Public institutions should lead the way towards a new model
A decaffeinated version of this article was published in EMBO Reports:
Ignacio Amigo & Alberto Pascual‐García, EMBO Rep. 2017 Dec; 18(12): 2081–2083. Published online 2017 Nov 20. doi: 10.15252/embr.201745008
Abstract
Despite great technological advances, scientific publishing has experienced little change in the last decades. While the strong push for Open Access has contributed to increase the expand the accessibility of science, most of the publication process is still largely opaque and subjected to economic and private interests imposed by journals. The momentum of pre-prints, together with the creation of online platforms to bypass journals, such as those from the Wellcome Trust and the Bill and Melinda Gates, are signs that we could be approaching a watershed. Here we discuss the problems associated with the current publishing model and present some of the alternatives that have bDespite great technological advances, scientific publishing has experienced little change in the last decades. While the strong push for Open Access (OA) has contributed to expand the accessibility of science, the way in which has been implemented has created a situation of conflict of interests which impacts the quality of the science produced. In particular, the Gold OA model, in which authors pay for making their work freely available, explicitly links the scientists’ possibilities of obtaining economic stability to journals’ revenues, through the ability that the formers have to allocate funder’s resources into journals. Thus, both journals and scientists have an interest in producing as many papers as possible, overlooking quality or integrity issues. The current momentum of pre-prints, together with the creation of new platforms such as those from the Wellcome Trust and the Bill and Melinda Gates Foundation, are signs that the publishing system could be approaching a watershed. However, these new models fail to address the heart of the matter and are likely to lead to new conflicts of interests. Here we discuss the problems associated with past and present publishing models, and analyse alternatives that have been emerging in the last years. We propose a model which we believe could create a scenario free of conflicts of interest and benefit the scientific community as a whole. Public institutions hold the key to the quality and speed at which such scenario could be reached.
Scholarly journals have been the bedrock of scientific communication for the last centuries. The first academic journals, Philosophical Transactions and the Journal des sçavans, date from 1665. Peer review, another pillar of scientific communication, was established in the 19th century, although the term and its current form – commissioned by journals and performed anonymously – did not become routine until late 20th century.
This model worked throughout most of the 20th century, when funding was abundant and scientists few: governments funded scientists, who published their results in scientific journals, and University libraries then purchased those journals, granting communication between scientists (see Fig. 1).

However, over the last decades there has been a concentration of journals in the hands of only a few publishers. A recent report shows that half of all the papers published in 2013 in the natural and medical sciences belonged to only three publishers. The proportion was even higher in the social sciences [1]. As a consequence of this oligopoly, publishers have engaged in the past in abusive practices, including excessive price hikes and the creation of controversial journal bundles [2]. For the interested reader, a detailed historical account of the events that led to this situation has been recently published [3].
At the same time, the increase in the number of scientists outpaced the creation of secured positions within academia. Competition between scientists on one hand, and limited funding from university librarians on the other, created a fertile ground for the development of metrics to evaluate the impact of research, including the now infamous impact factor. Thus, publishing in the best journals became the only way for scientists to access fixed positions and secure research funding. One of the consequences of this model was the emergence of a conflict of interests between journals in look for highly citable papers, and scientists, that were forced to adapt their researches to fit the most prestigious journals’ interests (Figure 2).

In this scenario, the increasing difficulties created by journals to access scientific information, both to scientists and to a growing industry, bolstered the emergence of the Open Access (OA) movement and, in the early 2000s, things began to change. With the advent of the internet, the costs of producing papers plunged and publication speed increased. The new scenario prompted the surge of new journals that embraced a model which is now known as ‘Gold OA’. Under this model, instead of charging readers to access the content, journals charge the authors a fee to cover for the publication costs, after which their work becomes freely accessible.
But despite having increased the overall accessibility to scientific literature, Gold OA has some important drawbacks. One of them is that it has failed to address the problem of the increasing costs of scientific publishing, which was one of the main reasons why it was implemented in the first place. Publication fees in many Gold OA journals are substantially high, considering that the cost of making papers is continuously dropping while fees keep steadily increasing. Another consequence of Gold OA has been the spread of low quality ‘predatory’ journals, that charge authors for publishing their work after flawed or non-existent peer review, discrediting both the OA movement and science as a whole [4]. Finally, Gold OA has only superficially tackled the existing problems with the editorial and peer review processes of journals, which still remain largely opaque. This perpetuates the scenario in which reviewers carry out the most important task of peer review without receiving any credit for it. This opacity, together with the increasing number of papers published, opens the door to situations of misconduct, conflict of interests or fraud.
In the last years, as governments legislated to make the research they fund accessible free-of-charge, Gold OA has become increasingly popular. Publicly funding this model is justified by governments appealing to an increase in the benefits-to-costs ratio: as research becomes more easily available, economic activities arise. However, a study has estimated that if authors made their research available simply by posting their articles online – what is known as ‘Green OA’ –, there would be a 40-fold increase in the same ratio [5]. Also, the reported profit margins of 37-40% of some publishing companies such as Elsevier, suggest that public institutions invest in publishing services far more than it would be needed [6].
In perspective, Gold OA is a model in which journals are financed by scientists using money from funders. For journals, adopting this model made their business more robust, no longer relying on subscriptions. However, the conflict of interests between scientists and journals has gotten worse with Gold OA (Figure 3). While high quality science requires time to be pursued, in the current scenario both journals and scientists benefit from publishing as many articles as possible. This is a natural environment for cheaters to arise on both sides, as we are seeing now with the emergence of predatory journals and the increasing number of cases of scientific misconduct.

As mentioned above, one of the alternatives would be to adopt a Green OA model. However, while cutting the middle man would alleviate the existing conflict of interests, journals – including those that adhere to Gold OA practices – offer a variety of services that would be left undone. These include: editorially reviewing papers, organising peer review, copy-editing articles and providing long-term archiving for papers. This apparent dead end has stimulated the development of new publishing alternatives.
Pre-prints are the most basic form of Green OA. In the last years, many researchers in the Life Sciences have began to upload their work to online repositories before submitting it to journals, thus making their manuscripts available to the public prior to peer-review. This approach has been popular in Physics for the last 20 years, and in Life Sciences the number of deposited papers in emergent repositories like bioRxiv or arXiv q-bio has been rapidly increasing. Repositories are also being used to store and make available large datasets, a move that could have great impact in future research. In theory, the use of repositories could be a way out to the current conflict of interests between scientists and journals. However, the fact that they lack peer-review discourages scientists from using them as the main vehicle to convey their results, thus limiting their current impact (Figure 4).

Born in the same year, F1000 Research aimed to specifically tackle the problems associated with anonymous peer review. Accordingly, what in some journal such as PeerJ is still optional in F1000 Research becomes default. In F1000 Research, manuscripts are promptly published after submission and peer review is performed openly by researchers identified by their name and institution. Once the paper has been approved by at least two referees, or one has approved it and two have “approved it with reservations”, the paper is indexed in PubMed, Scopus and other databases. The cost of publishing in F1000 Research is US$150 for articles up to 1000 words, US$1,000 for those over 2,500 words, and US$500 for those in between, substantially lower than in most Gold OA journals. Although it is still in the best interest of both the scientists and the platform to publish as many papers as possible, open peer-review partially alleviates this conflict of interest, because the reputation of the reviewers comes into question if a low quality paper gets published.
Recently, some large funders have embraced the model of F1000 Research to create their own publishing platforms. One is the Wellcome Trust, that last year launched an online platform where researchers funded by the charity can publish their research to be subject to free and open peer-review. The other is the Bill & Melinda Gates Foundation, whose platform is set to launch at the end of the year. A third platform, from the European Commission, could follow suit.
Although at first sight these initiatives might seem positive because they embrace open peer-review, it should be noted that, not only fail to address the issue of the conflict of interests, but they generate a new one (Figure 5). As the Wellcome Trust and the Bill & Melinda Gates Foundation platforms are only open to scientists funded by these institutions, if these platforms prove successful, the prestige associated with publishing in these venues will likely increase over the next years, competing with high impact journals. This would push scientists to align their research with the interests of these funders, that provide both funding and prestige through its publishing platform. Moreover, only the minority elite which is already funded by generous grants from these organizations will benefit from it, promoting a dangerous rich-gets-richer model that creates first and second class scientists.

Other initiatives are based in collaborative platforms. That’s the case of “Peer Community in”, a non-profit scientific organization that promotes the review and recommendation of articles in different fields. Its most successful branch, the Peer Community in Evolutionary Biology, allows peer-review of pre-prints free-of-charge. Once a manuscript is uploaded to a pre-print repository, authors can request a recommendation to the community. A ‘recommender’ then selects at least two reviewers and, according to their comments, decides whether to recommend it or not. If so, the paper is publicized and can be cited as peer-reviewed. A similar procedure can be applied to papers that have already been published, as a way of adding them value. Nevertheless, the platform does not publish negative reviews, which would be an interesting way to deal with low quality published results.
A more ambitious example of collaborative platform is the Self-Journals of Science (SJS). Articles submitted to SJS are posted online and open to peer-review by any registered scholar, identified with its real name. Reviews are displayed along with the text and subjected themselves to debate by other peers. Users can vote if they believe that a paper “has reached scientific standards” or if “still needs revisions”. Authors can then improve the paper, and the contribution of reviewers is acknowledged and visible to everyone in the next versions. SJS also allows publishing comments -both positive and negative- on previously published papers. Finally, any scientist can curate a group of papers converting them into a “Self-Journal”, thus making an editorial work. More importantly, all these roles are tracked and evaluated by peers, generating a self-organized process that pave the way for transparent publishing and fair evaluation.
While collaborative initiatives such as these seem to go in the correct direction to solve conflicts of interests issues (Figure 6), the lack of strong funding generates uncertainty in questions such as long-term archive, or if the articles published in these platforms will be indexed and considered by evaluators. It is difficult to think that these models can succeed side-lining journals, specially considering that publishers constitute an influential lobby for policymakers.

The times are changing. Public institutions and science funders have the power to set the pace of the change and encourage the adoption of new practices that safeguard free access to knowledge in the most effective way. They have already made clear that they support open access, as well as pre-print and databases repositories. In the US, the Fair Access to Science and Technology Research Act and the Public Access to Public Science Act support that research produced with public funds becomes freely accessible. The EU has also issued a similar mandate to make all publications funded by Horizon 2020 available to “read online, downloaded and printed”. It has also created free-to-access online repositories, such as OpenAIRE and Zenodo, to host data and published OA papers.
So why is there still resistance to promote a publicly-funded and free of conflict-of-interests scientific publishing model? Journalist Richard Poynder, an expert in OA, believes that publishers have taken advantage of the lack of a centralised voice in the OA movement. In the past, when governments and funding agencies have looked for ways of increasing the accessibility to the works they fund, they have turned for advice not to OA activists, but to publishers. Accordingly, the laws that are being passed are being, in many cases, tailor-made to the needs of the publishing industry, and the same will apply to any attempt of free peer-review implementation. One of the consequences is that, as recently happened in the UK, Gold OA is being promoted over less expensive alternatives [7].
In July 2017 F1000 launched Open Research Central whose “longer-term plan is to transition Open Research Central to being owned and governed by the international research community with broad representation across research funding agencies, research institutions, and researchers”. Still, how this stage will be achieved remains unclear, but the statement of intentions is quite clear. We should wonder why while publishers are already taking positions to compete for a new publishing scenario as the one demanded by scientists, public institutions remain idle.
We believe that the current situation is sufficiently worrying to request public institutions to take the lead towards a more ambitious publishing system, one that is not only free and public, but also transparent and without conflict of interests. A coordinated international movement considering all the actors involved would prevent conflicts as the one we are witnessing between Elsevier and German universities [8], or the emergence of publishing alternatives as the ones we described, which not only are unable to fully tackle the different problems but, in some cases, deteriorate further the situation.
Following this line of thought, we delineate a scenario which we believe is compatible with everyone’s interests. It considers a redistribution of funding and the role of the different actors (scientists, metric companies, librarians, …) to maximise the impact of their respective skills in the benefit of science, while still keeping the different economical activities likely profitable. We articulate it as follows (See Figure 7):

1. Research papers and scientific data should be published in several specialized open, internationally-supported and publicly-funded storage repositories (SR), guaranteeing long-term monitoring and storage of all scientific activity. These repositories won’t need to be centralised, taking advantage of the particular specialised services that each of them might offer. Librarian services would be critical in these platforms, and there should be specific funding to support research in their important activity. Although not necessary centralised, it is important to reach uniform standards and protocols. This is, for instance, the path that the Confederation of Open Access Repositories (COAR) is already following.
2. Peer-review should be self-organized by scientists in a centralised, international and publicly-funded platform (PRP). Similar to Wikipedia, no editorial work, type-setting, marketing, communication or rights management should be performed by external agents. Data and articles uploaded by scientists to SRs, or even published manuscripts, would be linked to each scientific profile in PRP, and openly subjected to scientific discussion. Thus, the PRP will be a space for scientific discussion where all the activity performed by each scientist – discussion in forums, publication of papers or peer-review for example – , will be tracked and publicly evaluated by other scientists, following a peer-to-peer spirit. A large number of successful self-organized projects such as Wikipedia, GNU-Linux or StackOverflow support the viability of this model. Metrics developed to evaluate scientists for their published scientific activity should take into account mainly results obtained from the activity in this platform which, keeping intact its independence, would constitute a safeguard against conflicts of interests. In addition, tracking the activity this way would allow to monitor misconduct more easily.
3.- Companies developing metrics to evaluate scientific impact would convert the self-evaluation of scientists in the PRP into simple metrics that can be evaluated by funders. They would also have the important role of estimating the impact of articles already published through these new standards, which would be one of the most important challenges that the model proposed envisages.
4. Free of peer-review and its associated costs, journals could focus on processing research to make it more accessible. This would allow them to expand their audiences to include industries and the big public, making a large contribution to society. Note that, although publishing in journals would not constitute the main evaluation for scientists, scientists would still be interested in collaborating with journals to generate reviews, perspectives and other journalistic products, that would give them more visibility among their peers and facilitate outreach. In summary, journals would be free to develop their business activity under the model that better suits them, without the current constraints imposed today by public funders, for instance in relation to OA policies.
5. Public institutions should take the lead towards this change. They should establish a clear roadmap for setting new evaluation procedures and deadlines, after which only publications in a PRP would be considered. In economic terms, the cost of implementing this model would be minuscule compared with current public investments.
In summary, we believe that freeing science from the existing scenario of conflict of interests is an urgent task, given the dangerous deteriorating tendency that the current model is generating. We propose a model in which, journals, evaluators, scientists, librarians and funders, among other actors, will find a space in which they can best develop the activity in which each of them is specialist, while separating their services and economical interests from the scientific activity per se. Science can only experience a healthy growth in such a scenario, in which scientists activity is free of conflicts of interest and their evaluation is transparent. We believe we should seize this opportunity to put science back as the best example of a cooperative human activity envisaged to bring to the next generations a better world.
References
1. Larivière V, Haustein S, Mongeon P (2015) The Oligopoly of Academic Publishers in the Digital Era. PLoS ONE 10: e0127502
2. Bergstrom TC, Courant PN, McAfee RP, Williams MA (2014) Evaluating big deal journal bundles. PNAS 111: 9425-9430
4. Bealls J (2016) Predatory journals: Ban predators from the scientific record. Nature 534: 326
5. Houghton, J.W. & Oppenheim, C. (2009) The Economic Implications of Alternative Publishing Models Prometheus 26 (1): 41–54.
6. Van Noorden R] (2013) Open access: The true cost of science publishing. Nature 495 (7442), 426.
7. Poynder R. (2014). The State of Open Access. Open and Shut. http://poynder.blogspot.com.br/2014/03/the-state-of-open-access.html
Conflict of interests: APG is working member of OpenScholar, a not-for-profit independent organization of scientists governing Self-Journals of Science. OpenScholar had no role in the preparation of the manuscript, and APG do not receive any economical reward for his activity in the organization.
Acknowledgements: The authors acknowledge useful comments in a preliminary version of the manuscript to Michäel Bonn, Pandelis Perakakis, Michael Taylor and Gary McDowell. We also thank Holger Breithaupt, editor of EMBO reports, for his insightful comments and suggestions.

