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