The Brief
from Clarke & Esposito 

January 14, 2019 • Issue #9
A monthly roundup of what we've been reading and thinking about
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The holidays were largely viewed as a welcome respite from discussions of Plan S in many quarters of the industry. In this, Robert Jan Smits, the chief architect of Plan S, has truly accomplished something. How often can so many people be said to have been looking forward to the holiday discussions with relatives? But now here we are in the New Year (happy New Year!), back at our desks wondering where did we leave off on the whole Plan S thing?

According to reporting in Science, federal agencies in the US and Canada have signaled that they will not be signing on to Plan S in the near future. This is a big deal as the fundamental question with regard to Plan S is how broadly its set of policies will be adopted. According to DeltaThink, the 15 funders that presently have adopted Plan S account for 3.5% of the global research output (there is a helpful graphic on global research output by country in the Science article). That is a significant number, to be sure, but it far from constitutes a tipping point. All eyes are now on China, which in addition to accounting for 18.6% of global research output, has recently indicated support for Plan S (but not, as yet, any specific policy changes). If China adopts Plan S it could lead to a two-tiered system, with China and Europe in one tier and the US and other countries in the other. If China does not adopt Plan S, the plan is likely to face increasing headwinds as researchers supported by cOAlition S funders bristle at the encumbrances of a policy out of step with the practices of their peers in the rest of the world (not to mention one that locks them out of most of the world’s most prominent publications). 
Source: Science, Nature

Scientific and scholarly societies, publishers, and other organizations have started to respond to Plan S. Notable responses so far include the German Chemical Society (PDF), the British Academy (PDF), EMBO, the Peace Research Institute Oslo (PRIO) and the Faculty of Social Sciences, University of Oslo (UiO), and Taylor & Francis. We anticipate many more statements from European and American societies and publishers in the coming weeks.
Source: Gesellschaft Deutscher Chemiker, The British Academy, The EMBO Journal, Peace Research Institute Oslo and University of Oslo, Taylor & Francis

The 101 Innovations group at Utrecht University published a gap analysis across disciplines for Plan S compliance. The researchers are thorough in laying out their methodology, and the resulting data, highlighting the difference in OA methods across disciplines, are valuable.
Source: Innovations in Scholarly Communication
On the read and publish front, the big news of the last month was the announcement by the University of California that it intends to let its system-wide license with Elsevier lapse unless it can reach agreement on a publish and read deal. Reportedly, access to Elsevier packages within the UC campuses remains active while negotiations continue into the New Year. This is an excellent and balanced article that nicely lays out the key issues at play and the challenges in coming to agreement.
Source: Inside Higher Ed

Meanwhile in Germany, while Elsevier remains deadlocked with regard to negotiations with Projekt DEAL (the German national consortium), Springer Nature has announced progress with same (but no DEAL as yet).

In other read and publish deal news, De Gruyter and Iowa State University ink what to our knowledge is only the second read and publish deal in the US (the first being between MIT and the Royal Society of Chemistry).
Source: Springer Nature, De Gruyter

PLOS released its 2017 financials. The open access publisher reported revenues down by $1.4 million (to $36.8 million) as compared to 2016. Phil Davis commented on this recently at the Scholarly Kitchen, highlighting declining submission volumes at PLOS. Of course this is a snapshot of PLOS in 2017 and it would not be amiss to ask why anyone cares here in 2019 (especially given PLOS has put in place new management and is very much in turnaround mode)? One reason to care is that PLOS was founded as a proof of concept for the gold open access model—so its trials and tribulations become viewed as proxy for the success or failure of gold open access publishing writ large (BioMedCentral predates PLOS, but BMC never released financials publicly and was then absorbed by Springer Nature). At this juncture, with gold OA adopted by nearly everyone, it is questionable whether PLOS remains a proxy for the gold model. That said, given its history, and the fact that there are few pure gold OA publishers (most have diversified portfolios) that are not privately held (e.g. Frontiers, Hindawi), the financial details of PLOS’s program continue to draw outsized interest.

A second point of interest is the $11.1 million write down related to Aperta, PLOS’s abandoned manuscript submission and review system. While the approximate level of investment by PLOS in Aperta could be gleaned from previous reports, the specific number was not known until now (and of course we still do not know how rigorous PLOS was in allocating all staff time spent on Aperta, so the $11.1 million figure may still be approximate). No matter how you look at it, $11.1 million is a big number and it highlights the challenges and risks of major software development projects by publishers, who are ultimately content and not software organizations. PLOS is, of course, in good company in terms of abandoned manuscript submission and review systems. Elsevier’s recent acquisition of Aries Systems follows Elsevier’s second (unsuccessful) attempt to develop such a system in-house.
Source: PLOS, Scholarly Kitchen

AI-supported information management solutions continue. Nature has a nice write-up of AI-based services to reduce publishing burden. Elsevier announced Entellect, a data platform that enables text mining, data normalization, and ontology mapping across multiple life sciences data sets. LexisNexis (a RELX company and sister division to Elsevier) announced a case-law language analytics solution that “analyzes tens of millions of court documents and extracts specific language that will resonate with a particular judge, including case language your judge cites most often and the rationale behind his or her rulings, to help you draft winning briefs or successfully argue motions.”
Source: Nature, Elsevier
eLife just this week provided an initial report on their opt-in peer review trial that started in June 2018 and closed for new submissions in early August. For the trial, once eLife editors made a decision that a manuscript should undergo in-depth peer review, the journal was committed to publishing the article plus the editor decision letter, peer reviews, and response to the reviews from the author. Authors could opt in to the trial at submission stage: 32% (313 of 978) of submitting authors chose to do so. What have we learned so far? The most common reasons for opting in to the trial were related to efficiency, support for innovation, and support for transparency; those who opted out most commonly cited not being aware of the trial, concern about higher rate of rejection, and concern about publication of reviews. Time to first decision took longer for trial articles—not surprising given that the initial editorial evaluation was in effect a decision about whether to publish the article (assuming the authors did not withdraw the paper after seeing the reviews). There was also some suggestion that late-career researchers were more successful at passing the initial evaluation and moving into peer review than early- and mid-career researchers. We look forward to more results as more articles from the trial continue through the publication process.

The Royal Society is mandating publication of peer review reports for Proceedings B and Royal Society Open Science for all manuscripts submitted as of 2 January 2019. (Open Biology introduced mandated open peer review in 2017.) Reviews are anonymous by default but reviewers have the option (and are encouraged) to sign their names. Royal Society Open Science has been encouraging (but not mandating) publication of reviews alongside articles since launch in 2014, with about two-thirds of authors selecting this option by 2018. The Royal Society reports no negative effect on publication times or reviewer recruitment during the trial period.

Genome Biology is adopting transparent review as permanent policy as well, after a pilot that suggested reviewers were not more likely to decline an invitation to review when told their review would be published with the article.
Source: eLife, The Royal Society, Genome Biology

In “How Do You Publish the Work of a Scientific Villain?,” Wired reports on the thorny question of whether to publish the human gene-editing work of Chinese scientist He Jiankui. Is it unethical to publish the work and the related data at all? STAT reports that He has been shopping a paper related to the work to journals.
Source: Wired, STAT


Inside Higher Ed and Gallup released its 2018 Survey of Faculty Attitudes. Among its many findings the survey found general support for Open Educational Resources (OER) in theory, but also reluctance to assign OER materials if they are of lower quality, and actual objection to limiting instructor choice. (We note that neither issue is a foregone conclusion with OER, though each needs to be addressed head-on for the model to succeed.) The other new textbook model emerging across the US, Inclusive Access, had support from a plurality—not a majority—of respondents, with 6 in 10 faculty believing it is too soon to tell either way. It's safe to say the major textbook publishers will be following these attitudes closely.
Source: Inside Higher Ed
De Gruyter continues to pursue its strategy of becoming a primary distributor for university press ebooks. Following closely on the announcement of its partnership with the University of Chicago Press, De Gruyter has now announced a similar arrangement with the University of California Press. All titles will be hosted on De Gruyter’s platform, including 2,250 backlist titles which will be digitized and distributed exclusively by De Gruyter for the first three years.
Source: De Gruyter

The shift of focus from textbooks to digital courseware is resulting in large academic publishers signing fewer textbook authors. One telling statistic from this report in Inside Higher Ed: Cengage published 120 first edition textbooks in the past four years but is scheduled to publish only 11 in 2020.
Source: Inside Higher Ed


A rumor broke in early December that the FTC was launching a “very preliminary investigation” of a proposed bid from Ingram to buy the retail arm of Baker & Taylor. Baker & Taylor, which was acquired by Follett in 2016, currently operates in both the library and retail space. The move may signal that the Follett/B&T group wants to slim down to focus on its strong positions in school and library distribution. Ingram, already the leading wholesaler and operator of significant distribution and print-on-demand businesses, would essentially become the only wholesaler in the US market if the deal were to take place. Undoubtedly such a development would be very concerning to bookstores.
Source: Publishers Weekly 

For the first time in 20 years, new creative works are entering the public domain. Many major writers will now have some of their works available without the necessity of seeking copyright permission or obtaining a license. The writers include Kahlil Gibran, Ernest Hemingway, Wallace Stevens, and Robert Frost; a long (but not comprehensive) list of titles can be found here. Some observers worry that the integrity of the original works may be lost through adaptation and bowdlerization, but the Times insists that the public domain status of these works will “be a boon for readers, who will have more editions to choose from, and for writers and other artists who can create new works based on classic stories without getting hit with an intellectual property lawsuit.” As for the debate surrounding copyright and the public domain, we see no end. In the words of Robert Frost’s “Stopping by Woods on a Snowy Evening,” which has just entered the public domain, we have “miles to go before [we] sleep.”
Source: New York Times, Duke University

Publishers keep a close eye on Plan S, other funder mandates, and piracy, but there is another front in the battle over the publishing business that comes from legal theory and philosophy. Samir Chopra of CUNY argues that we should “end intellectual property” as it interferes with the development of the public domain, for which it was intended. The argument is in part rhetorical: the phrase “intellectual property” invites us to transfer to copyrights, patents, and trademarks certain qualities that pertain rightfully only to physical property. Because of the generalization of “intellectual property,” “disaster has followed,” in the form of obstacles to creative work and the generation of new works. How does this dystopian vision account for the fact that, under the current IP regime, the number of books and articles published is growing at a rate beyond anybody’s ability to keep up? We are reminded of Abraham Lincoln’s wisecrack about General Grant when the president’s advisors recommended that Grant be relieved from duty because of his drinking. Lincoln’s response: Tell me what he is drinking so that I can send the other generals a few barrels.
Source: Aeon


DuckDuckGo released a fascinating white paper on bias in Google’s search engine, noting that the “filter bubble” is inescapable. A series of tests were conducted showing that even when a user has signed out of Google (and is therefore assumed to be searching anonymously), the search results continue to bear the impression of that user’s prior search experience. Thus there is no “objective” of unbiased search, at least on Google. We look forward to Google’s response.
Source: DuckDuckGo

A primer on machine learning. Noting that the term “deep learning” in research exploded in usage about 4 years ago, this article teaches the basics. Machine learning falls into 3 categories: supervised, unsupervised, and reinforcement. In supervised machine learning, the algorithm is told what patterns to look for in a large database. In unsupervised machine learning, the algorithm seeks patterns without a specific object. In reinforcement, the algorithm works through trial and error, seeking superior outcomes. A hat tip is offered to researcher Geoffrey Hinton, who invented the means to train neural networks.
Source: MIT Technology Review

China has been recruiting scientists from the U.S. and elsewhere in a bid both to bolster its reputation as a research powerhouse and to attract students from around the world to its universities. Researchers are attracted to the easier funding climate and students are attracted to tuition-free education. One sign that this effort is having an impact: a recent study out of the University of Oxford noted that China’s Tsinghua University is on track to be the number one producer of highly cited STEM papers within the next five years. Tsinghua University is already the top producer of highly cited papers in mathematics and computing, with four other Chinese universities in the field’s top ten.
Source: NPR, The Economist


As reported in Nature, a team of MIT researchers built and flew the world’s first solid state airplane. Powered by “ionic winds,” the new aircraft has no moving parts. The path to developing the new propulsion system reads like a science fiction story: As MIT researcher Steven Barrett recounts in this riveting piece for The Conversation, much of their work was based on “discarded” science from the 1920s and 1960s along with recent high school science fair projects.
Source: Nature, The Conversation

A still-active 4,000 year old termite megapolis the size of Great Britain has been noticed by researchers in Brazil. The little critters excavate a volume of earth that would fill the Great Pyramid of Giza—every year. The question we would like to see addressed in a follow-up study is, How is it possible that Brazilian researchers are only just now noticing a termite civilization the size of Great Britain that has been excavating a Great Pyramid–sized amount of earth every year for 4,000 years?  
Source: Current Biology

Question: Are standing desks overrated? Answer: yes.
Source: Journal of Occupational and Environmental Medicine

Despite the barrage of news reports to the contrary, the world is, by many measures, actually getting better. Need further evidence? We submit to you the coyote-proof dog vest. Game, set, match.
Source: New York Times, The Atlantic

Filter bubbles concern you? Consider this fact: More Americans now get news via social media than via print newspapers. But don’t worry, television news is still the most relied-on platform…
Source: Pew Research Center


Joe wrote on the Scholarly Kitchen about a recent article published by the New York Times in collaboration with ProPublica on unreported conflicts of interest in scholarly journals. The Times calls for journal publishers to increase their editorial oversight, but Joe points out that this new, large expense would come just as Plan S advocates are demanding a low ceiling on APCs. The result is that publishers are put in a “double bind”: It is not possible to satisfy one requirement without simultaneously violating the other.
Source: Scholarly Kitchen, New York Times

Michael wrote about the impact of Plan S on society publishers. Given the lack of access to transformative agreements (e.g. read and publish deals), Plan S privileges larger commercial publishers as compared to societies. Plan S is further biased toward a particular kind of volume-based, unselective publishing paradigm that flies contrary to the values and practices of most society journal programs. And finally, the prohibition against hybrid and mirror journals hits society publishing programs particularly hard. While it may be primarily aimed at the practices of commercial publishers, if Plan S were to be widely adopted it would have a particularly adverse impact on scientific and scholarly societies. 
Source: Scholarly Kitchen


We will be attending the following events. Let us know if you would like to set up some time to chat. We’d love to hear from you (

  • Academic Publishing in Europe, January 15–16, 2019, Berlin, Germany
  • AAP/PSP Annual Conference, February 6–8, 2019, Washington, DC
  • NFAIS Annual Conference, February 13–15, 2019, Alexandria, VA
  • STM US Annual Conference, April 10–13, 2019, Washington, DC
  • Council of Science Editors Annual Meeting, May 4–7, Columbus, OH
  • Society for Scholarly Publishing Annual Meeting, May 29–31, 2019, San Diego, CA
  • Association for University Presses Annual Meeting, June 11–13, Detroit, MI
Culture eats strategy for breakfast. —Peter Drucker
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