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Nature Policy update
Linda J. Miller, U.S. Executive Editor
Nature and the research journals
September 2005
Today’s speakers
Linda J. Miller, PhD Senior editor at Science Launch editor of Nature Immunology U.S. Executive Editor for Nature and the Nature
research journals
J. Myles Axton, PhD Oxford University investigator and lecturer Editor of Nature Genetics
Guide to today’s talks
General introduction to Nature journals Nature journal policies What is a good paper? What do we expect from out referees? Some specifics about Nature Medicine Nature Immunology Nature Genetics Nature Biotechnology
Nature’s mission circa 1869
Nature’s mission today
First, to serve scientists through prompt publication of significant advances in any branch of science, and to provide a forum for the reporting and discussion of news and issues concerning science. Second, to ensure that the results of science are rapidly disseminated to the public throughout the world, in a fashion that conveys their significance for knowledge, culture and daily life.
Common Policies at Nature journals
AuthorshipDeposition of dataSharing of materialsCopyright Manuscript transfer service Competing financial interestsPlagiarismImage integrityBiosecurity
Authorship
All authors are responsible for the paper
Changes to authorship need to be approved by all authors
Individual contributions can now be acknowledged in the published paper:
Deposition of data
SequencesGenBank, EMBL, DDBJ
StructuresPDB, SWISS-PROT
GenomesNCBI, ENSEMBL
MicroarraysGEO, ArrayExpress
Sharing of materials
Publication is a privilege & a pact Acceptance of manuscript implies
o Author provides access to readers of all new reagents described in the paper
o Reagents provided by biotech or other corporate partners be made available to all
o If access is conditional (such as small fees, Material Transfer Agreements, etc), conditions must be made explicit
If journal receives complaints, we will take action Contact author for explanation Contact funding agencies and institutes if warranted Post Editor’s Note with paper
Copyright and author license
Nature journal authors retain copyright on original research publications & grant NPG an exclusive license-to-publish.Authors can post the accepted version on their personal website and can republish in books or reviews they are writing - cite original source.Funding agencies and their institutions can post the accepted author’s version of the manuscript in their online archives 6 months after publication in a Nature journal.Nature journals are coordinating access policies with the deposition policies of major science funding agencies such as the US National Institutes of Health and the UK Wellcome Trust.
MS Transfer Service
Eliminates need for author to re-input a manuscript, if they are choose to submit their manuscript to another NPG journal
Authors provided with a link in their decision letter
Authors can choose any of the NPG or Nature journals
If the manuscript had been reviewed at the first Nature journal, and the author chooses to send the manuscript to another Nature journal, the reviews are automatically forwarded to the next Nature journal - this can save time in the evaluation of the manuscript at the second journal.
Competing financial interests
Authors required to fill out and sign a competing financial interests form before publication
Published papers contain a standard statement indicating whether or not a competing interest exists
Details of the competing financial interests are given online
Competing financial interests
Image integrity
Objective: Images in manuscripts accurately reflect the data
Beautification - Photoshop or other graphic tools used to alter a portion of an image (changing colors, brightness, contrast) in an attempt to make data clearer or remedy unsightly data
Deliberate fraud - manufacturing data that was never obtained experimentally
What’s wrong with this image?
Example 1: Gels
The original cause for concern:
Bands in lanes marked “+” and “-” were almost identical, but text stated that they were different
- +
What’s wrong with this image?
A close-up of the image revealed another potential problem
Artificially straight boundary between lanes - indicative of lane splicing
What’s right with this image?
Editor requested explanation and author supplied unretouched experimental data
Two problems resolved:
Lanes not cut Controls now run on same gel
- +
Guidelines for presenting gels
Publication-quality gels require that MW markers, negative and positive controls be run on the same gels (preferably full length)
Guidelines for presenting gels
Contrast should be set so that the background and ‘contaminating’ bands are still visible. Immunoblots often need boxes to demarcate the edge of the filter
Blot with indeterminate edges
Gel of too high contrast with box
Guidelines for presenting gels
Cut and repositioned (‘spliced’) lanes are discouraged. If absolutely unavoidable, gel discontinuities should be indicated with
boxes or inserted white space - and noted in the Figure legend.
Beautification becomes fraud when:
Graphic software is used to create images that misrepresent the actual data collected
Band sections cut and pasted into new positions- greenBands flipped and pasted into another lane - red
Fluorescence immunocytochemistry
Misleading manipulations include altering contrast or color in a portion of the photo or adding/deleting elements in photo
Manipulated image Manipulation of added cells revealed by contrast adjustment
Image integrity
What authors can do Provide more education to grad students and
postdocs Insist on seeing original data from which a
figure was built What editors can do Develop clearer guidelines and post in online
Guides for Authors and Referees Initiate internal inspections of all papers to
detect problems before publication
Plagiarism
Both self-plagiarism and plagiarizing others are increasing problems in science
Papers already published in non-English journals are unlikely to be published in high profile English-language journals; the original publication must always be cited
Give credit where credit is due
If in doubt, err on the side of too many, rather than too few, citations.
Biosecurity
2001 anthrax attacks changed public’s attitude, particularly in the US
Examples of papers that worried the media & public2002 J. Virol. paper - created a mousepox virus lethal even to mice already vaccinated against mousepox 2002 Science paper - de novo synthesis of polio virus without cells
Biosecurity
Is ‘Censorship vs Openness’equivalent to ‘Safety vs Risk’?
First step
January 2003 US National Academy of Sciences International journal editors Security experts
Agreed: Editors uphold integrity of scientific literature & ensure
reproducibility and verifiability Editors agreed to assess ‘manuscripts of concern’ for
risk of misuse vs benefit to public health
Joint journal statement
All papers in peer-reviewed journals must contain enough information to adequately reproduce the resultsCommitment to identification of papers before review and/or publication that have the potential for abuseFormation of clear policies as to the process to which such papers would be subjectedIf a paper is deemed inappropriate for publication as is, it would either be modified without compromising its reproducibility or communicated to the scientific community through other avenues.
What are ‘manuscripts of concern’?
October 2003 US National Academy of Sciences committee chaired by Gerald FinkIdentified some categories of experiments should be cause for concern: Render vaccines ineffective Confer resistance to useful antibiotics or antivirals Enhance virulence of microorganisms Increase transmissibility of pathogens Alter host range of a pathogen Render a pathogen harder to detect ‘Weaponize’ biological agents or toxins
More ‘dual-use’ publications
After the Jan 2003 meeting dual-use publication continues
May 2003 Nature - anthrax genome
May 2003 Science - SARS sequence
Mar 2004 Science - crystal structure of 1918 pandemic influenza HA
Oct 2004 Nature - construction of virulent flu with 1918 HA and/or NA
Nature journal policy
The editorial staff of Nature journals maintain a network of advisers on biosecurity issues. All concerns on that score, including the commissioning of external advice, will be shared within an editorial monitoring group consisting of the Editor-in-Chief of Nature publications, the Executive Editor of the Nature research journals, the Chief Biological Sciences Editor of Nature, and the chief editor of the journal concerned. Once a decision has been reached, authors will be informed if biosecurity advice has informed that decision.
Journal’s responsibilities
Be alert to papers whose risks of publication might outweigh benefits.Be alert to papers whose research materials’ dissemination might cause hazard.Ensure papers’ protocols adhere to local ethics rulesKeep in touch with debateBe transparent News section: scrutinize biodefense developments
Benefits of openness
Search for mechanisms of pathogenic organisms is critical to continue to protect public health
Open publication of genomes, as SARS genome has already proven, can have almost immediate health benefits
Science is international
Overly harsh regulation of publication in one country will be ineffective
International activities like science need international consensus in deciding what constitutes appropriate action
Editors and scientists both have the responsibility for protection of public health with minimal disruption of openness
“The traditions and structure of research in the U.S. today depends on replication and refutation, which means that sufficient data and methods to allow that must be published in peer-reviewed journals. Such publication also mitigates fraudulent results, sloppy science, and political biases guiding important policy decisions. Recent, well-publicized incidents of scientific misconduct underscore the merits of this system.”
Don’t throw out the baby with the bathwater
MRC GreenwoodChancellor, UC Santa Cruz
Immunology. All of it.
Nature Immunology is a multidisciplinary journal
Covers a wide range of subject areas in immunology, from immune receptor signaling to microbial immunopathology
Human immunology welcome
nature immunology
What are NI editors looking for?
NoveltyInterest to the general immunologistSizeable step forwardImpact in the fieldProvide new directions for researchProvide fundamental insights into the workings of the immune system
nature immunology
Elements of a “strong contender”
Clear presentation of an interesting questionIntro creates interest – why should reader care?Strong, well-controlled dataRules out some alternative explanationsSpeculation doesn’t “stretch the data”Discussion puts paper in perspectiveData is significant step forward with broader implications
nature immunology
Reasons for rejection
Lack of mechanistic insightCatalog of dataData do not support conclusionsRaises many interesting possibilities, but doesn’t begin to distinguish between themNew, but not a large enough step in fieldLacking in significant noveltyOnly of interest to specialists in a subfieldExperiments all performed in cell lines No broad conclusions
nature immunology
Editor(Juan Carlos Lopez)
6 manuscript editorsNew York, London, San Francisco
Nature Medicine editorial structure
• Cardiovascular• Infectious disease, immune system• Cancer• Metabolic disease• Neuroscience• And others
• Direct relevance to human disease• Mechanistic and molecular insight
Mechanisms involved in disease processesRelevant animal modelsHuman clinical samples or data from patients
New therapeutic agents or strategiesMechanism of action in vivo
What are we looking for?
Important question, new concepts Therapeutic advances, even in the absence of conceptual advance Technically convincing
Definitions: “The process of applying ideas, insights and discoveries
generated through basic scientific inquiry to the treatment or prevention of human disease” (NIH)
Taking ideas from clinical research back into experimental settings
We are eager to publish translational research Research involving humans is difficult High standards should be maintained
How does “translational research” fit in?
September 2004 editorial (10:879)
Create new disease model, but have not yet used it to learn something new about the biology of the disease
Experiments all done in cell lines, ex vivo
Compound works great, but mechanism is unclear
Gene or protein profiling Provocative changes, but functional importance in vivo is unclear For diagnostics, need prospective study, blinded samples
Mutation identification Effect of mutation on protein function or expression not clear Provides limited new insight into disease process
Probably not right for NM
January 2004 editorial (10:1)
What happens to submitted papers?
• ~280 papers received per month• Each paper read in detail by one editor, discussed by all• ~75-85% returned without review in 1-2 weeks• ~15-25% are sent for review, 2-4 referees• Decision for reviewed papers takes 4-6 weeks • ~ 5% of submitted papers are published
Most reviewed more than once Most are substantially revised