Theo Stroomer for The Chronicle

Jeffrey Beall, an academic librarian at the U. of Colorado at Denver, abruptly shuttered a blacklist of journals he deemed untrustworthy nine months ago. But while the project has ended, debates over its merit and impact live on.

Nine months after a dogged academic librarian quietly deleted his carefully tended list shaming more than a thousand scientific journals as unscrupulous, the Beall’s List Murder Mystery remains unsolved.Why, after toiling so hard for five years — and creating a resource cherished by scientists wary of exploitative publishers — did the University of Colorado at Denver’s Jeffrey Beall abruptly give it all up? Who, or what, forced his hand?

There are several prime suspects:

• His fellow university librarians, whom Mr. Beall faults for overpromoting open-access publishing models.
• A well-financed Swiss publisher, angry that Mr. Beall had had the temerity to put its journals on his list.
• His own university, perhaps fatigued by complaints from the publisher, the librarians, or others.
• The broader academic community — universities, funders of research, publishers, and fellow researchers, many of whom long understood the value of Mr. Beall’s list but did little to help him out.
• Mr. Beall himself, who failed to recognize that a bit of online shaming wouldn’t stop many scientists from making common cause with journals that just don’t ask too many questions.

In the end, all played important roles in the demise of Beall’s List. On one level, Mr. Beall’s saga is just another tale of warring personalities. On another, though, it points to a broader problem in publishing: Universities still have a long way to go to create systems for researchers to share and collaborate with one another, evaluate one another’s work, and get credit for what really matters in research.

Publicly, Mr. Beall has put most of the blame on his own university. As his professional home, that’s where he felt the longest and most direct pressure. Despite being a tenured associate professor of library science, Mr. Beall has spent the past two years working out of a small cubicle similar to a student’s study carrel, in daily fear, he says, of a new supervisor’s threats to make his conditions much worse.

The university, for its part, has said it values Mr. Beall’s work on his list, has spent many years defending it, and provides him a work space similar to that of other librarians. «There have been no documented cases of internal threats against him that leadership or university counsel is aware of,» says Emily Williams, a university spokeswoman.

Mr. Beall insists otherwise. «They’re trying to make me as uncomfortable as possible,» he said in an interview from an empty room down the hall, where he escapes for private conversations.But the Swiss publisher angry that it had showed up on his blacklist, Frontiers Media, may have played an even bigger role. In October 2015, Mr. Beall announced in a tweet that he had added Frontiers to his list, citing «wide disapproval from scientists.»

In explaining that decision, Mr. Beall cited a series of charges against Frontiers. Researchers complained of low-quality peer reviews at Frontiers journals. Reports described Frontiers as operating a factory of low-paid workers who churned out solicitations to academic authors. And the journals had published papers of disputed accuracy on topics that include creationism, climate change, and AIDS.

Kenneth W. Witwer, an assistant professor of molecular and comparative pathobiology at the Johns Hopkins University, is an ally of Mr. Beall’s. He is also an expert on AIDS, and he said he was especially bothered by a paper in Frontiers in Public Health questioning the long-established fact that HIV causes AIDS, and the journal’s subsequent decision not to retract it.

HIV is «the most-studied virus in the history of science,» Mr. Witwer said. It may be understandable that some people don’t want to admit its lethal nature, but such denialism «has been very damaging to the public health, especially in South Africa,» he said.

Yet other researchers defended Frontiers, making clear that while some of Mr. Beall’s additions to his predatory-journals list were relatively open-and-shut cases, Frontiers was much less clear-cut.And, more important, much less willing to take Mr. Beall’s assessment lying down. Frederick Fenter, executive editor in charge of open-access journals at Frontiers, quickly issued a statement decrying Mr. Beall’s «dubious actions» and defending its reputation.

When that didn’t win a reversal, Mr. Fenter traveled from Lausanne, Switzerland, to Denver in December 2015 to personally urge University of Colorado leaders to punish Mr. Beall. He accused the university of being «directly implicated in this absurd and slanderous action,» and demanded an investigation of Mr. Beall.

Roughly a year later, after continued pressure, the university accepted Frontiers’ demand and opened a research-misconduct case against the librarian. Mr. Beall responded almost immediately by killing his list.

The university took seven months to complete its review, which posed for Mr. Beall the threat of dismissal, even with his tenured status. After years of pushing back dozens of complaints, the university finally agreed to accept the Frontiers plea for a formal investigation into research misconduct on the grounds that Mr. Beall’s scholarship was «unethical and flawed,» said Ms. Williams, the university spokeswoman. «The Frontiers complaint was unique in its composition, length, detail, and complexity,» she said.

Ms. Williams said she could not comment on details of the investigative process, beyond confirming it ended in recent weeks with «no findings» or action taken against the professor. The experience nevertheless had its effect, leaving Mr. Beall unwilling to resume his list. Mr. Fenter had no comment on behalf of Frontiers.

The university initially served as a much more welcoming home for the project, which Mr. Beall began in 2012 after years of enduring the «spam» solicitations sent to researchers by the fast-expanding number of open-access publishers using an author-pays model. He chose the term «predatory,» feeling such journals were victimizing smart scientists who just didn’t have the time to weed through mounds of solicitations to find quality suitors for their work.

«For a very long time, his university supported him,» said Mr. Witwer.

But that tolerant attitude began to turn, Mr. Beall and Mr. Witwer said, as the list grew, case-by-case decisions became tougher, and better-financed publishers, such as Frontiers, more directly confronted him and his university.

Meanwhile, as his public recognition grew, Mr. Beall became increasingly outspoken in assigning blame for the spread of predatory journals — with his fellow academic librarians the main target. Mr. Beall was convinced that the push for open-access journals had become more than just a reform to foster better science. Instead he saw it as a «social movement.»

In Mr. Beall’s analysis, journal-subscription costs had been driven up by a variety of economic, academic, and demographic shifts, compounded by the failure of academic librarians to properly manage those shifts. Rather than admit that, Mr. Beall concluded, librarians had joined in unfair denunciations of large subscription-model publishers, such as Elsevier, for reaping unduly large profits.

Those librarians essentially adopted a political perspective, Mr. Beall argued, that led them to overlook a chief characteristic of open-access journals — a model in which authors, not subscribers, pay the cost of publishing. That model, according to Mr. Beall, creates dangerous incentives for corner-cutting and abuse.

Open-access advocates accept that criticism, to a point. The author-pays model does have obvious flaws and is not sustainable in the long term, acknowledged Heather Joseph, executive director of the Scholarly Publishing and Academic Resources Coalition. But less than 40 percent of open-access journals now use that model, and that percentage will continue to shrink as universities, research funders, and others recognize the need to support open-access publishing, she said.Ms. Joseph said Mr. Beall had provided a valuable service in helping researchers and publishers confront some of the disreputable actors in their midst. «I honestly think he was trying to do the right thing, which I applaud,» she said of Mr. Beall.

But the traditional publishing community, rather than open-access upstarts, deserves the primary blame for predatory journals, Ms. Joseph said. That’s because subscription-based publishers for years refused to contemplate open-access models, she said, thereby letting such journals grow in the largely ungoverned and unmonitored environment that Mr. Beall began to confront — largely on his own — in 2012.

Mr. Beall also has lost allies by casting researchers and their universities as victims of rapacious publishers. In fact, open-access advocates suggest, both groups shoulder some blame. Scientists could be a lot more careful before choosing a journal that makes unsolicited phone or email invitations, they argue, and universities could do a lot more to teach researchers about the risks.

«If you are a reputable researcher or a competent researcher, you know that that’s not how you get published,» Ms. Joseph said, referring to email solicitations. «Good journals are not going to come to you and beg you for your articles. That should be your first clue.»

In one of the many examples of predation cited by Mr. Beall, a Chilean researcher complained to him that the Journal of Bioremediation and Biodegradation — owned by OMICS International, a company on Mr. Beall’s blacklist — had quickly published his team’s manuscript, including key errors, after no review interaction. (OMICS later threatened to sue Mr. Beall for $1 billion.)

Yet the researcher also admitted, in a message to Mr. Beall, that his team had decided to «rush into publishing our current work» after receiving a solicitation from the journal. The team, he said, had felt it needed to publish to win more research funding — and so it moved so fast that its original version contained mistakes.

For some, that scenario raised an uncomfortable question: When a scientist elects to use a «predatory» publisher, who, if anyone, is the real predator? It may be cynical to admit, said Brian A. Nosek, co-founder and director of the Center for Open Science, but if researchers choose a low-quality journal «and receive the rewards that they desire from publishing, then nothing predatory occurred.»A researcher’s claim to victimhood could be stronger, for instance, if he or she had genuine reason to expect a quality peer-review process but did not receive one, Mr. Nosek said. A predatory act also could occur, he said, if researchers unexpectedly found that their universities «actually care about quality and integrity of peer review,» and deny career rewards to those published in poor journals.

Just last week, a research team at the University of Ottawa laid out evidence suggesting that while many low-quality journals are based in developing nations, it’s often scientists in wealthier nations who agree to publish in them. It’s hard to tell how many of those scientists are being genuinely misled, said one of the study’s authors, Kelly D. Cobey, an adjunct professor of epidemiology and public health at the University of Ottawa.

Even then, said a co-author, Larissa Shamseer, a doctoral student at Ottawa, some journals could have strong editorial standards but an amateurish web presence that mostly reflects a lack of financial resources. Either way, Ms. Cobey said, it seems clear that universities and funders are not doing enough to educate themselves and their researchers on the topic.

For researchers and universities wary of junk journals, Mr. Beall’s «blacklist» of bad actors provided some of that education. But to many of them, such a list was fundamentally more problematic than a «white list» of quality publishers, Mr. Nosek said. White lists have the benefit of «clear, explicit criteria» for inclusion, while blacklists seem «inherently riskier and more litigation friendly,» he said.

Mr. Beall discovered the greater risk. His online list of predatory journals described his general criteria for inclusion. But he said he had kept specific reasons in particular cases confidential because the details often came from researchers who feared retaliation if their complaints became publicly known.

He disputes, however, any suggestion that a white list is a better method. Leading examples of white lists include PubMed, the journal archive operated by the National Institutes of Health, and the membership lists of the Open Access Scholarly Publishers Association and the Directory of Open Access Journals, all of which use quality criteria to limit eligible journals.

PubMed contains either the full text or citation data for some 5,500 journals, chosen through an extensive grant-like review process. The number is limited to keep the task of archiving manageable. Exclusion from it should therefore not be taken as a sign of a low-quality journal, said Jerry Sheehan, deputy director of the National Library of Medicine.

The criteria for acceptance by the association and the directory are also subject to interpretation. The directory essentially requires its members to offer «high-quality» peer review. The association has a longer set of standards that includes a requirement that any direct marketing be «appropriate and well-targeted,» and a ban on any activities that could bring open-access publishing «into disrepute.» Yet both have accepted Frontiers and the Dove Medical Press, two publishers widely criticized for their editorial practices.

Claire Redhead, executive director of the association, said it had investigated complaints about Frontiers and Dove, and found that both meet its membership criteria.

A private company, Cabell’s International, has maintained its own series of journal white lists — available by subscription only — since 1978. In June it began offering a blacklist, largely to fill the void left by Mr. Beall, said Kathleen Berryman, a project manager at Cabell’s.

Cabell’s hoped to offer its blacklist free to the academic community, Ms. Berryman said. But it found it could not afford to match what Mr. Beall had done largely on his own time, often by rising at 4 a.m. daily to begin his work, she said. As for Frontiers, Cabell’s investigated and found it eligible for neither its blacklist nor its white list, Ms. Berryman said.

For now, the leading blacklist remains Mr. Beall’s, even after he took it offline. A scholar who is willing to be identified only as a postdoctoral researcher at a European university has resurrected the list at a new, publicly available site. But the successor, who said he had hidden his identity because he fears the type of threats Mr. Beall encountered, noted by email that he and others probably will not have much time to maintain such an undertaking. «Probably the Beall’s List will lose its relevancy over time because of that,» he said.

It’s one of many ways that finances loom as a major impediment to quality in open-access publishing. Open-access journals that do not use author fees or university subsidies typically depend on the benevolence of field-specific professional associations. «Often they operate on very tight budgets and rely excessively on volunteerism,» Mr. Beall said. «So they often do well for a while and then don’t do well.»

Mr. Beall’s list was, among other things, an attempt to ferret out journals that had failed to take peer review seriously. Beyond the list, however, is a more-fundamental question: What exactly should peer review do for science in the internet era, and how often is it really needed?

As soon as possible, said Ms. Joseph, of the scholarly-publishing coalition, open access in scholarly communications should be extended to refer not just to freely available journal articles or even scientific data but to «the entire range of communications.» In that future, she said, researchers would earn professional credit for all types of scientific contributions and collaborations, not just final articles.

Science is slowly moving in that direction, with the proliferation of online «pre-publication» websites on which research findings are presented without any pretense of wider peer review.

Some research teams might find value in eventually seeking affirmation of their work through publishing in journals with peer review, Ms. Joseph said. Peer-reviewed publications are not «inherently bad things,» she said. «But they’re the single currency right now» that denotes progress or quality in science and largely determines career advancement, she said. «That’s too heavy-handed at this point.»For Mr. Beall, after five years of battle scars, career advancement is now more a personal concern than a systematic one.

Having raised his hand at a time the research community seemed to need him, he now puzzles over many aspects of his treatment. Universities might want innovators, he said, but perhaps more important they like happy news. «They prefer things like ‘Students go to Haiti and dig a well to help poor people’ — they love stuff like that,» he said. «But they don’t like ‘Faculty member calls out predatory publishers.’»

Some critics weren’t sad to see Beall’s List go: It lacked scientific rigor, they said. But others admitted that there’s no real way to clearly define a predatory journal, and they gave the librarian credit for trying. It’s a subjective assessment, Mr. Beall said, and anyone trying to keep score just has to make the best case.

«That’s what I did,» he said. «I made the decisions.»

Paul Basken covers university research and its intersection with government policy. He can be found on Twitter @pbasken, or reached by email at paul.basken@chronicle.com.

Correction (9/13/2017, 11:43 a.m.): This article originally misstated when the University of Colorado at Denver opened an investigation into Jeffrey Beall. It was roughly a year, not a month, after an official with Frontiers Media visited the university. The article has been updated to reflect this correction.