Archive for March, 2013

An issue that regularly raises its head at Retraction Watch is the balance between corrections and retractions. The discussions that follow the excellent posts on Retraction Watch often revolve around the different reaction of journals to data re-use and/or manipulation.

One thing is certain: the reactions of journals are… …uncertain. So the re-use of data and data manipulation (not to be confused with data analysis, please), either within an article or between articles draw an inconsistent response.

Just to take some examples.
1. A recent case, described in a post on Retraction Watch, where data from fig 1a were re-used in fig 3 of the article in the Journal of Molecular Medicine, resulted in a retraction. Note that although the precise details are obscure, it was the authors who requested the retraction.

2. Serial image manipulation in the Journal of Biological Chemistry resulted in a substantial correction. In this instance the authors were subjected to an “investigation” (my quote marks) by their institution. This was instigated by peers publicising on the internet multiple instances of such image manipulation across several publications by these authors. The authors were not charged with misconduct by their institution. They now appear to be trying to clean up their record retrospectively. Judging from comments at various blogs, including under the Retraction Watch post, it would seem that not many of their peers agreed with the exoneration or with the retroactive clean up.

3. A Journal of Biological Chemistry article was retracted for image manipulation. The difference with the case above? The U Wisconsin researcher responsible was investigated for misconduct and formally found guilty. Then the paper was retracted.

3. A recent case in PNAS, which I posted on earlier, involved the reuse of data from one experiment in a previous Nature Materials paper, for a completely different experiment in the subsequent PNAS paper.
This earned the authors a correction: they substituted a new figure, which one assumes now actually has some bearing on the experiment described in the PNAS paper.

4. The after shocks of the Melendez scandal are a gradual retraction of his papers: now standing at nine, with this latest one for “Data presented in this paper have been manipulated digitally. Figures shown in this article have been replicated in other papers depicting different experimental conditions

I could go on, trawling the pages of Retraction Watch. There do seem to be some themes emerging.

First, if the authors request a retraction they get it. As I noted in a post a while back, there are some outstanding scientists who, when they get it wrong (we all make mistakes), take the simple step of retracting the paper. In other cases, where some form of misconduct has taken place, the authors occasionally request a retraction. Perhaps in such instances the institution has slapped their wrists hard, or they had failed to properly train an inexperienced member of the team regarding what is and what is not appropriate.

Second, if a researcher is formally found guilty of misconduct, then the papers start to fall, but not all of them, one should note. More than 18 months after the Melendez fraud came to light, only nine papers have been retracted. Diederik Stapel’s count is up to 50. In part, the slow rate of retraction may stem from the time it takes to go through each paper and establish the truth beyond reasonable doubt.

Third, corrections are issued, even when data are re-used for different experiments and that appears to be the end. In such cases there has often not been a publicly acknowledged investigation of misconduct, though I would note that the peers are generally unimpressed and there are continued calls for action on other parts of the research team’s oeuvre. For example, see comments at Retraction Watch under Case 2.

Fourth, the level of defensiveness of institutions, journals and authors, with respect to their reactions to clear evidence of data re-use and data manipulation, is quite astounding. Astounding, because we are engaged in science. One of the reasons we are employed is because we ask questions. This does not fit with defensiveness. Never did, never will.

With reference to this last point, we should note that once again science is becoming a small village. While the days when the world’s entire molecular biology community could meet at Cold Spring Harbor are long gone, the internet and social media bring back important elements of that time. We can all fit into “one room” albeit a virtual one, with many conversations happening simultaneously. This leads to far greater public scrutiny of scientific output (aka papers). While no one can read every paper, someone, somewhere has read your paper, very, very carefully. If there is something they are unhappy about, we will all know about it in due course.

This leads to self-evident conclusions. You publish BECAUSE people want to hear about your work and they will read your paper. Some will read it very carefully, so if you have got something wrong it will come to light. Defensiveness, silence, summoning the self-righteous shield of peer-review is more damaging than coming out into the open.


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I have just spotted a correction to A. Centrone, E. Penzo, M. Sharma, J. W. Myerson, A. M. Jackson, N. Marzari, and F. Stellacci, Proceedings of the National Academy of Sciences, 2008, 105, 9886–9891.
To quote:
Correction for “The role of nanostructure in the wetting behavior of mixed-monolayer-protected metal nanoparticles,” by A. Centrone, E. Penzo, M. Sharma, J.W. Myerson, A. M. Jackson, N. Marzari, and F. Stellacci, which appeared in issue 29, July 22, 2008, of Proc Natl Acad Sci USA (105:9886–9891; first published July 10, 2008; 10.1073/pnas.0803929105).
The authors note that Fig. 1 appeared incorrectly. The scanning tunneling microscopy image shown in the left inset has been replaced. The corrected figure and its legend appear below. This error does not affect the conclusions of the article.

Updated 3 November 2013

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The latest posting on Raphaël’s blog is the most comprehensive catalogue of data re-use in the papers by Francesco Stellacci on the phase separation of ligands on gold nanoparticles into stripes. As Raphaël notes, this information has been communicated to the Ombudsman of EPFL.

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The tension between peer-reviewed publishing and the reaction to papers once published in blogs, tweets and other internet media has come to light in comments on my postings on the stripy nanoparticle debate. This led me to post on the subject, “blogs and science“. An article on the last moves in the debate on the claims of DNA with a sugar-arsenate backbone by Rebecca Rosen last July. provides ample evidence for the importance of such debate. Note that the authors of the original flawed study stayed firmly behind the “wall” of the publishing process, stating that blogs, tweets and other media were not appropriate routes for scientific discourse.
Historically, science has spent more time engaged in various forms of informal discourse (letters, lectures, sometimes heated) than restricted to the sole channel of the peer reviewed literature.
In any event, Rebecca Rosen’s article is well worth reading.

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An excellent discussion has started on this Retraction Watch post on Brian Deer’s proposals to make life more difficult for dishonest researchers.

Retraction Watch

brian-deer-d-fullBrian Deer’s name will no doubt be familiar to many Retraction Watch readers. Deer, of course, is the award-winning investigative reporter known for his reporting on numerous medical issues, including Andrew Wakefield’s now-retracted research into autism and vaccines.

Deer is giving a talk next week at the UK’s “Evidence Live” conference,and has a proposal that he hopes will make it more difficult for dishonest researchers to hide their misdeeds — and make it easier for journals to retract fraudulent papers. He has expressed concern before that voluntary codes have no teeth. Deer is proposing an amendment to the ICMJE’s Uniform Requirements for the Submission of Manuscripts to Biomedical Journals:

View original post 70 more words

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either go through the ABG website, the University of Liverpool website or contact Dave Fernig directly.

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I have had time to ruminate. After I finished painting the walls of the bedroom, I indulged in some complex polymer chemistry with my eldest daughter – aka her first stab at a sponge cake.

What struck me after just a few brush strokes was a simple question. Who instigated the correction? The correction is extremely opaque. It just says “The error…“. Where, at what stage of the submission/production process, by whom?

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A number of events are worthy of a post, but the most urgent to bring to my readers’ attention is a development at Nature Materials. They have issued a correction to the 2008 paper by Francesco Stellacci, Nature Materials 7, 588 – 595 (2008). Thanks to Pep (despite stating he would no longer comment on this blog) for pointing this out in a comment on my blog entitled “Responses-to-evidence-of-self-plagiarism“. I have raised the issue of data re-use multiple times (no pun intended!) including these posts:

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Raphael notes in a post today on his blog entitled “On my [Pep Pàmies] comments on Lévy’s blog” that the apologia written in a private capacity by Pep Pamies, an editor at Nature Materials has been removed. A cached version has been unearthed and is posted for the record on Raphael’s blog.

To recap, Pep had been defending the data of Francesco Stellacci supporting the separation of ligands on nanoparticles into stripes; he eventually revealed himself to be an editor at Nature Materials, which surprised many and angered a few. As I commented earlier, one aspect I found worrying was the fact that Pep was not taking a strong line against data re-use.

So why the disappearance of his comments? My own speculation is that some giant has awoken from a deep slumber to find annoying disorder in his (or her) castle. As various fairy tales teach us, in such situations (quite common in fairy tales) giants tend to react somewhat violently towards anyone unfortunate to be within striking distance. We should not forget that giants have quite a long reach – that is why they are giants, after all!

Of course it may not be a giant – dragons, I understand from my reading of wise tomes such as Farmer Giles of Ham and The Hobbit, have similar tendencies as giants. Plus dragons can fly, so their reach is greater than that of a giant.

Nevertheless, I remain confident, perhaps over confident, that giants are only so big, dragons can only fly so far and that the world is far larger than their reach. The consequence is that there will always be a safe haven for information. After all, history teaches us that the movement of information out of the reach of an irate giant or dragon has been critical in preserving open debate and democracy and, hence, science. Indeed, the unexpected (temporary) disappearance of information often only serves to stoke the curiosity of Homo sapiens.

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There is a most revealing guest post on Raphael’s blog by Philip Moriarty, from the University of Nottingham entitled “Request for raw data: author’s and editors’ responses“. Philip Moriarty has apparently been trying to obtain some of the raw STM data of nanoparticles with stripy ligand shells since mid December from Francesco Stellacci.
Without success.
In his guest post, Philip Moriarty details the stonewalling from Francesco Stellacci and the editorial responses to his subsequent requests to the journals. This paints a rather disturbing picture. Funding agencies generally require that data be shared and certainly be available for a number of years, as do journals that subscribe to COPE guidelines. If the STM images that have been published by Francesco Stellacci do indeed support the formation of stripes on nanoparticles, then surely there can be no issues with sharing the raw data to allow others to analyse them? Indeed, giving such data to an SPM specialist might even generate further publications. Unfortunately, if there is nothing intrinsically wrong with the data and the ligands do indeed form stripes on nanoparticles, the refusal to share data to the point at which recourse has to be made to the journal editors (who can do no more than request the data) can only lead the onlooker to a rather dark conclusion. This conclusion is perhaps best summed up by Marcellus’ words in Hamlet, Act 1, scene iv (line 90 in the link) “Something is rotten in the state of Denmark“.

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