PLOS Genetics investigating paper by Ariel Fernandez

Ariel Fernandez, via Wikipedia
Ariel Fernandez, via Wikipedia

Ariel Fernandez‘s list of papers with editorial asterisks next to them grew again this week.

Fernandez has had one paper retracted, two papers subject to Expressions of Concern, including one from Nature, and another put on hold over data concerns. He threatened to sue us for covering one of the Expressions of Concern.

Here’s the “Notice from PLOS Genetics” for “Protein Under-Wrapping Causes Dosage Sensitivity and Decreases Gene Duplicability:”

Please be advised that PLOS is working with the authors on an investigation regarding one or more issues that have been raised with respect to the content or authorship of this paper.

We asked Fernandez for more details. He did not provide any, saying only that the criticisms of the work “have no scientific value” because they were made anonymously:

In regards to this case and the others that you have been covering in regards to my published record, my response remains pretty much the same:  All I know is that the challenger’s comments were made anonymously and were either not subject or did not pass peer review, so they have no scientific value. As a scientist I only address comments or challenges formulated in accord with scientific procedure, emanating from people versed in my subject.

PubPeer commenters did their own analysis of the data in the paper, and found it puzzling.

The paper, which has been cited 31 times, according to Thomson Scientific, had been subject to an earlier correction, in which the authors said the work was not supported by an NIH grant on which Fernandez was the PI. It was one of several papers by Fernandez with similar corrections, leading some to suggest that he made the corrections in an attempt to move any investigations out of the Office of Research Integrity’s jurisdiction.

Update, 10:15 a.m. Eastern, 1/9/15: Co-author Wen-Hsiung Li tells us:

I went to the website and I could not see any issue or comment except the note” Please be advised that PLOS is working with the authors on an investigation regarding one or more issues that have been raised with respect to the content or authorship of this paper.”. I don’t know what investigation you are conducting and I don’t remember any one ever challenged my part of the paper. What I knew is that there was a challenge to the part of the paper by Fernandez and he already responded to the criticism more than two years ago.

Hat tip: Rene Malenfant

65 thoughts on “PLOS Genetics investigating paper by Ariel Fernandez”

  1. To summarize the potential data issues here, these are the data distributions, as plotted by Peer 2 on PubPeer:
    1: http://imgur.com/UWte3QB
    2: http://imgur.com/GPr8s0L
    3: http://imgur.com/S3gHjT5
    4: http://imgur.com/MWqZPeA
    5: http://imgur.com/b0hczZ6
    6: http://imgur.com/dEgqDhk
    7: http://imgur.com/qRLDDDz

    A number are odd, but in particular, I have never seen biological data resembling #1 or #6. It should be noted that these graphs can be generated by using the data in the order given in the Excel files, and as far as I can tell there’s no reason to expect that the data would be ordered to create curvilinear trends.

    1. If this is not peer review (which is by definition anonymous) I do not know what would be. Maybe this guy should be reconfigured and sent back to graduation?…

  2. I can’t wait to read “Weishi Meng’s” take on all this. She, after all, is unquestionably “versed” in all matters Ariel.

  3. From Fernandez’s ppoetic CV on his company webpage (http://www.arielfernandez.net/cv.html): “He got his Ph. D. from Yale University in 1984, the fastest awarded doctorate at that institution. After his Yale graduation, Ariel Fernandez became a scientist at the Max-Planck Institute in Germany under the aegis of Nobel laureate Manfred Eigen, and later on, collaborated with Nobel laureate Robert Huber at the same institution. Until 2011, Ariel Fernandez held the Karl F. Hasselmann endowed chair professorship in bioengineering at Rice University in Houston, Texas. ”
    This and his impressive publication list demonstrates how easily things can go utterly and embarrassingly wrong in academia. Did nobody never ever become suspicious? Was everyone just too eager to believe he was a genius with magic hands?

  4. the criticisms of the work “have no scientific value” because they were made anonymously

    They would have been more scientific if the author had used a sockpuppet pseudonym.

  5. Paper 1
    Journal of Molecular Biology Volume 337, Issue 2, 19 March 2004, Pages 477–483
    Functionality of Wrapping Defects in Soluble Proteins: What Cannot be Kept Dry Must be Conserved
    Ariel Fernández
    Indiana University School of Informatics and Center for Computational Biology and Bioinformatics, Indiana University Medical School, 714 N. Senate Avenue Suite 250, Indianapolis, IN 46202, USA
    http://www.sciencedirect.com/science/article/pii/S0022283604001226#FIG1
    Elsevier

    Paper 2
    PNAS vol. 101 no. 9, March 2, 2004, pp. 2823–2827
    The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity in proteomic networks
    Ariel Fernández
    http://www.pnas.org/content/101/9/2823/F1.expansion.html

    Please compare Fig 1 of both papers.

    There is a PubPeer entry for this:
    https://pubpeer.com/publications/3FE98430D6B3361A9B9523163AA323#fb21050

      1. Note also in Crespo & Fernandez (2008), Fig. 10, in the “entropy-jolt” section that for both the 1 um and 10 um columns, the two experimental conditions (P-C-Kit D816V and C-Kit D816V) have identical bands that differ only in their displayed contrast/level.

        Is it asking too much for Ariel/Weishi/Liping/Laura/Doug/Haydee Fernandez/Meng/Larkin/Tobias/Blinky to provide a plausible explanation? If it is I’ll gladly accept an entertainingly implausible explanation from “Weishi,” especially if it includes irrelevant images of Ivan. 🙂

        1. If I am looking at this correctly, not only has the experimental data been duplicated between the articles, but it has be reused inconsistently. Look at the entries for untreated and imatinib in each case. The gel/concentration relationships have changed between the two papers. I guess cutting and pasting images is as hard as correctly reporting the funding source, meaning too difficult for Fernandez.

  6. did not pass peer review, so they have no scientific value

    Perhaps this equivalence between “peer review” and “scientific value” is why Fernandez is now editing an Omics journal, and promoting his work through Youtube.

  7. Can someone explain the analysis here as though I were a 12 year old?
    I think I get that such clean fits shouldn’t occur in nature, but need some help understanding what has been done here to reveal the issues.
    Thank you for your patience!

  8. Is Wen-Hsiung Li standing by this paper? I find that hard to understand if he has looked carefully at the issues that have been pointed out. From his comments, though, it sounds like he is not concerning himself because it is only “the part of the paper by Fernandez” that has been questioned. Does Li’s part of the paper, whatever that is, have any value if that data is flawed?

    1. That should be Neuroskeptic (o missing). Unfortunately, or fortunately, depending on which side of the stick one is at, Dr. Fernandez shows us the risks of carrying public identities while blowing the whistle. He cements the notion that anonimity is essential. Criticising or commenting openly with one’s true identity is no longer a viable, or safe, option. The anonymous movement is being heavily trolled and criticised, and being made to appear as the arch enemy of truth, even when it reveals the absolute ugly truth.

      1. Apologies to Neuroskeptic for the typo. In fact, anonymity works both ways. One also tends to believe, those who demand anonymity to be banned from PubPeer may be acting themselves anonymously or under assumed names, on PubPeer or elsewhere, the fictional characters Fernandez keeps inventing are just one example. In any case, I post under my real name and am looking forward to “Weishi Meng” and his friends to bring it on.

  9. On “Weishi Meng”‘s page, Ariel Fernandez has his alleged sock puppet say:
    “WM: Yes, they seem to dwell on whether I am a real person or whether you are actually me, or dual realities, or God knows what. Totally immaterial, like asking whether the characters in Plato’s dialogues are real or fake and take away merit if the latter were the case”.
    http://goo.gl/W5BU9L
    Now, this answer to a simple accusation of using a sock puppet of “maybe yes, maybe no, it doesn’t matter” is not professional and infantile. It does matter. I challenge Ariel Fernandez to make the same claim public, on “Weishi Meng” page or RW, which he made in his personal email to me from Feb 15th (s. below). There, it makes one wonder why Fernandez (who threatened to sue RW for alleged wrongdoing) claims to have a obscure female admirer in China (“Why do you think Oransky hates you? (Because you are good looking?)”), yet with a boyfriend “victimized by RW” (sic!). Well, question to Fernandez, “Weishi Meng” and maybe RW, who might this “victimized” boyfriend be?

    “Dear Dr. Schneider,
    I am not related to Dr. Weishi Meng. She is a patent lawyer from China.
    I believe her husband(?) or boyfriend may have been victimized by RW.
    Thanks for your attention and good luck with your research work.
    Ariel

    Ariel Fernandez, Ph. D.

    AF Innovation
    Pharmaceutical Consultancy

    Visit us: http://arielfernandez.net
    ____________________________________
    Disclaimer: I welcome comments on my published research. As a scientist, I shall only address comments that have passed rigorous peer review in a scientific forum where I get the opportunity for rebuttal under the same standards. Ariel Fernandez “

    1. Weishi Meng has now posted another ridiculous “interview” with Ariel Fernandez. Funny how half of “her” articles are about him when she is purportedly unrelated to him in any way and started the blog due to purported victimization of her husband/boyfriend by Retraction Watch.

      If anyone here speaks Chinese, I would love to see a translation of what is written about him in the Baidu Encyclopedia.

        1. Indeed, it is on the one hand funny but also somewhat pitiable, no? Yet somehow his shenanigans continue, and he even has a book coming out this summer.

          http://www.amazon.com/Biomolecular-Interfaces-Interactions-Functions-Design/dp/3319168495

          The author description is his typical self-promoting nonsense and even cites his publications that have been EoC’d. One wonders how much of the book relates to his many discredited works. Maybe Ivan should get a quote about it from Springer or an advance copy to compare with his more questionable papers (there is more on pubpeer about him than has resulted in Retraction Watch posts, go see for yourself.)

          1. It seems impossible for this book to not be infused with “data” and concepts from the EoC and retracted papers, and so it is, as they say, suspect. I nevertheless visited the Amazon site in an effort to determine the book’s contents, wherein I became thoroughly distracted by yet another, entertaining episode of “All My Sockpuppets.” Note in particular the reviews from “Forbes B” and “Ana Beaven,” neither of whom have any other reviews on Amazon yet found the energy to provide breathless praise for both book and author. The review by “Forbes B,” although grandly effusive in the classic style of El Gran Hombre, seems a simple revision of the book jacket description. “Ana Beaven,” however, steals the show. “Her” review, appearing only seven days after the book’s publication date, is entitled “Ariel Fernandez rocks (again) !!!” Why a fourth exclamation point was unavailable is not clear. If, as suggested by a simple Google search, “Ana” truly is the restaurateur from AF’s old stomping grounds of Houston, TX, she deserves some type of Merit Award for Amateurs for being so well informed on the intricacies of theoretical structural biology and protein chemistry.

          2. D Cameron
            It seems impossible for this book to not be infused with “data” and concepts from the EoC and retracted papers, and so it is, as they say, suspect. I nevertheless visited the Amazon site in an effort to determine the book’s contents, wherein I became thoroughly distracted by yet another, entertaining episode of “All My Sockpuppets.” Note in particular the reviews from “Forbes B” and “Ana Beaven,” neither of whom have any other reviews on Amazon yet found the energy to provide breathless praise for both book and author. The review by “Forbes B,” although grandly effusive in the classic style of El Gran Hombre, seems a simple revision of the book jacket description. “Ana Beaven,” however, steals the show. “Her” review, appearing only seven days after the book’s publication date, is entitled “Ariel Fernandez rocks (again) !!!” Why a fourth exclamation point was unavailable is not clear. If, as suggested by a simple Google search, “Ana” truly is the restaurateur from AF’s old stomping grounds of Houston, TX, she deserves some type of Merit Award for Amateurs for being so well informed on the intricacies of theoretical structural biology and protein chemistry.

            The reviews for his first book used the name of one of his former students and a former coauthor. Ana Beaven also gave a review there, using a different account that submitted only one review. Imagine doing all that work to assemble allegedly irreproducible data into a volume, and nobody but alleged Ariel sock puppets liked his book enough to give it a good review. It’s a bit sad, isn’t it?

            In any case, the allegedly fake reviews don’t seem to have helped sales of the book. It came out last year, and Amazon already marked it down to 30% of the original list price. From what I can see, it seems they only sold 8 copies out of their initial stock of 18.

          3. Has RW seen a more persistent sockpuppeteer than Ariel? The level of effort he puts into this grand fabrications is fascinating.

  10. I am not related to Dr. Weishi Meng. She is a patent lawyer from China.
    That is a coincidence; wasn’t Heidi B / Haydee Belinky also a patent lawyer, who met Ariel briefly through litigation, and was so impressed by his charisma as to take on the task of editing his Wpedia entry?

    1. Yes, that is correct. “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.”

      1. Link doesn’t work for me:

        Status: Forbidden (403) – Access denied – unable to verify rights to media.

        Perhaps a subsciption site?

  11. This Ariel/Weishi/Liping/Heidi mélange is at once bizarre, comical and disturbing. While part of me is addicted to following its sporadic update cycle, it must at the end of the day demand some formal expose. But until then…

    1. I feel kind of bad for the people who are having the back-and-forth conversation with several different sockpuppets at once, in the comment section of scienceretractions.wordpress.com . It’s bizarre.

    1. That is amusing. As “evidence” that he is not Fernandez, he wrote “I live and work in Germany”. But he accidentally exposed his IP address, which is located in…wait for it…Buenos Aires, Argentina, home of Ariel Fernandez.

  12. Well its official, spinrade is an arifer sockpuppet, despite all claims to the contrary. On reading the back and forth one can’t but be impressed with the patience and diligence of the Wikipedia editors.

    1. And yet with all the back and forth the self-editing, or more accurately self-promotion, has been successfull, as witnessed not just by the content of his page but also by self-promotional content added to topics such as “solvation shell”.

    2. Also, user WandaLan has been busy editing the spanish wikipedia page for Ariel while also posting on the english talk page. This is ridiculous

      1. It’s sort of amazing, isn’t it? No matter how many sockpuppets get banned, he keeps going on there with the exact same behavior. This is someone purportedly smart enough to publish 350 papers in statistical mechanics and related subjects!

        I suspect it would be helpful if there were other scientists commenting on the talk page, since the wikipedia editors took all his self-promotion nonsense and are lagging on updating the discussion of papers under investigation.

  13. It is all beginning to get a little insidious too, with the mantra that “scientists have papers challenged all the time’. it is not enough that the subject be shown to have done nothing wrong, its also necessary to show that all scientists are either capable or guilty of the same actions. As a fellow scientist I find this behavior most shameful and could by itself damage Fernandez’s reputation more with his peers than the cited EOCs.

  14. I suggest that the WP entry for Ariel Fernandez contain a specific section dedicated to proven cases of sockpuppetry. Since this is not conjecture and directly related to the presentation of information on WP it can hardly be determined as being overly negative content.

  15. So the sockpuppets strike again. Seemingly one WP editor has totally lost the plot, reverting the AF page based on a lack of consensus, a lack that exists due only to hysterical and threatening posts by sockpuppets of the subject. Disturbing on many levels

  16. A different editor seems to have reverted it back, noting that the only dissent is from the AF sock puppets. Still another editor is now battling AF sockpuppets in Spanish. It’s all very surreal and utterly disgraceful.

  17. As the sockpuppetry becomes one of the central aspects of the saga of this character, it should be discussed openly on the main wikipedia entry.

  18. And so it goes. On Jan 22 AF writes in one editor talk page: “Editor Bueller007 has made 70 (seventy) arbitrary changes yesterday to my BLP without seeking any consensus, while he fiercely refuses to add the sentence I requested in the interest of fairness and NPV. I would like to request that the 70 changes by Bueller are reversed until consensus is reached on the matter. I have asked the OTRS that my sentence be incorporated as per the policy that you cite in Talk page. Thanks again. Ariel Fernandez” – while the following day, regarding the exact same content he writes to Bueller007 ” I must say that you have done an exceptionally good job with the BLP. I may not necessarily agree with everything or like what is there but cannot deny that you have been extremely careful and thorough. I doubt there may be other edits of this quality in Wikipedia, where the editor takes the trouble to read professional papers. I regret our earlier differences and apologize for the troubles this has caused. On a positive note, the quality of the final product makes up for the earlier problems. AF”. The appropriate characterization is “Divide and Conquer”.

    1. Google, WordPress and Wikipedia are all blocked in China. It may be the only place on earth where Ariel can leave all his problems behind. Of course, WordPress being blocked in China sure does raise some questions about how Weishi Meng makes her blog posts, doesn’t it?

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