a majority) be improved upon? In particular, will the new CIHR Policy on Access to Research Outputs increase such percentages? (For access to the policy, see: www.cihr-irsc.gc.ca/e/34846.html) Outcomes of this kind from the policy won’t be available in the short term. What’s likely to be needed soon is a formative evaluation plan for the policy.

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OncologySTAT portal for cancer research

Elsevier provides free online access to 100+ oncology journals, Peter Suber, Open Access News, September 10, 2007. This news item is about OncologySTAT and includes Peter’s comments about this portal for cancer research.

See also: About medical publishing and advertising, Greg Dahlmann, blog.bioethics.net, September 10, 2007. Excerpts:

The web delivered a bit of a serendipitous dialectic today on the subject of how medical journals pay the bills. This morning, the New York Times published a story about the launch of OncologySTAT, Reed Elsevier’s new ad-supported portal for cancer research. The publisher’s plan basically goes like this:

1. Aggregate cancer research
2. Get doctors to register to use the site by providing free access
3. Tell pharmaceutical advertisers about all the doctors gathered in one place
4. Profit

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Alpha version of Freebase

Freebase is “an open, shared database of the world’s knowledge“.

From the Freebase FAQ:

1. What is Freebase?

Freebase is a uniquely structured database that you can easily search, add to and edit; you can also use the data in it to power your own projects. It’s a data commons in the way that a public square is a land commons—available to anyone to use.

Freebase covers millions of topics in hundreds of categories. It’s been seeded with a few million topics from open sources, including Wikipedia and Musicbrainz

Freebase Policies:
* Licensing Policy
* Copyright Policy
* Privacy Policy
* Terms of Service

Example: Search Freebase.com for “open access”.

The first two search results: Open access and Open access publishing.

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CIHR Policy on Access to Research Outputs

The Policy on Access to Research Outputs of the Canadian Institutes of Health Research (CIHR) was posted on September 4, 2007.

A press release: Open access to health research publications: CIHR unveils new policy.

Heather Morrison was, I think, the first blogger to post an item about the policy: Canadian Institutes of Health Research (CIHR) Policy on Access to Research Outputs.

Other blog posts:

Peter Suber, in Open Access News: OA mandate at the CIHR.

Michael Geist: CIHR Introduces New Open Access
Policy
.

Stevan Harnad: Canada’s CIHR: 31st to Adopt a Green OA Self-Archiving Mandate.

Alexandre Enkerli: Open Access in Canada: CIHR Weighs In.

Stephen Downes: CIHR Introduces New Open Access Policy.

Bayman (a graduate student in a cancer lab in Ottawa, Canada): Canadian Institutes of Health Research Moves to Back Open Access Science.

The next step: implementation of the policy.

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Genome sequence of an individual human

There’s an OA publication, The Diploid Genome Sequence of an Individual Human, by Samuel Levy and 30 co-authors, including J. Craig Venter, in PLoS Biol 2007(4 Sep); 5(10): e254.

This article has already attracted the attention of news media, and bloggers are beginning to post comments. Two examples:

J. Craig Venter, thoroughly exposed…, by Coturnix (Bora Zivkovic), A Blog Around the Clock, 3 September, 2007. Excerpt:

… the new paper actually uses his [J. Craig Venter’s] personal genome to do some nifty stuff, as this is the first time a genome containing the sequences from BOTH sets of chromosomes of a single individual has been sequenced, with some interesting insights …

In the Genome Race, the Sequel Is Personal, by Matt Dowling, Ontogeny blog, 3 September 2007. Excerpt:

Though there are now novel technologies for decoding DNA very cheaply, Dr. Venter’s genome sequence could set a high bar for a long time. It was decoded with an old method, known as Sanger sequencing, that is expensive but analyzes stretches of DNA up to 800 units in length. The cheaper new technologies at present analyze pieces of DNA only 200 units or so long, and the shorter lengths are much harder to assemble into a complete genome.

Many more comments from bloggers can be anticipated. The profile of OA (and, especially, Gold OA), will be elevated.

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