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January 25, 2007

"Publish" Videos of Experimental Protocols

The Journal of Visualized Experiments (2006-) is truly living up to the old adage that a picture is worth a thousand words. This online, open access journal is

publishing visualized (video-based) biological research studies. This publication aims to solve some of the most difficult problems in the contemporary life science research:
  • low transparency and reproducibility of biological experiments
  • time-consuming learning of experimental techniques

Each video-article will include step-by-step instructions on an experiment, a demonstration of equipment and reagents, and a short discussion by experts describing possible technical problems and modifications. Every scientist planning on a biological experiment will be able to access the database, find videos relevant to their work, and use them as protocols. High effectiveness of visualized instructions, as compared to currently used written protocols, will decrease failure rates for biological experiments, and, thus, facilitate significant savings in time and cost. It will also increase reproducibility of published experiments, one of the main problems in the current life science research.

There is no charge to authors to submit or have their protocols published. Each submission will be reviewed by members of an editorial board, but, at this time, will not be rigorously peer-reviewed (that will come later). The time lapse from the date of submission to the date of publication should be no longer than 7-14 days. At the present time, there are 17 videos available in JoVE.

Of course, researchers have been putting their videos up on their personal websites and in sites such as YouTube. See for yourself: search for microarray in YouTube or in GoogleVideo.

Posted by Katie Newman at 9:24 AM

January 24, 2007

Nature's Expose on Publisher's Tactics to Rout Open Access

Jim Giles, writing in a column in Nature (Vol 445, January 25, 2007, pg 347) reveals that a major group of sci-tech publishers (reportedly Elsevier, Wiley and the American Chemical Society) has hired a pit-bull PR firm to advise them on how to best combat the Open Access movement, particularly PubMed Central. Reportedly the publishers are spending up to a half-million dollars for the advice of Dezenhall Resources, a group that has had as clients in the past such illustrious folks as Jeffrey Skilling, the former Enron chief. According to the Nature article, Denzenhall is advising the publishers to give out the message that

“Public access equals government censorship”. He hinted that the publishers should attempt to equate traditional publishing models with peer review, and “paint a picture of what the world would look like without peer-reviewed articles”.
Read the full news item in Nature.

Commenting on the Nature Report, Peter Suber says in Open Access News:

  1. I've read this several times and still find it incredible. Why would the AAP pay $300-500k for advice on how to misrepresent the issue? The next time you see an AAP press release on OA, ask yourself this question.
  2. Does the AAP even need the advice? It has been falsely identifying government archiving with government censorship, and falsely identifying threats to publisher revenue with threats to peer review, at least since the debate over the NIH policy in 2004. For a more recent example, see its May 2006 public statement opposing FRPAA. (Also see my rebuttal.)
  3. I hope that publisher-members of the AAP will disavow these tactics and that journalists and policy-makers will understand the difference between intellectual debate and media massage.
  4. Kudos to Nature for uncovering and reporting this story.

Posted by Katie Newman at 1:41 PM

January 23, 2007

U.S. Court Upholds Copyright Law on "Orphan Works"

From Yahoo News 1/22/06:

A U.S. appeals court has rejected a bid by Internet activists to roll back federal laws that extended copyright protection over orphan works, or books and other media that are no longer in print.
The U.S. Court of Appeals for the Ninth Circuit affirmed a lower court decision to dismiss Kahle v. Gonzales, which argued that legal changes made in the 1990s had vastly extended copyright protections at the expense of free speech rights.
Orphaned works are a hot-button issue for the publishing industry, which has resisted efforts by Web companies Google Inc., Yahoo Inc. (Nasdaq:YHOO - news) and the Internet Archive -- working with major academic libraries -- to scan orphaned and out-of-copyright works to make them available for free on the Web.
Prior to 1978, the number of orphaned copyright works was limited by requirements that intellectual property holders renew their rights within a certain period of years. Otherwise ownership of these works would pass into the public domain.
Amendments to U.S. copyright law in the Sony Bono Copyright Term Extension Act of 1992 made renewal registration optional, rather than mandatory, in order to preserve copyrights. A 1998 amendment further extended the renewal term to 67 years.
Critics of the changes had mocked the law as an effort to prolong Walt Disney Co.'s copyright hold over Mickey Mouse.
The U.S. Supreme Court upheld the constitutionality of these changes to copyright law in a 2003 decision, Eldred v. Ashcroft, which the three-judge Ninth Circuit panel cited.

Posted by P. Kaufman at 10:51 AM

January 19, 2007

Editor of Open Access Scholarly Journal to Speak

Henry Hagedorn, editor of the open access journal, Journal of Insect Science, will present a talk entitled "Open Access: The revolution in academic publishing".

Monday, January 29th, 4:00 PM, Room B102, Chemical & Life Sciences Building, 601 South Goodwin Avenue, Urbana, IL.

In 2000 Hagedorn resigned as editor of the Archives of Insect Biochemistry & Physiology in order to launch the open access Journal of Insect Science. He recently retired from the University of Arizona, but continues to serve as editor of the Journal which is now supported in part by his new home base at the University of Wisconsin-Madison.

In an open letter published in the Journal of Insect Science, Hagedorn explains his motivation in starting the new journal in an open access mode.

Please note that the University of Illinois's Library Online Research Resources (ORR) lists three instances of the Journal of Insect Science: BioOne, from the Directory of Open Access Journals [DOAJ], and from PubMed Central. You may also access it by going directly to the Journal's home page,

The University also still has access to the journal from which Hagedorn resigned in protest, Archives of insect biochemistry and physiology, which is published by Wiley. It appears that both journals are publishing about the same number of articles / year.

Several University of Illinois entomology professors are associated with the Journal of Insect Science: May Berenbaum is on the Advisory Board while Hugh Robertson and Gene Robinson are serving on the Editorial Board.

Posted by Katie Newman at 12:40 PM

The Promise of Value-Based Journal Prices and Negotiation

The University of California libraries have tested the case that a journal's institutional price can and should be related to its value to the academic enterprise.

From the press release:
The report describes a value-based approach that borrows from analysis done by Professors Ted Bergstrom (UC Santa Barbara) and R. Preston McAfee (Caltech) on journal cost-effectiveness ( The UC approach also includes suggestions for annual price increases that are tied to production costs; credits for institutionally-based contributions to the journal, such as editorial labor; and credits for business transaction efficiencies from consortial purchases.
Through the report the libraries ask how an explicit method can be established, validated, and communicated for aligning the purchase or license costs of scholarly journals with the value they contribute to the academy and the costs to create and deliver them. In addition to describing the work done to date, the report provides examples of potential cost savings and declares UC’s intention to pursue value-based prices in their negotiations with journal publishers. In addition, the report invites the academic community to work collectively to refine and improve these and other value-based approaches.

Read the report

Posted by P. Kaufman at 8:28 AM

January 11, 2007

UK Book Trade

Richard Charkin of Macmillan comments on the British book trade, exports, and piracy:

In spite of the importance of the UK book trade, British publishers would not exist without their exports. And we do it really rather well in spite of having to contend with a very strong currency (vs our major competitor, the US dollar), threats from territorial erosion, piracy, dodgy dealers and restrictive practices in some countries.

The latest statistics show export growth of 14% in units and 10% by value with fastest growth in children's books and educational programs. Academic unit sales actually fell as a result of people switching to digital delivery but revenues held up. This year, subject to the usual provisos about political events and natural disasters should see further growth in Asia, Eastern Europe and the emerging markets in general.

The biggest issue (and cost) continues to be piracy and the Publishers Association (whose website will shortly reflect more obviously its merits!) leads the world's publishing industries in taking action where necessary and supporting legal and consitutional routes to the protection of authors' copyrights. It is expensive but vital. It is another example of a cost which commentators from within and without the industry tend to forget when calculating profits.

Chark Blog 1/11/07

Posted by P. Kaufman at 7:30 AM

January 9, 2007

Open Access: the View from a Scholarly Society's Journal Editor

Starting with the January 2007 issue of the journal Plant Physiology, all articles published by members of the scholarly society that publishes the journal, the American Society of Plant Biologists (ASPB), are open access at no additional cost to the member. Of the 43 articles in the January issue, 25 are freely available to all scholars with no lag period. Some of these may have been authored by non-members who paid $1,000* in order to provide open access to their article, but I suspect not many. [*$1000 if the corresponding author's institution does not subscribe to Plant Physiology, if it does subscribe it is $500.]

The editor of the journal, Donald Ort of the University of Illinois, wrote an editorial for the ASPB News, "Real-Time Plant Physiology: My View of What’s in It for Authors, the Journal, and ASPB". Following several avenues of analysis, he concludes that open access articles are more highly read than non-open access articles, which in turn he feels will enhance the stature of the journal. He also presents an interesting table listing the top 10 plant research journals and their open access option. Most have a provision for open access if the author pays; Plant Physiology will be the only one that offers free open access publishing to it's member authors. Of course, another perk with offering free open access publishing to members might be a jump in the membership count.

Interestingly, the editorial that Ort wrote for the ASPB Newsletter was only available online to members until he deposited it in the University of Illinois' digital repository, IDEALS, where it is now freely available to all. I would recommend it to the editors of other scholarly journals.

It can also be noted that the ASPB has for several years provided free online access to The Arabidopsis Book through a collaboration with BioOne.

Posted by Katie Newman at 3:14 PM