Wednesday, July 24, 2013

Retractions as references

A reader pointed out an interesting article to me that was published in October 2012 on PLoS:
Investigation of CD28 Gene Polymorphisms in Patients with Sporadic Breast Cancer in a Chinese Han Population in Northeast China by
Shuang Chen equal contributor, Qing Zhang equal contributor, Liming Shen, Yanhong Liu, Fengyan Xu, Dalin Li, Zhenkun Fu, Weiguang Yuan, Da Pang, Dianjun Li
Down in the article there is a statement that is referenced like this:
Compared with rs35593994 ‘G’, rs35593994 ‘A’ may promote transcription of the CD28 gene by the presence of a binding site available for the CCAAT enhancer-binding protein, but not GFI1 (which functions as a transcriptional repressor) [36]. 
Okay, I don't understand a word of this, but I can follow the reference:
36. Rathinam C, Klein C (2012) Retraction: transcriptional repressor gfi1 integrates cytokine-receptor signals controlling B-cell differentiation. PLoS One 7.
Retraction? Are they citing the retraction of the article as a reference for what had been stated in the article retracted? The retraction notice from July 2012 is pretty clear:
The authors wish to retract the article "Transcriptional repressor Gfi1 integrates cytokine-receptor signals controlling B-cell differentiation" by Chozhavendan Rathinam and Christoph Klein. PLoS ONE 2007, 2(3):e306.

After publication of the article, concerns were raised regarding the control bands in Figure 5A, and in particular, whether the bands represent total STAT5. Examination of the original Western blot data revealed that primary Western blot documents were not archived with due diligence. As a consequence, the doubts about the proper representation of the control bands in Figure 5A could not be unambiguously resolved. This course of action is in line with the recommendation issued by Hannover Medical School.
Retraction Watch noted in September 2012 that this was the second retraction for these authors, who often publish together. The retracted paper is listed on a CV of Rathinam's (that may, however, be automatically gathered from the web), but the retraction notice is not there. Klein has neither the retracted paper nor the retraction listed on his CV.

The question asked by my correspondent is: Does anyone actually READ the papers that are submitted to PLoS? It is supposedly a peer-reviewed online journal. Or is there a reason for quoting the retraction notice in this manner that escapes me?

Wednesday, July 10, 2013

The German Pseudodoctors

No, I'm not talking about the current situation, although it is getting bizarrer by the day. Nature published an anonymous editorial today, decrying the anonymous, mud-slinging plagiarism-accusers. Say what? Okay, I put in a comment, don't know that that will help.

I got the year wrong, though. I've got to learn to look up years and not trust my brain. I had the German historian Theodor Mommsen's letters in my head as 1867, but they were in 1876, as Ulrich Rasche noted in "Mommsen, Marx und May" earlier this year. It was also pointed out to me that the law about publishing the dissertation took a few more years.

In 1878 Max Oberbreyer put together a lovely collection of the letters and articles in Eisenach that had been published on the subject: Die Reform der Doctorpromtion - Statistische Beiträge von Dr. Max Oberbreyer. Google has scanned a copy and it makes fascinating reading. One of the articles by Mommsen is also available at Wikisource, Die Deutschen Pseudodoctoren. Plagiarism, as far as the eye can see. And since the end of the 19th century German academia has been discussing what to do.

Interestingly, the DFG published a second press release about the whistleblowing recommendation today. The press release emphasizes that the recommendation was ONLY about the ombud process, NOT about any other kind of scientific discussion:
Der Vorwurf, die DFG wolle über die Regelung zur Vertraulichkeit des Ombudsverfahrens Hinweise auf den Verdacht wissenschaftlichen Fehlverhaltens erschweren oder gar die Wissenschaftsfreiheit einschränken, entbehrt jeder Grundlage. (The accusation that the DFG wants to make it more difficult for whistleblowers to report suspicions of academic misconduct by regulating the confidentiality of the ombud process, or that they want to restrict scientific freedom, is completely unfounded. -- Translation by the author)
The lady doth protest too much, methinks. In the modern sense, not the Shakespearean.

Tuesday, July 9, 2013

Whistleblowing in Germany

The German research council DFG gave their yearly press conference on July 4, 2013. Among other topics, they also presented the 17th recommendation for good scientific practice, on whistleblowing. Since it is not yet available in English, I've taken the liberty of translating both the recommendation and the commentary, then I have some comments. Note that this is NOT an officially accepted translation! Many thanks to Margret Popp for her excellent corrections to the translation!
Recommendation 17: Whistleblower

Academics who give specific information about a suspicion of scientific academic misconduct (so-called whistleblowers) must not experience disadvantages in their own scientific and professional careers. The ombudspersons and the institutions that investigate an accusation must be committed to instituting appropriate means for protecting them. The accusation must be lodged in good faith.


Academics who lodge an accusation about a suspicion of academic misconduct with the appropriate institution perform an essential service in the duty of academic self-control. It is not the whistleblower who voices reasonable suspicion who does a disservice to science, scholarship, and the institution, but the scientist or scholar who commits academic misconduct. For this reason, a whistleblower's accusation must not result in disadvantages for their own  scholarly, academic, and professional careers. In particular, junior academics must not experience setbacks and obstacles during their education, the preparation of their final theses and dissertations as the result of voicing an accusation. This is applies in particular to their working conditions, as well as to possible contract extensions.

The accusations by the whistleblower must be made in good faith. Accusations must not be made without due diligence and without sufficient knowledge of the facts. A frivolous handling of accusations of academic misconduct, even more so for intentional false accusations, can itself be considered a form of academic misconduct. The body that receives an accusation made anonymously must weigh whether to examine the case. In general, a practical investigation needs the name of the whistleblower. The name of the whistleblower is to be kept confidential. Revealing the name to the accused person may be necessary in particular cases however, if the accused is otherwise unable to defend him- or herself. All participants must keep accusations confidential.

The confidentiality is for the protection of the whistleblower as well as the person accused. Before the investigation of an accusation of possible academic misconduct has been completed, it is imperative to avoid rushing to a judgment of the situation (see Recommendation 8, p. 15). It amounts to a breach of the  confidentiality of the process when the whistleblower publicly states a suspicion of academic misconduct without first informing the appropriate university or research institution. The investigating body must decide on a case-by-case basis how to proceed if the confidentiality has been breached. It is not acceptable for a premature publication of a case by the whistleblower to result in a loss of reputation for the accused person.
Not only the person accused of misconduct is in need of protection through the institutions, but also the whistleblower. Ombudspersons and the investigating bodies must provide this protection by appropriate means. Even in the case of unproven academic misconduct, the whistleblower must be protected, if the accusations were not apparently untenable. 

There has been a lot of commentary in German in the past days on the Internet (for German politicians: Neuland,  a virgin territory) and in the media.  Among them:
  • 28 June: Benjamin Lahusen, legal scholar, in his blog, "Gute wissenschaftliche Praxis"
  • 28 June: Sandro Wiggerich, legal scholar, in his blog, "Vertraulichkeit des Plagiats – Die HRK will weniger Öffentlichkeit"
  • 2 July ff: Forum bei VroniPlag Wiki
  • 4 Juli: Oliver Trenkamp in Spiegel Online, "Neue Regeln: Unis sollen anonyme Plagiatsjäger ignorieren"
    5 July: Laborjournal, "Don’t Shoot The Messenger" details a case in which a university did not get active until a case was published
  • 8 July: Peter Strohschneider, president of the DFG in Deutschlandradio Kultur, "Whistleblowing an Hochschulen nicht missbrauchen", including the statement "Sie können selbstverständlich in allen anderen Kanälen der wissenschaftlichen Kommunikation, anonym oder nicht anonym, und außerhalb des Schutzes von Vertraulichkeit Vorwürfe wissenschaftlichen Fehlverhaltens erheben, wenn Sie dafür denn Gründe haben." ("you can, of course, state accusations of scientific misconduct in all other channels of scientific communiation, anonymous or non-anonymous and outside the protection offered by confidentiality" -- translation dww).
  • 8 July: Stefan Hessbrüggen, a historian of philosophy and organizer of a petition about whistleblowing, in his blog, "Die DFG und die Whistleblower, oder: Mein Versuch, eine Empfehlung zu verstehen" and on SWR2, "Ein Maulkorberlaß?"
  • 8 July: Raphael Wimmer, computer scientist, in his blog "DFG-Empfehlung Nr. 17 – eine Analyse und ein Vorschlag"
  • 8 July: Blog "Erbloggtes", "Obmann Schummerlos Reise ins Neuland"
  • 8 July: Hermann Horstkotte in LTO Online: "HRK will anonyme Plagiatsjäger zurückdrängen"
I've probably missed half of the rest of the commentary, as I was traveling. Do drop more links in the comments area if you find them. Now for my comments:
  1. First off, I am very glad that science leadership in Germany is beginning to discuss whistleblowing. However, it would have been better if this had begun two years ago, but better late than never. It is problematic, however, that there are some confusing points in this recommendation.
  2. I am not really clear on what exactly a whistleblower is. Is this just someone who submits a case to a university ombud? Is it a scientist who points out errors in another scientist's paper in a learned journal? Is VroniPlag Wiki meant?
  3. Because of the complicated structure of German universities and research institutions they write "the body that receives an accusation". This is now so unspecific, that many officials could be meant. If I inform a university president (non-anonymously!) about a case now on the home page of VroniPlag Wiki, is the president now the "body"? At many universities it is not trivial to find the ombud for good scientific practice. I usually give up after about five minutes of searching and just write the president or rector. And now this body decides if an "anonymous" accusation will be followed up or not? How long do they have to decide?
  4. Why is the name of the whistleblower important for a substantiated (i. e. fact-based) accusation necessary? A sneaking suspicion is that this is only a problem for people for whom the Internet is, indeed, Neuland. Sure, a written anonymous accusation can't be questioned. But it is trivial to set up a John Smith email account and monitor it for questions. If this is just a technical problem, that needs to be stated. If there are other reasons, they need to be stated as well. 
  5. There is a contradiction about the confidentiality of the name of the whistleblower. First, it is to be kept confidential. Then, the name CAN be released if the accused feels that they can't defend themselves any other way. I'm sure all so accused need the name so that they can defend themselves. This must be made clear from the very beginning, whether confidentiality can be guaranteed. And anyway, universities don't have a good track record at keeping things secret.
  6. If I first write the university and then publish in my blog, I'll be keeping to the letter of this recommendation, won't I? Also if I inform the university and someone else informs the press, that's okay, too? In a collaborative setting there are more than one person involved in documenting scientific misconduct.
  7. If I look closely at this and Peter Strohschneider's comments, it becomes clear to me that VroniPlag Wiki is not affected by this. VPW is not an ombud. It is an additional venue. VPW is one possibility for documenting one particular type of scientific misconduct, plagiarism. At VPW, facts (text portions in published works) are documented; if there are sufficient grounds for publication, a name is named; the universities are informed (non-anonymously) as a courtesy by some of the contributors. If a university says: "case closed" without detailing why the documented text parallels are not plagiarism, it is perfectly acceptable to ask back: why?
I do hope the discussion continues. I found it unfortunate that the wording for this recommendation was prepared behind closed doors. Perhaps it can be made clearer in the near future.

You can still sign the petition, over 1100 signatories at the time of publishing this blog.