The Wall text on a background of a brick wall

The Wall: Barriers to publication and access to publicly funded research publications are driving researchers to preprint servers and depriving the public of information they funded

| 17 January 2024

Pink Floyd poster for the Live in Concert (the Worlds Largest concert spectacle) for their album ‘The Wall’. — Pink Floyd poster for the Live in
Concert in 1980-81 (the Worlds
Largest concert spectacle) for their
album ‘The Wall’.

If knowledge is power, if the media is the message, and if speed matters, the current model of scientific publishing is not working optimally for researchers or the public. Increasingly scientists are turning to preprint platforms to make their discoveries visible in a timelier manner to their peers and to the public, bypassing the delays and financial barriers inherent to publishing in conventional peer review journals. At the same time, information about new discoveries and medical treatments are being kept behind publishing paywalls, hidden from the public and decision makers. Is it time to change how we publish and share publicly funded research information? Should we seek to renegotiate the “deal” with a very small group of academic publishers who largely control the flow of publicly funded biomedical research information to academia and the public? I hope you will enjoy this blog, and I want to acknowledge input that I received from an expert in this area, Mr. Mark Swartz, a Scholarly Publishing Librarian, at Queen’s University.

Mark Swartz, a scholarly publishing librarian, at Queen’s University — Mark Swartz, scholarly
publishing librarian, at
Queen’s University
(0000-0001-8142-1613) -
ORCID

I publish a fair bit;15-20 publications a year. Most of my manuscripts are rejected at least once and usually pass through several journals and undergo two to three revisions before publication. This means the average time from my original submission to publication exceeds six months. Most of the “improvements” in my publications resulting from peer review are, in my opinion, minor. The slowness of the peer review publication system, combined with its the high rejection rates, is pushing researchers to “publish” drafts of their articles on preprint servers. These preprint services bypass both the delays and the quality improvement inherent in peer review process. In composing this blog, I stumbled down a rabbit hole of poor access to research publications that is a consequence of a cartel of academic publishers profiting from publicly funded research (i.e. there is a knowledge dissemination barrier even once a discovery is published). You may be surprised to learn that access to the fruits of publicly funded research is largely controlled by just five major publishers in what is now a $27 billion industry in which researchers pay to provide publishers with free content! In a June 27, 2017 Guardian article, Stephen Buranyi pointed out that the profit margin of Elsevier, one of the major publishers, was 36% or £2 billion, greater than that of Apple, Amazon or Google! So oddly the “geeky” specialized enterprise of scientific publishing is shockingly profitable! Buranyi’s article also quotes a 2005 Deutsche Bank report, calling it a “triple-pay” system, in which “the state funds most research, pays the salaries of most of those checking the quality of research, and then buys most of the published product”. This remains true in Canada today! This blog considers how one can accelerate knowledge dissemination and facilitate better access to the knowledge resulting from publicly funded research for researchers, the public and broader society.

First, a couple of definitions and facts.

1) Peer Review: Peer review refers to a process where experts in a field of research or medicine review and critique a manuscript that has been submitted to a journal for potential publication. The advice of two to four peers helps journal editorial boards decide whether to reject or recommend revision and resubmission of a submitted manuscript. If the manuscript is rejected the author sends it on to another journal; however, if the editor offers the chance of revision, the peer reviewers’ suggestions guide the authors as to what must be done to achieve publication (although no guarantee of success is offered). Peer review is usually an unpaid activity, and the opinion of the reviewers is usually given anonymously. While bias is not rare, since one’s peers are also one’s competitors, peer review it is widely considered to be the best of the bad systems available to optimize the validity of a manuscript and determine what should be published; but this may be changing!

2) Preprint Publication: This refers to online platforms, like bioRxiv and medRxiv, where authors can publish a publicly accessible version of their manuscript online without charge (and without peer review). The time from upload to public access is approximately one to two days. Preprint posting does not preclude subsequent submission to most conventional, peer-reviewed journals. While preprint submissions are not peer reviewed or typeset, they are screened to ensure they do not have offensive content and, in the case of human studies, have ethical approval from the sponsoring institution. Once posted these preprints receive a digital object identifier (DOI), so they are discoverable on search engines and can be cited (see an example below from my lab where we report the discovery of a new gene in which variants results in pulmonary arterial hypertension, posted Dec 31^st, 2023).

These preprints can be revised but cannot be removed. Researchers at the University of Minnesota documented in an eLife publication that the rate of use of preprint sites is soaring whilst Janda et al concluded, in a JAMA Network Open publication, that preprint content reliability is quite good (as defined by the finding that preprint manuscripts have content to the versions of the paper that ultimately appear as publications in journals).

There are two major preprint platforms in the biomedical world, one for medical discoveries (medRxiv) and one for biologic science discoveries (BioRxiv). medRxiv was founded by Cold Spring Harbor Laboratory (CSHL), a not-for-profit research and educational institution, Yale University, and BMJ, a global healthcare knowledge provider. medRxiv is owned and operated by CSHL. Preprint servers are also supported by the Chan Zuckerberg Initiative, which is dedicated to building open-source software tools to “accelerate science and generate more accurate and biologically important sources of data”. BioRxiv was also founded and is run by CSHL. The COVID-19 pandemic and the demand for rapid knowledge dissemination brought the preprint servers to public attention, although they were well-established pre-pandemic. Is the rise of preprint publication a rebuke of the pace and lack of open access of conventional peer reviewed publication? Read on!

3) Publicly Funded Research: While the industry, particularly Big Pharma, does important proprietary research, most research is publicly funded, meaning the money that funds the research is derived from the public purse, usually being awarded by universities themselves or directly by federal agencies like CIHR, NSERC or CFI (in Canada) or NIH in the USA. Admittedly, there is a rise in the relative contribution of pharmaceutical industry funded research of late, as summarized in this editorial in Science. Moreover, the researchers themselves, most of whom are faculty members at publicly funded universities write the articles which the journals publish for free. Furthermore, the journal’s peer reviewers also review the article without reimbursement. Thus far in the chain of knowledge creation, the public pays, and no one is making money. However, that changes when a manuscript is accepted. Rather than the journal paying the content provider, the author (researcher) must pay the journal “page charges” for the privilege of publication! These page charges range for $2000-8000/article and usually payment comes from the researcher’s grants, once again, derived from public monies. Additionally, the publishers charge subscriptions which researchers and university libraries must pay to access the publications. Without a subscription, and these are increasingly expensive, the only way to access the publication is to directly pay the publisher, since the papers are hidden behind “paywalls”. In general, Jane Q Public would not have a subscription to a medical or biomedical journal, and they are kept from the content by paywalls, relying on secondary information sources, like Facebook etc., for distillations of findings, which vary in accuracy.

4) Paywalls: Just as the name suggests, many publications are hidden behind a secure e-wall and can only be accessed by paying the publisher using a credit card. Charges vary but often are $40-$50 for a single article.

These introductory facts raise three important questions. First, are journals responsibly facilitating research or, because of their high rejection rates (often over 90%) and slow evaluation process (often four to six months from submission to acceptance in my experience) are they inadvertently slowing down research and discovery? Second, are large publishing houses unduly profiting from publicly funded research? Third, is the public getting fair access to published information; information that it ultimately paid for through taxation? (see figure below).

Barriers to accessing publicly funded research infographic — *A circular flow graph that describes the relationship between public funding and the ultimate publication of articles. Figure made in BioRender.*

The media that matters for dissemination of medicine and biomedical science are peer-reviewed journals, like: NEJM, Circulation, JAMA, The British Medical Journal, The Lancet, Nature, and Science. These journals have prestige and presumptive credibility. They were once typeset on paper, and, once the ink had dried, hard copies were snail-mailed to libraries around the world. When I was an undergraduate student at Queen’s University, my colleagues and I combed library stacks looking for relevant medical articles. We were guided by Index Medicus, a tome containing “all the world’s literature” (if you can believe it) to find the specific volume of a journal that contained the topic of interest.

Most (89%) journals are now online publications, as summarized in the graph below taken from the STM report 2021 (figure). Many journals don’t even offer the option to receive a paper copy.

The Market by format — This graph describes the percentage of publications in the scientific
literature which are paper based versus electronically based. It looks at the years 2019 and
2020, it shows that in the year 2020, 89% of all papers in the scientific literature are
published electronically. This reflects the fact that scientific and medical publications are
becoming an electronic media and raises questions as to why publishers limit page number
access.

Index Medicus was a very user-unfriendly forerunner to the online search engines scientists now use to find an author, title, or to search the literature by key words or topic of interest, notably PubMed and Google Scholar. Likewise, manuscript submissions are electronically transmitted to the journal’s portal and journals manage peer review online. In this e-world, one might expect radical decreases in delays prior to acceptance and publication; if that is your expectation prepare to be disappointed. One might also think that in the brave new world of e-publication, journals would be unfettered by page limits, making page charges a non-issue (there is no “page”) allowing journals to expand their offerings and thus accept a higher percentage of meritorious submissions. Here again, the truth is less rosy. Paradoxically, despite electronic publication, more authors are feeling the need to use preprint presses to establish the priority of their discoveries (time stamping when you knew what you knew) and share their findings with peers and the public. Preprint servers are free, fast and are the ultimate form of “open access” publication (meaning no subscription required and no paywalls used); however, they lack the Good Housekeeping Seal of Approval, conventionally provided by a peer review journal. The onus for evaluating the quality and veracity of a preprint manuscript is shifted to the reader-caveat emptor! Since preprints are preliminary reports of work that have not been certified by peer review, they should not be relied on to guide clinical practice or health-related behavior and should not be reported as “fact”. Despite this caveat speed matters!

Proof that Speed (of Publication) Matters? The COVID-19 pandemic created the perfect test for “the need for speed” in publication. When faced with a lethal pandemic, we needed to share new scientific and medical findings, and we needed them to be quickly shared across the globe, not only amongst scientists, but with the public and governments. How did preprint presses fare versus conventional publication? In March 2022, a team of researchers examined all COVID-19 preprints posted on medRxiv in 2020 and October 2022. They showed in JAMA Network Open that of 3,343 preprints put up on the preprint server in 2020, more than half (51.2%) were ultimately published as conventional peer-reviewed journal articles (by March 2022) (figure below). Moreover, of those preprints published, almost half (47.5%) appeared in top quartile journals (i.e. good journals). This appears to indicate the community felt the need to disseminate information more widely and rapidly than the conventional publishing apparatus allowed. That the preprint information was valid, is supported by the relatively high publication rate of preprint uploads, and publication did not lag far behind preprint posting.

Perhaps we need to take a lesson from COVID and look at ways to better accelerate the progression from discovery to dissemination for all biomedical research. Let’s look at the failings of peer review journals that have driven basic and medical researchers to preprint services. These failings include:

Unacceptable Acceptance Rates and Long Delays to Publication: Although journals are electronic and theoretically could publish more inclusively, many journals appear to manufacture scarcity (i.e. editors make their journal appear more prestigious by making acceptance hard to achieve). Elite journals brag about rejection rates that exceed 90%, leading to humorous responses such as the creation of the Journal of Universal Rejection.

While one needs standards, the world’s elite journals are more efficient at rejecting submitted science than the best vaccines are at preventing infection! Peer review is designed to improve the quality of publications, and many submitted manuscripts fall short. Thus, it may be a “good thing” that peers (who are experts) have considered a manuscript, suggested improvements and the authors have improved the product through their response. However, like all safety measures, there is a balance between safety and speed. A highway speed limit of 40km/hour would radically reduce traffic fatalities; but would also make the highways congested and impractically slow commerce! If rejection rates are too high, let’s say >90%, the journals risk becoming an impediment to knowledge dissemination.

Elsevier (one of the “Big Five” publishers) reviewed the acceptance rates of 2300 journals (over 80% of them published by Elsevier), and calculated that the average acceptance rate was 32% (range 1% - 93.2%). However, for established, high-impact journals, acceptance rates are very much lower. For example, for the leading cardiovascular journal, Circulation (acknowledgement: I am a member of the Circulation editorial board), the acceptance rate is only 7% while the sister American Heart Association journal, Circulation Research, is only slightly better at 12%. Likewise, general science journals, like Nature and Science, have acceptance rates of 8% and 6.1%, respectively. The world’s most prestigious medical journal is arguably the New England Journal of Medicine and they accept only 5% of the 5000 original submissions they receive each year. The average time from first submission to publication has become sufficiently long, with many papers being revised two to three times, that often over six months passes between submission and acceptance. Indeed a report of the fate of 8711 preprints from bioRxiv (2013 to 2017) by Herbert et al showed a median interval of 160 days to publication.

Preprint versus publication timespans inforgraphic. — A graph of medial interval between date of bioRxiv pre-print and date of publication in a journal, comparing preprints in direct and non-direct transfer journals. Pre-prints in direct transfer journal n=3438. Preprints in non-direct transfer journals n=5251. Note: 22 pre-prints were missing the necessary journal-level data for this analysis

These delays are aggravated by the consequences of serial rejection (i.e. once rejected by the first journal, one must repeat the submission process at a second journal). These delays hamper public access to knowledge and interferes with the researchers need to share their discovery. Researchers understandably want to demonstrate priority (i.e. that they discovered something first) and prove their productivity (to demonstrate to funding agencies their research is progressing so they can secure ongoing grant funding). Preprint presses solve the timeliness issue by allowing researchers to release their discoveries, as online “draft” manuscripts. These servers allow the public to see the work and colleagues to comment on the work, while the author searches for a journal “home”. In a tacit acceptance that reality has changed in the publication world, many conventional journals now offer the option of simultaneous preprint upload in parallel with journal peer review submission (see figure below).

Journals, like Circulation, allow prior preprint submissions.

The Future of Preprint: If we wish to see the future of biomedical prepress platforms we can look to ArXiv, a circa 1989 forerunner of the biomedical prepress services, as discussed in Scientific American in 2022. ArVix is home to preprints for the field of physics and has now handled two million papers! ArVix is housed at Cornell University and has existed for decades. Virtually all physics publications initially go through this preprint press. Indeed, by 2021, it was struggling to handle 1200 submissions daily, a victim of its own success! There are lessons to be learned by the biomedical platforms; from ArVix’s lack of infrastructure support, its burgeoning volume, and its overworked volunteer moderators. These moderators allow ArXiv to provide some quality control while maintaining speed. If there are no quality issues identified by moderators, the paper is online within a day or two; however, if one claims to have refuted Einstein or “created a theory of everything” delays are added and 6% of submissions are held while questions are addressed and ~ 2% are actually rejected (usually on the grounds their results are not credible or are pseudoscientific). If the future of biomedical publication involves preprint services, as appears almost certain, finding mechanisms for soliciting moderators in adequate numbers, supporting server growth, and provision of some quality control will be crucial.

Cost of Publication for a Scientist: As currently structured, scientists and universities are paying for open access (unless their university pays, they are charged thousands of dollars for this option) and paying for journal subscriptions. Meanwhile, the big five publishers: SAGE, Elsevier, Springer Nature, Wiley-Blackwell, and Taylor & Francis, are making record profits. Thus, scientists are unpaid content creators who must “pay to play” by virtue of ever-increasing page charges. In 2013, 53% of all natural and medical science publications were published by the five largest for-profit academic publishing companies. Paywalls and rising subscription costs are making fewer publishers more money. Annual revenues from English-language science, technology, and medical publishing journals in 2017 were estimated to be USD $10 billion and a 2021 STM report shows that the 2020 scholarly publishing market was $26.5 billion and is expected to grow to $28 billion in 2023 (see figure below).

Total STM market value graph — The graph illustrates the financial performance of the publishing industry from 2018 to 2024(forecasted), demonstrating a noteworthy increase in profits from $27 billion in 2018 to $29.5 billion in 2024. This highlights the lucrative nature of academic publishing in science and medicine, challenging common misconceptions about its size by revealing comparable profit margins to industry giants like Google and Apple.

STM is the leading global trade association for academic and professional publishers. It has over 140 members in 21 countries who each year collectively publish nearly 66% of all journal articles and tens of thousands of monographs and reference works. STM members include learned societies, university presses, private companies, new starts, and established players.

The number of English language journals the biomedical sphere is 35,000 and growing (see figure below). Approximately 39% of the global publishing market for science and medicine is in the USA, but China is the main producer of publications.

Growth in english journals graph — This graph shows the contrasts in the quantity of journals in 2010 with those specifically in
the fields of science and medicine in 2020. The graph illustrates the expansion of
worldwide journals in English language print, escalating from 25,000 in 2010 to 35,000 in
2020. Evidently, this signifies a notable area of growth, underscoring the profitability
observed in scientific publication.

Journals per country graph — The graph shows the distribution of the number of journals per country of origin according to Scopus derived data. It shows that the United Kingdom and the United States of America\ are by far the preponderant countries in which scientific and medical journals are hosted. With 5,856 journals from the UK and 5,712 journals from the US. Canada, by contrast, has 245 journals.

Most journals are based in the United Kingdom or the USA (figure above). How is Canada doing in the publishing business? Turns out we are doing better at hockey than science!

Comparing numbers of researchers graph — The graph is looking at the comparison of the number of articles produced, the number of researchers per million inhabitants in a country, and the number of journals that are active as of the year 2020. What it shows is that the United States and China have by far the most journals and publications. However, it shows that a country like Canada, despite having a high number of scientists per hundred thousand population, has relatively few journals and a modest production of scientific publications per scientist. Another interesting feature of this graph is that countries like India, which have relatively few scientists per population and very few journals, actually have high numbers of publications; reflecting the productivity of this country.

Canada has fewer journals and our scientists are producing fewer publications per capita than the UK, USA or China.

Where is this profit in publication coming from and why should we care? First, why should we care? “We the people” paid for most of the research that journals profit from. Our taxes fund the universities where research is performed and the granting agencies, that fund the research itself. Perversely, the public, researchers and publicly funded universities are paying subscriptions fees to publishing houses for materials that derive from public funding, are written by faculty at public universities, are peer reviewed for free by these same faculty and, to add insult to injury, the researchers pay “page charges” to share their discoveries. Despite the fact that the vast majority of funding derives from the public purse, often all the public can access of a publication using Google or PubMed (without payment), is the title and part of the abstract. To see “the whole thing” one needs to pay the publisher at a paywall. These fees limit access and the only entity that benefits are the publishers. The open access most university faculty members enjoy reflects the library at their school having purchased a subscription from a publisher; however, the budgets of libraries are struggling. The costs of subscriptions to journals are rising and, with poor funding of most libraries by universities, are unsustainable. For example, the library of Harvard University announced that the estimated $3.5 million in annual subscription costs were financially unsustainable and proposed that publishing in open access journals would be a wise response to counteract the control exerted by publishers and their expensive subscriptions and paywalls. Queen’s University pays over $4 million annually to four of the big five publishers, and have cancelled the journal package with the fifth (Springer-Nature). These subscriptions make up almost half of the yearly library acquisitions budget at Queen’s!

The 2021 STM report estimates that while university budgets have doubled in the past two decades the proportion of those budgets spent on libraries (who subscribe to the journals providing open access to faculty and students) has halved!

Library funding is in decline, making access to journal articles that are not open access more difficult. Without a change in the scientific publishing model, the control of the media by for-profit publishers threatens open access of academics and the public to biomedical research. If you are “just” a member of the public, you will have to pay or forgo the read.

Impact of Open Access — The front page of an open access article on peer review by Piwowar. The interesting fact in this paper is that open access articles receive 18% more citations than articles that are not open access. This reflects the fact that pay walls are bad: not only for the public getting access to scientific and medical information, but also for the person that publishes the paper, as their work tends not to be seen inside it as often as it would be if it were an open access.
A summary of the benefits of open access publication

Example of a Paywall: Roughly half of biomedical research publications are open access, meaning available online with just a click at no charge. The likelihood a paper is published “open access” style varies widely based on the type of science being published, being much lower if the topic relates to pharmaceuticals. Moreover, many journals only offer an open access option for publication for an additional hefty fee (beyond the page charge fee). Paywalls are bad for scientists and for the public. Articles behind paywalls are less often viewed or cited, reducing their impact, whereas open access publications receive 18% more citations than those behind paywalls.

Paywall Log in screeshot from the American Journal — This example of the American Journal of Respiratory and Critical Care Medicine illustrates a screenshot of a paywall. To access this paper, one must pay a fee of $40 for unlimited access to this single publication, these paywalls are increasingly seen by people in the public domain trying to access scientific and medical information and is an obstacle to the exchange of knowledge.

When one tries to download this Am. J. Resp. Crit Care Medicine article one must have a subscription (sign in), work for an entity that has a subscription, or pay $40 for access to that single publication (without even knowing if it worth reading or of definite value to the reader).

Moreover, paywalls impair public advocacy. With a more educated populace there is a demand for high quality medical information to allow informed consumerism and advocacy and to guide one’s own health care behaviours. This requires the public have timely access to high quality research and medical publications. Paywalls hamper patient engagement in their own health care, depriving them of trusted sources of information. Paywalls also impair transparent feedback to participants in research studies. Imagine participating in a research study and not being able to download the publication that results from it!

The Flip Side of Free Open Access Publication: Lest this blog be taken as a Utopian call for “free everything for everyone”, I recognize publishers have legitimate costs and making some profit is also legitimate. Charlotte Haug pointed out in a NEJM editorial (available by open access) that there is no free lunch i.e. journals need editorial staff, statisticians, and editors, and like any business, this requires revenue generation. Haug summarized the history of the open access publication movement, dating back to a 2001 conference in Budapest where it was envisioned the internet could transform access to knowledge, making it free for all. The following is a statement by the Budapest Open Access Initiative (BOAI), written some 10 years after the founding of the Worldwide Web, “An old tradition and a new technology have converged to make possible an unprecedented public good. The old tradition is the willingness of scientists and scholars to publish the fruits of their research in scholarly journals without payment, for the sake of inquiry and knowledge. The new technology is the internet.”. Haug notes, “Eliminating subscription-based publication models without having alternatives in place that can reliably produce independently vetted, cautiously presented, high-quality content might have serious unintended consequences for the integrity of the scientific literature.”

However, we have likely taken the wrong (passive) approach to requiring open access. Universities and government are allowing for-profit publishers to set their own subscription and page change fees. We academic dodos are willing to provide the content for free, perform peer review for gratis and, when we are fortunate enough to cross the 10% acceptance threshold, even find it in our hearts to pay rising page charges for the privilege of being published! These unfortunate conditions are not implicit in a healthy system of biomedical publication; they are however the reality we currently face. My colleague offered the following important insight regarding the cost of the open access system as currently structure:

“Another source of profit for the big 5 publishers is to charge authors “article processing charges” or “APCs” to publish their articles open access. Authors can now pay a fee to make their article open access in almost any journal, while some journals are purely open access, others are a mix of paywalled articles and open articles where the author elects to pay an APC. This is quickly becoming a major revenue source for publishers: a 2023 study found that global APCs payments to the five large commercial publishers (Elsevier, Sage, Springer-Nature, Taylor & Francis and Wiley) is $1.06 billion. The highest impact journals frequently have the most expensive APCs, for example, to publish an Open Access article in Nature Medicine, an author would have to pay $12290 US.” - Mark Swartz

Some “Dangerous Ideas” to Reform Publishing Models: Universities, governments and the public should have timely access to the discoveries and medical information they paid for! It is time to regulate publishing houses to reduce subscription fees, eliminate page charges for publicly funded research and ensure the fees for open access publication are modest and limited. While journal subscriptions and publishers are necessary, there is a need to act to accelerate publication, speed peer review, increase acceptance rates, and ensure that a small group of publishers are not the primary beneficiaries of billions in profit, which is essentially derived from content that is created from publicly funded research.

Mark Swartz offered two other important suggestions for how we might improve access to publicly funded research, stating: “One model for regulation proposed by Dr. John Willinsky at Stanford University involves creating a statutory licensing regime that regulates compensation for publishers for Open Access publications. An alternative to regulation is to change the Copyright Act and adopt ”secondary publishing rights”, to ensure that authors can immediately “republish publicly funded research after its first publication in an open access repository or elsewhere,” even in cases where this is forbidden by publishers.

The Bottom Line: We need a “New Deal” with academic publishers! Currently, we are de facto working for them and mistakenly acting as if we depend on them to transmit our discoveries to the world. Under a new deal, we need them to work for us (or at least with us), recognizing that without researchers and universities, they would have no content!