New publishing models will only work if authors embrace them

Complaints about the broken academic publishing system have been around for years and are getting louder. A common theme is that with the rise of open access publishing, commercial publishers have grasped the opportunity to grow their profits from article-processing-charges (APCs). Whereas in the past, journals competed to be the most highly respected outlet, now they compete to publish on the grounds of speed and quantity of publications (see e.g. Timmis et al, 2025).

In response, various new initiatives have arisen. My focus here is on the F1000 publishing model, which was adopted by the Wellcome Trust in 2016 for their journal Wellcome Open Research. In this model, the author deposits an article on the platform (in effect as a preprint), which then is updated to a published version if two positive peer reviews are obtained. The only editorial input is from office staff who check that the submission meets basic criteria and that the selected peer reviewers are appropriate. This system could quickly get overwhelmed with low quality submissions, but aims to avoid that by restricting submissions to authors funded by the Wellcome Trust, which agrees to pay their APCs. I've always been a fan of open access, and have published several papers in Wellcome Open Research, encouraged by the prospect of straightforward and free open access publication.

A check on the Dimensions platform shows that Wellcome Open Research has grown in popularity over the years, and now dominates outputs from Wellcome-funded researchers.

Figure 1. Plot of the top 5 journals, publications funded by Wellcome Trust between 2016-2025.

My funding by Wellcome Trust came to an end and in 2016 I took up an ERC Advanced Grant. Towards the end of that grant, in March 2021, the European Commission (EC) announced that they were setting up a new journal, Open Research Europe that adopted the same F1000 model and offered free open access publication for EC-funded researchers. In contrast to Wellcome Open Research, Open Research Europe has not been enthusiastically embraced. A search on Dimensions showed that a large proportion of EC-funded research is published open access with for-profit publishers (see Figure 2). Open Research Europe is not shown because the number of publications is relatively small: 213, 251, 290, 374 for the years 2021 to 2024 respectively. It rates 25th among journals used by EC researchers, whose favourite publisher appears to be MDPI.

Figure 2. Plot of the top 5 journals, publications funded by EC between 2021-2025.

This raises two questions: who is paying the APCs, and why don't researchers publish on their funder's platform, which offers them free open access?

Of course, Open Research Europe is relatively young, and its uptake may have been influenced by its launch coinciding with emergence from lockdown. It's possible that communications from the EC encouraging grantholders to publish there haven't been sufficient to raise awareness of this option. I'd be curious if any readers who have EC funding could comment on barriers to uptake. Meanwhile, between 2021-2025 around US$973 million* in APCs has gone into the coffers of publishers - money that could have been used to fund researchers in other ways. On a rough estimate, around US$197 million of this has been paid to the most popular publisher, MDPI.

*To obtain this estimate, I searched Dimensions.ai using search terms Funder = European Commission (EC), Publication Type = Article, and year range from 2021-2025, and then used Analytical views to generate a table of source titles. For the first 30 titles, I manually checked the APC and used a currency converter to convert to $US. For the remaining titles, I estimated the APC as equivalent to the average for the first 30 titles. I coded MDPI as publisher for titles I recognised, but I did not carefully check each one. A csv file with the relevant data can be found here: https://osf.io/rcxd3.

Reference

Timmis, K., et al. (2025). Journals operating predatory practices are systematically eroding the science ethos: A gate and code strategy to minimise their operating space and restore research best practice. Microbial Biotechnology, 18(6), e70180. https://doi.org/10.1111/1751-7915.70180 

 

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I don't care about journal impact factors but I do care about visibility

There's been a fair bit of discussion about Clarivate's decision to pause inclusion of eLife publications on the Science Citation Index (e.g. on Research Professional).  What I find exasperating is that most of the discussion focuses on a single consequence - loss of eLife's impact factor.  For authors, there are graver consequences.   

I've reviewed for eLife but never published there; however, I have published a lot in Wellcome Open Research, which is another journal that aimed to disrupt the traditional publishing model, and has some similarities with eLife.  Wellcome Open Research has never been included in Science Citation Index, despite the fact that it uses peer review.  Wellcome Open Research has an unconventional model whereby submitted papers are immediately published, as a kind of pre-print prior to peer review, and then updated after peer review.  It is true that some papers don't get sufficient approval to proceed to the peer-reviewed stage; the distinction between those that do and do not pass peer review is clearly flagged on the article.  In addition to peer review, Wellcome Open Research maintains some quality control by limiting eligibility to researchers funded by Wellcome.  

 

When Wellcome Open Research started up, all Wellcome-funded researchers were encouraged to publish there.  As someone committed to Open Research, this seemed a great idea.  There were no publication charges, and everything was open: access to the publication, data, and peer review. Peer reviewers even get DOIs for their reviews, some of which are worth citing in their own right.  I was increasingly adopting open practices, and I think some of my best peer-reviewed work is published there. 

 

I was shocked when I discovered that the journal wasn't included in Web of Science. I remember preparing a progress report for Wellcome and using Web of Science to check I hadn't omitted any publications.  I was puzzled that I seemed to have published far less than I remembered. Then it became clear: everything in Wellcome Open Research was missing. 

 

I was on the Advisory Board for Wellcome Open Research at the time, and raised this with them. They were shocked that I was upset.  "We thought you of all people didn't care about impact factors", they said. This, of course, was true. But I did care a lot about my work being visible.  I was also aware that any WOS-based H-index would exclude all the papers listed below: not a big deal for me, but potentially harmful to junior authors.  

 

The reply I got was similar to the argument being made by eLife  - well, the articles are indexed in Google Scholar and PubMed.  That was really little consolation to me, given that I had relied heavily on Web of Science in my own literature searches, believing that it screened out dodgy journals. (This belief turns out to be false - there are many journals featured in WoS that are very low quality, which just rubs salt into the wound).  

 

I have some criticisms of eLife's publishing model, but I would like them to succeed. We urgently need alternatives to the traditional journal model operated by the big commercial publishers.  Their response to the open access movement has been to monetise it, with catastrophic consequences for science, as an unlimited supply of shoddy and fake work gets published - often in journals that are indexed in Web of Science.

 

I agree that we need an index of published academic work that has some quality control.  Whether alternatives like OpenAlex will do the job remains to be seen. 

 

Papers that aren't indexed on Web of Science

Bishop, D. V. M., & Bates, T. C. (2020). Heritability of language laterality assessed by functional transcranial Doppler ultrasound: A twin study. Wellcome Open Research, 4, 161. https://doi.org/10.12688/wellcomeopenres.15524.3

Bishop, D. V. M., Brookman-Byrne, A., Gratton, N., Gray, E., Holt, G., Morgan, L., Morris, S., Paine, E., Thornton, H., & Thompson, P. A. (2019). Language phenotypes in children with sex chromosome trisomies. Wellcome Open Research, 3, 143. https://doi.org/10.12688/wellcomeopenres.14904.2

Bishop, D. V. M., Grabitz, C. R., Harte, S. C., Watkins, K. E., Sasaki, M., Gutierrez-Sigut, E., MacSweeney, M., Woodhead, Z. V. J., & Payne, H. (2021). Cerebral lateralisation of first and second languages in bilinguals assessed using functional transcranial Doppler ultrasound. Wellcome Open Research, 1, 15. https://doi.org/10.12688/wellcomeopenres.9869.2

Frizelle, P., Thompson, P. A., Duta, M., & Bishop, D. V. M. (2019). The understanding of complex syntax in children with Down syndrome. Wellcome Open Research, 3, 140. https://doi.org/10.12688/wellcomeopenres.14861.2

Newbury, D. F., Simpson, N. H., Thompson, P. A., & Bishop, D. V. M. (2018). Stage 1 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: protocol for a test of the double hit hypothesis. Wellcome Open Research, 3, 10. https://doi.org/10.12688/wellcomeopenres.13828.2

Newbury, D. F., Simpson, N. H., Thompson, P. A., & Bishop, D. V. M. (2021). Stage 2 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: testing the double hit hypothesis. Wellcome Open Research, 3, 85. 

https://doi.org/10.12688/wellcomeopenres.14677.4

Pritchard, V. E., Malone, S. A., Burgoyne, K., Heron-Delaney, M., Bishop, D. V. M., & Hulme, C. (2019). Stage 2 Registered Report: There is no appreciable relationship between strength of hand preference and language ability in 6- to 7-year-old children. Wellcome Open Research, 4, 81. https://doi.org/10.12688/wellcomeopenres.15254.1

Thompson, P. A., Bishop, D. V. M., Eising, E., Fisher, S. E., & Newbury, D. F. (2020). Generalized Structured Component Analysis in candidate gene association studies: Applications and limitations. Wellcome Open Research, 4, 142. https://doi.org/10.12688/wellcomeopenres.15396.2

Wilson, A. C., & Bishop, D. V. M. (2019). ‘If you catch my drift...’: Ability to infer implied meaning is distinct from vocabulary and grammar skills. Wellcome Open Research, 4, 68. https://doi.org/10.12688/wellcomeopenres.15210.3

Wilson, A. C., King, J., & Bishop, D. V. M. (2019). Autism and social anxiety in children with sex chromosome trisomies: An observational study. Wellcome Open Research, 4, 32. https://doi.org/10.12688/wellcomeopenres.15095.2

Woodhead, Z. V. J., Rutherford, H. A., & Bishop, D. V. M. (2020). Measurement of language laterality using functional transcranial Doppler ultrasound: A comparison of different tasks. Wellcome Open Research, 3, 104. https://doi.org/10.12688/wellcomeopenres.14720.3

 

 

 

A New Year's letter to academic publishers

My relationships with journals are rather like a bad marriage: a mixture of dependency and hatred. Part of the problem is that journal editors and academics often have a rather different view of the process. Scientific journals could not survive without academics. We do the research, often spending several years of our lives to produce a piece of work that is then distilled into one short paper, which the fond author invariably regards as a fascinating contribution to the field. But when we try to place our work in a journal, we find that it's a buyer's market: most journals are overwhelmed with more submitted papers than they can cope with, and rejection rates are high. So there is a total mismatch: we set out naively dreaming of journals leaping at the opportunity to secure our best work, only to be met with coldness and rejection.  As in the best Barbara Cartland novels, for a lucky few, persistence is ultimately rewarded, and the stony-hearted editor is won over. But many potential authors fall by the wayside long before that point.

But times are changing. We are moving from a traditional "dead tree technology" model, where journals have to be expensively printed and distributed, to electronic-only media. These not only cost less to produce, but also avoid the length limits that traditionally have forced journals to be so highly selective. Alongside the technological changes, there has been rapid growth of the Open Access movement. The main motivations behind this movement were idealistic (making science available to all) and economic (escaping the stranglehold of expensive library subscriptions to closed-access journals). It's early days, but I am starting to sense that there's another consequence of the shift, which is that, as the field opens up, publishers are starting to change how they approach authors: less as supplicants, and more as customers.

In the past, the top journals had no incentive to be accommodating to authors. There were too many of us chasing scarce page space. But there are now some new boys on the open access block, and some of them have recognised that if they want to attract people to publish with them, they should listen to what authors want. And if they want academics to continue to referee papers for no reward, then they had better treat them well too.

This really is not too hard to do. I have two main gripes with journals, a big one and a little one. The big one concerns my time. The older I get, the less patient I am with organizations that behave as if I have all the time in the world to do the small bureaucratic chores that they wish to impose on me. For instance, many journals specify pointless formatting requirements for an initial submission. I really, really resent jumping through arbitrary hoops when the world is full of interesting things I could be doing. And cutting my toenails is considerably more interesting than reformatting references.

I recently encountered a journal whose website required you to enter details (name/address/email) of all authors in order to submit a pre-submission enquiry. Surely the whole point of a pre-submission enquiry is to save time, so you can get a quick decision on whether it's likely to be worth your while battling with the submission portal! There's also the horror of journals that require signatures from all authors at the point when you submit a manuscript: seems a harmless enough requirement, except that authors are often widely dispersed - on maternity leave or sailing the Atlantic - by the time the paper is submitted. The idea is to avoid fraud, of course, but like so many ethics regulations, the main effect of this requirement is to encourage honest, law-abiding people to take up forgery.

Oh, and then there are the 'invitations to review' (makes it sound so enticing, like being invited to a party), which require you to login in order to register your response – which for me invariably means selecting the option that I have forgotten my password, then looking at email to find how to update the password, meanwhile getting distracted by other email messages so I forget what I was doing, and eventually returning to the site to find it wants me now to change the password and enter mandatory contact details before it will accept my response. Well, no.  I'm usually a good citizen but I'm afraid I've just stopped responding to those.

You'd think the advent of electronic submission would make life easier, but in fact it can just open up a whole new world of tiny, fiddly things that you are required to do before your paper is submitted. Each individual thing is usually fairly trivial, but they do add up. So, for instance, if you'd like your authors to suggest referees, please allow them to paste in a list. DO NOT require them to cut and paste title, forename, initial, surname, email and institution into your horrible little boxes for each of six potential referees.  It all takes TIME. And we have more important things in life to be getting on with. Including doing the science that allows us to get the point of writing a paper.

Even worse, some of the requirements of journals are just historical artefacts with no more rationale than male nipples.  Here's a splendid post by Kate Jeffery which in fact was the impetus for this blogpost. I thought of Kate when, having carefully constructed a single manuscript document including figures, as instructed by the Instructions for Authors, I got to the submission portal to be strictly told that ON NO ACCOUNT must the figures be included in the main manuscript. Instead, they had to be separated, not only from the manuscript, but also from their captions (which had to be put as a list at the end of the manuscript). This makes sense ONCE THE PAPER IS ACCEPTED, when it needs to be typeset.  But not at the point of initial submission, when the paper's fate is undecided: it may well be rejected, and if not, it will certainly require revision. And meanwhile, you have referees tearing their hair out trying to link up the text, the Figures and their captions.

The smaller gripe is just about treating people with respect. I do have a preference for journal editors whose correspondence indicates that they are a human being and not an automaton. I've moaned about this before, in an old post describing a taxonomy of journal editors, but my feeling is that in the three years since I wrote that, things have got worse rather than better. Publishers and editors may think they make their referees happy by writing and telling them how useful their review of a paper has been – but the opposite effect is created if it is clear that this is a form letter that goes to all referees, however hopeless.It is really better to be ignored than to be sent an insincere, meaningless email - it just implies that the sender thinks you are stupid enough to be taken in by it.

So my message to publishers in 2014 is really very simple. The market is getting competitive and if you want to attract authors to send their best work to you, and referees to keep reviewing for you, you need to become more sensitive to our needs.  Two journals that appear to be trying hard are eLife and PeerJ, who avoid most of the bad practices I have outlined. I am hoping their example will cause others to up their game. We are mostly very simple souls who are not hard to please, but we hate having our time wasted, and we do like being treated like human beings.

Time for academics to withdraw free labour

© www.CartoonStock.com

Jack is a sheep farmer. He gets some government subsidies, and also works long hours to keep his sheep happy and healthy. When his beasts are ready for slaughter, he offers them to an abattoir. The abattoir is very choosy and may reject Jack’s sheep, which is a disaster for him, as there is no other route to the market. If he is lucky the abattoir will accept the animals, slaughter them and sell them, at a large profit, to the supermarket. Jack does not see any of this money. The populace struggle to afford the price of meat, but the government has no control over this. When Jack feels like a nice piece of lamb, he buys it from the supermarket. Meanwhile, Jack provides his services for free as an inspector of other farmers’ animals.

Crazy story, right? But that’s the model that academic publishing follows. Academics work their butts off to get research funding, often from government. They then do the research and write up and submit it for publication. They run the gauntlet of picky reviewers and editors to get the work accepted for publication. Once it is published, it appears in a journal which is sold on to academic institutions for large profits. Post publication, the academic often has to pay a cost equivalent to several hardback books to get a formatted electronic copy of the article. Meanwhile, the journals justify this by arguing they have extensive costs. But in fact, it is the academic community that does the bulk of the work for free, acting as editors and peer reviewers. Increasingly, they are expected also to do copy editing and graphic design, tasks that were previously undertaken by professional journal staff.

It has taken many years for the torpid academic community to wake up to this ludicrous situation, but things are slowly starting to change. In some fields, academics are starting to take things into their own hands and cut commercial publishers out of the loop, but this still the exception rather than the rule. A more widely adopted innovation has been Open Access publishing. On the one hand, electronic publishing has made it possible for journal papers to be posted online and made freely accessible. On the other, major funders, notably NIH in the USA and the Wellcome Trust in the UK, have insisted that researchers whom they fund must make their published work Open Access. Obviously, something has to give: the publishers are not going to do their work for nothing. But the system does work, with a combination of new journals that are Open Access from the start, and older ones agreeing to make selected articles Open Access, in both cases for a fee. In general, the funders agree to pay the charge.

This week, however, a story broke suggesting that the traditional publishers are trying to fight back and force NIH to backtrack on its Open Access policy. Things hotted up with this post from Michael Eisen who noted that one major publisher, Elsevier, has been lobbying a NY Congresswoman, Carolyn Maloney, to persuade her to support a bill that would limit Open Access publishing. Harvard University gave a detailed response to the bill, which can be found here.

I want my response to this story to go beyond just tut-tutting and shaking my head.  Academics do have some power here. We provide the articles for Elsevier journals, and we do a lot of unpaid work reviewing and editing for them. None of us wants to restrict our opportunities for publishing, but these days there are a lot of outlets available. When deciding where to submit a paper, I suspect that most academics, like me, take little notice of who the publisher of a journal is. I focus more on whether the journal has a good editor, my prior experience of publication lags, and whether Open Access is available. But as from now, I shall include publisher in the criteria I adopt, and avoid Elsevier as far as I can. Also, if asked to review for a journal, I’ll check if it is in the Elsevier stable, using this handy website, and if so, I’ll explain why I’m not prepared to review. I suggest that if you are as annoyed as I am by this story, you do likewise, and refuse to engage with Elsevier journals.

Addendum, 10th January 2012

Some people on Twitter have asked if people should be paid for the work they do as author/editor/reviewer. Definitely not. It would just make matters worse, because publishers would factor in these costs and charge even more for journals.

No, I just want a change in the model whereby publishers make enormous and undeserved profits from academics. There are various ways this could be done.

1. The publishers could charge less: currently if you try and download a single journal article, you are charged around £20, even though the production costs are minimal.

2. Retain the current model but remove commercial publishers from the loop, with publication of research limited to learned societies, universities, funders.

3. Retain the current model but make all journals Open Access, with the funder or university paying a one-off publication fee.

4. More radically, move to a system such as arxiv, which I discussed here.

On the whole, academics are an interesting bunch. We’re not all that interested in money, but we are skilled and can produce things of commercial value. It’s a golden opportunity for someone who does want to make money to step in a make a profit. Publishers like Elsevier would have been fine if they hadn’t been so greedy and had charged modest sums for their product. Instead, they pushed costs as high as the market could bear, making huge profits, while at the same time giving authors less and less. (Copy-editors have become an endangered species). Instead of facilitating scientific communication, they have put obstacles in the way. But part of the blame lies with the academic community, who have been far too passive. We should have tackled this years ago before it got out of hand.