Preprint 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.

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.

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.

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.

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.

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

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.

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.

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.

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.