An early career researcher discusses issues with blinding and diversity in peer review, and ultimately whether including non-peer-reviewed preprints in science publishing can have beneficial effects…
Author: Paweł Borowicz, Researcher, Institute of Basic Medical Sciences, University of Oslo, Norway. Image credit: Pawel Borowicz. You can read more of his material on his personal blog.
Open Science – the movement to make scientific research available to all levels of society. Everyone has heard of it, some wish for it, and no one believes it will be achieved anytime soon. How come?
We live in the globalization era. The world has never been more integrated than now. The access to information is limitless. And yet, science is as hermetic as before. Many blame the commercialization of scholarly publishing for being the primary cause of this problem. Obviously, you cannot change the system without systemic changes. No single individual can introduce such changes, as one is powerless against the system. However, is it entirely true? Are we personally unable to make that change? Or is it just our sinful attitude?
Abandon all ideals, ye who enter here
Naturally, we could just blame the system for all the problems surrounding it. But let’s face it, we are to blame too. Who would actually bother publishing in high impact journals, if it was not rewarded with fame and higher chance of acquiring more funds by the scientific society? How many of us are sitting on data and unfinished papers in the hope of developing them into something better, while others might need this piece of information to push their research forward? At the same time, others “publish faster than they think” (just to quote Wolfgang Pauli) producing “salami publications”. It should not come as a surprise then, that some reviewers reject papers without giving the authors a chance to improve their piece of work. Especially, when the reviewers are themselves involved in the scientific rat race and do not have time to improve on others’ research.
While the everyday mood of a scientist is usually a frustration, the common representation of the scientist in the media is a resolute idealist. Have you been a resolute idealist when you started your scientific endeavors? Most likely, you will quickly nod “yes”. Are your senior colleagues still resolute idealists? Most likely, you will have to think about that answer a bit longer and it will not necessarily be “yes”. Have you not yet met those proud and famous scientists who behave more like businesspersons than scholars? Have you not heard from your senior colleagues how cruel, bitter and unfair academia is? The current academic system is not meant for idealists. It is made for determined people (obviously not a synonym of “idealist”). The race for grants, “publish or perish”, the hierarchic system, mistreatment of graduate students, bullying , and all the other aspects of academia do not make it easy for idealists. Therefore, from time to time, you should remind yourself about your ideals. World development, groundbreaking discovery, cure for cancer, understanding it all? You name it, you work for it! However, even the greatest idealists will not achieve much, if the entire system is against them…
Something is rotten in scholarly publishing…
The number of scientific publications is growing exponentially. Obviously, it is impossible to read all the papers in your field, not to mention more than 39M scientific articles from all the disciplines published in the last 100 years . Some estimates say that 90% of the papers are never cited and 50% have only been read by the authors, reviewers and editors . According to the Web of Science, out of these 39M articles published between 1900 and 2015, 21% are still waiting to be cited .
Surely, all of that science is important, right? With the growing number of publications, their credibility is actually going down. I do not mean the irrelevant or boring research published out of necessity and not the novelty, but the actual fraud. The number of fraudulent papers is increasing exponentially as well. Just to name the recent discovery of “paper mills” which caused retraction of hundreds of papers .
Above it all, the great paywall is hanging. We are commonly funded by the taxpayers in exchange for making our results available to the society. But how determined does someone have to be to read our paper if there is a significant price for the access? Not to mention that scandalous profit margins of commercial publishers, which are basically paid by the taxpayers . As a result, the fight against the paywall becomes the fight for open access. Fortunately, the numbers of openly available articles are rising. Currently, at least 28% of scientific articles are available in an open access (more than 19M in total) .
When fighting with commercial publishers, scholars forget that the publishing industry’s income is not the only problem here. The entire publishing system is archaic and has not evolved much since its beginnings. The review process itself does not befit the Internet era. Internet taught us that anonymity fuels animosities. Why not all publishers make manuscript revision completely transparent? Several interesting scientific notions are hidden in the review reports, but do not end up in the print as “not being relevant for the take-home message of the publication”. Not to mention the quality of the review process varying between publishers or even editors. Is it even possible to change a system broken on so many levels?
I am a policy-maker. Change my mind.
Recently I proposed a simple, but effective plan of complete restructuration of the existing academic publishing system – Plan X ( or ). In short, Plan X proposes making universities the primary publishing bodies. Such a move could potentially solve most of the current problems of scholarly publishing, create flexibility and facilitate future evolution of the publishing system.
While all the necessary means to introduce Plan X are already in place, to reach it might take a long time. The biggest obstacle is human nature – our avoidance of taking the initiative, fear of the new, and the fact that in problem solving, adding is favored over subtracting . I have been met with a lot of skepticism. It seems as if scientists’ pessimism about the policy makers’ good will only match people’s pessimism about the possible truce between USA and Russia. Unfortunately, there is some true in that, as the recent pandemic has shown. Before the UK government applied a mask-wearing rule in public transportation from the middle of June 2020 , scientists already argued in early April  that it should have been implemented in the regulations. If policy changes take more than two months during a world crisis, how much time does it take to change a policy, which affects only a percentage of a population and does not bring immediate profits?
Nevertheless, the policies are never changing “on their own”. The policy-makers effect necessary changes according to the dominating public will. So… How to make changes to the scholarly publishing system? Talk about it, convince others, and vote for people who want these changes to happen, or even propose such projects yourselves. Statistically speaking, your vote has more power over the policy of your university than over the policy of your country. However, if we cannot get to open science utopia with giant steps, we can always get there with small steps.
Hidden cost of free access
If every scientist only publishes all their future work via open access, the whole system of commercial publishers would collapse, as they would not be able to provide libraries with new content anymore. However, this is easier said than done. Publishing in open access is not a trivial matter. There is no such thing like publishing for free, someone always has to pay. It is either libraries or the author themselves. Yes, most likely it will again be the libraries who pay the publication fees. Recently, PLOS introduced a new model of payment, the membership fee, where the institution is paying a yearly fee for allowing its researchers to publish for free . While PLOS’ initiative might convince more scientists to publish in open access, there is a risk that commercial publishers will exploit this idea similarly to the “serials crisis” (when they constantly increase the subscription fees of regularly published academic journals paid by libraries).
Obviously, when choosing an open access publisher for our work, we are evaluating two factors, the impact factor of the journal, and the publication fee. However, there is yet another, probably even more important factor. Let us call it conscious publishing. For obvious reasons, you should avoid publish open access with commercial publishers. You should consciously choose non-profit open access publishers. Non-profit publishers usually share their financial reports publicly. For example, here is PLOS financial overview for 2019  and here you can find the eLife financial overview for 2019 . This allow you to see if your money is actually spent on publishing or on the new car of the CEO. Of course, PLOS and eLife are not the only non-profit publishers, but their journals are at the forefront of the scholarly publishing evolution as they constantly experiment with new alterations. However, even if you are not publishing via open access, you can still make your move toward Open Science via other routes.
Sharing is caring
Do you feel guilty for not publishing open access? Fear not! The game has changed a few years back. The pre-print revolution is already in place. Pre-prints are not only publicly discussed like proper research papers, but they are even accepted in the track records as legit publications. Moreover, many granting agencies accept it as a substitution for gold open access. You can even publish your pre-prints retrospectively, which I actually encourage you to do as soon as possible. The reason for that is simple and is called Unpaywall . It is a software, which searches the web for the free version of the research paper. By publishing your pre-prints after publication, you allow that software to present your pre-print as a free version of your article. Last, but not least, remember that you are legally allowed to share your papers with anyone PRIVATELY. It means, that you can always ask the authors to share their papers with you, and that YOU should share your work with anyone interested.
One thing is to allow people to freely access your hypotheses and their validation through experimentation, but the other thing (equally important for open science) is to grant people free access to your raw results. Data mining is a real thing and you would be surprised by how useful your results might be for other researchers. For the sake of scientific progress, share your datasets in the relevant repositorium. If you care about sending your own garbage for recycling, why should you not care about upcycling your precious data? One scientist’s trash is another scientist’s treasure! Also, for your own sake, try to learn how to make use of these repositories yourself. It might help to progress your own research as well. Similarly, you should post your methods and protocols online. Not all protocols are novel enough to constitute a scientific paper, but all of them could help others with troubleshooting. The most popular websites for that purpose are Scientific Protocols and Protocol Online.
Another important notion is that we should not be ashamed of our failed experiments. There are always lessons learned in every attempt. Not only for us, but also for other scientists attempting similar experiments. Therefore, it is possible to publish so-called “negative” results in a number of journals, such as Journal of Trial and Error  or The All Results Journals .
Sharing your work is important. No doubt about it. But people tend to forget that there is something much more important to share openly with your peers – your knowledge and insight.
Discussing is not harassing
What is the point of peer-review? Many will automatically say: to separate the grain from the chaff (or, if they do not weigh their words carefully, to reject the crappy papers). That is not true. The main function of peer-reviewing is to help other scientists improve their work. A reviewer should not be a judge, but an advisor. Why do most of us have different opinions about reviewing? The reason is simple. During our scientific education, we do not practice enough of how to review, advice, or discuss other people’s work. Therefore, practice it with your fellow colleagues whenever possible.
One of the best opportunities to discuss science is actually during a journal club.
By that, I do not mean the most common way of conducting the journal club, where one person is pretending to completely understand the paper and present it as their own. Sure, it can improve one’s presentation skills, but this format leaves little room for real scientific discussion. What I actually mean is to turn you journal club into an informal chat club!
To have a real scientific discussion everyone has to be on the same page (literally) and critically read the paper on beforehand. Senior scientists can lead the discussion by explaining concepts or methods that are more difficult, but everyone should be able to comment on any matter related to the article. It means that you can discuss/criticize the style, the figures, the concept, the argumentation, the hypothesis, the background, the authorship, the conflict of interests, the conclusions, and everything else. Yes, it would basically be a 1-hour-long-peer-review-session. Through that exercise, all the participants can learn much more than from a power point presentation.
You and your colleagues can gain a lot from such a scientific discussion, but why stop there? Ideally, your discussion is literally a post-publication peer-review of the paper, and the most interested party here are the authors themselves. You could send your comments directly to them, but there is an alternative and better way.
Internet – Connecting people
Did you ever hear about PubPeer? The “infamous” nest of whistleblowers, spotting bad and false science? Are you aware that the full name is “PubPeer – The online Journal club”? The site was developed with one purpose only, to publish your post-publication peer-reviews online. Although, scientists have forgotten about it, PubPeer is a perfect tool for proper scientific discussion:
- You can comment on ANY existing paper or pre-print (the only requirement is to have DOI)
- Your actions are announced via email to the authors (you can put the emails yourself if they are missing)
- You can post the comment anonymously if you are afraid of the repercussions (the only penalty is that your comment has to be verified by admins, which delays its publication)
- Your comments are not traceable via searching engines (even in PubPeer you can search only for papers, but not commentators). Your communication channel with the authors is secured and available only for the interested parties.
This brings me to the most curious thing of all-time. Why are scientists not to a larger extent using the World Wide Web for scientific discussions? One reason could be that the old-fashioned ways of scholarly publishing are rooted deeply in scientific community – treating scientific papers as a one-way-only dissemination. Consequently, nearly no journal allows commenting on papers on their websites! This may be why less than 10% of (bioRxiv) preprints have been commented on , which is shockingly low. It is as if scientists have nothing to say about science to each other! Sure, the COVID-19 pandemic has changed things a little , but mostly because the public and journalists wanted to quickly learn what scientists have to say.
Internet – Dividing people
Actually, scientists have a lot to say and regularly complain that no one listens. But that is not true. It is we who are not communicating in a right way. Carol H. Weiss pointed out already in 1979, that there is little to no chance at all that your paper would influence policy makers . In other words: policy makers do not read scientific papers. You can only reach their attention through (social) media.
What happens when scientists are not commenting on the science on the web? Terrible things. From the kind-of-funny-but-actually-pretty-sad examples when people ask under the cancer-related preprint, if they can use substance X described there to treat themselves, to serious public backlashes. Recently, the paper presenting a very interesting (and a valid from the scientific perspective) study on the soluble factors supporting pregnancy nearly was retracted from bioRxiv, because the authors could not stand the criticism on social media  (check out the authors response on PubPeer). Obviously, there was a trigger, which were these words: “male pregnancy”.
Could it all happen differently if other scientists more often engaged in the discourse? Most of the people “concerned” about the science behind the paper have no scientific background. It is definitely high time scientists regain the power over the science’s narrative. It is not enough to discuss science with fellow scientists. Our discussion must become visible (and understandable) for everyone. There is a number of platforms allowing scientific discussion. Aforementioned PubPeer is the most suitable for post-publication peer-review, but not even all scientists know how to use it, let alone other people.
Commenting directly under the published paper would have been more suitable, but such an option is rarely available (except on preprint servers, which generally have that option). It is much easier to search for scientific comments posted on ResearchGate (basically a LinkedIn for scientists). However, these comments are mainly focusing on the methods and troubleshooting, which is of no interest for the general audience. Similar discussions are handled on Protocol Online forum.
As I stated before, it is important to discuss science (online), but aforementioned websites are not designed to be a communication channel with non-scientists. For that purpose, one needs to become active on Twitter, Reddit, or any other social media where the scientific discussions are held. These channels of communication allow to share our knowledge with everyone, but be careful!
It is important to proceed with caution, as your participation may backfire. Talking with the science deniers is not easy, but even that kind of challenge can be mitigated . Although, your impact on the public through the social media might be limited, from time to time we all have a chance to talk in “real” media. Just remember to always say “yes”. Bringing science to masses should be a goal of every researcher.
If my arguments were not convincing enough for you, if you do not have time for that, if it is all too trivial for you, remember that – eventually granting agencies will start applying Open Science indicators for scientists’ assessment . Your time for redemption might come very soon. Better be ready than sorry!
|7 sins of scholarly publishing||Your redemption list|
|1. Lust for success||Reconsider your motivation for doing science (money, fame and power are the wrong answers!)|
2. Greed of commercial academic publishers
|Use your power as a policy maker|
|3. Envy of the unsuccessful scientists|
Try to always publish Open-Access, if not, make your preprints available online
4. Gluttony of data and results herding
|Make your data available online|
|5. Sloth of peers to discuss and review science|
Teach your students how to discuss science
6. Wrath of reviewers
|Use PubPeer for scientific discussion (it was made exactly for that!)|
|7. Pride of the successful scientists|
Be active in scientific discussion on (social) media
List of references:
 H. Else, “Does science have a bullying problem?,” Nature, vol. 563, no. 7733, pp. 616-618, 2018.
 R. Van Noorden, “The science that’s never been cited,” Nature, vol. 552, pp. 162-164, 2017.
 L. I. Meho, “The rise and rise of citation analysis,” (in English), Physics World, vol. 20, no. 1, pp. 32-36, Jan 2007.
 H. Else and R. Van Noorden, “The fight against fake-paper factories that churn out sham science,” Nature, vol. 591, no. 7851, pp. 516-519, 2021.
 J. Schmitt, “Paywall: The Business of Scholarship,” 2018. [Online]. Available: https://paywallthemovie.com/.
 H. Piwowar et al., “The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles,” PeerJ, vol. 6, p. e4375, 2018, doi: 10.7717/peerj.4375.
 P. Borowicz, “Alternate Publishing Model?,” PLOS BLOGS Your say, 22.01.2021 2021. [Online]. Available: https://yoursay.plos.org/2021/01/22/alternate-publishing-model/.
 P. Borowicz, “Plan X from Outer Space,” 2021. [Online]. Available: https://journalofideas.com/2021/01/20/planxfromouterspace/.
 T. Meyvis and H. Yoon, “Adding is favoured over subtracting in problem solving,” ed: Nature Publishing Group, 2021.
 T. R. H. G. S. M. Department for Transport, “Face coverings to become mandatory on public transport,” 04.06.2020 2020. [Online]. Available: https://www.gov.uk/government/news/face-coverings-to-become-mandatory-on-public-transport.
 T. Greenhalgh, M. B. Schmid, T. Czypionka, D. Bassler, and L. Gruer, “Face masks for the public during the covid-19 crisis,” Bmj, vol. 369, 2020.
 PLOS, “Community Action Publishing.” [Online]. Available: https://plos.org/publish/community-action-publishing-for-authors/.
 PLOS, “2019 Financial Overview,” 2020. [Online]. Available: https://plos.org/financial-overview/.
 eLife, “Annual Report: 2019 in review,” 2020. [Online]. Available: https://elifesciences.org/inside-elife/f07da98b/annual-report-2019-in-review.
 H. Else, “How Unpaywall is transforming open science,” Nature, vol. 560, no. 7718, pp. 290-292, 2018.
 Journal of Trial and Error. [Online]. Available: https://archive.jtrialerror.com/.
 The All Results Journals [Online]. Available: http://arjournals.com/.
 M. Malicki, J. Costello, J. P. Alperin, and L. A. Maggio, “From amazing work to I beg to differ-analysis of bioRxiv preprints that received one public comment till September 2019,” bioRxiv, 2020.
 N. Fraser et al., “The evolving role of preprints in the dissemination of COVID-19 research and their impact on the science communication landscape,” PLoS biology, vol. 19, no. 4, p. e3000959, 2021.
 C. H. Weiss, “The many meanings of research utilization,” Public administration review, vol. 39, no. 5, pp. 426-431, 1979.
 R. Zhang and Y. Liu, “A rat model of male pregnancy,” bioRxiv, 2021.
 L. McIntyre, “Talking to science deniers and sceptics is not hopeless,” Nature, vol. 596, no. 7871, pp. 165-165, 2021.
 P. Wouters, I. Ràfols, A. Oancea, S. C. L. Kamerlin, J. B. Holbrook, and M. Jacob, “Indicator frameworks for fostering open knowledge practices in science and scholarship,” Brussels: European Union., vol. 9, 2019. [Online]. Available: https://doi.org/10.2777/445286.