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New Communication Channels for Biology
The workshop will focus on the range of emerging approaches within e-science, community engagement in dialogue knowledge input/review or assessment, science blogs, and authenticated wiki-like research discussions and analysis, as well as the potential to formalize such community level contributions. These new approaches to communication are becoming important for biology as biological scientists attempt to address the inherent complexity of life, manage both high information content and high throughput data streams, and employ the opportunities emerging from advances in e-communication/networking and information technology. In part, this meeting has been stimulated by the success of the PSI KB Annotation Workshop, and by the general need within research both in metagenomics and structural genomics to understand the changing means of scientific communication and how we can best reach out to the community and have our work be enhanced in timely impact. The general case of getting input to genomic data from the entire community, third party annotation and not from only the original provider, is another driver for the need to extend communication beyond traditional publications, but the transformations in scientific dialogue / communication are much broader than just that within the genome community.

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Moshe Pritsker, myself, and many other great speakers will be giving 35 min talks on various subjects. The agenda can be viewed here and more details here

The workshop is open to the public (and free!) although they request that you register beforehand.

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California Institute for Telecommunications and Information Technology
Atkinson Hall (First Floor), Auditorium
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093-0446

June 26 – 27, 2008

The organisers are the Perimeter Institute for Theoretical Physics, not very “biosciences” but no doubt highly relevant to “publishing in the new millennium”. See more at conference website link above.

I want to send it to a new journal, that requests I suggest four potential reviewers.

Should these people be members of the “advisory board” or “editorial board”, of whom a certain number could be relevant, or could it be anyone? Or should the suggestion comprise a mix of both?

This paper has been painfully making the rounds for slightly over a year now, so I would like it to go to reviewers who are likely to actually do their review quickly as opposed to celebrities, who may not have the time or may pass it off to well-meaning but overly zealous grad students and postdocs.

the peer-review process is free, but only in a most superficial way. Reviewers get compensation from evaluating manuscripts for high-profile journals, provided that an initial screening of manuscripts takes place and truly identifies the contributions that will be of interest to the reviewers. The golden rule that there is no such thing as a free lunch also applies to our trade.

The conference aims to broaden researchers’ understanding and knowledge of the rapid changes in the scientific communication and publishing environment and its direct impact on the research community. The main sessions are centred on two themes – open access and metrics for assessing research.

There will also be a series of workshops on:
Open access and evaluating research
Writing a Science Paper, Ethics & Plagiarism
Web of Science, Journal Citation Reports, Scopus and the Faculty of 1000
Entrez databases – hands-on training
Peer review: what peer reviewers need to know
Nature Precedings and HeRA (Helsebibliotekets Research Archive)

Further details of the programme, speakers and registration can be found here

At Harvard, a Proposal to Publish Free on Web

The title is misleading, as it seems that what is at stake is not publishing, but archiving/self-archiving. (I assume that Harvard faculty are not interested in abandoning the peer-review model of publishing in favor of self-publishing on the Internet.) As described in the Times article, the proposal is ambiguous:

“Harvard would deposit finished papers in an open-access repository run by the library that would instantly make them available on the Internet”

A couple of questions immediately occur to me: Are “finished papers” equivalent to published papers? If they are published papers, are they the formatted journal version, or the post-peer-reviewed, but unformatted version? Or are “finished papers” those that are ready for submission to a journal (e.g. pre-prints)? If the proposal addresses published papers, does “instantly” mean immediately after publication, or after an embargo period? Will the proposal establish a repository like the University of Southampton’s Eprints Soton or function as an alternative to PubMed Central ?

Journal policies regarding when and how one can distribute manuscripts vary wildly (at least for journals in the biomedical sciences). Some journals forbid the author from distributing any version of the manuscript, either pre- or post-print. Other journals allow the author to distribute both pre-and post-print versions. Yet the majority of biomedical journals, including Nature, have a policy that falls somewhere in the middle. (The SHERPA/RoMEO project is a great resource and provides an overview of and links to individual publishers’ and journals’ policies.) How will the Harvard proposal fit with journal policies?

Allan Adler, a VP at the Association of American Publishers, suggests that the Harvard proposal is not antagonistic to traditional publishers. According to Adler, publishers reject “mandates”, but not giving authors a choice regarding archiving/self-archiving. (I assume this is because the author is given the choice of violating a journal’s policies or not, which may then have negative consequences for the author.) Publishers who don’t have policies forbidding archiving or self-archiving might still object to the idea that Harvard’s faculty will retain copyright and distribution/licensing rights for articles. An op-ed in the Harvard Crimson by Robert Darnton explains:

By mandating copyright retention and by placing those rights in the hands of the institution running the repository, the motion will create the conditions for a high deposit rate… The Harvard system would have all faculty members grant a non-exclusive permission to the President and Fellows of Harvard to distribute their articles… Anyone who wanted to retain exclusive rights to her- or himself could do so by obtaining a waiver. Of course, those who cooperate with the system will also retain full rights to the publication of their work. By sharing those rights with Harvard, they sacrifice nothing; and they will have the collective weight of Harvard behind them if they resist a journal’s demand for exclusive rights. We have designed a legal memorandum called an author’s addendum to reinforce them in negotiations with commercial publishers.

Since 2006, SPARC has provided just such an author addendum for negotiating with commercial publishers, yet my informal poll of authors and publishers suggests that authors rarely negotiate copyright with journals. This may change with the Harvard proposal. Darnton suggests that the Harvard proposal will give Harvard authors a stronger negotiating position with journals. Authors from other institutions may also benefit in their negotiations. Finally, the proposal seems likely to increase awareness that one can try to negotiate legal rights like copyright when publishing.

As Darnton notes, the Harvard proposal does include an “opt-out” policy, yet is unclear if this will allow authors to opt-out from archiving individual papers or on a global basis. I suspect that the details of policy will have have a huge impact on the number of manuscripts which are self-archived.

Universities have long been interested in retaining some of the fruits of their researchers’ work, whether it has been via institutional repositories, databases, or eprint servers. In addition to making the results of research openly available, and thus benefiting the community as a whole, this proposal seems in part to be an attempt by Harvard to also retain copyright and distribution/licensing rights for their researchers’ work. I’m curious to see how Harvard will license the manuscripts in their repository and what rights they will grant to users of the repository (re-use, re-distribution, read-only?). It will also be interesting to see how publishers respond, given Harvard’s clout in the research community.

Update: More information/commentary in articles/posts from Inside Higher Ed , The Boston Globe, The Chronicle of Higher Education blog, and Slashdot.

Update: Harvard has issued a press release about the initiative. It states that authors will retain copyright and not the university. Authors will instead provide the university with “a nonexclusive, irrevocable, paid-up, worldwide license to exercise any and all rights under copyright”. (Quoted by Chris Armbruster) Based on Robert Darnton’s op-ed in The Crimson, I (mistakenly) assumed that the university would hold the copyright rather than the authors. I have modified some of the statements above to reflect this fact.

Another update: The Scientist reports that the proposal will require authors to post manuscripts as soon as they have been accepted for publication. This implies that the repository is for post-peer-reviewed, but unformatted versions of manuscripts.

Update: Harold Varmus, who was the keynote speaker at the forum, has spoken about the Harvard proposal to Bloomberg.com. Varmus notes the distinction between author self-archiving and peer-reviewed, open access publishing.

Abstract: With an exponentially growing number of articles being published every year, scientists can use some help in determining which journal is most appropriate for publishing their results, and which other scientists can be called upon to review their work.

Jane (Journal/Author Name Estimator) is a freely available web-based application that, on the basis of a sample text (e.g., the title and abstract of a manuscript), can suggest journals and experts who have published similar articles.

Source and comment from Prof Suber

Mounir Errami and Harold Garner of the U of Texas Southwestern Medical Center report how they searched and analyzed more than 62,000 abstracts indexed in Medline and found that 1.35 percent of them were duplicates with the same authors (the authors give caveats for this analysis so please read the commentary). They say that with the rapid growth in the number of journals and papers, publishers and database curators have not kept up with the detection of duplicate papers. They call on journals to use new software tools to better identify duplicate papers and on the community to expose people who are clearly not following established publishing policies.

What do you think? Have you seen more duplicate papers published in your field?

Do you think this is a real problem?

Are there legitimate reasons to publish similar versions of the same paper in different journals?

What else can be done to prevent this problem from growing?

Before diving into the conversation, please have a close read of the commentary. The authors there give plenty of caveats for their Medline analysis, which I didn’t summarize fully in this post.

Everyone is calling for open access, and now they can have it, if they will support it financially.

Approximately 200 graduate student, post docs, professors and other interested parties gathered at the TMEC Amphitheater for “Publishing in the New Millennium: A forum on scientific publishing in the biosciences,” held on November 9, 2007. This forum, organized by five Harvard graduate students and funded by the Biophysics Program and HILS, brought together representatives from Cell, Nature, PLoS, Harvard, the Journal of Visualized Science (JoVE), and Science Commons, to discuss the current impact of publishing on biological research and its future.

The event was kicked off by two of the conference organizers, Kishore Kuchibhotla and Zeba Wunderlich, both fifth year graduate students in the Biophysics Program. Harvard Provost Steven Hyman then provided welcoming remarks in which he spoke about Harvard’s recent initiative, the Provost’s Committee on Scholarly Publishing. He laid out the challenges facing the scientific community today: a great deal of information is available; libraries have limited budgets, and researchers must be able to find the information they need quickly and efficiently. He then introduced the keynote speaker of the Forum, Dr. Harold Varmus, Nobel Laureate, former Directory of the NIH, PLoS co-founder, and President of Memorial Sloan-Kettering Cancer Center.

Using his perspectives as a scientist, publisher, and public policy-maker, Dr. Harold Varmus took the audience through a brief review of the history of scientific publishing and then laid out his vision of an optimal digital public library of science – an openly accessible, complete, searchable, sustainable archive of scientific knowledge. He then explained several different strategies aimed at creating this library, including PubMed Central, the NIH-sponsored repository for nationally funded research, and the PLoS family of journals and initiatives. Dr. Varmus described in great detail the reasons he believes the current subscription-based journal publishing system must change; he is a leader in the Open Access movement, which aims to make all published articles freely available over the Internet.

Two interactive panel discussions followed Dr. Varmus’ address. The first, “The State of Publishing,” featured Dr. Emilie Marcus, Editor-in-Chief of Cell Press; Robert Kiley, Head of Systems Strategy at the Wellcome Trust; Dr. Zak Kohane, Directory of Countway Library; and Dr. Stuart Shieber, Harvard Professor and Chair of the Provost’s Committee on Scholarly Publishing. The discussion largely centered on the open access initiative – should the content of journals be available by subscription or free to all? Dr. Marcus argued that the value added by a professional editing staff justifies the subscription costs, while Mr. Kiley asserted that open access journals make science more productive and are economically viable.

The second panel discussion, “Publishing 2.0,” featured representatives from four new publishing projects: Dr. Moshe Pritsker, CEO of JoVE, Hilary Spencer, Product Manager of Nature Precedings, a pre-print archive for biology, John Wilbanks, Executive Director of Science Commons, and Bora Zivkovic Community Manager for PLoS ONE. Each introduced their respective initiatives, as well as the impetus for starting each. Mr. Wilbanks made an interesting case for open access journals – open access allows information to be easily searched, synthesized and re-used. Ms. Spencer and Mr. Zivkovic discussed the benefits and challenges of getting the biology community to interact about research in online media, and Dr. Pritsker explained how online video protocols could accelerate the pace of research.

The conversation about open access, increased online scientific discussion and other issues continued into the evening at a reception sponsored by HILS and Nature Network, Nature’s science social networking site. The conference’s website, www.harvardpublishingforum.com will be updated shortly with pictures, audio, PowerPoint slides and other resources. The remaining conference organizers were Praveen Arany, Dental Medicine and HST; Kelly Anne Dakin, Neurobiology; and Anna Kushnir, Virology.

From the beginning of science up to the 70’s, scientists would publish their work without any major concern about the measuring of “impact” of the publication media. As the number of scientists increases competition drives the editorial broads of the ever increasing journals to accept the most influential research, the one that is or will become popular. On the other side of the coin, scientists will seek publications of high impact to out-compete their peers when applying for a job, tenure or funding. Academic appointment committees are selecting candidates from the bulk of the applicants based merely on publication records, which means the impact factors of the publications acquired. And there lies a mistake. The peer-reviewing process is the foundation of evaluation of scientific work. This is a consensus. But why doesn’t it form the absolute criterion of it? Why is the journal impact factor of the published work a main indicator of scientific excellence and not directly the reviews of scientific experts?
Charles G. Jennings a former executive director of Harvard Stem Cell Institute says on Nature (2006), doi:10.1038/nature05032: “It is common to bemoan the over-reliance on quantitative markers such as impact factors for assessing scientists’ abilities (and indeed there is much to bemoan), but until committee members have time to read every paper on every applicant’s CV, they will have to rely at least in part on proxy indicators.” In my opinion there can be effective proxy indicators, but journal impact factors are simply not ideal for that. Journal impact factors are related to the quality and novelty of the published work but they are not the most accurate measures for it. If the current trend continues the immense competition will lead to unfairness and arbitrariness in the scientific evaluation. What we need is a basis we can rely on; a unified reviewing system or an agency that will thoroughly, rigorously and objectively evaluate any given work to be published, using again specialized scientists as reviewers. Having an evaluation score from such an agency, scientists can include this score to their publication record. In addition, scientists can use the evaluation the reviewing agency provides and ask the journals to publish the evaluated work. If one journal is not interested, another one might be. Scientists will not loose their time to get into a new round of reevaluation and other scientists will not loose their time reevaluating a given work.

Can such a system work? I believe it can. NIH uses an evaluation score as a system to allocate funding. The cost of such a system is considerable; nevertheless it can be compensated by the cost of the editorial process. Martin Blume, an Editor-in-Chief of the American Physical Society at that time, wrote in the first of Nature Journals’ website (http://www.nature.com/nature/debates/e-
access/Articles/blume.html): “Peer review is expensive, and although reviewing by scientists is voluntary, we need to pay our editorial staff. It is more time consuming and hence more costly to review the 10,000 rejected articles than it is to review those that are accepted. Consideration is being given to other forms of peer review, but no savings are as yet obvious if quality is to be maintained.” As a proposed alternative, the cost of manuscript evaluation can be compensated by an equivalent reduction in the publication costs. If this is not enough, the scientists under evaluation or the government can compensate for the additional costs. The seeds for such an idea already exist. Cell press and PLoS journals now provide a small alternative: a scientist can get the reviews of a manuscript submitted to one their journals and forward them to the editors of another. In addition the Neuroscience Publishing Consortium introduced this past June in PubMed Plus Leadership Conference held in St. Louis will examine the feasibility of sharing reviews of submitted manuscripts within a group of journals that publish neuroscience papers. Nevertheless, such options would better serve the scientific community if they are not a privilege of a certain editorial press or consortium. Towards the same idea are the literature awareness tools “Faculty of 1000” (http://www.facultyof1000.com/) and “Science Watch & Hot papers” (http://scientific.thomson.com/products
/sw-hp/), which evaluate interesting and influential literature. Expanding this idea means to evaluate all the papers published. But it is much preferable if evaluation precedes publication.
As scientists, we have to reach to a point at which publication in high impact journals would still be preferable but not a “ticket” to scientific excellence. Let excellence in science be judged directly by the scientific experts without journals being the unnecessary and unwilling mediators in this process.

Review journals often commission articles on essentially the same topics year after year, simply updating the previous version.

Instead, why not have a wiki review that a selected group of experts in the field can update as needed. That way, the review is always up-to-date, and hyperlinking between related topics would be far easier than is currently the case.

I know some publishers are now experimenting with this. Could it work? Are there any show-stoppers (apart from the initial hurdle of convincing authors to take this approach).

We’ve been encouraging people to submit papers, posters, and presentations describing NoN-results to Nature Precedings. A recent blog post suggests that at least one researcher found a manuscript on Precedings to be helpful in this regard. However, as Goetz notes, sharing NoN-results “makes many scientists deeply uncomfortable, because it calls for them to reveal their ‘failures’”.

So are scientists likely to share these types of results? We hope that sharing them on a site like Precedings allows authors to turn non-publishable research into at least “citable” research, but is this enough motivation?