NSMB’s tips for revising your paper in response to reviewers

Posted on 27 Apr 2010 by Maxine Clarke

From: Nature Structural & Molecular Biology 17, 389 (2010)

Your paper went out to review, and after anxious waiting, you receive the letter asking for a revised paper. However, those ever-demanding editors and reviewers want more. One of the most important elements of a revision is the point-by-point response. Here are some tips for making it more effective.

Keep to the point. We [the NSMB editors] internally call this a point-by-point rather than a rebuttal, implying that it makes a series of points in response to each point raised by the reviewers. We will, and indeed have, read through 17-page point-by-points. But the longer the document gets, the more likely it is that the essence of your arguments will be lost in the mix.

Keep it objective. We have received comments from bewildered reviewers who do not understand why the tone of the point-by-point is so aggressive. Therefore, we will sometimes ask you to rewrite your response if it is overly pugnacious and we feel that this could affect the outcome of the review.

Keep things under control. There are definitely times for making a logical argument rather than adding new data and experimentation. That said, when fundamental technical concerns are raised or missing controls are being requested, the point-by-point is not the place for trying to dazzle your reviewers with argument and debate skills. Know when to go to the bench and when to argue.

The scope of things. Some requests might genuinely be beyond the scope of the manuscript or might simply be unfeasible. Make your response here as objective as possible. Say clearly and succinctly if something is unfeasible or if you think the results of such an experiment would be uninterpretable, and in both cases explain clearly why (pointing to the literature if needed) and how long the experiment will take to help make the case.

Some final points. There are some don’ts that should be obvious; but just in case, here are a few, in no particular order:

Telling us about your reputation, your pedigree, number of citations of your previous papers, your h-index, other Nature journals you have recently published in, etc. All interesting information but not pertinent to deciding the fate of the paper at hand.

Celebrity endorsements. Letting us know that a Nobel laureate enjoyed your talk at a recent meeting. Good to know but relatively meaningless. In fact, you never know—they could be moonlighting as your most critical anonymous reviewer.

Trying to guess who the reviewers are and then launching into a diatribe about their qualifications (or lack thereof).

And finally: “You recently published an even worse paper.”

All of these can be amusing to varying degrees but will do little to further your case.

Overall, it can be helpful to put yourself in the reviewer’s shoes and compose a response s/he would find appropriate, where the concerns raised are considered and fully addressed. In its ideal state, the review process is a positive and constructive back and forth, an intellectual discussion in which the manuscript is the ultimate beneficiary. Although it can be frustrating to be told at this stage that further revisions and experiments are a condition for publication of work that you felt was complete enough to submit, a common refrain after publication is for authors to express that, with the benefit of hindsight, the review process strengthened the paper. And a strengthened paper submitted at revision is the strongest rebuttal of all.

How Nature selects papers for publication

Posted on 25 Feb 2010 by Maxine Clarke

This is a shortened version of an editorial in Nature ( 463, 850; 2010 ; free to read online).

One myth that never seems to die is that Nature‘s editors seek to inflate the journal’s impact factor by sifting through submitted papers (some 16,000 last year) in search of those that promise a high citation rate. We don’t. Not only is it difficult to predict what a paper’s citation performance will be, but citations are an unreliable measure of importance. Take two papers in synthetic organic chemistry, both published in June 2006. One, ‘Control of four stereocentres in a triple cascade organocatalytic reaction’ (D. Enders et al. Nature 441, 861–863; 2006), had acquired 182 citations by late 2009, and was the fourth most cited chemistry paper that we published that year. Another, ‘Synthesis and structural analysis of 2-quinuclidonium tetrafluoroborate’ (K. Tani and B. M. Stoltz Nature 441, 731–734; 2006), had acquired 13 citations over the same period. Yet the latter paper was highlighted as an outstanding achievement in Chemical and Engineering News, the magazine of the American Chemical Society.

Indeed, the papers we publish with citations in the tens greatly outnumber those in the 100s, although it is the latter that dominate our impact factor. We are proud of our full spectrum.

Another long-standing myth is that we allow one negative referee to determine the rejection of a paper. On the contrary, there were several occasions last year when all the referees were underwhelmed by a paper, yet we published it on the basis of our own estimation of its worth. That internal assessment has always been central to our role; Nature has never had an editorial board. Our editors spend several weeks a year in scientific meetings and labs, and are constantly reading the literature. Papers selected for review are seen by two or more referees. The number of referees is greater for multidisciplinary papers. We act on any technical concerns and we value the referees’ opinions about a paper’s potential significance or lack thereof. But we make the final call on the basis of criteria such as the paper’s depth of mechanistic insight, or its value as a data resource or in enabling applications of an innovative technique.

At the same time, we operate on the strict principle that our decisions are not influenced by the identity or location of any author. Almost all our papers have multiple authors, often from several countries. And we commonly reject papers whose authors happen to include distinguished or ‘hot’ scientists.

Yet another myth is that we rely on a small number of privileged referees in any given discipline. In fact, we used nearly 5,400 referees last year, and are constantly recruiting more — especially younger researchers with hands-on expertise in newer techniques. We use referees from around the scientifically developed world, whether or not they have published papers with us, and avoid those with a track record of slow response. And in highly competitive areas, we will usually follow authors’ requests and our own judgement in avoiding referees with known conflicts of interest.

Myths about journals will continue to proliferate. We can only attempt to ensure that the processes characterized above remain as robust and objective as possible, in our perpetual quest to deliver to our readers the best science that we can muster.

Protein Data Bank policies for disputed structures

Posted on 04 Feb 2010 by Maxine Clarke

Helen M. Berman, director of the RCSB (Research Collabatory for Structural Bioinformatics) Protein Data Bank, and co-authors wrote a Correspondence to Nature ( 463, 425; 2010) to clarify the PDB’s correction procedures and policies in the light of a current investigation. Their letter is reproduced here.

Your News story ‘Fraud rocks protein community’ (Nature 462, 970; 2009) discusses allegations that 12 Protein Data Bank (PDB) entries are based on fabricated data. Pending verdicts on these entries from the US Department of Health and Human Services Office for Research Integrity, we wish to clarify PDB policies and actions.

The PDB archive, which is managed by the Worldwide PDB (wwPDB), houses more than 62,000 entries for macromolecular structure models and their experimental data. It is maintained for the public good. Deposited structures are validated using community-developed standards, and any related corrections are made by depositors before release and publication.

Entries can be replaced on written request from the depositor(s) if better data have become available or the interpretation of existing data has changed. Entries can be withdrawn (that is, rendered obsolete) by the senior author, or by journal editors when the published paper describing the entry is retracted.

An author’s employer (in this case, the University of Alabama at Birmingham) may request removal of an entry, but this request must be fully documented and the original paper describing the entry must be retracted. This ensures due process for the author(s) and the scientific integrity of the PDB archive. To date, the paper describing one of the 12 PDB entries in question has been retracted (J. Biol. Chem. 284, 34468; 2009), and the corresponding PDB entry (PDB code 1BEF) has been made obsolete by the wwPDB at the request of the publisher.

To ensure that PDB entries are validated using state-of-the-art methods, wwPDB validation task forces have been convened for X-ray crystallography and nuclear magnetic resonance spectroscopy. Their recommendations will be reviewed and incorporated into wwPDB’s deposition and annotation procedures.

wwPDB encourages all journals publishing macromolecular structures to stipulate accompanying submission of wwPDB validation reports. These will help editors and referees to assess the reliability of structural data and their interpretation. A few journals have already indicated their interest.

With the support of the structural-biology community, the mission of the wwPDB is to safeguard the integrity and improve the quality of the PDB archive. It is the public availability of atomic coordinates and experimental data that enables errors and possible fabrications to be detected in the first place. Current validation procedures were designed to identify occasional honest mistakes, not to guard against rare cases of malfeasance.

Full authorship of this Correspondence:

Helen M. Berman, Director, RCSB PDB, Rutgers University, Piscataway, New Jersey 08854-8087, USA

Gerard J. Kleywegt, Head, PDBe, EMBL–EBI Hinxton, Cambridge CB10 1SD, UK

Haruki Nakamura, Head, PDBj, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan

John L. Markely, Head, BioMagResBank, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA

Stephen K. Burley, Chair, wwPDB Advisory Committee, Eli Lilly and Company, San Diego, California 92121, USA

About the PDB archive.

Note from Nature: Nature would like to make clear that the misconduct investigation by the University of Alabama concluded in December 2009 that H. M. K. Murthy acted alone in generating allegedly falsified protein structures. He denies the allegations.

Cite well, says Nature Chemical Biology

Posted on 27 Jan 2010 by Maxine Clarke

NChemBio Feb 10.gif

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.

Integrating with integrity, according to Nature Genetics

Posted on 19 Jan 2010 by Maxine Clarke

Data worthy of integration with the results of other researchers need to be prepared to explicit export standards, linked to appropriate metadata and offered with field-specific caveats for use. The Editorial in the January edition of Nature Genetics ( 42, 1; 2010) explores the extent to which, to be useful at generating new analyses and hypotheses, data sharing needs to be about standardized formats as much as simply being made ‘available’. For example, the Editorial states, “Sample sizes, selection criteria, statistical significance, number of hypotheses tested, normalization and scaling procedures, read depth and sequence quality scores are all important considerations that can be misunderstood or missed in combining and reanalyzing data. Whether integrative approaches are useful may depend upon whether integration preserves or destroys essential information….

Integration is of most value in two areas: bioinformatic modeling, to predict the effects of genetic and environmental perturbation, and clinical utility, to increase the speed and accuracy of the transfer of preclinical knowledge to clinical trial. Funding bodies hope that encouraging researchers to integrate their results will reduce duplication of effort. Trivially, researchers can agree to work on the same systems and samples or to use agreed standard control materials, but this can be problematic in practice….

Researchers can enable integrative studies by publishing their quality metrics and exchange standards in a timely way in regularly versioned, citable preprints; and by holding integration workshops between data producers and data users from different fields. These exchanges should focus on honest assessment of what data are ready for use and explain the quality metrics used and where the pitfalls lie in using the data. In return, data producers can increase the citability of their datasets by better understanding the metadata needed by users. Requirements for open data deposition and integration that do not include mechanisms to agree on, publish and use data standards risk inflating inconsequential ‘integrative’ bubbles.”

Nature Genetics website

Nature journals’ policies on availability of data and materials

Scientific integrity in Iran

Posted on 15 Dec 2009 by Maxine Clarke

nature 10 Dec.jpg

Nature continues to report on allegations of scientific plagiarism by Iranian authors. An Editorial in this week’s (10 December) issue calls for Iran’s institutions to investigate the allegations as a matter of urgency (Nature 462, 699; 2009, free to read online) in the light of fresh evidence that senior officials in the Iranian government have co-authored scientific papers that show signs of plagiarism (Nature 462, 704-705; 2009). This follows similar revelations in October (see Nature 461, 578–579; 2009). What follows is an extract of this week’s Editorial:

The first wave of alleged plagiarism cases was widely discussed both inside and outside Iran, and provoked dismay among the country’s researchers and reformist bloggers. The cases were also reported by Iran’s mainstream media, which deserve credit for airing the story despite the present regime’s record of shutting down newspapers, arresting journalists and otherwise intimidating free inquiry.

The regime’s research institutions, however, have done little to investigate the allegations. This is perhaps not surprising, given the extreme political sensitivity of the accusations. One of the disputed papers was co-authored by transport minister Hamid Behbahani, who supervised President Mahmoud Ahmadinejad’s PhD. Other questionable papers were co-authored by science minister Kamran Daneshjou, who oversaw this year’s disputed presidential election. An official investigation is needed to clarify the circumstances of these and the new cases of alleged plagiarism. Senior scientists also have a responsibility for what happens in their labs, and for papers on which their names appear.

One can only speculate over what might cause such plagiarism. In some cases, using texts to help counter a poor command of English may provide extenuating circumstances. And in Iran, as in several developing countries, there is a cultural expectation that officials should have strong academic credentials. Another factor could be the politicization of Iran’s research system after the 1979 Islamic revolution and the deterioration of the research environment since Ahmadinejad took power in 2005. In the aftermath of this summer’s protests over the election, Iran’s universities have become a hotbed of opposition — a prime focus for the government’s crackdown.

Leading researchers inside Iran are keeping their heads down. But many are quietly pressing for the authorities to investigate the plagiarism allegations, which, they note, would be consistent with wider demands by academics for the current regime to be more accountable and respectful of the republic’s values and civil rights. They are also pushing for merit-based promotion practices, and are having some success in persuading Iran’s academic institutions to emphasize ethics in the practice of research and publishing.

Iran’s researchers, both inside and outside the country, are to be applauded for their defence of excellence and scientific integrity in such difficult political conditions. The actions of a few must not be allowed to soil the reputation of the majority of Iran’s scientists. Rather, the international scientific community must redouble its efforts to support and collaborate with its Iranian colleagues.

Consortium to address author ambiguity

Posted on 11 Dec 2009 by Maxine Clarke

Via press release:

Various members of the research community have announced their intent to collaborate to resolve the existing author name ambiguity problem in scholarly communication. Together, the group hopes to develop an open, independent identification system for scholarly authors. This follows the first Name Identifier Summit held last month in Cambridge, MA, by Thomson Reuters and Nature Publishing Group, where a cross-section of the research community explored approaches to address name ambiguity. A follow-on meeting of this group took place in London last week to discuss the next steps.

Accurate identification of researchers and their work is seen as key for the transition from science to e-science, wherein scholarly publications can be mined to spot links and ideas hidden in the growing volume of scholarly literature. A disambiguated set of authors will allow new services and benefits to be built for the research community by all stakeholders in scholarly communication: from commercial actors to non-profit organisations, from governments to universities.

The organizations that have agreed to work together to overcome the contributor identification issue include: American Institute of Physics, American Psychological Association, Association for Computing Machinery, British Library, CrossRef, Elsevier, European Molecular Biology Organisation, Hindawi, INSPIRE (a project of CERN, DESY, Fermilab and SLAC), Massachusetts Institute of Technology Libraries, Nature Publishing Group, Public Library of Science, ProQuest, SAGE Publications Inc., Springer, Thomson Reuters, University College London, University of Manchester (JISC Names Project), University of Vienna, Wellcome Trust and Wiley-Blackwell.

Previous Nautilus post on author identity.

Authors’ surnames and citation indices.

Nautilus posts on authorship.

NPG News archive.

NPG press release archive.

Nature Medicine’s wake-up call on intellectual property rights

Posted on 12 Nov 2009 by Maxine Clarke

Intellectual-property protection is a key driver of innovation, and researchers are always keen to file patents to shield their discoveries. Yet scientists often have an uninformed view of the value of their intellectual property. This naiveté slows down translational research. So concludes the November Editorial in Nature Medicine (15, 1229; 2009).

An informal poll conducted by the Nature Medicine editors revealed that “about two-thirds of scientists, particularly in Europe, don’t know who owns the intellectual rights to the discoveries made in their labs. A similarly high proportion don’t know if there are any provisions in their job contracts assigning them any rights over their discovery. And roughly half don’t even know whether they are legally entitled to open a company based on their research.” Ironically, states the Editorial, these are the very same scientists who dream of patenting their work and reaping the financial benefits. Before thinking about licenses (the essential first step), the Editorial continues, “it’s important to realize that the decision to file a patent seldom rests with the scientists, but rather with the technology transfer office (TTO) of their institution. Strangely enough, although most of the scientists we surveyed were interested in patenting their work and knew about the importance of the TTO to this end, over 60% admitted to never having interacted with that office.” After highlighting some of the problems concerning technology transfer offices and investor caution, the Editorial concludes:

“Translational researchers never shy away from the chance to present their science to anyone who might want to invest in it. But they would be well advised to start listening to companies, investors and their own TTOs to develop a better understanding of what they must bring to the table in order to attract financial support. Admittedly, there are very few places where scientists can learn how to engage in this dialogue, but the excuse that provides should be cold comfort given how important this is to the progress of translational research. The creation of forums of this sort should therefore become a priority for universities and research centers alike. A high-profile paper may allow you to get your foot in the door, but it won’t be enough to open it.”

See also the free Nature Medicine podcast, this month looking at the law in the context of the “patent cliff” which pharmaceutical companies are facing.

In other Nature Medicine news, the journal is organizing a colloquium on Systems Biology and HIV Vaccine Development on 8-10 February 2010 in Peachtree City, Georgia, USA. Participants will include HIV researchers and scientists using systems approaches in other areas of biomedical research, who will address how systems biology has provided insight into the immune response and into other areas of medicine, such as cancer and autoimmunity. Also on the agenda for discussion are the technical and bioinformatic challenges associated with using systems biology approaches; the gaps in HIV immunology that need to be resolved to develop an HIV vaccine; whether systems approaches can help to address these questions; and how ‘systems vaccinology’ approaches can be implemented in HIV vaccine development and clinical trial monitoring.

Authors warned to keep their online identities secure

Posted on 11 Nov 2009 by Maxine Clarke

This is the text of a Correspondence in Nature (462, 35; 2009) by Irene Hames , an editor at The Plant Journal.

Goudarz Molaei is right to express concern in his Correspondence about simultaneous submission of manuscripts to different journals (Nature 461, 723; 2009). As a professional journal editor with more than 20 years’ experience, I would like to highlight here a worrying new problem I recently encountered: duplicate submission arising from author impersonation.

Unfortunately, online submission and review systems inadvertently encourage this unwelcome activity. For example, a co-author or colleague may be given the corresponding author’s account password in order to submit his or her manuscripts — perhaps because of the corresponding author’s lack of time or unfamiliarity with file creation and uploading. These people are then able to change the author’s accounts, including the passwords, and submit manuscripts in that person’s name without their knowledge.

So, authors, be wary of who has access to your account. Keep a check on what’s happening and change your password after files have been submitted.

Polymath Project and Google Wave: open-source science

Posted on 16 Oct 2009 by Maxine Clarke

Two examples of open-source science are the subject of Opinion articles in this week’s Nature. In the first of these, Timothy Gowers and Michael Nielsen describe their ‘Polymath Project’, which showed that many minds can work together to solve difficult mathematical problems, and reflect on the lessons learned for open-source science (Nature 461, 879-881; 2009). In the other article, Cameron Neylon says that Google Wave is the kind of open-source online collaboration tool that should drive scientists to wire their research and publications into an interactive data web (Nature 461, 881; 2009).

“Solving the current problems in science communication requires the intervention of strong companies such as Google”, he writes. “But it will take more than technical advances to provoke scientists into taking full advantage of the web. We need pressure, and perhaps compulsion, from journals and funders to raise publishing standards to the new level made possible by such tools. Google Wave may not be, indeed is probably not, the whole answer. But it points the way to tools that build records and reproducibility into every step. And that has to be good for science.”

Both these articles are free to read online for one week from the publication date (15 October).

nature.com blogs

Category Archives: Authorship