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The Dark Side

The Ugly State of the Literature These Days

So how’s it going out there in the land of the journals that will publish any flippin’ thing you send them? Apparently pretty well. I’m not sure if we’re still in the log phase of their growth or not, but there’s no shortage of quasi-open-access titles out there, the ones that (like reputable OA journals) do charge you for publication and make the resulting paper freely available (if the web site stays up). But the key difference is that they skip that pesky stage where they actually review the papers. Or even look at the papers at all. It’s much easier to make all such editorial decisions on the basis of “Have the funds deposited?”

My wife likes to quote an Iranian saying to the effect that “A thief robs a thief, and God smiles”, but not everyone who publishes in the junk journals is looking to hoodwink some faculty review committee or government agency into thinking that they have a legitimate trail of academic papers. That’s what I take away from this article, which shows that there are more people publishing in these papers than you’d think from institutions that should know better. For example, only 17% of a survey of such papers listed any sort of funding, but among those, the number one source was unfortunately the NIH. India was the number-one source of publications in the total sample, but the US was a solid runner-up.

Now, if you adjust for the number of papers produced by each country, the proportion of US scientific papers going to predatory journals is still low, but it’s definitely higher than it should be. (As a percentage of total scientific output, the countries that look worst are India and Nigeria). And in case you’re thinking that the US papers must be from Wassamatta U. and the Univ. of Southern North Dakota at Hoople, Harvard was among the top US institutions with such publications. The article itself doesn’t hide its conclusions:

Whether authors are being duped or are overzealously seeking to lengthen their publication lists, this represents enormous waste. Just the subset of articles that we examined contained data from more than 2 million individuals and over 8,000 animals. By extrapolation, we estimate that at least 18,000 funded biomedical-research studies are tucked away in poorly indexed, scientifically questionable journals.  Little of this work will advance science. It is too dodgily reported (and possibly badly conducted) and too hard to find.

The authors  show that the papers that show up in this layer of scientific publishing tend to report less well controlled experiments with fewer details, making their value even less than you might have thought. They’re calling for funding agencies, governments, and university administrators to start paying more attention and stop rewarding such publications as if they were legitimate. That’s the only way that anything will happen; if the benefit of publishing such stuff starts to disappear, but we’ll see if that happens, and on what time scale.

In the meantime, thousands upon thousands of these things flood out every month. I realize that seeing a paper in an expensive, hard-to-publish in journal like Nature complaining about cheap open-access publishers might be open to charges of self-interest. But these complaints are still valid even if you fold the page down so you don’t see where they’re coming from: this stuff really is a waste of time and resources.

But here I’ve been talking about the problem being localized in academia, while this article from Bloomberg tells me that I’m being too complacent. It’s focused on the Omics Group, a rather large publisher these days that owns a number of other nameplates. In the past, they’ve let all kinds of unreviewed craziness through, and listed people on their editorial boards who had no idea that they’d been so honored. These aren’t just problems from their early days; here’s a story from June. And there’s more:

In August 2016, in U.S. District Court in Nevada, the FTC raised the stakes, accusing Omics and Gedela of violating the FTC Act by engaging in “deceptive academic publishing practices.” The agency calls Omics’s peer-review processes a “sham,” whereby manuscripts get approved within days of submission instead of the weeks or months it takes at more credible venues. It alleges that Omics claims distinguished experts as editorial board members and as speakers at its conferences without their consent; fails to disclose publishing fees ranging from hundreds to thousands of dollars until after articles are accepted; cites phony impact factors (a measure of prestige indicating how often a journal’s articles get cited elsewhere); and maintains that journals are indexed in PubMed when they aren’t.

Otherwise, things are pretty above-board, I guess. The company’s founded, Srinubabu Gedela, also seems like an interesting character himself:

In Hyderabad, where Omics’s headquarters are spread over 250,000 square feet in two buildings, Gedela is convinced of a win. “The FTC is following the fake news,” he says. He exudes nervous energy as he walks the halls, rarely making eye contact with employees and cutting off conversations abruptly. For years he’s promoted a postdoctoral study he did at Stanford to boost his credibility. The school confirms he held a position for five months, an unusually short time, in 2009, a year after starting Omics. Gedela is cagey when asked about the details, saying he left early to return to India to build his company. But when he hooks his laptop up to a large TV screen in his office to show emails proving the dates of his Stanford sojourn, he accidentally projects an adviser’s email threatening to terminate his contract after saying he took vastly more vacation than allowed. When questioned, he brushes the discrepancy off.

Excellent, a real pro. But the problem, as the article shows, is that a number of biopharma companies have published papers in Omics journals, participated in its sponsored conferences (there are over a thousand every year!), and thus lined the pockets of this guy. This isn’t good. The implication is that the people doing the publishing are either clueless or trying to place papers somewhere where they know that they’ll get published no matter what, and neither of those burnishes anyone’s reputation. The closer such papers get to marketing, the worse this looks. Some of these papers have even appeared since the FTC lawsuit, and although it’s not clear when they were submitted, the Omics folks are not one of your wait-months-to-hear publishers. No, this is another thing that the industry has to watch out for; we’ve got enough people mad at us already without kicking the ball into our own nets. Ditch Omics. Ditch all of these people.

Mind you, the rest of the scientific publishing world is not such a quiet place these days, either. I wanted to note this study, which suggests that the number of pirated papers on the Sci-Hub site is now so large as to pose a potentially irreversible threat to the big publishing houses and their business model. They’d better adapt quickly – I don’t like the looks of the people who are coming up from the bottom looking to take their place.



Note: All opinions, choices of topic, etc. are strictly my own – I don’t in any way speak for my employer

51 comments on “The Ugly State of the Literature These Days”

  1. old chemist says:

    Not to condone “fake news” or predatory publishers, but there is a need for reputable journals that do not charge authors to publish and which are available free to readers. Only well-funded universities and companies can afford to be well-published and well-read these days.

    1. Derek Lowe says:

      Hard to work that intersection out, though – where’s the funding to come from?

      1. Jacob says:

        External sources? “Free to read, free to publish” describes arXiv and other pre-print services of similar nature (bioRxiv, chemRxiv). Of course those are not peer-reviewed, and personally I have noticed the quality of publications is often extremely poor.

        1. old chemist says:

          Good points – another have’s and have not’s issue – and even for nonprofits capitalism is often the major driver of day to day survival. It does make one think seriously about moving entirely over to ‘free’ venues such as those that Jacob mentioned, hard as it is for those of us who are old-school.

        2. anon says:

          At least in mathematics there are arxiv overlay journals, some of which are of extremely high quality (Discrete Analysis, for example).

          Of course arxiv needs funding, which is provided by several universities and grants from foundations, but the cost per preprint is only something like ten dollars. I don’t understand what supposedly non-profit open-access journals do with >$1000 article charges.

      2. CR says:

        Advertising, like everything else on the internet?

      3. Marc Couture says:

        One possible source: scientific societies. As few seem to know, Elsevier now offers publishes 500 OA journals, a majority of them subsidized by societies (or academic institutions) and not charging APCs. However, no information seems to be available as to the costs involved, thus we don’t know if it’s a good deal for a society (I expect that it is for Elsevier, though).

        1. Isidore says:

          I am not sure the OA journals are a good deal for Elsevier either, at least not financially. I was told by someone who seems to know what she’s talking about (someone involved at a high level with an Elsevier-published journal of a scientific society) that Elsevier is either losing money or just breaking even with the majority of their OA journals, subsidizing these from their other for-profit publications. However, they believe that this is worth it for its positive PR and for binding Elsevier to many scientific societies.

    2. Hugo says:

      I don’t think the cost of publishing is the real problem. Even though something like “Scientific Reports” charges a hefty 1495$ publishing fee (and the Royal Society of Chemistry charges up to 2500 gbp to make a review open access…), the fee to publish in many “Omics” journals is also >1000$. Maybe it’s a bit cheaper, but compared to the actual cost of research it’s still not that much. If you really wanted to save your money you could always send your manuscript to a real niche journal in your field that has some problems filling its pages.

      The fact that they have no real peer review is the main reason why they have so many submissions. Submit and forget, no questions asked. This makes publication easy (and that might even be good thing), but it lets a lot of questionable content through.

      A second reason is that a lot of researchers are really out of touch with literature, have no idea about suitable journals for their research, and don’t spend 2 minutes looking up Omics on wikipedia.

    3. Emjeff says:

      How , exactly, do you do that? Are you expecting people to work for free?

    4. Ray Threllkell says:

      I estimate that 20% of federal funding could be eliminated with no negative impacts on science. Most universities could easily reduce spend 25% with increased efficiencies.

  2. Cato says:

    “he accidentally projects an adviser’s email threatening to terminate his contract after saying he took vastly more vacation than allowed”

    I wonder if that was a legit complaint or just because he didn’t come in on Saturdays!

    1. Bagger Vance says:

      Yeah, maybe he accidentally projected Carreira’s famous “Dear Guido” letter by accident, reporter wasn’t hip enough to get the reference

    2. Daniel Barkalow says:

      Sound like he left early to build his company and said he was on vacation.

  3. SirWired says:

    Even the “reputable” publishers have a problem… When Elsevier has journals for Homeopathy and “Acupuncture and Meridian Stuidies”, they aren’t exactly strengthening their case as the world’s best gatekeepers for scientific publishing.

    1. kriggy says:

      Not saying that homeopathy works but I remember from lecture I attended that for example strigolactones (plant hormone) work at very narrow concentration range so actualy “less is better” which could be called homeopathy. This might be the case with other compounds as well (probably in very specific examples.

      1. AC says:

        Homeopathy is not “less is better” or hormesis. Homeopathy is based on the idea of “water memory”.

        1. kriggy says:

          I see. I always understood it in a way that the lower the dose the higher the effect is. Thats why would you dilute so much. Still weird that they have journal for it. Is it still online?

  4. LF Velez says:

    I absolutely loathe these predatory publishers, and steer my colleagues away as much as possible. Yet it’s interesting to see demands for high quality publishing to be ‘free’ in the same place where there are frequent explanations of why pharmaceutical products need to cost significant amounts of money. There is genuine work involved in receiving, reviewing, editing, formatting, typesetting, and production, even for online publications. The people performing these tasks are entitled to fair compensation.

    Why it is unreasonable for there to be costs associated with these activities?

    [No, I do not work for a publishing house.]

    1. a. nonymaus says:

      Receiving: An automated email processing script followed by expenses to be filed under editing.
      Reviewing: Done by unpaid volunteers, coordination of these is by the editor.
      Editing: Manuscript editing as one typically thinks of the term is done by the authors in response to the reviewers. The journal editor is the only real expense in this chain and decides which articles to send out for review, evaluates the reviewer responses, and generally organizes the process. So, about 1 – 3 FTE for any given journal.
      Formatting: Done by the authors according to a template.
      Typesetting: Mostly automated, although some journals use copy-editors in their workflow to add errors that the authors must fix once they receive page proofs Perhaps another FTE here.
      Production: This reduces to running a website and contracting out for short-run periodical printing.
      Making a Fermi estimate, if FTEs cost US$ 100k each and journal subscriptions cost US$ 10k, this journal will break even with only 40 subscriptions and no other revenue. At a typical current rate of US$ 40 / article download, the journal will break even with 10k downloads/year and no institutional subscriptions.
      Given that, it is not that people are complaining about journal staff being fairly compensated but about rent-seeking by publishers.
      On the topic of article availability in the event of publishers going out of business or otherwise ceasing distribution, this is one of the reasons to support Sci-Hub and other distributed ways of mirroring published articles. A truly open-access publisher would support distribution by e.g. bittorrent seeded from various libraries.

      1. Hugo says:

        I think your Fermi estimation shows that the current price for journals or the open access fee is not even that far off.
        10k downloads seems like a reasonable number, but that’s 250 articles per year @ 40 downloads each for full price, and with subscriptions you’d expect people to pay less, not more. Maybe Nature & Science can reach those numbers, but your favorite niche journal will be nowhere close. And the amount of work doesn’t scale with impact factor (although it might if you factor in the omics group…).

      2. NJBiologist says:

        I think the numbers in your Fermi estimate are off, but not by much. I’d put subscription prices lower by a factor of two. Downloads are tougher to estimate. The only data point I know is a journal I used to associate-edit; they’re an established clinical+research journal operated by a professional society, and I think they got ~2k downloads a year.

        Bottom line: I think you’re close, and the numbers seem achievable.

      3. Emjeff says:

        There is “type-setting”- publishing software for journals is enormously expensive. Not to mention website hosting, storage and advertising. I’ll ask the same question- are you expecting people to work/provide services for free?

        1. Some guy says:

          Journals expect their reviewers to work for free, so tournabout seems like fair play.

    2. HTSguy says:

      Compensation for reviewing? Have any of your ever received that? My experience is that journals expect reviewers to work for free (I have been offered free access to some of the literature for a limited period, but that’s not of value to those of us at universities). No “typesetting” either for online publications.
      But yes, organizing reviews and refereeing disagreements between them, editing, formatting, and hosting the resulting publications does require and deserve reasonable compensation. However, some scientific publishers have stretched the meaning of reasonable.

  5. anon says:

    I don’t think sci-hub deserves to be in the same category with these predatory journals in a post titled “The Ugly State of the Literature”. It is the result of the ugly state of publishing and the greed of publishers.

  6. anonymous says:

    I’d be curious to see how many people listing their institution as Harvard in the joke journal articles are actually at Harvard. If they are, are any other authors on the publication respected faculty members that signed off on it, or did one person just come up with some garbage and slap the unsuspecting authors names on it? Same thing for the listed NIH funding.

  7. Curious Wavefunction says:

    Try searching for Srinubabu Gedela on YouTube. And watch the video where he’s fêted like de Gaulle entering Paris.

  8. dave w says:

    Seems like the journals once provided a unique service in printing and distributing the literature, but these days they mainly cling to existence based on the “need” to be “published in a recognized journal”… except for that, I suspect that everyone would just be posting papers in PDF files on the net and reviewing them via a blog-comment mechanism.

    1. Ian Malone says:

      I half agree, in that the need to be in a ‘good’ journal is what keeps the publishers going. I’d be unlikely to spend time doing in-depth reviews of articles unless they were sent to me though, and a blog comment approach would have the downsides that: a. only a few papers would really get in-depth attention, b. it’ll be dominated by a few noisy people with time to kill, c. self selection, any article halfway controversial will inevitably have sensible analysis flooded out by reactionary comments from interest groups (see recent responses to an article here which happened to involve US tribal lands…).

  9. cynical1 says:

    Naive question: Are the articles published in these “fake journals” indexed by the various firms that index the scientific literature? If they are, would simply stop indexing them make any difference or potentially solve the problem? How much impact factor could a journal have that wasn’t even indexed? If PubMed, Medline, EMBASE, etc. just simply stopped indexing them then their Impact Factor would be zero right?

  10. Anon says:

    “Harvard was among the top US institutions with such publications”

    Does anyone seriously think that any of these desperadoes who pay to publish fake papers in fake journals are actually associated with ANY real institution? If you’re gonna pay to fake a scientific track record, you may as well fake a great one!

  11. Silias J says:

    So what, when you fuse a flourophore to a super reactive group, throw it in a cell, and look at it, and call that a nature paper not once, but 50 times or so….why shouldnt anything go, including non peer reviewed. As you will learn young grad students, all of science is marginal, except at the very cutting edge which is luck
    However, that cutting edge does not employ our massive workforce. So, we make stuff up.

    1. Turn the crank says:

      Or find a way to generate a radical and then add it to acrylates, heterocycles etc

  12. Chrispy says:

    The predatory journals are a symptom of a much greater problem. Frankly, most of what is in the “good” journals is garbage, too. Peer review is only so helpful. Sure, it is better than nothing, but the push to get positive data and publish it is so great that it has occluded the notion that we need to write nonfiction. In some ways, the big-name journals are the worst for drug discovery, as the right set of cherry-picked data and gamed models serve as an advertisement for the inevitable biotech spinout. The pathetic state of the literature is a real problem for scientific progress.

    1. Nick K says:

      Excellent comment, thank you. The corruption in the scientific enterprise extends far deeper than merely OA journals.

  13. TSRI alum says:

    A start could be training students to write and generate ideas. At TSRI, profs openly derided any attempt at creativity, instead encouraging you to ” churn and burn ” and ” be intense”: throw you head against a wall every day to no end. Ultimately, the talented who unfortunately listened to elder advice fell out of the system. The stupid, who didnt listen, are now publishing in said journals.

    1. Lt. Hayden Thurston says:

      I hear your pain. Try to look beyond it. Don’t lose sleep over these silly, self-important “scientists.”

  14. TSRI alum says:

    ” We dont think, we do “. ” it does not matter what you think ” — two prominent TSRI professors. Exactly why the literature is crap now. This is how we train our future scientists.

  15. TSRI alum says:

    ” if i could have my way, we would have no graduate school classes”– Jamie Williamson, former TSRI dean of grad school. Now, figure out why the literature is crap, geniuses.

  16. Morten G says:

    They won’t die until reputable institutions start writing in the job postings that publications in journals on Beall’s list won’t be considered when evaluating applications.

  17. The problem with research is that much of it is geared to finding the magical chemical which often causes more adverse effects than corrective measures. The substances found naturally in the body are not investigated to determine if changing their balance might correct the problem. This applies both to biochemistry and the biome not to mention the Viome, parasites or molds found in the body which we know nothing about.
    This is astounding b/c only 2% of the DNA in the body is human. Further, less than 25% of the genes found in the body are active so 75% of research on genes is occurring on inactive genes.
    The above would indicate that much of the money is wasted.

  18. JB says:

    One of the worst articles I’ve ever seen was just published in Science Communications. The authors apparently made an entirely brand new class of antibody against a type of PTM that has never been done before, yet never tested the antibody on cell lysate. How in the heck does that pass peer review? The article also contained all sorts of iffy mass spec data buried deep in the supplement.

  19. Run of the mill toxic prof ( no tenure ) says:

    There in only one way to be and that is me. Let me teach you, or else ( er, i dont have time, so lets let this postdoc teach you). Maybe you will have your own lab one day, but until then, i call all the shots. Oh, by the way do these 50 western blots ill be traveling for the next two weeks at conferences, so i doubt if i will awswer you email. Also, jobs are drying up, so it looks like your going into industry ( ie. Grad school lasting 30 y). Also, your place is in the lab, no conferences for you. I be here on saturday for 10 min to make sure you are. Want to make sure there is no life for you.

    1. Silias J says:

      Perfect satire of many profs these days. Remember, If someone is arrogant enough to think you are doing everything wrong and they have all the answers, they are arrogant enough to not care one iota about your well being. It may seam like they may, but it will change on a dime one day without warning.

  20. Insilicoconsulting says:

    The fact that reviewing weeks or months and the costs to get published are a big part of the problem. Pay top qualified reviewers well and ensure reviews within a week. I used to wait months for a review only to hear silly arguments from 1 of the two or three reviewers which again took a long time to resolve.

    To check against malpractice, make it mandatory to submit all data for crosschecking and implement some rudimentary checks for plagiarism and image analysis for suspicious images. Latter is harder but may be worth the effort.

    There’s always pressure to publish so help by making the process better for good journals so that people turn away from the fraudulent ones. Chinese and Indian Governments are very cognisant of abuse by publishing to these, so just writing to the research or education department may get these journals in the blacklist.

  21. Bruce Fisch says:

    I’ll never forget my favorite mentor referring to the NEJM as the Acta Retracta. That was 25 years ago…and it was as true then as it is now.

  22. Jane Baker says:

    Something has to be done about these ” prof-tards”— supposedly hypersmart PhD scientists that work at our nation’s top institutions but on the other hand generate literal research garbage and are emotionally 15 y/o highschool girls.

  23. MTK says:

    OK, so we all know the situation isn’t good. That’s apparent.

    It’s not completely hopeless, however, IMO. The (relatively) new NIH biosketch format, for example, is a step in the right direction where one highlights the five most important contributions to science and is limited to 4 cited publications for each contribution, so at least it tries to emphasize quality over quantity.

    One would think that as money is less tied to quantity that researchers and evaluators, meaning grant reviewers and tenure committee members would follow.

  24. DCRogers says:

    This is applicable:

    Peer review is a relatively recent invention, and was invented mostly to assist the editor, whose name on the nameplate of the journal was the true imprimatur that gave value to the journal. These days, the involvement of the editors seems often like a paper-shuffle rather than a true stamp of approval of a particular paper.

    Perhaps the name of the responsible editor should be published with each paper, so that they have some skin in the game? Though really, with the internet, any “editor” who wants to set up a “journal” could do it, and publish what they whilst, and be read, and respected, only if they provide interesting content, with Google AdSense providing any coverage for the minimal costs. (More like Derek’s blog, really…)

    Or maybe, we ditch the entire current system, and just have each lab “publish” their own work on the internet, with the reputation of the lab the only guarantor of quality. A record in provides the persistence.

    1. Curt F. says:

      You make a very important point. Peer review is really a service to editors, not to readers or authors. The editors should put their name on their articles.

      When every lab puts all their junk on chemRxiv or biorxiv or wherever, it will still be valuable to have trustworthy editors draw our attention to the most important new manuscripts in a particular field. I think professors would be well-positioned to do this, since “service” is already a component of their jobs.

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