Nature issues Expression of Concern for paper by author who threatened to sue Retraction Watch

Ariel Fernandez, via Wikipedia
Ariel Fernandez, via Wikipedia

Nature has issued an Expression of Concern for a paper co-authored by a scientist who threatened to sue us last year for writing about another Expression of Concern for one of his other papers.

Here’s the “Editorial Expression of Concern” for “Non-adaptive origins of interactome complexity:”

Dr Michael Lynch has indicated that he no longer has confidence in the original data presented in this Letter, and would like to have his name removed as a co-author. Dr Ariel Fernández has conducted his own statistical analysis, firmly stands by the data and has claimed that differences in interpretation are at the basis of this disagreement. Nature’s editors have concluded that it is necessary to alert the readership to this controversy until further clarification is obtained.

The paper has been cited 57 times, according to Thomson Scientific’s Web of Knowledge.

Fernández tells Retraction Watch that he has posted the following “Open Data and Post-Publication Information” in response to the Expression of Concern:

In an addendum appended to the letter on November 26, 2014, the Editors of Nature have upheld the work while pointing to a controversy between the two authors. The paper and its addendum may be found at the url:
http://www.nature.com/nature/journal/v474/n7352/full/nature09992.html
To clarify the controversy issue, I have posted on the web the step-by-step instructions and the code required to reproduce and analyze the primary data and I have also published at the same website the raw data, statistical analysis of the raw data and the resulting interpretation. The information may be found in my tutorial at the url
http://colbas.academia.edu/ArielFernandez/Tutorial-for-Nature-474,-502-505-(2011)
By posting this tutorial, I am fulfilling the open-data mandate (not enforced by Nature at this time) and I am also inviting the readership to generate more information that would shed light on the controversy. Should readers have further questions or requests, they can contact me at ariel@afinnovation.com

It’s not clear to us that Nature has “upheld the work,” as Fernández claims, and it’s not what they wrote in the Expression of Concern. Such Expressions of Concern are often posted when there are questions about whether the data exist at all.

Lynch, who removed the paper from his CV two years ago, tells Retraction Watch:

At this point, I’ll just say this is not a matter of “confidence in the data” or in the statistical analysis or interpretation of the data.

In April 2013, Fernández had a paper in BMC Genomics subjected to an Expression of Concern after

it was brought to the Editors’ attention that the data generated by the first author, Ariel Fernandez, seemed anomalous. One of the author’s institutions found that the data were not reproducible from the described methods, but an investigation by the author’s other institution did not find the data or their interpretation suspicious.

Fernández threatened to sue us for covering that Expression of Concern, and has since posted a document at Academia.edu that claims to be the conclusions of an “in-depth analysis” of the paper. He had earlier claimed in a now-removed post on the same site that the

paper was critically reviewed by a senior faculty member at the University of Chicago at the behest of BMC Genomics. The paper was found to stand on firm ground. The professor found the work to be correct and reproducible. Therefore, the paper will not be retracted and the record will not be corrected.

The senior faculty member at the University of Chicago was, however, Ridgway Scott, with whom Fernandez has collaborated. (A PNAS paper the two co-authored has been retracted for duplication.)

Fernández also had another paper put on hold for concerns over anomalous data, and has corrected the funding sources in several papers, in an apparent attempt to disclaim support from the NIH.

71 thoughts on “Nature issues Expression of Concern for paper by author who threatened to sue Retraction Watch”

  1. I see a pattern emerging. Threaten to try to reduce spread of information, change funding acknowledgements to keep ORI off back. The comment form Lynch, the co-author of the Nature paper speaks volumes, particularly that which is not mentioned.
    There will doubtless be updates to this here on RW!

    1. I’m not sure what you mean. I read Mike Lynch’s comment and found it quite confusing, as he says basically says that the problem is not the data, the analysis, or the interpretation. What else could possibly cause an author to retract his name?

    1. Just use his! Based upon his colorful history of “anomalous” data, “thought leadership,” and legal threats I’m confident that El Hombre Grande will take it as a compliment.

    1. Thank you for the link, wherein we learn that El Hombre Grande believes that the freedom of speech (and perhaps also the freedom of the press) provided by the first amendment to the US Constitution is “a travesty of Constitutional protection.”

      Can this fellow become any more ridiculous?

      1. Can this fellow become any more ridiculous?
        Well, he could write of the “wanton difficulty” of the protein-folding problem… no, wait, he has already done that.

    2. I note that it also includes a link to the blog of Weishi Laura Meng, who twice commented on the Nature piece.

      There’s something about not understanding that <meta> tags are supposed to be invisible that I find to reliably augur over-the-top frothing on the way, and this is no counterexample. In one nice touch, although the comment form states “Address never made public,” she proceeds to do precisely this with a long, one-off pseudonym.

      1. The most amusing aspect of that blogpost, for me, was the three comments — one from a spambot and two earnest replies from Weishi Meng.

  2. RW readers, I hope you can review this and correct me as needed: But isn’t this the first ever Editorial Expression of Concern that that most venerable and august of science journals, to whit Nature, has actually issued!!?

    Was there an EoC for STAP cells? Were there any EoCs for anything, ever, pre-2014?

    Ye scientists; ye researchers; ye grunts chained to the lab bench; ye seekers after truth: It is important to get the facts right before the overly excitable amongst your ranks indulge in wanton, prolonged, and most unseemly celebration. But if, indeed, this be Nature’s first toe in the water regarding EoCs, then is this not anything other than a monster new milestone for PPPR?

      1. No one has yet confirmed here whether or not this is the first EoS for Nature. It might be, but I am not sure, and I really don’t want to get this wrong. If it is, then they are on new ground.

        EoSes are a statement by the journal whereas (as we usually choose to forget here) retractions are traditionally by the researchers and/or their institutes. EoSes can be issued even when there is going to be no retraction by those traditionally responsible for the content of scientific papers. And EoSes can be issued much faster than retractions by a willing journal. There are advantages vis-a-vis retractions for protecting the research community.

        I will defer to no one in my deep cynicism of Nature’s underlying motives and their parasitic business model: But if they are finally making this move, it is a hugely significant step. It would be a belated realisation that they have to do more to serve the scientific community than merely provide their vanity publishing service.

        En passant, is NPG ramping up the costs of their vanity journals for your library this year too, as they have done to us throughout the last several years of economic crisis?

        1. Exactly, there is a good reason Nature leaves it entirely up to authors to retract or not, whatever the accusations. So with this EoC they did their bit for the good of science, now they can forget the Fernandez case and move to other pressing issues. Or do you expect Ariel and his imaginary friends to call for retraction here? About subscription costs: no idea, I am not an active scientist anymore, unfortunately.

  3. The paper and its addendum may be found at the url:
    I followed the link. No sign of any appendum (unless it’s behind the paywall).

  4. Is Ariel Fernández the same as Weishi Meng or Weishi Laura Meng? A couple of blog sites have hinted at this, and certainly trends in comments and criticisms of RW would lend support to this hypothesis.

      1. October 24 and 25 were a busy couple of days at the Wookiepedia, with Fernandez demanding that the entry be removed if he could no longer dictate its contents (having “absolutely no interest in being featured in Wikipedia”);
        followed in quick succession by Doug Larkin Tobias and Liping Laura Meng vouching for the independent existence of Fernandez’s chief cheerleader Heidi / Haydee;
        then by Heidi B herself praising AF, complaining of “harassment and abuse” and threatening legal consequences for “slander, abuse of power and harassment proceeding internally as appropriate and ex-oficio by elevation to the proper Civil Court”;
        and finally by appeals to “Constitutional rights” from Haydee’s alternative IP-only identity.

        All from Buenos Aires IP addresses.

  5. From my viewing of the first post on the “scienceretractions” site, I have been convinced that “Weishi Meng” is actually Ariel Fernandez. Now, with lightning speed, “Weishi Meng” has posted an “interview” with Ariel Fernandez about the Retraction Watch post. Now I have this delightful vision of Fernandez repeatedly switching seats as he obsequiously “interviews” himself. Thank you Ariel Meng, this made my day!

      1. We have it from no less an authority than Doug Larkin Tobias that “Ariel Fernandez is George Clooney, they kind of look alike”.

    1. I asked above, “Can this fellow become more ridiculous?” With this information and the amazing Wikipedia “dialogues,” I now have a clear answer.

      1. The wikipedia Talk page is crying out to be adapted into a stage production. Ideally with John Gielgud voicing all the parts, as in “Prospero’s Books”, but you can’t have everything.

        The legal-threats toys-out-of-the-cot stage is a highlight, with “Heidi B” claiming (a) to be a different person from Ariel Fernandez; (b) to be a pseudonymous admirer; and (c) to have suffered personal defamation and loss of repute from the editorial skepticism at Wikipedia, finishing in lawyeristic posturing identical in form to that favoured by Ariel Fernandez.

        But the opening scenes are not to be ignored, such as the part where an “AriFer” weighs in, claiming to write on behalf of the horde of anonymous entities who had been improving Fernandez’ entry, and explaining that they were all employees of his company, editing it on his behalf to avoid any conflicts of interest or biased viewpoints. Not sockpuppets at all.

        1. The legal-threats toys-out-of-the-cot stage is a highlight

          Indeed. Leaving aside the humdrum failure to understand what slander is (much less the Texas long-arm statute), there’s this:

          “I learned about AF and took interest in his work after I became acquainted with his consultancy work in a patent litigation case in 2011, where I volunteered an opinion outside the Court” (emphasis added).

          Beg pardon? The only sensible way I can parse this is that “she” was standing outside the building while opining. I also can’t find any cases in which Fernandez has actually served as an expert witness, but whatever.

  6. However is the current or potential employer of Fernandez, I do hope they read these comments and ask him a couple of questions about his online activities and his (imaginary) friends Weishi, Heidi, Doug and who knows, maybe even Zaphod Beeblebrox.

  7. Meng’s blog is called “Science Retractions – Restoring a healthy research environment for scientific pursuit.”

    Well, Ariel, there’s one thing you can do that would help improve the scientific environment immeasurably… and it rhymes with ‘design’.

    1. Consider his recent employment history. Who leaves an endowed chair at Rice for a visiting position at Chicago? After that he was briefly employed at another place before now claiming he is “retired” from science a per the Wikipedia talk chain. His only current affiliation is with COLBAS, which seems about as real as his online defenders.

    2. He hasn’t left Science completely; he is still on the Editorial Board of the Journal of Biological Physics and Chemistry (a journal spawned from the “Collegium Basilea” vanity association).

      Not to mention the editorial board of “Metabolomics”, one of the journals from the questionable Omics press.

      His blurb there still cites Rice University as his academic affiliation. It also makes a deal of the fact that in 2007 he edited a Special Issue of Frontiers in Bioscience (consisting of three issues, two of them his own).

      And now he offers expertise as “expert consultant in pharmaceutical patent litigation”. It’s an interesting career path.

  8. Ahh, my good friend “Weishi Meng”, about whom I posted recently

    https://ferniglab.wordpress.com/2014/11/11/my-opinion-pure-bovine-excrement/

    and in return “Weishi Meng” has sent me some e-mails. Unfortunately, these e-mails broke that most robust of instruments, my “Bull-O-meter”, by pushing it beyond its upper design limit. I have ordered a new one at great personal cost, as I have no grants for this. Happily the new instrument has a greater range and it is due to arrive before Christmas. I look forward to pressing it into service.

    He does suggest a most interesting scenario: we publish and we accept everything that is published as infallible. The appropriate retort is “eppur si muove”.

  9. Given this individual’s apparent tendency to create online personas to spring to his own defense, perhaps someone should look into whether he has pseudonymously reviewed his own papers? Obviously that would be an entirely different level of offense than merely posting on Wikipedia under a fake name or interviewing oneself on a blog with a fake interviewer (and – to be clear – there’s no evidence for it at the current time), but it would be consistent with the online MO we seem to be seeing.

    1. Excellent point. Although the likelihood seems vanishingly low that any journal(s) would make such an investigation, perhaps some editors do take their obligations seriously …

      Would it be asking too much to hope that “Doug Larkin Tobias,” “Weishi Meng,” and “Heidi/Haydee Belkin/Belinky” are among those editors?

      1. “perhaps someone should look into whether he has pseudonymously reviewed his own papers”. Excellent idea. However, how do you propose doing that without illegally having to hack into publishers’ editorial accounts or the author’s personal accounts to discover this truth? Assuming that a legal route can in fact be found, would publishers volunteer to check the e-mails and veracity of the “peer” reports that led to the acceptance of his papers? Most likely “no”. If anything, in the absence of a scoop or a leak, the publishers will try to not investigate, or to release peer reviewers’ identities and reports. All under the legal guise of “privacy concerns”.

  10. Put love of nature above personal vanity, and you probably won’t find yourself in a situation like this guy finds himself in.

    Sure, the community is disrespected by this, but it also strikes me as disrespectful of nature itself.

  11. This is clearly a faked interview.

    “WM: Doctor, I heard rumors that you and I are the same person.

    Ariel Fernandez: Well, let’s see. You surely sound quite different from me and I don’t have any Chinese ancestry to speak of…

    WM: Thank you doctor, have a good evening.”

    1. As if having Chinese descent is a prerequisite for pretending to be a Chinese person in a fake interview, hah.

      He’s also masqueraded here before as one “Xi Han Wang” in order to comment that “Dr. Fernandez is a deep original thinker,” among other things.

      1. In addition to glowing comments toward Fernandez, “Xi Han Wang” has expressed great disdain for ORI: http://retractionwatch.com/2013/10/21/marc-hauser-corrects-a-tiny-part-of-the-scientific-record/#comment-14154

        Interestingly, others have suggested that removing NIH from a list of funding sources (as recently occurred with a number of Fernandez articles) is likely to avoid ORI investigation:
        http://retractionwatch.com/2013/10/17/researcher-who-threatened-retraction-watch-with-lawsuit-corrects-funding-source-for-several-papers/#comment-26844

        And for what it’s worth, the list of articles with changed funding includes this potentially problematic one under discussion at PubPeer: https://pubpeer.com/publications/13AD6E4F308D67FBDE961A23EDBA39

        All merely coincidence, I am sure.

  12. Narad
    Appendix 3: “RAW DATA AND STATISTICS (EXCEL FILES)
    FORMAT NOT SUPPORTED BY THIS SITE
    AVAILABLE UPON REQUEST at
    ariel@afinnovation.com

    ” raw data and statistics in Excel” – that alone should be worth of expression of concern for paper with “omics” subject

  13. With regards to the Expression of Concern for Fernandez’ earlier BMC-Genomics paper, commenter Biochimie pointed out the anomalous nature of the data — a central “spine” of data points following an exact error-free linear or curvilinear function, surrounded by a “halo” of data points forming a rectangular distribution around that spine. That is, for a given value of [eta], the Ks[nu] values follow a rectangular distribution centred on a delta-function spike. Almost as if the data had been generated from a theoretical curve, with noise added in a half-assed way.

    In fairness to AF, he belatedly became aware of this feature of his observations, and in 2012 he appended a Reader’s Comment to the original paper:
    http://www.biomedcentral.com/1471-2164/12/604/comments
    — postulating a dual population of buffering regimes, with some genes constrained to conform precisely to the theoretical curve while for others “alternative post-transcriptional regulatory mechanisms participate in the buffering process”.

    “Further studies from my laboratory will be forthcoming to address these issues and classify genes according to their buffering (single or mixed) strategies”. So it’s all good!

  14. A summary of Ariel Fernández papers being discussed at PubPeer (with all publically available information).

    #1
    https://pubpeer.com/publications/13AD6E4F308D67FBDE961A23EDBA39
    Liang H, Plazonic KR, Chen J, Li W-H, Fernández A (2008) Protein Under-Wrapping Causes Dosage Sensitivity and Decreases Gene Duplicability. PLoS Genet 4(1): e11.
    doi:10.1371/journal.pgen.0040011
    http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.0040011
    Han Liang, Wen-Hsiung Li
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
    Kristina Rogale Plazonic
    Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey, United States of America
    Jianping Chen
    Program in Applied Physics, Rice University, Houston, Texas, United States of America
    Ariel Fernández
    Department of Bioengineering, Rice University, Houston, Texas, United States of America
    Ariel Fernández
    Department of Computer Science, University of Chicago, Chicago, Illinois, United States of America
    Corresponding Authors
    Email: whli@uchicago.edu (WHL)
    Email: arifer@rice.edu (AF)
    Competing Interests
    The authors have declared that no competing interests exist.
    Author Contributions
    HL, W-HL, and AF designed the research. HL, KRP, JC, and AF performed the research. HL, W-HL, and AF wrote the paper.
    Acknowledgments
    The help of Anuphap Prachumwat in gene family classification is gratefully acknowledged. We would like to thank the three reviewers for their valuable suggestions.
    Funding: This research was supported by National Institutes of Health (NIH) grants to WHL and AF.

    #2
    https://pubpeer.com/publications/056676E65D0DD70A9728089687BF72
    Subfunctionalization reduces the fitness cost of gene duplication in humans by buffering dosage imbalances
    BMC Genomics 2011, 12:604
    doi:10.1186/1471-2164-12-604
    Ariel Fernández123*, Yun-Huei Tzeng4 and Sze-Bi Hsu5
    * Corresponding author: Ariel Fernández ariel@morgridgeinstitute.org
    1 Instituto Argentino de Matemática “Alberto P. Calderón”, CONICET (National Research Council of Argentina), Buenos Aires, 1083, Argentina
    2 Department of Computer Science, The University of Chicago, Chicago, IL 60637, USA
    3 Morgridge Institute for Research, Madison, WI 73715, USA
    4 Graduate Institute of Biostatistics, China Medical University, Taichung 40402, Taiwan
    5 Department of Mathematics and National Center for Theoretical Science, National Tsing-Hua University, Hsinchu 300, Taiwan
    http://www.biomedcentral.com/1471-2164/12/604
    http://www.ncbi.nlm.nih.gov/pubmed/22168623?dopt=Abstract&holding=f1000,f1000m,isrctn
    Expressions of concern:
    http://www.ncbi.nlm.nih.gov/pubmed/23594279
    http://www.biomedcentral.com/1471-2164/14/260
    Competing interests
    The authors declare that they have no competing interests.
    Authors’ contributions
    AF conceived the work, developed the theoretical framework, collected the data and wrote the paper. YHT analyzed the data. SBH critically assessed the theoretical concept, contributed to the model. All authors read and approved the final manuscript.
    Acknowledgements
    The research of AF is supported in part by funds from the Morgridge Institute for Research (USA) and by CONICET, the National Research Council of Argentina. The collaborative work of AF, YHT and SBH was made possible through a travel award by the National Tsing-Hua University (Taiwan). Discussions with Prof. Michael Lynch and Prof. Wen-Hsiung Li are gratefully acknowledged.

    #3
    https://pubpeer.com/publications/6923CF71EEC91447810DC34AD72623
    http://www.nature.com/nature/journal/v474/n7352/full/nature09992.html
    Non-adaptive origins of interactome complexity
    Ariel Fernández1, 2, & Michael Lynch3,
    Nature 474, 502–505 (23 June 2011)
    doi:10.1038/nature09992
    Affiliations
    1. Department of Computer Science, The University of Chicago, Chicago, Illinois 60637, USA
    2. Department of Bioengineering, Rice University, Houston, Texas 77005, USA
    3. Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    o Michael Lynch
    Contributions
    A.F. and M.L. conceived the project and wrote the paper. A.F. collected the orthologue groups across 36 species with sufficient structural representation, performed the structural analysis and determined the interaction propensities across orthologues.
    Competing financial interests
    The authors declare no competing financial interests.
    Corresponding authors
    Correspondence to: Michael Lynch or Ariel Fernández
    Received 24 August 2010 Accepted 09 March 2011 Published online 18 May 2011
    EOC addendum (the topic of this RW story):
    http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13141.html

    #4
    https://pubpeer.com/publications/5E683F587ACC73DA5F4CAF6C0A67DA
    http://www.annualreviews.org/page/genet/111212-133310
    “It has come to our attention that some key concepts reviewed in the manuscript entitled “Supramolecular Evolution of Protein Organization” by Ariel Fernández (scheduled to appear in Volume 47 of the Annual Review of Genetics) derive from at least one article in the primary research literature currently under dispute due to unsettled anomalies in the data and/or interpretation. Annual Reviews, with concurrence of the review’s author, has decided to withhold final publication pending satisfactory resolution.”

    1. at least one article in the primary research literature currently under dispute due to unsettled anomalies in the data and/or interpretation

      It is over a year since AnnRevGen “withheld final publication pending satisfactory resolution”.

      Are we to infer from the delay that satisfactory resolution is not possible?

  15. One wonders whether Nature’s recent comments about retractions and lawsuits are referring to him, at least in part.

    In addition to this paper, I found it very questionable that one of the two investigations of his BMC Genomics paper was conducted by one of his former collaborators. How is this an unbiased independent investigation?

      1. Yes, well I suspect Weishi Meng is about as real as Haydee Belinky (the name of one of his wikipedia sockpuppets, which is why I post using this name.)

          1. Alejandro Belinky appears to be a real person (one of Fernandez’s former coauthors), but I doubt he actually wrote the review. Sean Sessel is a former PhD student, and Ana Beaven owns a restaurant in Houston. I have no idea who David Plane is. Actually, I do know who David Plane is. He is George Clooney!

  16. An interview between Meishi Weng and Ivan Oransky, or an interview between Ariel Fernandez and Ivan Oransky, moderated by Meishi Weng, would be very useful to clarify all three individuals’ positions. This should also clarify the sock-puppetry concerns, especially the latter option, because then there would forcibly be three individuals in the room.

    1. Hilarious is putting it mildly. Ariel’s…oops, I mean Weishi’s…painfully aggrandizing “report” ends with what might be the funniest line I’ve seen all week: “Dr. Fernandez, come back [to China]. We miss you!”

      I can’t help but be reminded of the great Dan Hicks’ song, “How Can I Miss You When You Won’t Go Away?”

    2. Too bad he didn’t spend as much time generating reproducible data as he does on all this sockpuppetry nonsense. Does he really think the rest of the world is so far beneath him intellectually that we cannot see the truth? For someone who purports to have 151 IQ, he is not so bright.

  17. Not-Ariel has updated all of his newest articles to include images of Ivan, apparently to contrast their looks. Because he clearly has the maturity level of a child.
    http://scienceretractions.wordpress.com/

    He also changed the logo of the blog to 怒, which is the Chinese symbol for “anger”. One would think that 真 (=truth) would be a better choice, but apparently that’s not what “Science Retractions” is about.

  18. No news, in over 6 months? His sock puppet blog is as richly entertaining as always, but I’m surprised we don’t have any news about the many papers that are under investigation.

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.