Journal news 28 January to 3 February

Your journal-related news for the week.

F1000Research

Faculty of 1000 (F1000), the well established post-publication peer review service, has announced a new service that will publish original research papers. According to the initial announcement, this will differ from traditional journals in that all papers will be published immediately, before peer review (as long as they pass a ‘sanity check’), and peer review will happen openly after that. Publication of datasets will also be encouraged. Fees are still under discussion. Retraction Watch discussed the proposal and received many comments, including from two members of F1000 staff, Rebecca Lawrence and Sarah Greene, who thanked commenters for helping them to develop the idea further. This looks like an experiment worth watching – if it takes off it could herald a big change in publication of peer-reviewed papers. (Via @F1000Research.)

Arsenic Life (or not) in arXiv

Microbiologist Rosie Redfield has been trying to replicate the experiments presented by Felisa Wolfe-Simon et al. in late 2010 about a bacterium (called GFAJ-1) that could apparently grow using arsenic instead of phosphorus. Redfield has now submitted a manuscript to Science and at the same time uploaded it to the preprint server arXiv. She has found that there is no arsenate in the DNA of arsenate-grown GFAJ-1 cells. She is inviting comments on the manuscript on her blog, as an experiment in open peer review. (Via @RosieRedfield.)

More on the boycott of Elsevier

See my post earlier this week for the background on this. The list of researchers who have pledged not to support Elsevier journals has now reached over 3800. An article by Josh Fischman in The Chronicle of Higher Education on Tuesday included responses from Elsevier (Alicia Wise and Tom Reller). Kent Anderson of the Scholarly Kitchen criticised the boycott, saying that other publishers have prices as high as Elsevier, bundling of journal subscriptions is useful rather than being wrong, and other publishers also support the Research Works Act. Elsevier also put their case in this blog post by Chrysanne Lowe. Meanwhile, Michael Eisen, one of the founders of the Public Library of Science, gives some historical context in his blog. (Various sources.)

Launch of Cell Reports

In an announcement that got rather lost in the furore about the boycott, Cell Press (part of Elsevier) launched a new open access journal, Cell Reports. According to its information for authors (pdf), it publishes ‘thought-provoking, cutting-edge research, with a focus on a shorter single-point story… in addition to a longer article format’ and also ‘significant technical advances’ and ‘major informational data sets’. Authors can choose between two Creative Commons licences for their papers: Attribution (CC BY) and Attribution-Noncommercial-No Derivative Works (CC BY-NC). Are there now any major scientific publishers left that don’t have any open access journals? Possibly not. (Via @WiseAlic.)

Gyrations in Life

A controversial paper was published this week in the little known open access journal Life, apparently after peer review, that claims to explain just about everything using a simple geometric figure, the gyre. It has been taken to pieces by John Timmer in Ars Technica and PZ Myers in Pharyngula. Following these and other criticisms, the editor has now responded, saying that peer review was thorough, and Retraction Watch has discussed the response. (Via @tdechant and @leonidkruglyak.)

Mind your Editorial Board

Evolutionary biologist Jonathan Eisen pointed out something not quite right about the biography of an editorial board member on a journal called Molecular Biology, published by OMICS Publishing Group. The expert in ‘oximological microbiology, non-linear submorphological endosaccharomorphosis, applied endoplutomomics’ turned out to be a fictional creation of the German satirical magazine Titanic. How the journal administrators could take him seriously when his biography says that he ‘has successfully completed his Administrative responsibilities as vice president of the universe for scientific publication ethics and spamology’, we may never know. His name is still on the editorial board page as I write. It may be relevant that OMICS has been described as a ‘predatory open access publisher‘. (Via @phylogenomics.)

Journal news for 20-27 January

A brief summary of recent news related to journals and scientific publishing.

Datasets International

The open access publisher Hindawi has launced Datasets International, which “aims at helping researchers in all academic disciplines archive, document, and distribute the datasets produced in their research to the entire academic community.” For a processing charge of $300 authors can upload an apparently unlimited amount of data under a Creative Commons CC0 licence (and associated dataset papers under an Attribution licence), according to comments on Scott Edmunds’ Gigablog. The new journals currently associated with this initiative are Dataset Papers in: Cell Biology, Optics, Atmospheric Sciences and Materials Science, though no doubt more will follow. (Heard via @ScottEdmunds.)

Peerage of Science

A company run by three Finnish scientists this week has a new take on improving peer review. Peerage of Science is a community of scientists (‘Peers’), formed initially by invitation, who review each other’s papers anonymously before submission to journals. Reviews are themselves subjected to review, which means that reviewers receive recognition and ratings for their work. The reviews can even be published in a special journal, Proceedings of the Peerage of Science. Journals can offer to publish manuscripts at any point, for a fee – this is how the company aims to make a profit. (Heard via chemistryworldblog, via @adametkin.)

Peer review by curated social media

Science writer Carl Zimmer (@carlzimmer) reported last week in the New York Times on a recent (open access) study in Proc Natl Acad Sci USA about the generation of multicellular yeast by artificial selection in the lab. He has now posted a follow-up article in his Discovery blog, in which he presents the conversation that followed on Twitter about this paper (using Storify) and invites the author to respond, which the author does. The comments on the latter post continue the conversation, and the author continues to respond. It’s an interesting example of the author of a controversial paper engaging constructively in post-publication peer review. (Heard via @DavidDobbs.)

Research Objects

Tom Scott (@derivadow, who works for Nature Publishing Group) has published a detailed blog post outlining a proposal for a new kind of scientific publication: the Research Object. This would be a collection of material, linked by a Uniform Resource Identifier (URI), including an article, raw data, protocols, links to news about the research published elsewhere, links to the authors and their institutions, and more. He credits the Force11 (‘Future of Research Communications and e-Scholarship’) community for the idea, which is developed in greater detail here (pdf). These elements may or may not be open access, although the sophisticated searches Scott envisages will be difficult if they are not. (Heard via @SpringerPlus.)

Analysis of F1000 Journal Rankings

Phil Davis of The Scholarly Kitchen has done an analysis of the journal ranking system announced by Faculty of 1000 (F1000) in October. The analysis includes nearly 800 journals that were given a provisional F1000 Journal Factor (called FFj by F1000) for 2010. Plotting the FFj of each journal against the number of articles from it that were evaluated by F1000 shows that the two numbers are closely related; in fact, the number of articles evaluated explains over 91% of the variation in FFj. Journals from which only a few articles were evaluated suffer not only from this bias, but also from a bias against interdisciplinary and physical science journals that publish little biology. It seems to me that these biases could easily be addressed by taking into account (a) the number of articles evaluated from each journal and (b) the proportion of biology articles published in it when calculating the FFj. F1000 would be wise to study this useful analysis when reviewing their ranking system, as they plan to do regularly, according to the original announcement. (Heard via @ScholarlyKitchn.)