Weekend reads: Waste in research, a praise-worthy swift correction in NEJM, and more

booksThe first full week of 2014 featured a slew of stories and commentary about scientific publishing and related issues. Here’s a sampling:

Update, 4:15 p.m. Eastern, 1/12/14: As noted by commenter JATdS, the Journal of Bone & Joint Surgery item was slightly inaccurate and has been changed to reflect what the journal meant by “who reviewed the article.” Journal publisher Kent Anderson tells us:

The JBJS peer-review statements only list the roles of the peer-reviewers involved. We have no plans to lose what we think are benefits to a confidential peer-review process.

18 thoughts on “Weekend reads: Waste in research, a praise-worthy swift correction in NEJM, and more”

  1. If we shut down the NIH, the fantasy that researchers benefit public health and science will be eliminated,
    That will lead private industry to do the studies and everybody at least knows their true motives. Its all just one junk science report after another—useless studies with ulterior motives of greedy agendas.

    1. I am not a proponent of shutting down the NIH, and I am not even a US citizen. For one simple reason. It does much more good than bad. Look at PubMed, for example. It does the world a positive service. Much more benefit is derived than the inherent evils that may exist due to beaurocracy. That is like saying that Springer or Elsevier should stop being publishers and should stop to exist simply because the number of retractions in their journals is increasing. No, the NIH, like some large corporate publishers, or even Thompson Reuters, have an importance in science, publishing and society. What needs to happen is reform. Change that makes them more efficient, less wasteful, more resourceful, and less exploratory. More openness, better communication and PR, more accountability and most importantly, honesty (or at least a move towards it). Frauds should be called out (whistle-blown?), expunged from the system and the resulting message should be a no-nonsense policy. There is no reason why the private sector and the government sector cannot exist alongside each other. That would simply stimulate more competition, which is healthy. Extinction of a service or institute, or company will occur naturally as a natural life cycle. When it is no longer needed it will fall by the way side. The problem is when such behemoth institutions are being propped up by exploratory policies and wasteful funds. If you can prove, in dollars and cents, that this is taking place, then present your case, rather than call for an irrational call to terminate something that does more good than bad.

      1. Separately related to the JBJS story. JBJS (Journal of Bone & Joint Surgery) has made a TINY step forward towards re-instilling trust in the peer review process. But of what value is the honesty of one journal when the other thousands trend the other way? How does ensuring quality control of one journal stem the tide of the pay-to-publish business model of many non peer reviewed open access publishers on the Beall list http://scholarlyoa.com/2014/01/02/list-of-predatory-publishers-2014/) ? That’s like adding one drop of water to a pool of pure salt and expecting the salinity to somehow decrease. One of the greatest failures of modern science publishing is the gradual erosion of accountability on the part of editors and peer reviewers. Publishers only move in the direction of assuming responsibility in order to save face. The latest trend is to vilify authors, and slap on an academic tax, a retraction. Although on this blog the authors are most often vilified, to be frank, peers, editors and publishers, who are supposed to serve as the gate-keepers of quality and verification, have shown that their systems (and they themselves, too) have some levels of failure. Therefore, to ensure that peer review is conducted thoroughly, and responsibly, no better way than to actually name the peer reviewers. This holds them accountable forever. This is an excellent solution for publishers still using the traditional publishing model so that later on, when there are problems, or disputes about ethical issues such as duplication or scientific content, peers can be called upon for a response (provided that they are still alive). In other words, there is a false impression in science publishing that the responsibility of a peer or an editor reaches an end-phase the minute that a paper is published. This is the biggest fallacy of the science publishing kingdom. Responsibility and accountability are carried forward to the last living day of a peer and a reviewer. They must always be held accountable for their gate-keeping, even long after retirement as an editor. As equally an author must carry their own responsibility for what they have published to the day they die. In some ways, new-age publishers like f100Research try to emulate the open peer review system prior to publication by showing the names of peer reviewers and, more importantly, their peer reports. I do not mean to disrespect them for their effort, but what JBJS did is not a significant improvement. It simply showed some accountability. The true test would be to publish the peer reviewers’ reports and the authors’ responses, alongside the original paper. That would be a true test of accountability by the publisher and would possibly also make the journal more cautious about what is accepted, or not.

        1. Peer reviewing is a freely given academic service. I am constantly annoyed that there seems to be an movement to shift the blame for cases of deliberate fraud to the reviewer! Last year I reviewed slightly over 20 manuscripts (including re-submissions), that is (for me) a lot of time. I do as good a job as I can (every year I catch one or two papers for outright fraud or fabrication). Can there be improvements? Sure. As a reviewer I caught a case of deliberate image manipulation. Clear cut, no question. Four months later the same paper is published in a different journal with the offending figure cut. ONLY! Trying to shift more responsibility to reviewers will simply result in more people clicking the “no thanks” button when invited to undertake a review of a manuscript. Keep the blame and responsibility squarely where it beongs: On the originators of the fraud itself. It belongs in no other place.

          1. PWK, scientists can always choose NOT to review, or charge a fee for their services. Where is it stated that professionals have to be the slaves of publishers as the gate-keepers of quality control? And for free, at that? This is a perverse abuse by for-profit publishers of professionals. As if we somehow have to be the Mother Teresa’s of science! If you work in any other sector of the economy, professionals like us are paid for our work, like a consultancy service, Simple. And not paid lightly, either. Publishers make profits, and they sit back (and I guess laugh) while we take care of quality control for them, for free. All they do is activate their automatic mail spoolers to get authors processed and editors managed. Why do you think authors have to process papers through online submission systems and editors are also processed through the same meat-grinders? This is my comment regarding the unfair nature of the current system. It is predatory, and abusive. Time to charge publishers for quality control, or boycott their journals. This includes Springer, Elsevier, Wiley, Taylor and Francis and countless others.

            Now, on the issue of responsibility. If you do a job, you face the consequences. Just because no money is involved doesn’t mean that you aren’t responsible. We should all take FULL responsibility for the papers we let through. Kindly note, I never stated that responsibility should be SHIFTED. It must be SHARED. So, an author that commits plagiarism must be almost totally responsible. But a publisher that claims to do background checks on plagiarism, and fails to detect it, or editors who are also – as part of their peer reviewing repertoire – meant to detect for such issues, should also be held accountable for a failure of the system. You take the glory, don’t you, for doing the job? Well, so too should you also assume the responsibility. The equation is as simple and logical as that. Emotions aside.

        2. RW stated that “The Journal of Bone & Joint Surgery will begin naming reviewers, as part of an effort to make it clear what peer review means there.” In fact, this is slightly inaccurate. The journal only lists who performed the peer review, but does not disclose the actual names. See the editorial by Vernon T. Tolo:
          http://jbjs.org/article.aspx?articleid=1790466

          This can be clearly verified by any article, for example the first paper of the January issue:
          http://jbjs.org/article.aspx?articleid=1790468, which states, in the View Disclosures and Other Information section “Peer Review: This article was reviewed by the Editor-in-Chief and one Deputy Editor, and it underwent blinded review by two or more outside experts. It was also reviewed by an expert in methodology and statistics. The Deputy Editor reviewed each revision of the article, and it underwent a final review by the Editor-in-Chief prior to publication. Final corrections and clarifications occurred during one or more exchanges between the author(s) and copyeditors.”

          Does this actually advance our knowledge? Is this information even useful, except to prove that peer review actually took place and was not bogus?

          So, actually, it doesn’t do much. It should name all entities exactly by name, otherwise there is no real transparency and accountability (sorry if this hurts the feelings of those who review freely). Could this be a fear of legal consequences and libel suits against editors, reviewers or staff arising from claims should a retraction occur later on?

          1. I have no words to describe my disappointment. I naively understood that “naming reviewers” meant “quoting names and affiliations of reviewers”. The expertise field of a reviewer, e.g. “an expert in methodology and statistics” is almost useless. I suppose that The Journal of Bone & Joint Surgery has very few experts in Medieval history in his reviewers board.

      2. typo: Thomson Reuters, in place of Thompson Reuters (like J.J. Thomson, the hypothesizer of the plum pudding model).
        “What needs to happen is reform”: I couldn’t agree with you more.

      3. JAT: Your ideas are good and lofty, but they do not factor in politics, grantsmanship, publish to get tenure and stature. I caught a group of NIA funded “investigators” red handed
        on fraud and violation of regulations. Google Hebrew rehab/OHRP. For their violations they were sent out for retraining! Can you make a reckless crook an ethical investigator?? So my call is not irrational but founded
        on empirical evidence. ORI, HMS, and JAMA are giving us a snow job.

          1. “I fault the Editors of JAMA Psychiatry, Joseph Coyle, MD, and of JAMA, Howard Bauchner, MD, for the non-rigorous standard they applied to the notice of Failure to Disclose. They acquiesced in another dissembling response.” Hold editors accountable. Raise a brouhaha. Demand at least a corrigendum. With enough revolt, and should a corrigendum be issued, those who are vocally strongly against corporate corruption that hides COIs and fails to make appropriate disclosures can then try to progress towards demanding a retraction. By trying to force a corrigendum by exposing the truth, you will first force them to admit to guilt and error. And with such a public admission in hand, the rest could be simple, provided that you can gather the momentum by other peers. And finally, try and convince Coyle and Bauchner to offer a public response on the blog. Nice work, Bernard.

  2. More weekend read: 10.1021/om4000067. The Reto Dorta’s paper, which was released on the web 6 months ago (July 12, 2013), is still alive, in the ASAP page for Organometallics. Do you remember? “Emmaaaaaa… just make up an elemental analysis…”
    The bottom of the ASAP barrel is an interesting section of editorials, something like the limbo of papers:
    http://commons.wikimedia.org/wiki/File:Follower_of_Jheronimus_Bosch_Christ_in_Limbo.jpg
    If I remember correctly, the “NaH as an oxidant” paper was also available for one year (or so) in the limbo of the JACS.
    And currently,
    Chem. Commun. has a manuscript accepted on 02 May 2013 (10.1039/C3CC41498A), not yet published. What happened?

    1. And here’s two cases for Sunday tea-time conversation. Bear with me, the plot is thick. So perhaps some scones with the tea would be in order.

      Case 1

      A paper in an open access journal not listed at Beall’s http://scholarlyoa.com/individual-journals/ was supposedly retracted:
      Authors not indicated
      ARE WE AWARE HOW CONTAMINATED OUR MOBILE PHONES WITH PATHOGENIC BACTERIA
      Int J Pharnacy and Pharmaceutical Sciences (IJPPS)
      http://www.ijppsjournal.com/Vol3Suppl4.htm (pages 275-276)

      The retraction notice states “This Article has been removed from publication due to Copy Right Violence.” (which is a fat laugh in itself).

      If we do a little research on Google, we quickly discover that the plagiarised article, in fact wholly duplicated (in this case an act of publishing PIRACY), we find the original to be a BMC journal, Annals of Clinical Microbiology and Antimicrobials (http://www.ann-clinmicrob.com/content/8/1/7). In my opinion, that paper is such a trash study, just some basic swabs made on mobile phones. Nonetheless, it turns out that the authors of the original paper also committed an act of plagiarism and got a correction for it: http://download.springer.com/static/pdf/322/art%253A10.1186%252F1476-0711-8-31.pdf?auth66=1389676742_28c4bb35f388f3f0da8e909b0d865230&ext=.pdf

      Ironically, if you swing through a few more Google/Yahoo pages with the title, you still find the PIRATED text:
      VIRENDER SINGH1*, P. K. CHAUHAN2, ROHINI KANTA3, ABHINEY PURI4 AND JASWANT SINGH SAINI
      http://www.ijppsjournal.com/Vol3Suppl4/2445.pdf

      Shocking, isn’t it?

      Case 2

      Sticking with IJPPS, on exactly the same page (journal issue) as Case 1, we find a second retraction!

      Authors not indicated
      PHARMACOGNOSTICAL EVALUATION OF CALOTROPIS GIGANTEAN (LINN). LEAVES
      http://www.ijppsjournal.com/Vol3Suppl4.htm (pages 167-174)

      The retraction notice states exactly the same laughable wording as Case 1: “This Article has been removed from publication due to Copy Right Violence.”

      Yet the paper PDF still exists online:
      SWAPNA P* AND ELUMALAI A
      http://www.ijppsjournal.com/Vol3Suppl4/2383.pdf

      Despite attempts to identify the original paper, I found none, begging the question, whose copyrights were violated? I did find another paper by the same authors in another publisher:
      http://www.ijpsr.com/V2I11/33%20Vol.2%20(11),%20IJPSR%20,RA-883,%202011,%20Paper%2033.pdf

      The plot gets thicker, but if this first part can appear on RW, then this will form an important part of a follow-up.
      .

      1. Eleven (11) more retractions from the same journal, IJPPS (verbatim reasons for retractions are listed as per the publisher)

        1. SYNTHESIS AND ANTIFUNGAL ACTIVITY OF 1-ALKYL/H-2[4-(ALKYL/ ARYL-PIPERAZIN-1-YL)-METHYL]-BENZIMIDAZOLE DERIVATIVES
        http://ijppsjournal.com/Vol2Issue2.htm Vol 2(2) 84-92 (2010)
        Reason: This Article has been removed from publication due to Copy Right Violence.
        Despite officially reported retraction, the PDF was still available through Google and Yahoo searches:
        http://www.ijppsjournal.com/Vol2Issue2/461.pdf
        SUNIL V AMRUTKAR1*, UMESH D BHAGAT1, PRITI PARGHARMOL1, SANDEEP S KOTGIRE1, M S RANAWAT2
        *Asistant Professor, MGV’s Pharmacy College, Nashik (Maharashtra), India, 1 Department of Pharmaceutical Chemistry, MGV’s Pharmacy College, Nashik (Maharashtra), India, 2 Department of Pharmaceutical Chemistry, B.N. College of Pharmacy, Udaipur (Rajasthan), India.
        Copies or duplications of the paper not searched for.

        2. SYNTHESIS AND ANTIMICROBIAL ACTIVITY OF NEW IMIDAZO [2, 1-B] THIAZOLE DERIVATIVES
        http://ijppsjournal.com/Vol2Suppl1.htm Vol 2(suppl 1) 65-69 (2010)
        Reason: This article has been removed from publication due to violence of rules.
        Despite officially reported retraction, the PDF was still available through Google and Yahoo searches:
        http://www.ijppsjournal.com/Vol2Suppl1/311.pdf
        SENTHILRAJA M* AND GIRIRAJ P
        Department of Pharmaceutical chemistry J. K K. Nataraja College of Pharmacy, Salem Main Road, NH47, Post Box # 151, Koamrapalayam638183, Namakkal, Tamilnadu, India.
        Copies or duplications of the paper not searched for.

        3. DEVELOPMENT AND EVALUATION OF MUCOADHESIVE BUCCAL TABLETS OF SALBUTAMOL SULPHATE
        http://www.ijppsjournal.com/Vol2Suppl2.htm Vol 2(suppl 2) 40-42 (2010)
        Reason: This article has been removed from publication due to copy right voilence [sic]
        Despite officially reported retraction, the PDF was still available through Google and Yahoo searches:
        http://ijppsjournal.com/Vol2Suppl2/456.pdf
        R K ARYA1, AKANKSHA GARUD2, NEETESH K JAIN2, NAVNEET GARUD*2
        1Institute of Pharmacy, Bundelkhand University Jhansi (U.P.), 2 IPS College of Pharmacy, Shivpuri Link Road, Gwalior (M.P.), India
        Copies or duplications of the paper not searched for.

        4. FORMULATION AND EVALUATION OF METFORMIN HYDROCHLORIDE FAST DISINTEGRATING TABLETS BY USING POLACRILIN POTASSIUM NF FROM DIFFERENT SOURCES AS SUPERDISNTEGRANTS
        http://www.ijppsjournal.com/Vol2Suppl2.htm Vol 2(suppl 2) 55-57 (2010)
        Reason: Article has been disqualified from the publication
        No PDF could be traced.
        Any link to the following two:
        http://www.pharmasm.com/pdf_files/01_neha%20maniyar.pdf
        http://www.irjponline.com/admin/php/uploads/1174_pdf.pdf

        5. STUDY OF THE EFFECTS BY FIXED DOSE COMBINATION OF ZYDOTUM (CEFTAZIDIME -SULBACTAM) IN ALBINO MICE
        http://www.ijppsjournal.com/Vol2Issue3.htm Vol 2(3) 173-176 (2010)
        Reason: This article has been removed from publication due to violence of copy right
        Despite officially reported retraction, the PDF was still available through Google and Yahoo searches:
        http://www.ijppsjournal.com/Vol2Issue3/645.pdf
        RAJINDERJIT SINGH AHI, R. PATHAK, DEEPAK ARORA, RAJIV KUMAR*
        Department of Biochemisty, Adesh Institute of Medical Sciences and Research, Department of Physiology Bhojia Dental College, Baddi (H.P), Department of Microbiology, Adesh Medical College & Hospital, Bathinda. Punjab INDIA
        Copies or duplications of the paper not searched for.

        6. PATHOGENESIS OF DIABETIC NEPHROPATHY
        http://www.ijppsjournal.com/Vol2Suppl4.htm Vol 2(suppl 4) 24-29 (2010)
        Reason: This article has been removed from publication due to voilence [sic] of copy right
        Despite officially reported retraction, the PDF was still available through Google and Yahoo searches:
        http://www.ijppsjournal.com/Vol2Suppl4/872.pdf
        ATUL ARYA1*, SAHIL AGGARWAL2, HARLOKESH NARYAN YADAV1
        1*From the Cardiovascular Division, 2 Nano Technology Research Centre, Department of Pharmaceutics, ISF College of Pharmacy, Moga (Punjab)142001 India
        Copies or duplications of the paper not searched for.

        7. CENTRAL VENOUS CATHETER RELATED BACTEREMIA IN HEMODIALYSIS PATIENTS
        http://www.ijppsjournal.com/Vol2Suppl4.htm Vol 2(suppl 4) 168-171 (2010)
        Reason: This article has been removed from publication due to copy right violence
        Despite officially reported retraction, the PDF was still available through Google and Yahoo searches:
        http://www.ijppsjournal.com/Vol2Suppl4/876.pdf
        DR POOJA GUPTA, DR REENA SET, DR DEEPAK ARORA, DR KALPANA MEHTA, DR RAJIV KUMAR
        Dept. of Microbiology AIMSRBathinda151001, Dept. of Microbiology NAIR Medical College, Mumbai, Dept. of Nephrology NAIR Medical College, Mumbai, India
        Copies or duplications of the paper not searched for.

        8. POTENTIAL ADVANTAGES OF NOVEL INTRACORNEAL DRUG DELIVERY SYSTEM IN MANAGEMANT OF FUNGAL KERATITIS – AN OVERVIEW
        http://www.ijppsjournal.com/Vol3Suppl2.htm Vol 3(suppl 2) 12-17 (2011)
        Reason: This article has been removed from publication due to copy right violence
        Despite officially reported retraction, the PDF was still available through Google and Yahoo searches:
        http://www.ijppsjournal.com/Vol3Suppl2/1078.pdf
        ROHIT BISHT*, SUMIT DURGAPAL
        Siddhartha Institute of Pharmacy, Sahastradhara Road, , Himalayan Institute of Pharmaceutical Science and Research, Dehradun, Uttrakhand, India (e-mail missing)
        Copies or duplications of the paper not searched for.

        9. PHYTOCHEMICAL AND PHARMACOLOGICAL EVALUATION OF THE SEEDS OF ANNONA SQUAMOSA LINN.
        http://www.ijppsjournal.com/Vol4Suppl3.htm Vol 4(suppl 3) 92-94 (2012)
        Reason: Article has been removed from publication due to misconduct
        Despite officially reported retraction, the PDF was still available through Google and Yahoo searches:
        http://www.ijppsjournal.com/Vol4Suppl3/3144.pdf
        Authors names omitted, but running head indicates Debnath et al.
        http://www.ijppsjournal.com/Vol4Issue2/3297.pdf
        Was this the duplication or original?
        http://ijrpbsonline.com/files/RV2.pdf (2011)
        http://anvpublication.org/RJPP/RJPP_1_3_2009_Abstract.pdf (2009)
        The reference list of this recent paper in another predatory OA journal is revealing:
        http://www.irjpas.com/view_content.php?quat=3&date=Volume-3:Issue-4 (Jul-Aug, 2013)&issue=4 (web-links a mess)
        PHYTOCHEMICAL ANALYSIS OF ANNONA SQUAMOSA SEED EXTRACTS. Biba V. S; Lakshmi S ; Dhanya G.S and Remani P

        10. DESIGN AND EVALUATION OF A 3-COMPONENT COMPOSITE EXCIPIENT “MICROCRYSTARCELLAC” AS A FILLER-BINDER FOR DIRECT COMPRESSION
        http://www.ijppsjournal.com/Vol4Suppl4.htm Vol 4(suppl 4) 160-170 (2012)
        No reason: This Article has been removed from publication
        No PDF could be traced.
        Any link to the following:
        Design and Evaluation of a 3-Component Composite Excipient “Microcrystarcellac” as a Filler-Binder for Direct Compression Tabletting and it’s Utilisation in the Formulation of Paracetamol and Ascorbic Acid Tablets. Shittu, A.O., Oyi, A.R., Isah, A.B. & Ibrahim, M.A (2012) Global Journal of Medical Research vol 12 Issue 7 Version 1.0 Global Journals Inc. (USA) A publisher on Beall’s list.
        Copies or duplications of the paper not searched for.

        11. IN VITRO ANTIOXIDANT AND FREE RADICAL SCAVENGING ACTIVITY OF ISOLONGIFOLENE FROM MURRAYA KOENIGII LEAVES
        http://www.ijppsjournal.com/Vol5Suppl4.htm Vol 5(suppl 4) 276-279 (2013)
        Reason: Article was withdrawn from publication on author request
        Despite officially reported retraction, the PDF was still available through Google and Yahoo searches:
        http://www.ijppsjournal.com/Vol5Suppl4/7883.pdf
        KOWSALYA RANGASAMY1, ELANGOVAN NAMASIVAYAM1,*
        1Department of Biotechnology, Periyar University, Salem 11, Tamil Nadu, India

        Similar topic here:
        http://www.sciencedirect.com/science/article/pii/S0308814607006450

        Erratum http://www.ijppsjournal.com/Vol2Suppl3/Erratum.pdf (2010)
        An odd authorship erratum also exists that purportedly left out one author, but then the notice fails to explain what is the actual correct order of authors.

        Corrigendum: http://www.ijppsjournal.com/Vol5Issue1/corrigendum.pdf (2013)
        Another odd authorship issue.

        The originals of all these cases need to be identified. The publisher has removed the names of the authors. But maybe the PDF files can be traced. This open access publisher has problems. Seriously. I have not examined the quality of all papers, but the quality of some is atrocious, i.e., based on scientific quality alone, a lot from this journal should be retracted. So the above retractions refer exclusively to the really obvious ethical violations like copyright violation or duplication. I suspect that the only reason why they are retracting papers here is because they are desperately trying to seek an Impact Factor (see the home page where they are apparently listed on JCR). Securing an IF would secure BIG MONEY as they then would seek to increase APCs (article processing charges). Guaranteed. This has been the “plot” employed by several predatory open access publishers, and others like MDPI. It is this publishing model that is threatening science integrity. There are also so many links between frauds in one journal and others, the web of fraud is complex. Maybe Thomson Reuters might be interested in a parallel web to the Web of Science, the Web of Fraud of WoF. So take note very carefully.

        Someone should contact Jeff Beall about this. Someone should also alert Thomson Reuters about this.

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