When to preprint?
At what stage in the life of a research paper should you preprint it? It depends on the circumstances of the study, but there are roughly four options.
Cite as: Kamoun, S. (2022). When to preprint? Zenodo https://doi.org/10.5281/zenodo.6980124
In the digital age, anyone can be a publisher. You can write a paper, a book, a blog post, film a video, and then with just one click upload them to the internet. Et voilà! Anyone with internet access can read and watch your production.
Around 1990, when I was a PhD student, I bought a Sony Handycam camcorder — a pretty impressive video camera by that day’s standards. I filmed a few short movies, which I thought were quite fun to watch. But hardly anyone could view them. I would have loved to share them with a wide audience, but back in those days, unless you were a cinematographer or connected to a TV station, your audience will be limited to friends and family. I estimate that at most 10–15 people watched my camcorder videos.
Contrast that with today’s digital age. You can tweet a video clip or post it on YouTube and you may get thousands of views from friends and strangers alike. This impromptu video of world beefsteak expert and fellow plant scientist Sebastian Schornack reviewing Burger King’s Impossible Whopper — the meat-like burger made from plants by Impossible Foods— gathered almost 5,000 views, most of them within a day of posting.
The same transformation has impacted academic publishing. In the old days, filtering the literature was necessary because it was expensive to print articles and books on paper and ship them around the world to subscribers and libraries. Nowadays, you can simply post your paper, your mini-paper, your datatset, your poster, your photos, your videos on one of the popular academic open access publishing platforms like bioRxiv or Zenodo, and anyone can read or watch them. And it’s all free of charge. Free to publish and free to read. It doesn’t cost you a dime to publish in bioRxiv or Zenodo, and anyone can read or watch your productions anytime at no cost.
These modern day academic publishers also allow you to share your work under Creative Commons Attribution (CC) licenses. This is important because CC licenses allow the reuse of material that would normally be prohibited due to copyright laws. CC licenses are critical to the open science movement. You still get full credit for your work and generate a citable academic output but anyone can reuse and share your productions as long as they follow the specified attribution rules.
Also, think what this does to the traditionally restricted literature. Even after you publish your preprint in a journal, you and others can reuse the content under the CC license of the pre-publication thereby bypassing any copyright restrictions the journal may enforce. I still remember the days when lecturers couldn’t easily distribute copies of journal articles to their students for fear of breaking copyright rules. Even today, the current copyright rules remain complicated. But when the article is preprinted, forget about the journal version, just reuse the preprint along with its figures and images.
I wrote that the digital age has impacted scientific publishing. Well, sort of. Academic publishing is still in a transitional phase. Many academics remain reluctant — either by habit or lack of knowledge and understanding of the new options — to fully transition from filter and publish to the publish and filter model and embrace truly transformative initiatives like Plan U — funder preprint mandates. Indeed, the academic community as a whole has been to some degree slow at embracing this cultural revolution. Many of our habits, such as the view that peer-review by 2 or 3 anonymous experts is the only mode of filtering and triaging the literature, have stuck around despite spectacular large-scale failures from glam-mags publishing nonsense to the paper mills.
I discussed this and related topics at an August 2022 workshop on alternatives to classic journal publishing hosted by the dynamic team at the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa. The outrageous article page charges (APCs) billed by the major publishers are hurting everyone, siphoning limited research funds from scientists to the publisher’s deep pockets. Communities, like the FABI scientists are stuck. On one hand, they feel the need to publish in the renowned journals and cough up the hefty fees because this is how they get evaluated and secure funding. On the other hand, FABI and the great majority of the scientists I talk to realize how broken and immoral the system is. Their dilemma is universal. To a younger generation accustomed to the ways of the internet, instant and free publishing comes naturally. In my view, the current publishing culture is one of the main reasons Early Career Researchers (ECRs) drop out of academia and related science jobs. Just think about the worship of the journal impact factors with their 3 decimals. How can any self-respecting scientist feel inspired to join a community that embraces such a toxic, idiotic and non-scientific metric.
What’s the solution? How can we move towards a full embrace of open science and open access? One solution is preprints, arguably the most exciting development of the last decade in academic publishing in the life sciences.
Preprints were of course key to the discussion with the FABI scientists. Preprints are free to publish and free to read. They are central to this new digital era when scientists can freely and openly share anything they produce while retaining credit and producing different types of citable scholarly outputs. Publish and filter. Post your preprint, share it with your colleagues and gather community feedback before you even consider publishing it in a classical journal.
When to preprint?
A pertinent question popped up at the workshop and prompted this post: when to preprint? At what stage in the life of a research paper should you preprint it? The answer varies depending on the circumstances of the study and the paper. But, roughly, we can define four options.
Option C — Classic: simulatenous preprinting and journal submission
The classic way of preprinting and as explained in the ASAPbio FAQ is that the preprint is submitted to a journal around the time it is published on the preprint server. Generally, the version submitted to the journal is identical to the one that is published as a preprint. I would guess that the majority of published preprints belong to this category.
There are now processes that facilitate the transfer of articles between preprint servers and journal. For instance, bioRxiv allows you with one click to submit your Preprint to a Journal or Peer Review Service.
The life science journal eLife has taken things further. They now only peer-review articles that have been previously posted on a preprint server. As they wrote:
“…as of July 1, , we would only be reviewing in-depth articles posted as preprints…we have focused on taking advantage of the unique opportunities preprints provide to build a more open and effective system of peer review… if required, eLife staff can upload articles to bioRxiv or medRxiv on behalf of the authors.”
Option 0–Preprint without submitting to a journal
In what appears to be an increasingly popular option, a preprint is posted without the authors having any intention of publishing it in a journal. This is option 0 (zero). It may involve preprints describing negative or confirmatory results, which are traditionally difficult to publish in journals but can be useful to the community. In fact, bioRxiv lists Confirmatory Results and Contradictory Results as formal article categories. In such cases, the authors may want to share the information with the community without going through the hassle, time commitment and financial expense of publishing in a journal. Perhaps, M.Sc. and Ph.D. students can consider publishing their minor thesis chapters as Option 0 preprints.
Option -1 — Preprint an early version of the paper
Option -1 (minus 1) is when you preprint a short paper, a poster, a dataset, a method or any other research output that you do not intend to submit to a journal as is, but will consider incorporating into a full-fledged paper at some point in the future.
As I wrote before, mini-papers — one descriptor for Option -1 outputs — are undervalued by academics for reasons that escape me:
“Mini-papers are the underrated scholarly outputs of academia. For many Early Career Researchers (ECRs), publishing a full fledged research article is a daunting task. So, why not break down this task into smaller, less intimidating units and publish them as datasets or method papers?”
To take an example related to work taking place at FABI. Imagine you isolated a new strain of a plant pathogenic fungus, have completed the phylogenetic analyses but are still awaiting pathogenicity assays. You may post a version 1 (v1) of your preprint that only describes the the molecular work, and later on the v2 with the full paper, which will be the one you submit to a journal. Note that although preprints become permanent publications and cannot be removed once published (according to digital object identified or doi rules), you’re free to post as many versions as you wish until the article is published in a journal.
Option +1–Preprint after the paper is accepted
Preprinting after the paper is accepted by a journal is a controversial and, in my view, the least advisable method of preprinting. To a large degree this defeats the idea behind preprints serving as a way to accelerate the dissemination of scientific knowledge (the ASAPbio movement) and the use of preprints to receive feedback from the community prior to (or alongside) journal peer-review. In fact, as biophysicist Kresten Lindorff-Larsen tweeted, bioRxiv doesn’t allow updating (or posting) preprints after acceptance and some journals don’t want you to post the revised version as a preprint. One argument for Option +1 is to openly share the paper with the community, especially if the article will be published behind a paywall. But then again, why not share the original version a few months earlier?
Do not post premature or incomplete work
No matter what option you chose, do not post premature or incomplete work. Just like a talk, a poster, or a journal article, the preprint will be the currency by which your peers will judge and evaluate you. This will be your billboard, and as such it deserves to be taken as seriously as any other publicly available scholarly outputs you publish.
Now that we addressed the question of when, I look forward to seeing your preprints whether full paper or the mini version. And don’t forget to tweet a thread about them.
Option K — There is a fifth option according to my colleague and fellow plant scientist Ksenia Krasileva.
Ksenia tweeted “we preprint a full finished ms few weeks before submitting to the journal. The goals is to incorporate peer reviews from community before we submit. Typically, we get 3–4 reviews that way send to us via email.”
I agree, this option was missing from the list above. I think it should be called Option K for Ksenia! It highlights how preprints have reinvented peer-review. Nothing prevents anyone at any career stage to review preprints and chip in with their feedback on the paper.
Notes and acknowledgements
I’m grateful to the incredibly enthusiastic team at FABI for organizing the workshop and inspiring me to write this post.
Any discussion on preprints inevitably circles back to peer-review. For more on the topic, check this post on the call to end once for all “pre-publication peer-review”. As my colleague Detlef Weigel tweeted: “do not confuse publication with peer-review”.