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Journalology

Journalology #67: Reviewed preprints

Published 3 months ago • 16 min read


Hello fellow journalologists,

This week we start off with an assessment of eLife’s new editorial model and finish with an excerpt from what may well be the most interesting academic conference of the year.

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News

Scientific Publishing: The first year of a new era

It is perhaps worth remembering that when we went public with our plans, there were predictions in every direction. Some thought that our new publishing model was too risky and that authors would not submit their work. Others were sure that we would be flooded with low-quality articles – or that the opposite would happen and that only those researchers who had the most confidence in their work would submit to us. There were also worries that editors and reviewers would not want to be involved in a system where there was no accept/reject decision and where authors were under no obligation to revise the article in response to comments from reviewers.
A year on, the reality is a lot more encouraging. We received more than 6200 submissions to the new model in its first year of operation, with last month (January 2024) being the best to date. About a third of these have been reviewed in depth, which is comparable with the fraction selected for review under our previous model, and we estimate (based on the ratings for significance and strength of evidence) that the quality of submissions has not changed significantly.

eLife (Timothy E Behrens, Yamini Dalal, Diane M Harper, Detlef Weigel)

JB: The accompanying report contains some interesting data, although I would have liked to have seen equivalent numbers for the period when a more conventional peer review model was used. 6200 submissions in the past year is certainly encouraging, but how does that compare with previous years?

If you’re new to this topic and want to better understand how eLife’s editorial model works, this blog post from January should help you to orientate yourself: eLife’s New Model: What is a Reviewed Preprint?.

As a reminder each paper is assessed in the following way:

To help readers quickly assess the merit of the research, eLife assessments indicate the significance of the findings using common vocabulary: from “useful” for findings with focused importance and scope, to “landmark” for findings likely to have deep and widespread implications. Similarly, the strength of the support for the findings are described: from “exceptional” for exemplary use of methods, to “inadequate” where the research does not support the claims of the article. We highlight these terms in bold for ease of reference, and where different elements of a preprint warrant different evaluations, our assessments may use more than one of these terms as required.

There’s no filter on the website to allow readers to choose which papers to see. As I reader I wouldn’t want to see “inadequate” papers, for example. Unfortunately, readers are generally considered to be less important than authors in this brave new world, which is a missed opportunity in my opinion.

The report provides graphs on the proportion of papers for each category in the controlled vocabulary. Here’s the data for significance. Note that the lowest rating is “useful”. There’s no such thing as “useless” piece of research, apparently.

And here’s the data for strength of evidence:

Eyeballing the second graph, it looks as though around one quarter of papers that are peer reviewed are “inadequate” or “incomplete” when it comes to the strength of the evidence.

That figure is lower than I expected. After all, sound science journals like PLOS One and Scientific Reports have acceptance rates of around 50%. This suggests there must be some kind of editorial screening done before peer review at eLife that filters out some of the poor quality work. That’s not a bad thing, but eLife is adamant that this doesn’t happen:

It is important to note that we don’t ascribe value to the decision to review. Our aim is to produce high-quality reviews that will be of significant value but we are not able to review everything that is submitted.

That’s the one part of the model that makes no sense to me. If eLife really believes in avoiding any kind of quality assessment before peer review, then surely it should randomly allocate papers to “desk reject” and “peer review”. I can’t see authors liking that approach, though.

eLife is doing an interesting and important experiment. These new data suggest that some research groups are more than happy to submit to eLife under the new model, which is a useful indicator in and of itself.

However, the Clarivate Sword of Damocles may still be hanging over them. Remember that there’s now no accept or reject decision at eLife, which could mean that eLife will lose its impact factor.

Take a look at this page and scroll down to the ‘Coverage of journals/platforms in which publication is decoupled from validation by peer review’ section.

My reading of this is that Clarivate will want to re-evaluate eLife for inclusion in Web of Science, if it hasn’t done so already. If eLife loses its impact factor, it will be fascinating to see what happens next. All the historical evidence suggests that submissions would fall off a cliff, but eLife is an unusual journal and perhaps it would buck the trend. We shall see.


American Physiological Society to Launch Subscribe to Open Model for Research Journals

The American Physiological Society (APS), a nonprofit organization that publishes 16 scientific journals highlighting critical advances in physiology and related fields, announces a strategic shift to a Subscribe to Open (S2O) publishing model. As part of its mission to advance scientific discovery, understand life and improve health, APS is working closely with the library community to implement this open access publishing model, beginning in 2025, for 10 of the Society’s primary research journals.

American Physiological Society (press release)

JB: A big disadvantage of the S2O model is that it makes it hard for publishers to grow revenues. However, many society publishers working in traditional biomedical disciplines — like physiology, biochemistry, pharmacology and anatomy — have seen their article outputs fall dramatically over the past decade, with new fully open access publishers, especially Frontiers, taking significant market share. S2O could be a way to lock in existing subscription revenues at a level where the revenue per article is higher than would be the case under an APC business model, while also transitioning the portfolio to open access.


Introducing Dimensions Research GPT and Dimensions Research GPT Enterprise

For many researchers, the excitement surrounding Generative AI (GAI) has been mixed with skepticism because of concerns ranging from hallucinations to ethical AI development. In response, Dimensions has developed its custom GPT solutions, uniting the robust data from Dimensions with ChatGPT’s AI platform: Dimensions Research GPT and Dimensions Research GPT Enterprise. These solutions mean that researchers can now access an advanced literature discovery workflow that merges the scientific evidence base of Dimensions with the Generative AI functionality of ChatGPT – reducing the likelihood of hallucinations and providing click-through scholarly references for each statement to enable quick and easy validation and further discovery.

Digital Science (press release)

JB: It’s worth reading Daniel Hook and Simon Porter’s blog post on the announcement: Launching a new way to interact with scientific content on OpenAI’s ChatGPT platform. The free version of the tool (calledDimensions Research GPT) only uses open access articles.

In the case of Dimensions Research GPT, data related to research articles from the open access corpus contained in Dimensions is used to provide context to the user’s question and discover more. This free tool gives users the ability to interact with the world’s openly accessible scholarly content via an interface that ensures that answers refer back to the research that underlies the answer. This provides two important features: Firstly, the ability to verify any assertions made by Dimensions Research GPT, and secondly, the ability to see references to a set of articles that may be relevant to their question so that users continue to be inquisitive and read around a field. Basing this free tool on content that is free-to-read provides the greatest chance for equity and impact.

Simon Linacre wrote a blog post about the tools too: Fast forward: a new approach for AI and research.


BC Partners revives plans for $9.7 bln Springer Nature sale, sources say

Springer Nature’s private equity backer is dusting off plans to list the German academic publisher, amid growing optimism around initial public offerings, four people familiar with the matter told Reuters. BC Partners is in the early stages of exploring options for its 47% stake in Springer Nature, including a potential IPO as soon as the second half of the year, the people said, speaking on condition of anonymity.
Springer Nature, the publisher of science journal Nature and Scientific American, could be valued at up to 9 billion euros ($9.7 billion), including debt, one of the people said. Deliberations are still preliminary, and there is no certainty that a transaction will happen, the people cautioned.

Reuters (Amy-Jo Crowley and Pablo Mayo Cerqueiro)

JB: Springer Nature Eyes IPO in H2, Valuation Could Hit 9 Billion Euros Amid Market Optimism is also worth reading.

If you’re not familiar with the backstory, this quote from Jaime A. Teixeira da Silva and Yves Fassin’s 2022 Learned Publishing article should help you to get up to speed.

In late 2017, Springer Nature planned to enter the stock market, accompanied by news of an initial public offering (IPO), which was set to take place in the middle of 2018. The estimated value of the IPO in late 2017 was €4–5 billion, increasing to €7 billion in early 2018, with news that the company desired to speed up the IPO with a listing on the German stock exchange in Frankfurt by June–July 2018. With assistance from reputed banks and ‘bookrunners’, the Springer Nature IPO gave the impression of a done deal. However, despite high revenues and excellent EBITDA (earnings before interest, taxes, depreciation and amortization), the €3 billion debt could not be ignored. Fluctuating values of the IPO were accompanied by pessimism by Springer Nature in late April and early May 2018 regarding volatility in European IPOs and increasing trends of instability in academic publishing. On 8 May 2018, 1 day before the expected launch of the IPO, Springer Nature cancelled the IPO.

The current owners of Springer Nature tried again in 2020:

Several media sources (Reuters, Nasdaq) reported a second IPO attempt in 2020, which was postponed twice and then cancelled, citing the pandemic as the reason.

If they’re able to IPO at somewhere close to €9 billion, then the owners will have doubled their money in just over 6 years.


DataSeer.ai and IOP Publishing Collaborate on Open Science Indicators and Open Data Pilot

The pilot project will help build an understanding of how researchers are adopting open science practices across IOP Publishing’s portfolio of proprietary journals. Supported by DataSeer ai’s advanced analytics platform, it will explore the use of open science indicators with a focus on open data practices. The findings will help enhance knowledge of current practice and indicate future directions for supporting open research.

IOP Publishing (Faye Holst)


Cambridge launches new Sustainable Web Design guidelines

The Sustainable Web Guide has been developed to help ensure web projects are energy efficient and produce the least amount of carbon emissions possible in support of the organisation’s commitment to sustainability, which includes being carbon zero on all energy-related emissions by 2048.
The guide includes sections on benchmarking, design, content, development and hosting, and refers to Cambridge’s sustainable design principles; ‘sustainable thinking’, ‘inclusive design’ and ‘carbon efficiency’. It is publicly available for anyone to access and use.

JB: You can read the guide here. This week, CUP also won the OpenAthens UX Award 2024.


Plan S: Annual Review 2023

The “Gold” route remains the most widely used method for delivering OA, amongst cOAlition S-funded researchers, with more than 40% of all articles published OA in 2023 made available this way, as shown in Figure 1. The number of articles made available via the “Hybrid” route has increased, likely due to the transformative arrangements, such as Read and Publish agreements and transformative journals. In the future it will be interesting to see if this number declines following the statement from cOAlition S that, post 2024 it will no longer financially contribute to such arrangements.

Plan S (report)


Is ChatGPT making scientists hyper-productive? The highs and lows of using AI

And there is a drawback to the productivity boost that LLMs might bring. Speeding up the paper-writing process could increase throughput at journals, potentially stretching editors and peer reviewers even thinner than they already are. “With this ever-increasing number of papers — because the numbers are going up every year — there just aren’t enough people available to continue to do free peer review for publishers,” Lancaster says. He points out that alongside researchers who openly use LLMs and acknowledge it, some quietly use the tools to churn out low-value research.

Nature (McKenzie Prillaman)


Kotahi Unveils AI PDF Designer: A New Era for PDF Production

The Kotahi AI PDF Designer, transforms PDF design into a straightforward, interactive process. Click on any part of your article—like text or images—and simply tell the AI what you’d like to change, for example, “make this text green and bigger.” The AI instantly understands and applies your design choices, letting you see the effects right away. You can then choose to render the PDF with each change or on-demand. This means you can quickly adjust and refine the look of your PDF, ensuring it’s both beautiful and easy to read, without needing to know complex design software.

Robots Cooking (Adam Hyde)

JB: Kotahi is sponsoring this week’s newsletter, so perhaps I have a conflict of interest here. I would have linked to this announcement, regardless.


Springer Nature announces unified open code policy to better support open research practices

All journal articles will now feature a Code Availability section and authors will be encouraged to share code publicly, using permanent identifiers, and citing code they have used. Journals with existing code-sharing policies will see no changes. For journals without an existing policy, a gradual implementation will occur via integration into Snapp (Springer Nature’s Article Process platform - the publisher’s next generation peer review platform) providing a simplified and singular workflow for authors to manage their article submissions with the publisher.

Springer Nature Group (announcement)

JB: Bravo Erica Pastrana!


Other news stories

GeoScienceWorld Celebrates 20 Years of Advancing Geoscience Collaboration and Scholarly Publishing (GeoScienceWorld, press release)

CSE 2024 Annual Meeting: Communicating Science for a Sustainable Future (Science Editor, Jennifer Workman and Heather DiAngelis)

Participate in the IGI Global Annual Academic Publishing Trends & Open Access Survey 2024 (IGI Global

ALPSP Response to ICO Consultation (ALPSP, Wayne Sime)

ResearchGate and Canadian Science Publishing announce Journal Home partnership for open access journals (ResearchGate, press release)

Preprints ‘should be factor in academic hiring’ (Times Higher Education, Jack Grove; paywall)

Thank you to our sponsor, Council of Science Editors

Don’t delay—register for CSE’s 2024 Annual Meeting in Portland, OR! Held on May 4-7, the meeting is chock full of excellent programming, including a special closing general session on generative AI. Register now—early-bird registration ends April 4th.

Learn more

Opinion

United2Act Against Paper Mills: Fighting Fraud that Corrupts the Scholarly Record

The Working Groups reflect what is so important about United2Act – it does not only oppose paper mills theoretically; it sets out an agenda to proactively address the problem. As Professor Jennifer Byrne, a medical researcher from the University of Sydney who has been flagging suspect papers for around a decade, explained: “Although many of us have been fighting paper mills on many fronts for some time, what’s been missing and what United2Act provides is coordination and dedicated resourcing towards tackling this worldwide problem. I’m very pleased to chair the Research Working group, where we will advocate for research to better understand the problem and to design real-world, effective solutions.”

The Scholarly Kitchen (Lisa Janicke Hinchliffe and Deborah Kahn)


Publication Ethics and Updates at MDPI

Two of the procedures implemented by MDPI in 2024 to enhance the quality of SIs [special issues] include greater oversight and the verification of Guest Editor credentials. But what does this mean in practice?
The new guidelines require that Editors-in-Chief (EiCs) take on the responsibility of overseeing Special Issues, as they would oversee the other content published in journals. They may select another Editorial Board member to provide oversight instead where appropriate and to take on responsibility for the Special Issue.

MDPI Blog (Shaheena Patel)

JB: A few weeks ago I noted that MDPI can feel like a black box and suggested that it would be helpful to have more insight into what goes on within the publisher. The above article is one of four published in February covering topics related to ethics and research integrity. The other two were: (1) Ethics in Publishing by Daniella Maritan-Thomson;(2) Ethics in Open Access Publishing by Jack McKenna; and (3) Artificial Intelligence: Ethical Considerations In Academia by Nat Kelly. More please, MDPI.


Other opinion articles

The Transformational Line of Progress Curved to Form a Circle: A Middle Way for Technological Advancements in Journal Production (Science Editor, Scott Curl)

A Standard Terminology for Peer Review: Supporting Transparency and Trust (Science Editor, Nettie Lagace)

Society Publishing’s Weakness (The Geyser, Kent Anderson; paywall)

What cartel research tells us about how journals serve the needs of research users (Impact of Social Sciences, W. Benedikt Schmal)

Give It to Me Straight: Plain Language Summaries and Their Role in Scholarly Journals (Science Editor, Emilie Gunn)

Chef de Cuisine: Perspectives from Publishing’s Top Table (The Scholarly Kitchen, Robert Harrington interviews Niko Pfund)

An Interview with CHORUS on joining OASPA (OASPA, Carol Green interviews Howard Ratner)

What do we know about DOIs (CrossRef, Martin Eve)

When will we be transformed? Reflections on the experience of working with transformative agreements as a cross-library working group (Insights, Julie Baldwin and Paul Cavanagh)

On the challenges of open access monitoring (Insights, Athanasia Salamoura and Giannis Tsakonas)

A meeting of brilliant minds (Research Information, Vicky Reich and David Rosenthal)

Toward an open-science ecosystem (Bonfire)

Charting the Growth of Open Access in ACS Journals (ACS Publications Chemistry Blog, David Armstrong and Meredith Rountree)

From Singapore to Athens via Hong Kong: The Itinerary of Research Integrity from Scientific Research to Real-life Applications and Policy Making (The Scholarly Kitchen, Panagiotis Kavouras et al)


Journal Club

Does it pay to pay? A comparison of the benefits of open-access publishing across various sub-fields in biology

Based on our findings of access type and other model parameters, we suggest that, in the case of the 152 journals we analyzed, paying for open access does confer a citation advantage. For authors with limited budgets, we recommend pursuing open access alternatives that do not require paying a fee as they still yielded more citations than closed access. For authors who are considering where to submit their next article, we offer additional suggestions on how to balance exposure via citations with publishing costs.

PeerJ (Amanda D Clark et al)

JB: So much depends on the which subscription journals are included in the comparator group. Subscription journals that have deep penetration in the academic library market, like The New England Journal of Medicine or Science, are unlikely to have much of a citation disadvantage. By contrast, authors who are considering submitting to The Journal of Obscure Results, whose largest institutional subscriber is Aberystwyth University, would probably be better off publishing OA.


Recommendations for accelerating open preprint peer review to improve the culture of science

Just 10 years ago, preprinting in many disciplines barely existed. Today, preprints are becoming more commonplace, are indexed by major bibliographic databases, and are encouraged (or even required) by many funders. Although preprint review is in its infancy, momentum is building rapidly, and we feel the potential benefits are already evident. Building on the growing enthusiasm within the community, the time is right to promote the growth of this practice so that scholarly publishing may become more constructive, equitable, and transparent.

PLOS Biology (Michele Avissar-Whiting et al)

JB: Take a look at Figure 1 and compare 2022 with 2023. Do you agree with the statement “momentum is building rapidly”? I know I keep coming back to this point, and probably sound like a stuck record, but preprint peer-review advocates often over-inflate the impact that preprints are having. To be clear, I’m not against the approach, but I do think that scientists shouldn’t make over-hyped claims that aren’t substantiated by the data. 300 peer reviewed preprints per month does not constitute a revolution. Perhaps it will happen one day and this paper will help to accelerate progress.


The publication facts label: A public and professional guide for research articles

We are calling it a publication facts label (PFL). It is intended to appear with each research article. It emulates the look and feel of the Nutrition Facts label on food products in the United States. At this point in its development, the PFL draws data and links from the journal’s publishing platform on eight critical elements for scholarly publishing and presents to readers: (a) the publisher’s identity; (b) the journal’s scholarly editorial oversight; (c) the journal’s article acceptance rate; (d) the indexing of the journal; (e) the article’s number of peer reviewers and reviewer backgrounds; (f) the article authors’ competing interests; (g) the research study’s data availability; and (h) the funders of the research

Learned Publishing (John Willinsky and Daniel Pimentel)


Endorsements of five reporting guidelines for biomedical research by journals of prominent publishers

Currently, there is no universal endorsement of reporting guidelines by biomedical publishers nor ways to demonstrate adherence to the endorsed reporting guidelines. There is also a lack of agreement on what constitutes an endorsement; finer nuances for the types of endorsements are needed.

PLOS One (Peiling Wang, Dietmar Wolfram, Emrie Gilbert)

JB: tl;dr Publishers need to do MUCH better.


Other journal articles

How transformative are transformative agreements? Evidence from Germany across disciplines

Scaling up open access publishing through transformative agreements: Results from 2019 to 2022

How open are hybrid journals included in transformative agreements?

A network-driven study of hyperprolific authors in computer science

Emerging plagiarism in peer-review evaluation reports: a tip of the iceberg?

Regional disparities in Web of Science and Scopus journal coverage

Information accessibility and knowledge creation: the impact of Google’s withdrawal from China on scientific research


Webinars

I’ve started to create a list of upcoming webinars, which should help our community engage more with each other. The webinars that are happening over the next fortnight are shown below. If you’re holding a webinar that you’d like me to include here, please send me an email.

Ask the Experts: Ask a Publishing Executive (March 6, Society for Scholarly Publishing)

Early Career Community of Interest Meeting | Public Speaking Tips (March 8, Society for Scholarly Publishing)

Coalition for Diversity and Inclusion in Scholarly Communications (March 13, Society for Scholarly Publishing)

Equity, Diversity and Inclusion Survey results and next steps (March 19, European Association of Science Editors)

Preprints across the globe; landscapes, perceptions and challenges (March 19, ASAPbio Community Call)

Publishing Integrity (March 19 and March 20, Charleston Hub)

Open Access Evolution, Revolution, or Demise? (March 20, Society for Scholarly Publishing)

Author Engagement Outside of the Publishing Process (March 21, ChronosHub)

Horizon Planning: Preparing for the Users of the Future (March 21, Renewd.net)


And finally...

This probably wins the prize for the best academic conference of the year:

The Swiftposium was a hybrid academic conference on the topic of singer-songwriter Taylor Swift. It was hosted by the University of Melbourne, days before Swift was set to perform in Melbourne, Australia. The idea came from a casual conversation when tickets for Taylor Swift’s Eras tour were released for sale in Australia and our desire to offer academic analysis surrounding her stardom, celebrity and unique social influence.

The topic of my PhD was incredibly dull in comparison.

Until next time,

James


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Journalology

James Butcher

The Journalology newsletter helps editors and publishing professionals keep up to date with scholarly publishing, and guides them on how to build influential scholarly journals.

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