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Handful of Biologists Went Rogue and Published Directly to Internet

16 March 2016

From The New York Times:

On Feb. 29, Carol Greider of Johns Hopkins University became the third Nobel Prize laureate biologist in a month to do something long considered taboo among biomedical researchers: She posted a report of her recent discoveries to a publicly accessible website, bioRxiv, before submitting it to a scholarly journal to review for “official’’ publication.

It was a small act of information age defiance, and perhaps also a bit of a throwback, somewhat analogous to Stephen King’s 2000 self-publishing an e-book or Radiohead’s 2007 release of a download-only record without a label. To commemorate it, she tweeted the website’s confirmation under the hashtag #ASAPbio, a newly coined rallying cry of a cadre of biologists who say they want to speed science by making a key change in the way it is published.

Dear Dr. Greider, We are pleased to inform you that the above manuscript has passed screening and will be online shortly. Cant wait #ASAPbio

— Carol Greider (@CWGreider) Feb. 29, 2016

Such postings are known as “preprints’’ to signify their early-stage status, and the 2,048 deposited on three-year-old bioRxiv over the last year represent a barely detectable fraction of the million or so research papers published annually in traditional biomedical journals.

But after several dozen biologists vowed to rally around preprints at an “ASAPbio’’ meeting last month, the site has had a small surge, and not just from scientists whose august stature protects them from risk. On Twitter, preprint insurgents are celebrating one another’s postings and jockeying for revolutionary credibility.

. . . .

For most of the history of organized scientific research, the limitations of technology made print journals the chief means of disseminating scientific results. But some #ASAPbio advocates argue that since the rise of the Internet, biologists have been abdicating their duty to the public — which pays for most academic research — by not sharing results as quickly and openly as possible.

. . . .

Unlike physicists, for whom preprints became a default method of communicating discoveries in the 1990s, biomedical researchers typically wait more than six months to disseminate their work while they submit it — on an exclusive basis — to the most prestigious journal they think might accept it for publication. If, as is often the case, it is rejected, they try another journal. As a result, it can sometimes take years to publish a paper, which is then typically available for a time only to colleagues at major academic institutions whose libraries pay for subscriptions. And because science is in many ways a relay, with one scientist building on the published work of another, the communication delays almost certainly slow scientific progress.

Researchers say they participate in the process in large part because the imprimatur of highly selective journals like Science, Nature and Cell has come to be viewed as a proxy for quality science. Like a degree from certain colleges, a study in an elite journal can be a passport to jobs, funding and promotions.

. . . .

The delays prevent scientists from showing off their most recent work to prospective employers or benefactors. They have also, some researchers say, begun to look faintly absurd against the general expectations for speed and openness in the not-so-new digital age. With the rapid spread of the Zika virus, for instance, several journals signed a statement promising that scientists would not be penalized for immediately releasing their findings, given the potential benefit for public health, in turn prompting some scientists to ask, why draw the line at Zika?

Link to the rest at The New York Times and thanks to Meryl for the tip.

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38 Comments to “Handful of Biologists Went Rogue and Published Directly to Internet”

  1. As with traditional publications, this antiquated practice favors the publisher, who to a large degree wields monopoly power over publishing of results much like traditional publishers in fiction. Unlike traditional publishers, to a large extent the journal, rather than the author, gains readership reputation from the work, which presumably gives the publisher an even tighter stranglehold. If you were to seek publication in a law review, by contrast, there exist mechanisms by which authors can shop publications to multiple journals simultaneously–better for the author and quicker to publication (since one need not iterate an entirely new version after each rejection). Thus, better models are clearly possible, but then, despite for-profit publishers adding little to no value (they typically edit little if at all, and they prey off academic faculty to get their articles peer-reviewed for free) publishers wouldn’t want to jeopardize their golden goose with improvements to benefit the public who pay for the research or the scientists who actually do the work.

  2. While I applaud the openness and speed this idea brings, I have to ask; Without peer review before publication do we not open the door to pseudoscience?

    After-all, it was one guy and one paper that started the whole vaccines-cause-autism craze. Yes, he was soundly discredited, his paper was yanked and his license revoked, but the damage was already done. People bought into it and despite him being discredited they continue to, and now kids are paying the price.

    I don’t see the potential harm of a Stephen King novel or a Radiohead song causing damage if thrown out on the internet, but scientific papers can be dangerous if not handled properly. Pseudoscience is an industry that makes billions every year, I think this will just give them the means and incentive to produce more.

    • Bless your heart, I find it charming that you think peer review prevents the publication of pseudoscience.

      Einstein’s Zur Elektrodynamik bewegter Körper, the paper which includes his statements of the mathematics of Special Relativity, was reviewed by only two men before publication: the editor and assistant editor of the Annalen der Physik.

      Contrariwise, Lysenkoism was derided as pseudoscience when I was a schoolboy. Now I hear that though Lysenko was wrong about how, it is almost certain that he got the what right.

      Besides, peer review has not stopped and will not stop men from following money, pseudoscience or no.

      Peer review is a corrupt system. In my view, you cannot reform a corrupt system. You can only destroy it.

      I say kill it.

      • Oh, never said it would stop it, but it does keep it from running wild. Just because the faucet is dripping doesn’t mean you give up and open it wide.

        I don’t see how killing peer review would be a good thing. If anything it needs tougher guidelines. There will always be those who game the system (KU anyone?) but giving up and opening the floodgates doesn’t strike me as a sound decision. Not in the world of medicine anyway. Your talking to a guy who spent his prior career in that field, the battle against quack medicine is ongoing and only getting worse.

        Did you know you can cure any type of cancer by sticking bleach up you a$$!?! Yes, there are people who actually believe that, and there’s a quack out there publishing a paper to support it. Giving him the green light is something I can’t get on board with.

        Oh, almost forgot, bless your heart too.

        • I’ve seen some of the open access journals are also using an open peer review process, where the research is posted, and then the reviewers post their reviews under their own names, so everyone can see their credentials as well and the scholarly dialog. I think that is an excellent solution to this problem, and I hope it spreads. (I wish I could remember which journals are doing it that way)

        • The best you can say about modern peer review is that it slows down the worst offenders a bit. Mostly by letting different cliques snipe at each other.
          The ever increasing number of retracted fake reports don’t speak favorably of the journals’ gatekeeping. A more open crowd-vetted approach can hardly do much worse.

          It certainly seems to work well for Amazon’s video projects. 😉

        • The best you can say about modern peer review is that it slows down the worst offenders a bit. Mostly by letting different cliques snipe at each other.
          The ever increasing number of retracted fake reports don’t speak favorably of the journals’ gatekeeping. A more open crowd-vetted approach can hardly do much worse.

          It certainly seems to work well for Amazon’s video projects. 😉

        • The best you can say about modern peer review is that it slows down the worst offenders a bit. Mostly by letting different cliques snipe at each other.
          The ever increasing number of retracted fake reports don’t speak favorably of the journals’ gatekeeping. A more open crowd-vetted approach can hardly do much worse.

          It certainly seems to work well for Amazon’s video projects. 😉

          • Hmm. Browser went bonkers there.

          • This past year, publishers have discovered numerous problems with peer-reviewed papers. (Google search link).

            They’re also discovering that a lot of results from the “soft sciences” such as psychology can’t be replicated, casting doubt on their accuracy.

            • An article in the Atlantic talked about this, in their profile of Dr. John Ionnides, a meta-researcher who looks into the credibility of medical research:

              … He and his team have shown, again and again, and in many different ways, that much of what biomedical researchers conclude in published studies — conclusions that doctors keep in mind when they prescribe antibiotics or blood-pressure medication, or when they advise us to consume more fiber or less meat, or when they recommend surgery for heart disease or back pain — is misleading, exaggerated, and often flat-out wrong.

              Sobering read.

        • Randall is right. Peer review is imperfect but it matters. Fortunately, peer review and open access publication are not mutually exclusive. Fancy journals organize peer review, but they don’t do it themselves. Scientists do it for them. For free. Open access can be structured with peer review. They can publish anything that qualifies. No need for gatekeeping based on page count or prestige. Besides, the biggest advantage of open access isn’t necessarily to increase the number of papers being published, but to make them free (or cheap) to the reading public. The established journals make exorbitant amounts of money off journals, even though they neither produce the content nor review it.

      • Thank you Antares and Felix

        You hit it.

    • I think fostering education is probably a better counter to pseudoscience than trying to limit information. Better educated people will be able to more quickly and easily identify pseudoscience.

      • Second the motion!

        • I’m all for that, but it seems to be heading the other way.

          Take the “Food Babe” for example. This is a woman who advised her fans to sit near the front of the plane because that’s were the pilot controls the oxygen distribution to the passengers. Yup. On top of this she points out that the airlines are cheating/poisoning you by not giving you 100% oxygen. (Its over half nitrogen, she screams!)

          http://gawker.com/the-food-babe-blogger-is-full-of-s***-1694902226

          She has millions of devoted followers. Head-desk.

          • @ Randall

            “Its over half nitrogen, she screams!”

            Seventy percent, actually. Been pretty much the same since the Carboniferous.

            But even 100% oxygen can’t help the brain-dead. 🙁

            • True.:)

              There’s even a group called “Banned by the Food Babe” (if you call her out on her website she bans you as a “Monsanto Shill”, whatever that is) so they started their own group to basically watch and, well, laugh at her stupidity. Its both fun and sad at the same time.

              Still, shes making millions off these people.

            • ETA: Precisely 78.084% N, 20.946% O, the rest is everything else (mostly CO2).

    • If Peer Review included trying to duplicate the results of the tests or things like that there would be value in it.

      but since all it does is read the paper that was written and the documentation that the authors claim came from the study (frequently without such critical information such as the computer program that analyses the raw data to produce the results they are writing up) it’s pure GIGO (Garbage in Garbage out)

      The only thing peer review can catch is minor mistakes. Beyond that it boils down to the question of if it agrees with the existing viewpoint or not.

      • Exactly.
        Pseudo science isn’t really a threat in professional outlets like the website cited. Bad and faked data is and peer review rarely delves into the data.

        Where pseudo science comes into play is the non-professional sites and, most critically, the mainstream media.

      • You are correct that if the paper’s authors lie or report inaccurate data, no amount of review can catch that. But you do not appreciate that peer review is much more.

        Good peer review examines methodology, and makes sure that the authors’ conclusions are supported by their data. Authors have a big incentive to say in words more than is actually said by their numbers. They also might design a study poorly, say, with inadequate controls or bogus statistical analysis. This is extremely important as most medical research these days ultimately relies on statistics and good study design to draw meaningful conclusions.

        As an extreme example, what if someone ate nothing but blueberries for three days, and on the third day came down with a cold. They write up a paper concluding that blueberries cause the common cold. Good peer review would reject a paper like this not because it is “pseudoscience” but because it is poorly done science.

    • @Randall– IIRC, the guy who published the paper linking vaccines and autism was published in the British Medical Journal (I was an assistant medical librarian at the time). So even with peer review, pseudoscience still got an airing– along with the validation of a well-respected medical journal.

  3. *sudden enlightenment* So that’s why indie publishing seemed so familiar to me! I spent ten years in physics research. One of the tasks of a graduate student is preparing research papers for publication, including the data graphs. (You kids have it so easy with your Paint and Photoshop and all…we used tape and copiers!) After dealing with the arcane requirements for my thesis (25% rag paper, for example), and a torture technique known as the “camera-ready manuscript” using LaTex, self-pub is like falling off a log. (If you want to hear profanity that would make a hardened drill sergeant blanch, ask me what I think of LaTex).

    Randall, the premise of a preprint is the research *will* be submitted to a refereed journal. If it isn’t that is scientific misconduct and we do police our own. The other aspect to non-simultaneous submissions is other researchers are doing the reviewing for publication. If you sim-sub you are wasting a lot of other people’s time, and it is inconsiderate. I have both published papers in the reviewed journals and been a reviewer, so I am familiar with the process. 🙂

    • From what I read this process would be done on an open forum though, correct? If I read this wrong I’ll stand corrected.

      If I’m right though this opens the papers interpretation to anyone with an internet connection. So we now have the uneducated spinning the data to support their own goals. What snake-oil salesman would not love to have a paper from a reputable source supporting their pseudoscience product or treatment?

      I also fail to see how this would be policed by the people involved. If the initial paper was wrong, or for that fact just easily misinterpreted by a layman, the damage is done. They pulled Wakefield’s paper but that didn’t stop the spread of his BS.

      I just think this is something we should be careful with.

      I just re-read this, is there a step in the process that I’m missing?

      • What you fear has always been the case, alas.[1] And my experience is with physics–the preprint culture may indeed be different than bio, and the writing style tends to be very dense. The best journals have page charges or page limits, and the audience is of our peers, so the text is opaque to most non-specialists.[2] Also fewer people think they can make use of electron-phonon coupling mechanisms in supercooled doped fullerene films, but *everybody* has a body they’d like to have work better 🙂

        [1]Radithor, a patent medicine containing actual radium(!) circa 1918. Do a search for the full horror show, including the article “The patient was fine until his jaw fell off”.

        [2]This actually happens, even with peer-reviewed papers. We can’t win…

      • silly edit timer cut me off!

        The “policing” is done via ostracism/shunning/your career is dead. We have a high trust culture in science and if that trust is violated you don’t work in that field again, nobody cites your work, nobody gives you grants…you become a non-person in the field. Look up what happened to Pons and Fleischmann of the cold fusion debacle. It’s a serious punishment. Not done lightly, so we are careful about making accusations, but misconduct that egregious is not tolerated. Again, my experience is with physics and the hard sciences. YMMV.

        • One, that link is priceless. (already stolen)

          Two, I see where you are going.

          One remaining question. What if your motivation is money? What if you couldn’t care less about being shunned, you perhaps even welcome it as it feeds into the whole “they ostracize me because I’m revealing the truth” marketing meme. Wakefield is still making a good living peddling his BS despite being dismissed by his peers as a fraud. Oz gave up a great career as a heart surgeon in favor of peddling miracle snake oil. He’s now a joke among the surgeons I know, some who actually studied under him.

          I think this openness might work in some fields but not in others. Not to make light of the infraction, but I have yet to hear of someone being killed by the Pons paper. But medicine is different, when people buy into the woo it’s consequences are real. I’ve treated kids with diseases that should no longer be possible, all because Mom trusted the internet over her doctor.

          I’ll have to do some more reading on this subject. Thanks for your insight.

          • There is plenty of that already around.
            Always has.
            (Hollow Earth “theory”, without going too far.)

            But the fastest way to a quick buck through pseudo science is through the Manhattan publishers. (Just ask Von Daniken and his precursors, like Cayce.)

          • I did not know you were in the medical profession! That is cool, and you might be very interested in the Radithor history. For one thing, it illustrated how different people exposed to the same amount of hard radiation can have radically different symptoms (some people naturally get rid of radioactive material before it has time to do as much damage) I worked with radiation sources so I got lots of safety training–it’s a fascinating area of medical research. And apparently the “burst of energy” is a known symptom of bad radiation damage, so that part of the patent medicine was actually valid. You die of the side effects, though 😉

            In tight communities like physics, the money and the esteem of your peers are closely linked. It’s hard to sell what we do on streetcorners. Also, not a lot of politics. In other fields, it is either hard to do experiments (climate change) or there is a lot of emotional drama inherently part of the topic (vaccines/autism) and politics can have a debilitating effect on research and funding.

            In the end, scientists want to do cooler stuff, and if they can’t reproduce your cool stuff they complain long and loud. That’s what torpedoed cold fusion–nobody could reproduce it. We all thought it would be neat if it worked!

          • I had no idea that Dr. Oz was a real doctor. I thought the “Dr.” part was a persona. That’s sad what he’s done to himself, then.

            There was an episode of “House” where he’s talking to a mom who’s against vaccines. She thinks they’re products of Big Pharma. He says that instead of enriching the pharmaceutical industry, she’s actually enriching the funeral industry.

            “More parents like you make a bigger market for child-sized coffins,” or something to that effect.

            I’ve heard that doctors are starting to fire patients who think like her. I hope that’s working. It has to be disheartening to see a child pointlessly suffering from polio.

  4. I am not a scientist, nor do I play one on TV, but I try to keep as informed as a lay person can.

    It seems to me if we bat this “peer-reviewed” versus “internet-reviewed” issue back & forth enough, we’ll get to the conclusion that it’s medium of the review that matters, not its validity. Isn’t this a similar argument to the one we hold, that the story is the words? That the delivery system matters less than the story itself?

    Of course there are openings for scam artists. I’m reminded of the guy who appeared on Bill Maher last month claiming that he’s cured chikungunya virus and can cure all forms of cancer the same way. Yeah. Okay. Right.

    I hope, though, that Sabrina is right and the system will self-police in the disruptive environment as effectively as it currently does.

    • Any system will work well if saints work it. The problem is that saints are in short supply.

      I know my way around data and numbers. You give me your raw data and your stats derived from those data, and I can tell you in minutes if the data will support your conclusions. If you don’t publish your raw data, you are just blowing smoke.

      Peer review is an appeal to authority, a logical fallacy. The real test is repeatability.

  5. And here’s what can happen when people with a particular ideology or worldview Start to twist and manipulate science for their own benefit, http://youtu.be/oACng87P9I0
    And extreme example I know, but I think this is why we need objective scientific reviewers especially in the field of biology, to stop dangerous drugs like this being produced.

    • FWIW I once interviewed for a job with a Bay Area company that specialized in running stats for pharmaceutical firms to qualify their drugs for FDA approval. All smiles as the interviewers (2) reviewed my qualifications and experience. Then they asked how I would handle outliers. I told them I would footnote each outlier with an explanation. The smiles disappeared. They never called me back.

      Pay no attention to that man behind the curtain. If your data are honest and your methods work, your results can stand the scrutiny of king and commoner alike. If you are a charlatan, the odds of being exposed increase toward unity the more people see what you are doing. The current peer review system restricts the allocation of grant monies to them as is in the club.

  6. appreciate the comments. Have to say as a peer reviewer, and having been reviewed and having sat in on editorial for med journal, that the same issues that are out of control in gen’l genre publishing, are far far too often also rampant in peer vetted pub.

    My.02, self-policing wont work, bec, in part, peer review is often far too wobbly already re ethics, favoritism, narrow intent about what kind of research ought be disseminated, sometimes like a phallanx of scolds and other times like a small squadron sotted with envy and thereby obstructionism and trivial nit picking on carious, inc language, for instance.

    My .02, is also that like paris review and other ‘literary’ rags, there is an ‘in’ group at most every kind of journal I’ve seen up close from the inside. Somewhat like facebook, [agh] there are friends of friends. And then there are truly original researchers/ experimenters/ testers who are unknown, and often remain so. Esp in ink on paper ante-dilivian process that still prevails [only so much room in paper pages, they say.]

    I think the part I’m for most is that journals are not behind an absurdist pay wall that cost’s an individual a king’s ransom to read. Not sure why, but many a vetted journal reminds me of country club 1950s of ‘inclusion of our kind’ only. Given there are hundreds of thousands of legit researchers worldwide, and very few are ever heard from in print… seems like indie author way through would be such a disruption to ‘the old way’ that is calcified as it stands.

    I wouldnt be so afriad of ‘false science’ as the believers will always be with us, whether eating a teaspoon of dirt off a silver spoon [Roma[, or ill health coming if a person enters a place, any place, where a person has died [Navajo] or that huge amount of rads of electricity to the brain will ‘cure’/help’ depression even though it leaves the patient often somehow half disappeared.

    Plenty was gotten wrong in medical so-called science over the years, vetted journals/ fda and other govt units, regardless. Prob we all need to be smarter about analyzing claims…. To know how to. Surely the days of relying on a person with a title to ‘tell us the real deal’ is over. I dont know the answers about how to protect everyone from even themselves, but I hope all can be sheltered in ways of good or better health that actually work.

    And Dr. Oz? Ask any person of sudden fame or bestsellerdom if it’s true that soon after, the devil shows up. Most say no to the demon. But some say yes. The yes is evident in the subsequent vapidity, circus sheen.

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