Nature Neuroscience on gaps in ethical oversight of research

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Although institutional review boards are important ethical gatekeepers of human patient research, there is little data to evaluate their effectiveness. More coordination and a more transparent decision-making process is critical if review boards are to make appropriate and consistent decisions – so says the Editorial in this month’s (February) issue of Nature Neuroscience (13, 141; 2010). From the Editorial:

“An ethical overview is meant to be more than just another bureaucratic hurdle in doing research; it is a guarantee that all research is held to certain minimum standards and, particularly for human patient research, it is an assurance that the participants’ welfare is being looked after and that the risk to them is minimized. However, there is very little oversight of how well this overview meets its stated aims, especially for human research. Moreover, what little data exists points to some worrying inconsistencies; a study that submitted a mock functional magnetic resonance imaging human neuroimaging protocol to 43 Canadian review ethics boards found that the protocol was unconditionally approved by 3 boards, approved conditionally by 10 and rejected by 30. Given the increasingly knotty ethical challenges that neuroscience advances present, it is critical that we try to improve this situation by encouraging review boards to make their decision-making process more open and by encouraging greater cross-talk between different ethical review boards……

What is urgently needed is some real data on how the current process is working. Providing a searchable database of current protocols of the sort already provided for clinical studies would be a good first step by providing guidance to local review boards about decisions made on comparable cases, while still retaining the flexibility required to make case-by-case decisions. It would also highlight decisions that differ from the norm. Along with greater cross-talk between local ethical review boards, such publicly available information would also help reassure the public that ethical review is indeed doing what it sets out to do, by ensuring the welfare of subjects while advancing our knowledge of how the human brain works.”

Nature Neuroscience journal website.

Cite well, says Nature Chemical Biology

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Scientists need to devote more attention to the citation lists of scientific papers—the connectivity and usefulness of the scientific literature depend upon it. The February Editorial in Nature Chemical Biology ( 6, 79; 2009) explores how “citations of published work link together the concepts, technologies and advances that define scientific disciplines. Though information technology and databases have helped us to better manage the expanding scientific literature, the quality of our citation maps still hinges on the quality of the bibliographic information contained in each published paper. Because article citations are increasingly used as metrics of researcher productivity, the citation record also affects individual scientists and their institutions. As a result, all participants in the scientific publication process need to ensure that the citation network of the scientific literature is as complete and accurate as possible.”

The Editorial goes on to discuss the factors that stand in the way of good citation practices, and explains how the journal ensures that the reference lists in the papers it pubishes are accurate and balanced. But although editors can help, authors are ultimately responsible for the work they cite in their papers, ensuring appropriateness, transparency and accuracy. Yet "the responsibility for maintaining and enhancing the citation network of a discipline resides with all participants: authors, referees, editors and database managers. Thoughtful attention during the writing and review processes remains the first and best approach for ensuring citation quality and the appropriate assignment of credit in published papers. Yet new publishing and database tools that lead us to an interactive multidimensional scientific literature will become essential.

As publishers move toward integrating functionality such as real-time commenting on published papers and creating ‘living manuscripts’ that preserve the snapshot of a research area through the lens of a published paper, while permitting forward and backward linking, the scientific literature is poised to become a richer environment that will support future scientific progress."

Nature Chemical Biology journal website.

Nature Chemical Biology guide to authors.

The Nature journals’ publication policies.

Nature Chemical Biology on assigning responsibility and credit

The journal’s October Editorial outlines new policies that refine the responsibilities of authors and require author contribution statements in Nature Chemical Biology research papers ( Nat. Chem. Bio. 5, 697; 2009):

“When a manuscript is submitted to Nature Chemical Biology, one author assumes the role of corresponding author. This individual, typically a principal investigator of the study, serves as the central point of contact for the manuscript and manages communication with the journal while the paper is under consideration. Corresponding authors also take responsibility for coordinating communication among the paper’s authors and for certifying that all authors have agreed to the contents of the manuscript prior to submission. Our ”https://www.nature.com/authors/editorial_policies/authorship.html">updated authorship policy now clarifies the corresponding author’s role in managing the manuscript’s author list: prior to submission, the corresponding author “ensures that all authors are included in the author list, its order has been agreed by all authors, and that all authors are aware that the paper was submitted”.

Why are these changes needed? Because publication records remain an important metric for assessing the research productivity of individual scientists, it is essential that author lists are accurate and are determined in an objective and open manner. Most authorship disputes result from lack of clarity on two main points: (i) defining whether an individual’s scientific contributions warrant authorship and (ii) determining the order of the author list. Obtaining agreement on these points is made more challenging by differences in authorship models among disciplines and individual laboratories, and by the fact that collaborative papers in interdisciplinary areas often include data from multiple research groups."

The Editorial goes on to describe further details of these policies, including the introduction of authors’ contributions statements in published articles.

Nature journals’ authorship policies.

Nature Chemical Biology guide to authors.

About the Nature Chemical Biology editors.

Nature Methods announces online methods

Nature Methods follows in the footsteps of Nature by ushering in an online methods section, fully integrated with the paper, for all original research articles. Details of the service described in the journal’s current (May) Editorial (Nature Methods 6, 313; 2009), and the editors welcome comments on the service at Methagora, the Nature Methods blog.

Daniel Evanko, Chief Editor of Nature Methods, writes: “We are relieved that we will no longer have to relegate important methodological details to Supplementary Information and we expect our authors will appreciate being able to include more citations in their papers. A potential downside of this change is that the print and online versions of papers have quite different levels of methodological detail. What do you think? Those of you who are online readers may not have very strong opinions on this, but what about our print readers? If anyone who regularly receives a print copy of the journal is reading this, we would ”https://blogs.nature.com/nmeth/methagora/2009/04/methods_section_remake.html">like your feedback as well."

From the Editorial: “We expect that our readers and authors will appreciate the advantages that Online Methods bring to Nature Methods. With this change effectively increasing the length of Nature Methods papers—and more than doubling the length of Brief Communications—our authors will have far more space to communicate their new methodologies and cite previous work. But by limiting the increase in length to the methods section we continue to emphasize the value of succinct scientific reports. The body of the paper will remain short enough that casual readers can easily obtain the important information. The details required for more in-depth understanding or reproduction of the work will be easily accessible if needed. We hope our authors and readers are as excited by this change as we are.”

Nature Methods journal website.

Nature Methods guide to authors.

Nature‘s formats for methods.

Methods in full, the Editorial announcing Nature’s introduction of this service (Nature 445, 684; 2007).

Nature Photonics on combating plagiarism

In its May Editorial, Nature Photonics (3, 237; 2009) describes some of the ways in which the Nature journals combat scientific misconduct and practices such as ‘guest’ authorship. Part of the Editorial concerns plagiarism:

“Many forms of plagiarism exist, but the goal is generally the same — to garner false or undue credit. Plagiarism sometimes involves reuse of another author’s published work, but it is commonly thought that the most typical tool of the plagiarist is self-plagiarism: the reuse of substantial parts of an author’s own published work, particularly without appropriate referencing, and less commonly, duplicate publication, in which the results are recycled in their entirety.

The peer-review process provides a net for catching offenders, but it cannot provide a fail-safe barrier. As a result, Nature Photonics is now starting to use the plagiarism-detection software ”https://www.crossref.org/crosscheck.html">CrossCheck, which makes comparative checks between provided manuscripts and those previously published and in an existing database. Any manuscript that seems to show an abnormally high match will be immediately investigated. Unfortunately, plagiarism can also occur without verbatim duplication of words or data. And it is here that the lines between normal and acceptable activity and plagiarism become smeared, and the likelihood of detection and punitive repercussions is diminished.

Using another researcher’s arguments and logic, even if the text is not identical, without due reference is intellectual plagiarism. This type of plagiarism can be subtle and as simple as not including a reference to a highly relevant previous paper. Citation-related plagiarism, whether it is intentional, or due to gross negligence, can give an untruthful impression of precedence, reassigning credit from the original discoverer to another person.

When reporting scientific messages, it is an author’s responsibility to find and acknowledge the critically relevant literature, or at least to have endeavoured to do so with rigour. Failing this can result in falsely apportioned claims, albeit caused by negligence.

If plagiarism is suspected in research results published by us, it is our policy to conduct an immediate investigation and if deemed appropriate to contact the author’s institute and funding agencies and consider a formal retraction of the paper. Although it is often the first authors who have historically borne the brunt of confirmed misconduct allegations, our editorial policies highlight the serious responsibilities of all coauthors: “submission to a Nature journal is taken by the journal to mean that all the listed authors have agreed to the content”. It is unreasonable to expect each author to be responsible for every aspect of the paper, but it is the responsibility of the corresponding author to manage the understanding that all authors are expected to have made reasonable attempts to check the findings submitted to a journal for publication."

The full text of this Nature Photonics Editorial.

Nature Photonics guide to authors.

About the Nature Photonics editors.

Nature journals policy on plagiarism.

Nature journals policy on authorship.

Clarifying authors’ duties and making “contributions statements” mandatory

Here is the text of an Editorial in the 30 April issue of Nature (458, 1078; 2009 – free to access online):

The Nature journals encourage authors to treat their data and their collaborators with the respect that their communities demand. High-profile journals have a duty to reinforce the trends towards greater transparency and to help scientists to fulfil their responsibilities as researchers and authors. We are therefore introducing small but important changes in our policies to reflect these goals.

In a previous Editorial (Nature 450, 1; 2007), we asked for feedback about whether we should require senior or corresponding authors to sign a statement that they had taken some specific ‘integrity insurance’ steps before the manuscript was submitted. Some applauded this idea, but most were not in favour. (Some of the feedback can be seen here.) Major doubts were expressed about the ability of corresponding authors to take on such responsibility given the diversity of collaborations. The belief was also expressed that such signed statements would too often be worthless box-ticking exercises. Although we regretfully accept these realities, we believe that we should go further in spelling out the responsibilities of co-authors, and in requiring an implicit acceptance of them.

Accordingly, we have modified the Nature journal policy on authorship, which is detailed on our website. For papers submitted by collaborations, we now delineate the responsibilities of the senior members of each collaboration group on the paper. Before submitting the paper, at least one senior member from each collaborating group must take responsibility for their group’s contribution. Three major responsibilities are covered: preservation of the original data on which the paper is based, verification that the figures and conclusions accurately reflect the data collected and that manipulations to images are in accordance with Nature journal guidelines, and minimization of obstacles to sharing materials, data and algorithms through appropriate planning.

Corresponding authors have multiple responsibilities, but we now make it clearer that the author list should include all appropriate researchers and no others, and that the order has been agreed to by all authors. They are expected to have notified all authors when the manuscript was submitted, they are the point of contact with the editor and they must communicate any matters that arise after publication to their co-authors.

Another change is that we have strengthened our policy for statements of authors’ contributions. This policy was first introduced nearly 10 years ago (Nature 399, 393; 1999) to make the credit due to individual co-authors more explicit. Since then, authors of Nature papers have had the opportunity to include in their papers a statement that details each author’s role in the published work. Over the past 10 years, the proportion of authors who choose to include this has risen dramatically.

This acceptance, and discussions with authors who have chosen not to include such a statement, has led us to change our policy. Rather than ‘strongly encouraging’ such statements, we now require them for publication of original research papers in Nature and the Nature research journals. The detail provided can vary tremendously and authors are left to structure them as they see fit. We insist only that no author be left out.

To ensure that authors are familiar with these changes, we will shortly require the corresponding author to confirm that he or she has read the Nature journal policies on author responsibilities and is submitting the manuscript in accordance with those policies.

Nature journals’ authorship policies.

Discuss Nature’s Commentaries on innovation

Are you interested in innovation and how to promote and predict it? Check out Nature ’s series of commentaries on the subject and tell us what you think at a Nature Network forum for online discussion.

In June, Bill Destler, president of the Rochester Institute of Technology discussed his school’s plan to foster innovation through academic-industrial partnerships.

In July, Lan Xue director of the China Institute for Science and Technology Policy argues that pushes to globalize science must not threaten local innovations in developing countries.

In August, David Guston of Arizona State University discusses the inherrent contradictions in the idea of introducing innovation policies, and offers ways of anticipating change without predicting it.

In September, Fred Gault and Susanne Huttner discuss some of the ways the OECD is looking to apply metrics to measure the impacts of innovation policies.

Podcast Extra!

David Goldston talks with experts about policies to implement innovation in this run up to the US presidential election.

Do you think innovation can be directed? Can it be predicted? Encouraged? Measured? Join the discussion at Nature Network.

The Nature commentaries are collected in this web focus.

Nature Methods recommends deposition of proteomics data

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 ”https://www.ebi.ac.uk/pride">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.

Author contributions audit

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)

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Molecular Systems Biology’s new author licence

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.”