Nautilus

Starting this month (March 2008), Nature Methods strongly recommends deposition of proteomics data to public repositories before manuscript submission. From the Editorial in the March issue of the journal (Nat. Meth. 5, 209; 2008):
"Several proteomics data repositories are now available that differ in terms of their goals, structure and the formats they accept. They include PRIDE, PeptideAtlas, Global Proteome Machine Database (gpmDB) and the file distribution system Tranche. The newest addition, Human Proteinpedia, is a community-based annotation tool that hosts experimental data (Nat. Biotechnol. 26, 164; 2008).
Importantly, the major database administrators have shown their willingness to work with users and with each other to facilitate data deposition. At this stage, the process can still be labor-intensive, but a repository like PRIDE provides extensive technical assistance. Under the umbrella of the ProteomExchange consortium, the major repositories are also devising ways to share their data in a collaborative fashion, capitalizing on their complementarities to minimize submission hassle while maximizing benefits.
We support these efforts and consider it premature to recommend a particular repository. Rather we will rely on community experience to determine which database or combination of databases emerges as the most useful. However, there are specific features that editors favor. In particular, we like the possibility currently offered by PRIDE and Human Proteinpedia to provide peer reviewers with access to datasets associated with a manuscript before public release, in an anonymous fashion, and to coordinate public release of the data with publication. "

Nature Methods welcomes comments on this Editorial, and the recommendations it makes, at the journal's blog Methagora.
The Nature journals' policies on data and materials availability, including links to editorials on these policies, can be found at the author and reviewers' website.

Posted by Maxine Clarke on March 10, 2008
Categories: Data availability, Disciplines, Partners, Policies | Permalink | Comments (0)

As part of our ongoing discussion about the accountability of authors and co-authors (comments are still very welcome), I decided to take a snapshot look at the popularity of Author Contributions statements in Nature. We strongly encourage authors to make these statments, specifying the ways in which the authors contributed to the paper, but we do not make it mandatory. Should that change? Part of the answer to that question lies in how useful authors find the idea. So it is of interest to note that in the past three or four issues of Nature, about half of the Articles and Letters (primary research) carried contributions statements. Here are some examples, all from the same issue of Nature (1 November 2007):

J.L., J.R.S. and J.W.L. conceived the Brainbow strategies. J.R.S. and J.W.L. supervised the project. J.L. built initial constructs and validated them in vitro and in vivo. T.A.W. performed all cerebellar axonal tracing and colour profile analysis with programs developed with J. Lu. H.K. performed all live imaging experiments. R.W.D. generated Brainbow-1.0 lines expressing cytoplasmic XFPs, and R.A.B. generated Brainbow-1.1 constructs and lines. J.L., T.A.W. and R.W.D. screened mouse lines.

S.H.C. designed and performed experiments, analysed data and wrote the paper; N.C., M.T. and J.M.G. designed and performed experiments; D.R. and M.B.G. developed analytical tools; and C.I.B. designed experiments, analysed data and wrote the paper.
(more on the post continuation page)

Continue reading "Author contributions audit" »

Posted by Maxine Clarke on November 05, 2007
Categories: Authors, Authorship, Categories, Policies | Permalink | Comments (3)

Via Seven Stones blog:
Molecular Systems Biology (published by a partnership of the European Molecular Biology Organisation and Nature Publishing Group) has changed its publishing licence for all articles accepted after 1 October 2007 (see updated instruction to authors). The new procedure allows the journal's authors to choose between two Creative Commons licences: one that allows the work to be adapted by users ("attribution-noncommerical-share": by-nc-sa), the other that does not allow the work to be modified ("attribution-noncommercial-no derivative": by-nc-nd). The first articles to be published under the new licence are appearing online at the beginning of this month. The journal's content is therefore not only freely available to all, but also authors can decide to make their research fully open for reuse and adaptation.

Thomas Lemberger, EMBO editor of Molecular Systems Biology, who runs the Seven Stones blog, notes that he initially wanted to make this announcement only after the first paper published under the new licence (accepted after 1 October) had appeared online, but in light of a recent Editorial in PLoS Biology (“When Is Open Access Not Open Access?”), reviewing in detail the subtleties of publishing licenses and the concept of “open access”, he bought forward the announcement of Molecular Systems Biology's new policy. "Unfortunately, this Editorial, at the time of its publication (16 October), included erroneous information on Molecular Systems Biology, given that we had updated our policy on 1 October.", Thomas writes. "In any case, it is somewhat ironic that MacCallum chose to stigmatize Molecular Systems Biology as an example of a journal that “promulgates” confusion about open access. As it turns out, Molecular Systems Biology is dedicated to the concept of making research freely available and to engage authors themselves in decisions that would achieve this goal with their own research. It is in this spirit of openness and respect for authors that we have recently adapted our license to publish."

Posted by Maxine Clarke on November 02, 2007
Categories: Access, Policies, Publishing | Permalink | Comments (0)

This week's Nature addresses how the responsibilities of co-authors for a scientific paper’s integrity could be made more explicit (Nature 450, 1; 2007). The text of the (free access) editorial:

The two most notorious frauds of modern science, by the stem-cell biologist Woo Suk Hwang and the physicist Jan Hendrik Schön, both brought into question the responsibilities of co-authors in the oversight of their colleagues’ work. But despite the concerns raised after these episodes, there remains a need for a clearer understanding, both within a collaboration and by readers of the eventual papers, of the various contributions made by the authors not only to the research but also to safeguarding its integrity.
One welcome development in transparency was pioneered by the medical journals. Authorship of a paper is justified when a researcher has contributed significantly to the work being described and to the writing or approval of the manuscript. But the traditional publication style is entirely opaque as to which co-author contributed what. Concern about ‘honorary authorship’ — in which an author is unacceptably included for reasons other than any scientific contribution — and about this lack of transparency has led to the increasing use of statements in papers that specify authors’ contributions. Some medical journals require them, and others, including the Nature family, strongly encourage their use and may yet make them compulsory.
Such statements delineate contributions to the work but do not underwrite its integrity. Something more is needed.
It is too glib to state that every co-author of a paper shares full responsibility for its content. A researcher who specializes in the radio-active dating of rock strata cannot necessarily be expected to vouch for a palaeontologist’s analysis of fossils within them — especially if the work has been carried out in labs on different continents.
The fact that simple trust may no longer suffice is a sad reflection on recent scientific history, but anything that supports public confidence in research has to be welcomed, provided that its burden is not too great. What follows is a proposal in that direction, on which we invite readers’ comments.
We suggest that journals should require that every manuscript has at least one author per collaborating research group who will go on record in a way that collectively vouches for the paper’s standards. Each would sign a statement with reference to Nature’s publication policies as follows:
“I have ensured that every author in my research group has seen and approved this manuscript. The data that are presented in the figures and tables were reviewed in raw form, the analysis and statistics applied are appropriate and the figures are accurate representations of the data. Any manipulations of images conform to Nature’s guidelines. All journal policies on materials and data sharing, ethical treatment of research subjects, conflicts of interest, biosecurity etc. have been adhered to. I have confidence that all of the conclusions presented are based on accurate extrapolations from the data collected for this study and that my colleagues listed as co-authors have contributed and deserve the designation ‘author’.”
Principal investigators traditionally bask in the glory of a well-received paper. We are proposing now that they willingly open themselves to sanctions that could be brought to bear should the paper turn out to have major problems.
Misconduct investigators go out of their way to spare anyone apart from the direct perpetrators, but they have indicated concerns over the degree of oversight within collaborations. If the damage to reputations were more widespread in the event of fraud, researchers would be even more fastidious about the data emanating from their labs and the due diligence they would impose. The chances of major frauds, with their disproportionate impact on the reputation of science as a whole, would be diminished.
We invite comments from readers on this editorial.
(The Nature journals' current policies can be seen at Nature's Guide to Authors and at the Author and Reviewers' website.)

Posted by Maxine Clarke on October 31, 2007
Categories: Authorship, Ethics, Policies | Permalink | Comments (23)

Juan C. Gallardo of Brookhaven National Laboratory, New York writes in this week's Correspondence (Nature 449, 572; 2007):

As chair of the American Physical Society's Committee on International Freedom of Scientists, I wish to express my alarm about the kafkaesque situation confronting the Russian biologist Oleg Mediannikov, reported in your News story 'Russian scientists see red over clampdown' (Nature 449, 122–123; 2007).
The American Physical Society is the biggest organization of physicists in the United States, with a large international membership. The society is independent of any government, and its international freedom committee is responsible for monitoring the human rights of scientists throughout the world, including the United States, and assisting those in need. In the past couple of years our efforts have been partially focused on Russia, where several scientists collaborating with foreign researchers have been intimidated and prosecuted.
As well as Mediannikov, we are actively assisting Valentin Danilov, Oscar Kaibyshev, Igor Sutyagin and Oleg Korobeinichev. We are committed to defending our colleagues at risk and we will continue to raise our voices whenever scholars encounter a prohibition on travelling, publishing or pursuing research. We call upon scientific human-rights organizations to join us to protest at restrictions, by any government, on the free exchange of ideas, be it by denying visas or barring scholars from attending conferences or taking academic positions.

Posted by Maxine Clarke on October 29, 2007
Categories: Ethics, Policies | Permalink | Comments (0)

Dr M. Nabeel Ghayur, of McMaster University Ontario, writes: I would like to add some points to Nature's News Feature "Human-subjects research: trial and error"(Nature 448, 530-532; 2007), on the important topic of clinical-trial review by regional versus central review boards. I feel that the main question is not about who conducts the review, but about it being performed thoroughly and diligently.
It is more than 40 years since the unanimous approval of the Declaration of Helsinki, yet we are still faced with many challenges in this area of research on human subjects. Episodes such as the fatal testing of gene therapy on Jesse Gelsinger in 1999 and the TeGenero fiasco in 2006 of severe side effects of a phase-I monoclonal antibody in six men, demonstrate that the need for stringent measures when it comes to clinical trials involving humans cannot be over-emphasized.
The need for stringent oversight is even more vital at a time of widespread outsourcing of trials from the West to developing countries, particularly in Africa and Asia. Many of these countries remain without concrete laws and legislation, sometimes without even functioning ethics committees in individual health-care institutions. It is imperative that trials are monitored to the best standards available worldwide.
We hear of cases such as that of Ru Huang of Johns Hopkins, accused of being engaged in unethical trials involving testing of drugs in India without formal consent (see Nature 412, 466; 2001). More recently, the pharmaceutical giant Pfizer was sued by Government of Nigeria for $9 billion for allegedly carrying out trials in children without parental or official approval. These examples surely reflect the importance of strict ethics review of clinical trial proposals irrespective of the authority responsible for performing it.
However, as outlined in your News Feature, it does not make sense to have unnecessarily time-consuming bureaucracy, as delays can be equivalent to introduction of beneficial therapies. Informed consent forms should be kept as simple, short and meaningful as possible. Increasing the length of a form so as not to miss any information can make it harder for the patient to grasp, particularly a potential participant from a country where people are less well-educated and who will struggle to read and understand scientific and ethical jargon. There is a dire need to make the process of ethics review extensive, yet concise and effective, both for investigators and patients.

Posted by Maxine Clarke on September 07, 2007
Categories: Ethics, Policies | Permalink | Comments (0)

This week's Nature (449, 8; 2007) features a News story about a plaigiarism scandal involving more than a dozen theoretical physicists at four universities in Turkey. Almost 70 papers by 15 authors have been removed from the popular preprint server arXiv, where many physicists post their work, by the server's moderators. They allege that the papers plagiarize the works of others or contain inappropriate levels of overlap with earlier articles. This is probably the largest single incident of its sort ever seen on the server, according to physicist Paul Ginsparg of Cornell University in Ithaca, New York, and founder of arXiv. "What these guys did was way over the line," he says. See here for the full version of the story (site licence or subscription required).
According to the Nature News story, Ginsparg says that it's not uncommon for scientists with a poor command of English to plagiarize introductions or background paragraphs from earlier work, often adding an appropriate citation. He thinks that although such practices are ethically questionable, it is inappropriate to be overly draconian. A recent analysis turned up numerous examples of plagiarism on the arXiv server (see Nature 444, 524–525; 2006).
The Nature journals' policies on plagiarism can be found on our free-access author and referees' website. The policy page contains links to various (free access) Editorials written in the Nature journals on the topic which, taken together, we hope provide a useful guide for authors.

Posted by Maxine Clarke on September 06, 2007
Categories: Ethics, Policies | Permalink | Comments (0)

Dr Robin Rose writes: Recently, the scientific community was presented with a paper containing the names of no fewer than 21 authors in Nature. The race for recognition in certain areas of study appears to have many scientists battling for authorships on as many papers as will accept them. Any number of journals seem to find this acceptable. Thinking back through my long career in science I cannot recall ever seeing an article or "letter," in this case, with so many authors: 1/21 would suggest an average 4.76% contribution, with some contributing more and some less (!). While collaboration is often praiseworthy, I found myself asking more than a few questions:

(1) How does a paper with so many authors actually get written, accepted for review, and then revised? What does author mean in such a case?
(2) How does such a paper 'count' in terms of value in academic promotion and tenure? Did 20+ people have the same idea at the same time?
(3) What level of credit does each author take when such a paper is part of a resumé or when citation statistics are considered?
(4) After the first three to five authors, how is the contribution of the rest gauged?
(5) Does the author order have some significance when there are 20+?
(6) Is research more credible with 20+ authors? Should journals allow for 30+ authors?
(7) Are 20+ authors meant as some sort of statement, whether scientific, political or scientifically political?
(8) Were authors added as a way to strengthen the conclusions, but also implying that a few did most of the work, more did a bit of the work, and the rest did very little?
(9) Are the authors part of a collective group? Why not use the group name as the author?
(10) Are we witnessing "author inflation?"

Such questions are important for scientists, journal editors, and their supervisors to sort out. Maybe papers with high author counts are intended to display some harmony that exists in the international academic and research community. Maybe we need to stop using the vague "et al" and go to "first author name plus 20" (the specific number of co-authors) so as to better clarify multiple contributions. There may be more issues, questions, and possibilities but I'll leave those to countless other authors.

Dr Robin Rose, Research Cooperative College of Forestry, Oregon State University.

Maxine Clarke, on behalf of the Nature journals, adds: we welcome responses (in the comments section below) to Dr Rose's points. Our authorship policies do not specify a particular order or maximum number of authors, but we do strongly encourage authors to include a statement in the end notes to specify the actual contribution of each coauthor to the completed work.

Posted by Maxine Clarke on August 21, 2007
Categories: Authors, Authorship, Policies | Permalink | Comments (8)

This month's Editorial in Nature Cell Biology (freely available at Nature Cell Biology 9, 721; 2007) explains to biologists the role of the preprint server, that mode of communication familiar to physicists, astronomers, astrophysicists and chemists. This post is an edited version of of the section of the Editorial about Nature Precedings, and how posting preprints and other documents to that site affects submission to Nature journals.

Nature Precedings aims to facilitate sharing and discussing prepublication data. Notably, the site hosts a diverse set of formats, including slide presentations, preprints, posters and stand-alone data. The postings are citable (DOIs) and attributable to an author, and although they are screened by in-house curators for scientific legitimacy (not novelty or quality), they are not peer reviewed. As a result, content can be posted in less than a day. The content carries a 'Creative Commons Attribution' licence, which requires only proper citation. The Nature journals, like many others, do not consider a posting on the site as a formal publication that would prevent consideration of a submitted manuscript for publication (but authors cannot post to Nature Precedings subsequent pre-accept versions that evolve due to the journal's editorial process).
A strong focus of Nature Precedings is on browsing, searching and alert functionality, with Web 2.0 features such as authored comments, voting, subject tagging and RSS feeds. No submission charge is levied and the long-term open availability of the content is guaranteed.
In essence, biologists are now getting a taste of what has been an integral part of the physical sciences community for decades in the form of preprint servers such as arXiv, now with more than 100,000 articles. Some will argue that Nature Precedings will provide poster presenters with global exposure and serve to 'time stamp' data and ideas, whereas others will feel that researchers in highly competitive areas will not gamble on such a wide exposure in the race to publication. After all, many big conferences already suffer from a dearth of unpublished data. However, there is good cause to be optimistic, as even traditionally secretive research areas, such as pharma-research, are occasionally opening up with laudable open-access projects such as Synaptic Leap — a site that facilitates sharing data on neglected tropical diseases. We are keen to hear your views.

Posted by Maxine Clarke on July 04, 2007
Categories: Policies | Permalink | Comments (0)

In a post entitled Nascent: Word 2007 and the STM Publisher Ecosystem, Howard Ratner, Chief Technical Officer of Nature Publishing Group, writes about how he has become involved in "a very lively conversation with Microsoft staff about why Word 2007 is not being actively endorsed by STM publishers. It has recently come to Microsoft's attention that Nature , Science and many other scholarly publishers do not accept files from authors in Word 2007. Both Science and Nature Publishing Group have been in correspondence with Microsoft staff on this important issue. The staff there have been very willing to engage in this conversation."

The rest of Howard's Nascent post is the text of a letter to Microsoft by Bruce Rosebaum of Inera, which well explains the issues for science and technical publishers attempting to integrate this format with their typesetting and web coding systems. The letter concludes: "Those of us in the scientific community look forward to a dialog to articulate scholarly publishing requirements to Microsoft so that Microsoft can provide products that serve the needs of the entire scholarly community."

James McQuat, London Nature journals' Editorial Production Director, draws attention to an article by Margaret Heffernan at The Huffington Post, one of the world's most popular blogs, on this issue. It is a much more upfront analysis of the situation, but encapsulates it well.

In a comment to the Nascent post, Bruce D'Arcus writes: "There's another issue with backwards compatibility for scholarly workflows. Word 2007 supports new citation and bibliography fields. But if you open such files in previous versions of Word, the fields are converted to plain text. This means scholarly collaboration becomes impossible unless all parties are using Word 2007. I'm sure MS thought this a smart business decision, but I beg to differ. I think it'll mean many scholar won't bother with Word 2007, or its citation features."

Posted by Maxine Clarke on June 21, 2007
Categories: Policies, Publishing, Writing | Permalink | Comments (1)

The authors of a controversial paper on stem cells publish a correction of their work in this week's issue of Nature (447, 880-881; 2007) but state in it that the errors do not affect the conclusions of the article. A News story also in this week's issue (Nature 447, 763; 2007) describes how the paper in question, published in 2002, claimed to find evidence for so-called 'multipotent adult progenitor cells', or MAPCs, in mouse bone marrow (Y. Jiang et al. Nature 418, 41–49; 2002). The work was led by Catherine Verfaillie, now director of the Stem Cell Institute at the Catholic University of Leuven.
From the News story: The paper challenged the prevailing idea that only stem cells derived from embryos were highly flexible. Some of its results have been reproduced by other labs, but no one has been able to replicate the work independently in its entirety. "I believe that despite the hype over the mistake, we and Nature made the conclusion that the final findings of the paper still stand," says Verfaillie.
This February, an investigation convened by the University of Minnesota — Verfaillie's former institution — found that her group had used incorrect procedures in the Nature paper, and that some of the data contained in it might be flawed. The investigation was a response to questions from a reporter from the magazine New Scientist, who pointed out that the figure from the Nature paper that has now been corrected was partly reproduced with different labels in another paper in another journal, Experimental Hematology (Y. Jiang et al. Exp. Hematol. 30, 896–904; 2002).
In response to the investigation, Nature convened a peer-review panel to analyse the data from the 2002 paper. According to Nature, the experts concluded that although the figure data were flawed, the paper's conclusions are still valid. No allegations of fraud or misconduct have been levelled at Verfaillie or anyone from her group. Verfaillie says her group cannot explain how the errors in the Nature paper occurred: "Why this happened, we have not been able to determine," she says.

Posted by Maxine Clarke on June 14, 2007
Categories: Data availability, Disciplines, Ethics, Policies | Permalink | Comments (0)

The current issue of EMBO Reports features a Talking Point collection of articles on the use of animals in scientific research. Frank Gannon writes in his introduction:
The balance between the rights of animals and their use in biomedical research is a delicate issue with huge societal implications. The debate over whether and how scientists should use animal models has been inflammatory, and the opposing viewpoints are difficult to reconcile. Many animal-rights activists call for nothing less than the total abolition of all research involving animals. Conversely, many scientists insist that some experiments require the use of animals and want to minimize regulation, arguing that it would impede their research. Most scientists, however, try to defend the well-established and generally beneficial practice of selective experimentation on animals, but struggle to do so on an intellectual basis. Somehow, society must find the middle ground—avoiding the cruel and unnecessary abuse of animals in research while accepting and allowing their use if it benefits society.
In any debate, one should first know the facts and arguments from each side before making an educated judgement.
The article continues here.
The other articles in the Talking Point are:
Animal research: a moral science by Bernard E. Rollin.
The ethics of animal research by Simon Festing and Robin Wilkinson.

Posted by Maxine Clarke on June 06, 2007
Categories: Animal experiments, Policies | Permalink | Comments (0)

In its June Editorial, which is freely available, Nature Chemical Biology (3, 297;2007) reports on new online features to enhance interdisciplinary communication and to increase the accessibility of chemical information for readers.

Most published chemical content is traditionally contained in the schemes, figures and tables of scientific papers. Authors also use abbreviations, acronyms or numbering schemes to identify specific molecules. Though these shorthand notations simplify the presentation of chemical information, they tend to make chemical papers less accessible to the general reader. This is a concern for chemical biology articles, which are intended to attract an interdisciplinary audience. Moreover, since the advent of the Internet, the way by which scientists acquire scientific information has changed. Though some scientists continue to read journal articles in print, most turn to the online HTML and PDF versions of published manuscripts. This expanded use of electronic resources offers an excellent opportunity to make chemical information more accessible and user-friendly to readers of scientific papers.

The Editorial provides details of the resources now available to authors and readers, and asks for your evaluation of what has been done so far, and your 'wish list' for new chemical or biological functionality that will foster communication and collaboration between researchers at the interface of chemistry and biology.

Posted by Maxine Clarke on May 30, 2007
Categories: Access, Author benefits, Data availability, Policies | Permalink | Comments (0)

Here is the full text of an Editorial in today's Nature (447, 1-2 ;3 May 2007), which is freely available. For further details of the Nature journals' policy on fraud and fabrication, see the Author and Reviewers' website. Comments on this editorial are welcome.

The use of electronic laboratory notebooks should be supported by all concerned.

Too often when errors or cases of fraud occur in science, the lab data required to reconstruct what happened have gone astray. And too often, the co-authors failed to exert due scrutiny on their colleagues' activities in order to prevent such misfortunes. The damage to personal and institutional reputations can be severe and, in rare high-profile cases, public trust can be eroded.

It is therefore in everyone's interest to pre-empt such cases as far as possible. Electronic laboratory notebooks offer a partial solution — and have other advantages too. This is despite the fact that maximizing their benefits will require a change in culture that many researchers will no doubt initially resist.

Continue reading "Share your lab notes" »

Posted by Maxine Clarke on May 03, 2007
Categories: Communication, Data availability, Ethics, Policies, Publications | Permalink | Comments (4)

Euan Adie, on his Nature Network blog FnL, posts about Shelley Batts' Retrospectacle review of a paper about treating fruit with natural volatile compounds to make it last longer, in which she included a figure and chart from the paper (the source was cited). An editorial assistant at the Journal of the Science of Food and Agriculture – where the paper was published – threatened her with legal action unless she removed the images immediately. The blogosphere reacted with predictable speed and free-expresssion, documented in Euan's FnL post.
Euan goes on to ask whether the reaction is, in the cold light of a couple of days later, reasonable, looking at the incident both from the point of view of the publisher concerned as well as the blogger. As he puts it: "Storm in a teacup or dark conspiracy?" There is a good debate in the comments to the FnL post, so if you are interested in weighing up these pros and cons, and would like to add your take, please take a look.

Posted by Maxine Clarke on May 02, 2007
Categories: Access, Policies, Public and media, Publishing | Permalink | Comments (1)

Rebels hold their own in journal price war : Article : Nature (Subscription or site licence required.)

In a News story in the current issue of Nature, "Rebels hold their own in journal price war", Declan Butler looks at what has happened since last August, when the entire editorial board of the Elsevier journal Topology quit in a row over pricing. Now the board is setting up a non-profit competitor to be published by the London Mathematical Society. The Journal of Topology, announced last week, will launch next January and will cost US$570 per year, compared with Topology's $1,665.

Over the past eight years, continues the News story, around a dozen cheap or open-access journals have been created to compete directly with an expensive commercial journal, many by editorial boards that had quit the original publication in protest. (See the News story for a table of these journals.) But do the cheaper journals fare better than their rivals?

As far as scientific credibility is concerned, the answer is often yes — many of the challengers have obtained impact factors (a measure of the citations its papers receive) higher than their competitor. Nevertheless, the rebel journals often get poor support from libraries, with subscriptions being an uphill battle for them.

Source: Nature 445, 351 (25 January 2007) | doi:10.1038/445351a; Published online 24 January 2007.

Posted by Maxine Clarke on January 29, 2007
Categories: Access, Policies, Quality measures | Permalink | Comments (0)

Following the MIAME (minimal information about microarray experiments) standards for reporting microarray data, various scientific communities are engaged in producing similar guidelines. Some of these standards papers are under consideration for publication in Nature Biotechnology. Because data-reporting standards are only as useful as the community finds them, we want to know what you think. The papers are freely available for at least a month, and your comments are welcome. New papers are added to the list on the Nature Biotechnology website as they become available, with a commenting facility for each one. The papers cover standards for 'minimum information about a genome sequence', proteomics, protein modification data, mass spectrometry, mass spectrometry informatics, gel electrophoresis, functional genomics, molecular interactions, and in situ hybridization and immunofluorescence experiments.

The Nature journals' policy on data availability, including MIAME standards, is available at the author and referees' website.

Posted by Maxine Clarke on January 29, 2007
Categories: Data availability, Policies | Permalink | Comments (0)

Juan-Carlos Lopez, Chief Editor of Nature Medicine, discusses the question of data integrity of figures in his post on Spoonful of Medicine: The figure police.

Juan-Carlos discusses an editorial in the Journal of Cell Biology, which takes the line that "the progress of science depends on the reliability of the entire published record, and journal editors must do their part to ensure that reliability", urging editors to "participate in this dialogue with the scientific community, to help devise effective and practical standards that can be applied to the published literature".

Should scientific journals screen every image in every paper, as the Journal of Cell Biology editorial recommends? Or is a spot-checking system, such as used by the Nature journals, preferable, on the grounds that the vast majority of the papers published are not fraudulent, and that the journal could invest more usefully in other author and publication services? (This last point is particularly critical for small, society-owned journals that have limited resources.) Or is the responsibility that all research work is honest, and that the papers produced accurately reflect the work done, that of the scientific institution and/or the funder?

The Nature journals' policies on image integrity can be found at our Author and Referees' website.

Posted by Maxine Clarke on January 22, 2007
Categories: Data availability, Ethics, Policies | Permalink | Comments (0)

Today's issue of Nature (vol 445, pp 229 and 240-246; 2007) contains an Editorial and several news stories about scientific misconduct. These articles, with links to the journal content (subscription required) are listed at Nature's newsblog so that readers can comment.
From the Editorial: ...."most important of all, as the first scientific studies of the factors behind good conduct confirm, is the example set by senior researchers themselves. It is here in the laboratory — not in the law courts or the offices of a university administrator — that the trajectory of research conduct for the twenty-first century is being set."

Posted by Maxine Clarke on January 18, 2007
Categories: Ethics, Policies | Permalink | Comments (0)

Philip Ball's column in news@nature.com this week is about Richard Doll, and whether he should have stated in his publications that he received consultancy fees. The Nature journals' policy on competing interests is summarized here. As ever, we welcome comments from scientists about the practice of declaring such interests, whether financial, ethical or personal, in published papers. How relevant are any or all of these conflicts to the strength of the scientific conclusions reported in a peer-reviewed paper? In particular, we welcome feedback about our own policy, via comments to this post.

Posted by Maxine Clarke on December 19, 2006
Categories: Competing interests, Policies | Permalink | Comments (0)

Q. Dear Editor
My collaborators and I just submitted a paper to Nature. We would like to know whether we can send the present paper on the physics arxiv web site (see for example xxx.lanl.gov) or if -- to respect Nature policy-- we should wait for the editorial decision.

A. Dear Author

Thank you for your message. It would be fine for you to send your preprint to the arxiv site, or any other recognised community preprint server. Please provide the arxiv reference number to the editor handling your paper for his/her information, though.

Our policy is here:

"Contributions submitted to, in press with or published in Nature must not be posted on any web site, except for preprints posted on recognized preprint servers (such as ArXiv) where this is community practice. The server concerned must be identified to the editor in the cover letter accompanying submission of the paper, and the content of the paper must not be advertised to the media by virtue of being on the preprint server, as explained fully in Nature."

Best wishes
Nature.

Posted by Maxine Clarke on December 18, 2006
Categories: Access, Policies, Policies Feedback | Permalink | Comments (2)

There is much comment in Nature and elsewhere this week about the two fraudulent stem-cell papers published in and retracted from the journal Science. Science's editors commissioned an external committee to report on its handling of the papers, in the light of which the journal is likely to begin extra scrutiny for "high risk" papers. For more details, see Nature's news story in the current issue (vol 444, pp 658-659; 7 December 2006), and this special feature.

Other opinions about the panel's report can be seen in a statement by Don Kennedy, Editor-in-Chief of Science, at the journal's website; at the weblog Nobel Intent; and in The Scientist's online news service. The report itself can be seen here.

Inevitably, much of the discussion centres on the role of journals and peer-reviewers in their combined ability to detect fabricated results. Everyone would agree that published papers have to be entirely above suspicion. But what of the authors' perspective -- how much data, methodology or calculation is necessary to provide a convincing case for a conclusion? Especially in fast-moving fields such as stem-cell research, how much time and effort is needed to accumulate such evidence and submit it to a journal -- a journal that may have to decline 90 per cent of submitted papers?

The Nature journals' policies on data availability can be seen here. As we scrutinize these policies in the light of current events, we welcome suggestions from authors, past, present or future, as to what you believe to be reasonable for a journal to demand to ensure that conclusions are solid. Please make your suggestions in the comments to this posting.

Posted by Maxine Clarke on December 08, 2006
Categories: Data availability, Policies | Permalink | Comments (0)