2020-06 update: Thanks to Oya Rieger, Alex Mendonça, Emily Marchant, Iratxe Puebla, John Inglis, Martyn Rittman, Mate Palfy, Sowmya Swaminathan, Alice Meadows, Katie Funk, and Allison Leung for input into this revision.

Have a question that isn’t answered below? Please feel free to email it to jessica.polka@asapbio.org.

General

  1. What is a preprint?
  2. Are preprints compatible with journals?
  3. Can a preprint help my journal submission?
  4. Why do people use preprints? What is their value?
  5. What constitutes a preprint and when should I submit my work as a preprint?
  6. As a journal, institution, or funder, do we have to run a preprint server?
  7. As a journal, how can we make sure that we are open for submission of preprints?
  8. Do preprints work with double blind review?
  9. Do funders and job search committees give credit for preprints?
  10. Why publish a paper if the work is already a preprint?
  11. Where can I find preprints? Will preprints be integrated with PubMed or a similar service?
  12. Can preprint commentary harm my paper?
  13. What are the main arguments against preprints or possible unintended consequences?
  14. What are the preprint servers for biology?
  15. Without peer review, how do I know if a preprint is flawed?
  16. Do preprints establish priority?
  17. How should I cite a preprint in a journal publication?
  18. Are preprints open access?
  19. What if incorrect information gets disseminated to the broader public?
  20. Can I preprint if I want to patent my work?

Submitting preprints

  1. What should I consider before preprinting?
  2. How should I prepare my preprint before hitting the submit button?
  3. Can I submit to multiple preprint servers?
  4. Which journals allow preprints?
  5. What license should I choose for my preprint?
  6. Does a preprint differ from a journal submission?
  7. When should I preprint?
  8. Do I need to submit all of the information on how the work was done (e.g. all Methods)?
  9. What about sharing data, code and reagents described in a preprint?
  10. What about co-submission of papers from different laboratories?
  11. What if I want to revise my preprint?
  12. What if I want to withdraw my preprint?
  13. What if I have been “scooped” by another paper appearing in a journal or a preprint server? Should I submit a preprint?

Scooping

  1. Introduction to scooping FAQ
  2. ArXiv founder Paul Ginsparg’s thoughts on scooping
  3. Can preprints help in cases of unintentional “scooping” (two groups are working on the same problem; work from one lab appears first)?
  4. How can preprints help cooperation between competing groups?
  5. In establishing priority, could I be unlucky and get scooped during the publication process itself?
  6. Will my preprint be seen? How do I know if my work is not cited because it was wrongly ignored or because other scientists are just not looking at preprints?
  7. Will preprints result in lots of small, poor quality postings just to prevent getting scooped and claiming priority?
  8. Can my journal submission be scooped by the appearance of a preprint from another group, leading to editorial rejection of my paper?
  9. Can preprints help prevent scooping from presentations at meetings?
  10. Would my preprint enable my competitors to catch up?

What is a preprint?

A preprint is a scientific manuscript that is uploaded by the authors to a public server. The preprint contains data and methods, but has not yet been accepted by a journal. While some servers perform brief quality-control inspections (for more details on the practices of individual servers, see asapbio.org/preprint-servers), the author’s manuscript is typically posted online within a day or so without peer review and can be viewed (and possibly translated, reposted, or used in other ways, depending on the license) without charge by anyone in the world. Most preprint servers support versioning, or the posting of updated versions of your paper based upon feedback and/or new data. However, most servers also retain prior preprint versions which cannot typically be removed to preserve the scholarly record. Preprints allow scientists to directly control the dissemination of their work to the world-wide scientific community.
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Are preprints compatible with journals?

Yes. While both preprints and journal articles enable researchers to disseminate their findings to the research community, they are complementary in that preprints represent an opportunity to disseminate at an early stage. 

In most cases, the same work posted as preprint also is submitted for peer review at a journal. Thus, preprints (rapid, but not validated through peer-review) and journal publication (slow, but providing validation using peer-review) work in parallel as a communication system for scientific research. 
In many fields, the majority of journals allow submission and citation of preprints. To get a sense for preprint policies, you can check SHERPA/RoMEO, Transpose, or Wikipedia’s List of academic journals by preprint policy. However, before submitting a manuscript, always check the journal’s website for recent changes or any nuances of their policy.


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Can a preprint help my journal submission?

Many preprint servers are integrated with one or more journals, making it possible to submit to both a server and a journal at once. View these integrations in the Preprint Server Directory.

Preprint servers can also serve as a “marketplace” for journal editors to invite submissions to their journals. PLOS Genetics has “preprint editors,” described in this article. Proceedings of the Royal Society B also have a preprint editor. Read more on our page about journal policies and practices.

Commentary on preprints (whether on the preprint site, on social media, or on sites such as preLights, PREreview, or Peer Community In) can help authors to improve their paper, and could also be used to inform the journal peer review process. For example, PLOS is piloting a program in which authors can opt-in to having community comments on preprint servers considered by editors along with traditionally-submitted peer review. The Review Commons platform (a collaboration between ASAPbio and EMBO) allows authors to post refereed preprints which can also be submitted to affiliate journals.


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Why do people use preprints? What is their value?

Because journal publication can be slow and the peer review process unpredictable, preprints provide a mechanism for rapidly communicating research with the scientific community. This is good for science overall, since disseminating new knowledge or techniques leads to new discoveries. However, there are tangible benefits to the scientist who uses preprints, a subset of which are described below. Many of these points are also articulated in a commentary in Science Magazine (May 20, 2016).

  • Speeding up discovery of interim work when timely information is particularly valuable (such as the COVID-19 pandemic – see ASAPbio resource on COVID-19 and preprints)
  • Evidence of productivity and accomplishment. A preprint provides funding agencies and promotion and hiring committees with public evidence of your most recent accomplishments, which is pertinent for their decision-making.
  • Increasing visibility and attention. Posting a preprint increases social media attention and citations (Serghiou 2018, Fraser 2019, Fu 2019). It also promotes invitation to meetings since organizers are often looking for recent work not published in journals.
  • Feedback on your work. You can send the link of your public preprint to fellow scientists and ask for comments. Sometimes scientists might contact you through email or through commentary on the server. These type of interactions and feedback can help you to improve your final journal publication beyond the two or three anonymous scientists who review your paper for a journal.
  • Establishing priority of discoveries and ideas. Preprints are the main mechanism for disseminating work and establishing priority in the physics community, and we anticipate this developing in biology (see draft document from the recent ASAPbio meeting and an eLife article by Vale and Hyman).
  • Potential for developing new collaborations earlier. Once your technique or results are in the public domain, new interactions can occur which can advance your work.
  • Free access to your work. Your research is made available to all scientists without requirement of subscription or journal-imposed paywalls.

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What constitutes a preprint and when should I submit my work as a preprint?

A preprint is usually the same manuscript that is submitted to a journal, although other types of information that are currently difficult to publish (e.g. negative results) could be transmitted. Please see our related questions in the “Submitting preprints” section.


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As a journal, institution, or funder, do we have to run a preprint server?

Many publishers have launched their own preprint servers (including Wiley’s Under Review, Springer Nature’s use of the Research Square In Review service, and MDPI’s preprints.org).
However, there is no need for a journal to launch their own preprint server as there are many repositories that can fulfill this function. For a list of servers relevant to the life sciences and their characteristics, see the Preprint Server Directory.


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As a journal, how can we make sure that we are open for submission of preprints?

Design a clear and comprehensive preprint policy and include it in the Instructions to Authors. You may want to consider elements such as:

  • What version of the manuscript can be posted? First submitted, after peer review, all versions (including postprints), etc?
  • What licenses on preprints are supported? 
  • Can preprints be cited in the reference list?
  • Are authors free to post on any server?
  • What type of media coverage of the preprint can or should authors engage with?
  • Do you wish to offer any scoop protection policy, such as is offered by EMBO Journal, eLife, and PLOS Biology?

For sample preprint policies, see eLife, PLOS, and Nature Research.

Ideally, collect preprint information (such as the DOI or other identifier) upon manuscript submission. Consider technological integrations with preprint servers to facilitate manuscript transfer (eg B2J and/or J2B for bioRxiv and medRxiv, SWORD protocol to link to PKP’s OPS, etc).


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Do preprints work with double blind review?

A review process is considered “double blind” if neither authors nor reviewers are aware of one another’s identities. Though it is relatively rare in the life sciences, it is more prevalent in social science and the humanities. Double blind review is one approach to mitigating biases in review, which can range from a bias against female corresponding authors (noted in studies of Frontiers, eLife, and AGU journals) to a bias towards authors within reviewer’s own co-author networks. For those journals and disciplines that use double blind review, it is an important part of their peer review process.

However, double blind peer review cannot eliminate all biases since many decisions fall with editors, and because many reviewers can already successfully guess the identity of authors. As summarized by Hilda Bastian: “The rate of failure of blinding [in 8 trials] was high: average failure rates ranged from 46% to 73% (although in 1 journal within one of the trials it was only 10%).” The rates of blinding failure may be influenced by how stringently authors obfuscate their identities in the manuscript, for example in referencing previous work.

Preprints might make it more difficult to preserve blinding. Currently, no preprint servers enable anonymous posting; doing so could compromise many of the benefits of preprints, such as visibility and recognition, and raise challenges related to ethical disclosures. COPE discourages pseudonymous preprint posting for similar reasons. That said, there are also many other sources of information that could compromise blinding. For example, seminar announcements, conference abstracts or programs, or social media posts are all searchable on the web. It is expected, however, that referees participating in double blind review will not attempt to discover the identities of manuscript authors, and will recuse themselves from reviewing papers with authors known to them.

This means that any early visibility of work can either harm the integrity of the double blind review process (if reviewers ignore requests to avoid attempting to identify authors) or make it more difficult to find suitable reviewers. While exacerbated by preprints, this problem is by no means unique to them.


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Do funders and job search committees give credit for preprints?

We are tracking the policies of both funders (including NIH, HHMI, Wellcome, MRC, HFSP, CZI, CIHR, Simons, EMBO, Helmsley, Cancer Research UK, & BBSRC) and universities that have considered preprints in assessment processes (including UC Davis, NYU, UCSC, UT Austin, and the Rockefeller University).

For example, On March 24, 2017, the US NIH released NOT-OD-17-050, which clarifies that “The NIH encourages investigators to use interim research products, such as preprints,” which can be “cited anywhere other research products are cited.” More details can be found in a subsequent NIH blog post

In the UK, preprints constitute valid output for REF2021.

Some funders (CZI, MJFF, and Aligning Science Against Parkinson’s) now require preprints. In 2021, Wellcome will begin to require preprints in case of a “significant public health benefit.”


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Why publish a paper if the work is already a preprint?

In the present day reward system, journal publications play a major role in funding and promotions. For such reasons, the vast majority of research-paper preprints in physics (ie, not meeting proceedings, reviews, etc) are also submitted to journals (see slide 13 in Paul Ginsparg’s talk), even though work is one’s field is generally always seen and discussed first as a preprint.

However, journals provide many services for improving and validating work, which are labor-intensive:

  • Journals provide an infrastructure for peer review and quality control. Journal-based peer review remains the present-day gold standard of validation, despite its shortcomings.
  • Many journals offer copyediting and other production services that enhance the final version, or Version of Record.
  • Visibility of work is promoted by broad journal readership or added journal features (highlights, perspectives, coordination of press releases, etc).
  • A paper can improve through revisions and editorial corrections.
  • A journal can provide assurance that the authors have complied with standards of the field for database depositions, conflict of interest disclosures, and other issues.

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Where can I find preprints? Will preprints be integrated with PubMed or a similar service?

Europe PMC began indexing preprints in July of 2018. Preprints are also indexed in search tools such as Google Scholar, PrePubMed, and OSF preprints.

On June 1, 2020, NCBI announced a pilot to include NIH-funded preprints in PubMed Central, beginning, in the first phase, with preprints relevant to COVID-19.


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Can preprint commentary harm my paper?

Some preprint servers discourage anonymous commentary. This mitigates potentially harmful commentary, since the individual is disclosed and will have to stand by their remarks. Indeed, in some cases, commentary might help a submitted paper (see Can a preprint help my journal submission?”). However, the usefulness and perhaps unintended consequences of commentary on preprint servers should be evaluated especially when more data has been acquired on this important issue. The sources of commentary received and desired by authors was documented in a survey of bioRxiv authors.


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What are the main arguments against preprints or possible unintended consequences?

The following have been raised as possible negative consequences of preprints.

  • Poor quality and irreproducible data will be posted in preprint form.
  • Scientists will rush out data pre-maturely to claim priority and get credit.
  • Scientists will try to “scoop my work” if I post as a preprint.
  • Reporters and other non-specialist will use the findings without recognizing the interim nature of papers.

Poor quality publications, irreproducibility, and scooping are already issues with our journal system, but there is no current evidence that the situation will worsen with preprints. Most of these (with the exception of human research) have been tested with physics research and have not come to pass with arXiv; nor is there any indication that these problems are surfacing in biology preprints. See the Q&A on scooping by Paul Ginsparg, founder of arXiv.

In practice, these tendencies are mitigated by the powerful driving force of scientists to develop and maintain a good reputation within the scientific community. Reputation is the single most important factor for developing a sustained career in the sciences. Even for scientists who voice the above concerns, when asked if they might be tempted to behave in such manners they immediately respond “no.” In fact, in some instances, poor quality/irreproducible work might be spotted by the community and corrected before reaching final publication in a journal.

Note that preprints are considered public disclosure for the purposes of patenting. See “Can I preprint if I want to patent my work?” below.


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What are the preprint servers for biology?

There are many options. bioRxiv has been steadily growing in preprints posted per month since 2014, and the more recently-launched Research Square (populated by the In Review service used by Springer Nature) has been rapidly expanding. medRixv is a sister to bioRxiv hosting clinically-relevant preprints. Each server varies in its disciplinary scope, screening and withdrawal policies, and technological features. To learn more, visit the Preprint Server Directory.


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Without peer review, how do I know if a preprint is flawed?

You do not and you should be aware that it could be flawed. However, you should apply a similar wariness to journal publications since peer-review often misses important flaws in papers.

Preprint commentary by experts in the field, whether in the preprint server’s comment section, on a third-party review site, or on social media, can help to put findings into context.


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Do preprints establish priority?

In the physics community, preprints posted on arXiv clearly establish priority of discovery since they have a time stamp, are publicly available and are widely cited (for more on arXiv, see Paul Ginsparg’s comments on scooping). An article on the topic of priority in the life sciences community by Ron Vale and Tony Hyman has appeared in eLife.


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How should I cite a preprint in a journal publication?

Most journals allow citation of preprints in the reference list of the article in question, similar to journal articles. The NIH has recommended a preprint citation format that makes clear the status of the work as a preprint and includes its DOI. While ArXiv does not use DOIs, they have their own persistent identification system.


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Are preprints open access?

While all preprint servers relevant to life sciences currently allow readers to access the text for free, many preprints do not conform to the original definition of open access, which allows redistribution and reuse. In order to enable these functions, authors can choose to apply a Creative Commons license. For more information, see our Preprint Licensing FAQ. Furthermore, some preprint servers require readers to register before use (see the “Reader Registration” field in the Preprint Server Directory).


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What if incorrect information gets disseminated to the broader public?

There are legitimate concerns that preprint servers may become venues for posting and providing some validation for “pseudoscience,” low-quality research results, or even papers that pose serious ethical or national security concerns.

Many preprint servers screen papers before posting. arXiv has faced these issues with climate science and has largely managed to block or mitigate issues surrounding attempts to propagate misinformation. 

Since the potential public impact of papers relevant to public health increases the dangers of posting misleading information, the medical preprint server medRxiv carries out more stringent screening than bioRxiv. While there are dangers inherent in distributing medically-relevant information prior to peer review, the server has also been influential in increasing early feedback and visibility of important COVID-19 research and thus played a major role in pandemic response. See ASAPbio’s resource on preprints in COVID-19.

Furthermore, some preprint servers display disclaimers on the top of each article to make clear that preprints have not been certified by peer review. In fact, it can be much more damaging when misinformation is conveyed through a journal, which carries an implicit stamp of approval from the scientific community (a case in point being the connection of vaccines to autism which was published in a major medical journal).

Many preprint servers also have policies about when content can be completely removed for ethical or legal reasons. The leak of personal data from the dating website OKCupid under a scientific pretense provides an example of behavior in this category.

For more information about screening, withdrawal/removal, and disclaimers, see the Preprint Server Directory.


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Can I preprint if I want to patent my work?

Preprints, like journal articles, are considered public disclosures, which can affect a patent application. Therefore, if you intend to file an application to patent work disclosed in your paper, discuss the situation with your technology transfer office before preprinting.


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What should I consider before preprinting?

Before preprinting, we suggest completing the following steps:

  • Double check journal policies on when and where preprints may be posted. 
  • Choose a preprint server. Consider visibility, funder recommendations, and features like preservation and indexing, which are cataloged in the Preprint Server Directory.
  • Choose a license.
  • Get all authors on board with preprinting. Refer to the resources in the Preprint Info Center (including these FAQ) to address any unanswered questions. 
  • Upload any code/data/reagents you want to share to appropriate repositories.
  • Post the preprint!
  • Invite feedback via social media or email.

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How should I prepare my preprint before hitting the submit button?

Prepare your manuscript as carefully as you would for a journal submission, if not more so. In bioRxiv, all versions submitted are retained and can be viewed.

Unlike a journal submission, which will be seen by only two or three anonymous peer reviewers, your posted preprint is public and the scientific community will be able to judge your work immediately. Thus, be sure that your preprint meets the benchmarks of rigor and quality that you aspire for yourself or your laboratory. A well-constructed preprint will help to build your scientific reputation. In contrast, a hastily submitted preprint with scientific errors (or even grammatical mistakes) might be detrimental. An editor and the peer reviewers can help to correct mistakes as part of the services of journal submission; however, for a preprint, the burden of quality control belongs to authors. We recommend that the submitting authors perform a rigorous internal review process, which can involve lab members or scientists outside of your lab.

Also ensure that the author list provides appropriate credit to contributors, as you would for a journal article or meeting abstract submission.


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Can I submit to multiple preprint servers?

Posting on multiple preprint servers can cause challenges both for authors and readers. Authors may find it difficult to keep all versions updated, and it can cause citations and other usage metrics to be split between multiple copies, making it harder to track downstream impacts of the work. Indexing services and search tools may also have to manage duplicate copies, potentially giving preference to the display of one over the other.

The impetus for submitting to multiple preprint servers is often to increase the potential exposure of a paper. This can be more easily accomplished by sharing the preprint with colleagues through email and social media.


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Which journals allow preprints?

Many journals that publish biological research allow preprint submissions. To get a sense for preprint policies, you can check SHERPA/RoMEO, Transpose, or Wikipedia’s List of academic journals by preprint policy. However, before submitting a manuscript, always check the journal’s website for recent changes or any nuances of their policy.


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What license should I choose for my preprint?

You can refer to the Licensing FAQ and discuss these options with your co-authors before beginning the submission process. Note that the NIH has encouraged the use of CC BY licenses, and we are not aware of any journals preventing the posting of preprints with a Creative Commons license. You can see which licenses are offered by which servers in the Preprint Server Directory.


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Does a preprint differ from a journal submission?

In most cases, they are the same in content. However, the preprint could offer more freedom in terms of format. For example, the short communication format of many journals has strict guidelines for length, formatting and often has only a paragraph of introduction and conclusion. However, in a preprint, you could extend the introduction, conclusion and references to provide more context for the work. Additionally, a preprint can be uploaded in a single PDF file without the complicated forms for uploading separate images that are common for journal submissions.

Furthermore, preprints do not need to be tied to journal submission, meaning that you can post a complete scientific manuscript and continue to revise it until you are ready to submit to a journal.


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When should I preprint?

This is your decision and depends on when you have complete scientific work ready to share. In many cases, where the manuscript will be sent to journals as well, preprints are submitted close to the time of journal submission. Several journals have enabled one-click manuscript transfer from bioRxiv. Some scientists may want to post a preprint publicly for a few weeks before submission and point their community to this version for initial feedback. Some editors invite submissions from preprint servers, and some journals have even appointed specialized “preprint editors” to do this work.

Some investigators may decide to submit after receiving the first set of reviews. However, it is important to note that some journals do not allow new versions to be submitted after peer review for continued consideration at the journal. 

It’s important to consider the policy of the preprint server as well. For example, bioRxiv allows submission anytime prior to journal acceptance, but not after. If the version posted to another server is the one that was accepted by a journal (equivalent to the AAM, or “author accepted manuscript”), this is considered a postprint instead of a preprint. You can check journal policies about self-archiving (also known as Green Open Access) at journal websites and SHERPA/RoMEO.

Whatever you decide, it’s best to be transparent with the journal editor about your preprint by notifying them when you post or in your cover letter.


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Do I need to submit all of the information on how the work was done (e.g. all Methods)?

A preprint should fairly and completely disclose the data and methods that are necessary to evaluate and replicate the work, just as in a journal publication. If properly performed, then authors should also receive credit and be properly cited for their discovery. As with the formatting question above, a more complete description will help a scientist to build a positive reputation for thorough and open scientific communication.


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What about sharing data, code and reagents described in a preprint?

This is a grey area and one that might change over time. Currently, authors may benefit from sharing reagents, code, and data after a preprint posting but are not required to do so, in contrast with most journal publications. Sharing ahead of publication may seed new collaborations, accelerate discovery, and also enhance the group’s reputation for being cooperative. A large survey conducted by the Center for Open Science found that links to data and materials improved perceptions of a preprint’s credibility. 


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What about co-submission of papers from different laboratories?

With preprints, it is simple to co-submit and have work from different groups appear at the same time. In contrast, a journal may not want both papers or one paper may be delayed to referee requests.


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What if I want to revise my preprint?

Most preprint servers allow new versions of the manuscript to be uploaded. Thus, you can update your paper based upon new experiments or input received from the community or through a journal-based peer review process, unless specified otherwise by the journal. For example, on bioRxiv it is quite easy to tell when a new version has been posted, which reduces concerns about multiple versions. However, the original and all subsequent versions of the paper are retained and can be viewed. Most journals will not allow the final copy edited, journal-approved version to be uploaded. Please check the exact policy of the journal to which you submitted your work.


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What if I want to withdraw my preprint?

In order for preprints to be considered permanent research objects that are able to be cited and used to demonstrate productivity for grants or job applications, readers must be able to cite them without fear that they will spontaneously become unavailable. Therefore, removal of preprint files is typically reserved for cases where there are significant ethical or legal concerns with the original paper.

Instead, most servers allow authors to post a new version of a preprint, which is in some cases displayed preferentially even though the old version can still be viewed and cited. Some servers enable withdrawal of preprints (similar to retraction of a paper) by posting a new version of the paper that is effectively a withdrawal notice. See details on servers versioning and withdrawal/removal policies in the Preprint Server Directory.


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What if I have been “scooped” by another paper appearing in a journal or a preprint server? Should I submit a preprint?

Many scientists are working in the same area, and papers from two or more groups that appear within a short period of time are usually recognized as having been performed independently. The advantage of a preprint is that you can post your work without any delay and therefore close to the publication date of the other work. Of course, any manuscripts submitted (whether to a journal or preprint server) should fairly cite and discuss related work regardless of where it appears.


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Introduction to scooping FAQ

ASAPbio receives many inquiries regarding preprints and “scooping.” As jobs and grants become very competitive, there is increasing worry among biologists about scooping, ie that their ideas/results will be published by others and that they will not receive proper attribution.

Here we try to break down the issue of scooping into specific scenarios and points of view. However, it is worthwhile prefacing these remarks that scooping, while it can occur, is less prevalent than one might think. Most work is unique or unique enough that concerns of scooping do not compromise publication. Furthermore, even though reagents have become more available and assays easier to perform, most work is not that easy to replicate in a few weeks by an unscrupulous scientist.

The key question is whether preprints will have unintentional consequences of engendering bad behavior and making biologists more vulnerable to scooping compared to a journal-only publication. Our argument is that this is unlikely, and indeed there is likely to be greater protection and overall fairness in establishing credit for work by submitting both to a preprint server (for fair and timely disclosure) and to a journal (for validation by peer review), as discussed below.


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ArXiv founder Paul Ginsparg’s thoughts on scooping

Since arXiv has a long track record and experience, we asked the following question to Paul Ginsparg, physicist and founder of the preprint server arXiv:

“Many biologists worry that they will get “scooped” if they place their work on a preprint server. How common is it for someone to see a study posted on arXiv and then try to rush their own paper to a journal to claim credit and try to receive more recognition for the work?”

His response:

It can’t happen, since arXiv postings are accepted as date-stamped priority claims.

Eventually I came to understand that biologists do not use “scoop” in the standard journalistic sense, where it means an exclusive news item of exceptional importance or surprise, with no unethical connotation. Instead “scooping” in the context of biology research appears to mean using information or ideas without proper attribution. This is dishonest, of course, regardless of the source. Similarly, when biologists are described as “competitive”, it is apparently connotes some form of unscrupulous behavior. I’d long responded that physicists are as or more competitive, in the sense of being eager to be first to discover some new phenomenon and get credit for it, but now clarify that competitive ordinarily stops well short of cheating or stealing. On the other hand, while fear of such unethical behavior may seem widespread in biological circles, it’s not at all clear how prevalent the behavior is in reality, or for that matter would be if preprints were widely available.

Whether or not the concerns are exaggerated, though, the long-term solution could still be systematic posting of preprints, and consensus of the community that it counts for staking intellectual precedence. There might be some intermediate pilfering phase, but a few high profile cases of admonishment and censure would quickly establish a proper ethos.

Once preprints achieve higher number, visibility, and easier searchability within a subcommunity, no one can plausibly claim they “did not see it”. Vale and Hyman have recently discussed the principles for establishing “priority of discovery”, disentangling disclosure from validation, and examine how journal publication dates can obscure priority.

Biology partitions into subcommunities with sizes ranging from many hundreds into the thousands of researchers, just as in physics and other research areas, so the self-policing mechanisms can be just as effective.

As for concerns that research in biology is fundamentally different from other fields, there are many ideas or calculations in theoretical physics that are much easier to reproduce and claim than would be an experiment in biology. And various tabletop experiments in condensed matter physics might be roughly comparable to those in biology in that regard.

But the experience has been that unexpected or rapid progress leads to increased preprint usage within communities, precisely to stake priority claims, and that increased usage remains the norm afterwards.


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Can preprints help in cases of unintentional “scooping” (two groups are working on the same problem; work from one lab appears first)?

This happens to every scientist at some point. We look at PubMed or examine the latest table of contents in Journal X and find a similar study. Often, there is no bad intention, just different labs in a similar field converging on the same topic. Naturally, this scenario can be very dispiriting to the student or postdoc from “second group” whose work is not yet published.

With Preprints: If the “second” group is close to the completion of their work, then they can post their findings on a preprint server. The “first” preprint or journal publication should be cited in this work. If the “second” work appears within a few weeks, it is clear that this work was performed independently as the time span between the two disclosures is too short for the “second group” to have initiated and completed the study de novo after the announcement of the first paper. Some journals offer “scoop protection” policies that honor the priority claims of preprints even if published literature has appeared in the intervening time.

Without Preprints: If the “second” group tries to make their disclosure in a journal, then the situation is less predictable. First, many journals might reject the work editorially or after peer review because it is too similar to already published work (even though it was performed independently and at approximately the same time). Furthermore, the journal publication will take time (potentially months), thus creating a larger time gap between the first and second study and making more ambiguous what the second group achieved independently at the time of the disclosure of the first group.


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How can preprints help cooperation between competing groups?

This is an ideal and not infrequent situation where two groups become aware of similar work and wish to “co-disclose” or “co-publish” together to obtain a similar time stamp.

Preprints: This situation is very easy to navigate with preprints, since the disclosure is under the control of the scientists. The groups simply have to agree upon a date when they will submit to a preprint server. The coordinated submissions then receive the same time stamp and are made available to the scientific community concurrently. There are no hassles and no unpredictability.

Journals: The same outcome can be achieved with journals, but with greater difficulty and uncertainty, since:

  • The different scientific groups may decide to submit to different journals, based upon journal preference or likelihood of being accepted. Coordination the timing of publication date between two or more journals is possible but often becomes difficult. Generally, one journal must be pressured to speed up its publication pipeline for fear of being second.
  • If submitted to the same journal, the journal may ultimately decide to only accept one of multiple submissions given demands for journal space.
  • The referee process can be unpredictable in the same or different journals, making it difficult or impossible to coordinate timing. One paper might also get rejected at the very end of the pipeline.

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In establishing priority, could I be unlucky and get scooped during the publication process itself?

Let us imagine a scenario in which two groups with similar discoveries backed by similar quality of data submit to two separate journals at the same time. For one group, the journal sends out the work for review, the reviews are favorable, and the work is published quickly. However, the other group is less fortunate and subject to the “samsara” of resubmissions and revisions; two journals reject the work and the third journal requires lengthy revisions. While imaginary, most scientists have done an even better controlled experiment of submitting the same paper and receiving different outcomes- rejected by top journal X and top journal Y, then proceeding rapidly to publication in top journal Z.

By submitting only to a journal, the scientist loses control of the timing of when their discovery is made public. That decision is made by a journal editor. In some cases, one can be lucky and it might sail through. In other cases, it may have to undergo many rounds of journal submissions and revisions. There is also perception and (perhaps a reality) that the top scientists at top institutions have an easier time getting work published quickly in top journals, whereas younger scientists and scientists from less well-known institutions can have a harder time. Preprints provide transparency, equity, and reliable timing of disclosure.

Furthermore, the initial manuscript submissions to journals are lost from the historical record. A scientist cannot claim “I made the discovery at the same time as scientist Y” but my paper took longer to get published. The journal review process occurs “behind the curtain”, the community and history will never know exactly what a scientist discovered or how data was interpreted <u>when</u> he/she initially submitted the work to a journal; there is no public record of this submission. Perhaps an injustice occurred when the journal delayed publication, thus delaying the transmission of an important discovery. However, perhaps there were fundamental problems in the data or in the original interpretation which came to light during the review. We simply don’t know.

Although not the intention of this article, Eric Lander’s article The Heroes of CRISPR (Lander, 2016 Cell) illustrates the unreliability of using journals for establishing the timing of disclosure with several examples:

“Mojica went out to celebrate with colleagues over cognac and returned the next morning to draft a paper. So began an 18- month odyssey of frustration. Recognizing the importance of the discovery, Mojica sent the paper to Nature. In November 2003, the journal rejected the paper without seeking external review; inexplicably, the editor claimed the key idea was already known. In January 2004, the Proceedings of the National Academy of Sciences decided that the paper lacked sufficient ‘‘novelty and importance’’ to justify sending it out to review. Molecular Microbiology and Nucleic Acid Research rejected the paper in turn. By now desperate and afraid of being scooped, Mojica sent the paper to Journal of Molecular Evolution. After 12 more months of review and revision, the paper reporting CRISPR’s likely function finally appeared on February 1, 2005 (Mojica et al., 2005)”

[…]

“The authors proposed that the CRISPR locus serves in a defense mechanism—as they put it, poetically, ‘‘CRISPRs may represent a memory of ‘past genetic aggressions.’’’ Vergnaud’s efforts to publish their findings met the same resistance as Mojica’s. The paper was rejected from the Proceedings of the National Academy of Sciences, Journal of Bacteriology, Nucleic Acids Research, and Genome Research, before being published in Microbiology on March 1, 2005. 

Finally, a third researcher—Alexander Bolotin, a Russian emigre who was a microbiologist at the French National Institute for Agricultural Research—also published a paper describing the extrachromosomal origin of CRISPR, in Microbiology in September 2005 (Bolotin et al., 2005). His report was actually submitted a month after Mojica’s February 2005 paper had already appeared—because his submission to another journal had been rejected.”

[…]

“Siksnys submitted his paper to Cell on April 6, 2012. Six days later, the journal rejected the paper without external review. (In hindsight, Cell’s editor agrees the paper turned out to be very important.) Siksnys condensed the manuscript and sent it on May 21 to the Proceedings of the National Academy of Sciences, which published it online on September 4. Charpentier and Doudna’s paper fared better. Submitted to Science 2 months after Siksnys’s on June 8, it sailed through review and appeared online on June 28.”

Some journals, including EMBO Press titles, offer scoop protection at the time of preprint posting.


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Will my preprint be seen? How do I know if my work is not cited because it was wrongly ignored or because other scientists are just not looking at preprints?

Many physicists, mathematicians and computer scientists use arXiv and as Paul Ginsparg articulates in his comments about scooping, it is not plausible to claim that “I never saw it.” Preprints are undergoing a transition in some fields of biology where the numbers are still small and many scientists do not know about them. This situation will likely change in the future as they are integrated into more search tools and become more  discoverable. However, even now, preprints are permanent public documents with DOI. They are a record of an accomplishment that can be pointed out to any other scientists, cited in journals, and in funder applications and reports


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Will preprints result in lots of small, poor quality postings just to prevent getting scooped and claiming priority?

There is no indication that this type of behavior has emerged in the physics, mathematics, and computer science communities as a result of wide-spread use of preprints. Scientists do not engage in quick posting of low quality work because they are wary of developing a bad reputation in the community. Furthermore, if the work is poor, then it will likely just be ignored by the rest of the community. A discovery is not just a date stamp; there has to be clear data supporting the discovery and clear articulation of the nature of the discovery in order to make an impact on the scientific community.That said, preprints could potentially allow authors to post (and update) papers throughout the process of their development, enabling them to share findings with the community before polishing them into a more comprehensive story.


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Can my journal submission be scooped by the appearance of a preprint from another group, leading to editorial rejection of my paper?

Another group posts a preprint on a similar work to my own. I decide that I do not want to submit a preprint but rather go straight for a journal publication. Will the chances of my publication be jeopardized by the appearance of this earlier preprint?

We have discussed this scenario with several journals and the response received so far is that editors consider only peer-reviewed work in applying criterion of originality. They do not use preprints as a basis of deciding whether to send work out for review and ultimately accept it. For example, Nature Research’s preprint policy states that “Manuscripts posted on preprint servers will not be taken into account when determining the advance provided by a study under consideration at a Nature Research journal.” 

We note that intentionally ignoring and failing to cite the earlier preprint in an appropriate way in one’s own journal article (or preprint) would be deceitful, as it would be intentionally ignoring work from a scientific colleague in order to advance one’s own work. Such behavior is not tolerated in the physics community (see comments by Paul Ginsparg). It should not be tolerated in biology as well.


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Can preprints help prevent scooping from presentations at meetings?

Scientific meetings are increasingly becoming dominated by published or soon to be published data (e.g. manuscripts that are accepted). Many scientists are wary of sharing earlier stage work, even if they have a manuscript in hand, since they have no idea how long it might take to get published. Meeting presentations and posters are generally not citable and only a limited number of individuals have access to the talk/poster, making it difficult to use these formats to establish priority. In contrast, a preprint is a public, globally-accessible document and is citable. Thus, if a scientist wishes to disclose new data at a scientific meeting, they have the option of also reporting that data either before or after the meeting in the form of a preprint. In contrast, if the presented work is only submitted to a journal, the time until public disclosure is not certain.


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Would my preprint enable my competitors to catch up?

Naturally, the answer is yes. But the same is true for a journal publication. Once work is public, the entire scientific community can make use of the new knowledge; this is how the scientific enterprise advances as whole. That is why preprints are valuable for science, society, and the public and funding agencies who pay our salaries and enable our research.


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