An accountability problem

In a Times Higher Education article two weeks ago, Paul Jump discussed the current legal threats on post-publication peer review highlighted by “the case of Fazlul Sarkar, a distinguished professor in cancer research at Wayne State University in Detroit [who] claims that anonymous comments posted on PubPeer this summer led to the withdrawal of a $350,000 (£220,000) a year job offer by the University of Mississippi.”

Rebecca Lawrence, Managing director 0f F1000 Research, responded to the above article with a letter entitled “An anonymity problem“, suggesting that anonymous commenting was not appropriate when “scientists’ livelihoods are at stake because of competition for funding and jobs“. Similarly, in an article at The Conversation, Andy Tattersall, Information Specialist at University of Sheffield, presents the fact post-publication peer review may have an impact on scientists as a potential cause for concern.

It should not be a cause for concern. It is normal (but not the norm) that what we publish (rather than the impact factor of the journal in which it is published) and how we respond to critiques of our work, should have an impact on our careers.

The problems in Sarkar’s papers are numerous. The fact that some scientists respond to reasonable criticism of their published work with abuse, legal threats or lawsuits are a clear demonstration of why anonymity is in some cases necessary. Are Rebecca and Andy really suggesting that scientists should not be accountable for what they publish?


Nanostripe controversy in new twist

Simon Hadlington, writing for Chemistry World, reports on our new paper:

A simmering controversy over whether certain nanoparticle structures are merely instrument artefacts has boiled over into a bitter dispute, with a senior scientist alleging that he has become the victim of a personal vendetta, something that is strongly denied by researchers on the other side of the argument.

A significant section of the report deals with such accusations. These are not new. More interestingly, given the very small number of scientists who have expressed a public view on the controversy, it was notable to read the following from Paolo Samori, from the University of Strasbourg:

In my laboratory we have imaged Professor Stellacci’s particles and found that these particles indeed have stripes on them. The images show clear features that are invariant with imaging parameters (scan rate, scan angle, feedback loop, etc) and hence they can ascribe to true tip sample interactions […] (he then goes to discuss power spectral analysis, this is thoroughly address in Stirling et al, e.g. see fig 10)

I would like to invite Prof Samori to share these images “that indeed have stripes on them”, e.g. using FigShare. In the meantime, we can only relie on the published evidence. To my knowledge, the only image of stripy (?) nanoparticles published coming from Samori’s lab is from Biscarini et al and is reproduced below next to stripy nanoparticles from the original 2004 Jackson et al paper.

left from Fig 1a of Jackson et al (2004), right from Biscarini et al (2013)

left from Fig 1a of Jackson et al (2004), right from Biscarini et al (2013), fig 1d

Reactions to this 2013 Biscarini et al were somewhat incredulous:

Mathias Brust: “And yet there are stripes

Quanmin Guo: “Where are the stripes

Philip Moriarty: “The Emperor’s new stripes

The Rights Stuff: Copyright, Scientific Debate, and Reuse; By Damian Pattinson and Cameron Neylon

Damian Pattinson, Editorial Director of Plos One, and Cameron Neylon, Advocacy Director for PloS

We’ve all monkeyed around trying to sort out the ownership of published content. In the scientific community, copyright and its (mis)application in publishing has authors, publishers, and readers grappling with questions of what is legally possible, what is desirable, and what is “allowable” by any particular party.

The most recent example of these challenges can be found in a PLOS ONE article published yesterday by Stirling et al., which focuses on a re-analysis of images used by other research groups as evidence for the creation of “striped nanoparticles”. The scientific controversy is fascinating and has been covered on blogs and in social media, but the copyright issues that cropped up during the paper’s publication process are also noteworthy.

In the study, the authors re-analyzed key results from previous work written up in the literature by other researchers and wanted to share their findings by publishing them, formally adding to the scientific literature on nanoparticles. To provide context and more effectively discuss the data, the authors of the re-analysis included figures (images) from previous studies in their own paper. However, the original figures were published in journals that owned the copyright of all the written content. And here is where we ran into a problem, and one that was far from simple.

Read more at the PloS blog

Looking at Nothing, Seeing a Lot. [Brian Pauw]

Brian Pauw

Today is a day of relief for Dr. Julian Stirling and his eight co-authors (with many looking forward to the response, including Raphaël Lévy). The paper released today opposes ten years of prolific work from a group claiming to have made and observed stripes on the surface of nanoparticles (c.f. Figure 0, Figure 1 in this post). While most of the work revolves around scanning probe microscopy (SPM), small-angle scattering also played a minor role (c.f. Figure 2 and this paper). This, coupled with modern approaches to publication, led to my inclusion in the (otherwise amazing) list of authors. Here is how this came to be.

Find out here

New paper published today: a major turn in the stripy controversy… or a non-event?

The article by Stirling et al is published today in PloS One [I have the privilege of being a co-author]. The publication occurs after several months of delay due to copyright issues (see here, here, here and here); the negotiations between publishers have been hard and the resolution is hailed as a victory for open access.

The paper is undoubtedly an important piece of work. It analyses in exquisite detail the stripy nanoparticle evidence (from the abstract):

Through a combination of an exhaustive re-analysis of the original data with new experimental measurements of a simple control sample comprising entirely unfunctionalised particles, we conclusively show that all of the STM evidence for striped nanoparticles published to date can instead be explained by a combination of well-known instrumental artefacts, strong observer bias, and/or improper data acquisition/analysis protocols.

Why do I ask whether its publication might be a “non-event”?

A preprint version of this article was uploaded to the arXiv nearly a year ago. This arXiv version was the subject of post-publication peer review. This arXiv article remains the article with the highest number of comments on the post-publication peer review website PubPeer (276 comments at the time of writing). The PubPeer thread has over 20 000 individual IP views. Two comprehensive and very supportive reports from PloS One referees reports were shared two months ago.

Given that the article has been in the public domain for nearly a year, validated through super-extensive-peer-review-beyond-anything-that-will-ever-happen-in-a-journal, what difference does it make that it is now officially published in a scientific journal?

First, the final version is not identical to the arXiv version. The most important difference is in the small angle neutron scattering section. This has been improved thanks to the inclusion of a new author, Brian R Pauw… [see how he became involved in this in his latest blog post].

Second, papers remain a career currency as discussed in a previous post (Scientific journals no longer necessary?). I am extremely pleased that Julian’s enormous work is recognized through the publication of this article. I am also very pleased that Predrag Djuranovic is a co-author. He was the first to question the existence of the stripes when he was a student in Stellacci’s group at MIT, and his criticisms, from almost a decade ago, are finally vindicated ‘in print'”.

Third, although it’s been two years since Stripy Nanoparticles Revisited (Cesbron et al) and one year since the release of Stirling et al on the arXiv – and that therefore everyone who needs to know should know that there is no solid evidence for the existence of stripes — articles based on the stripy concept continue to be accepted and published as if none of this had ever happened.  For example, Francesco Stellacci’s group published in ChemComm this year an article where the first sentence of the abstract reads “Scanning tunnelling microscopy studies have found stripe-like domains on gold nanoparticles coated with certain binary mixtures of ligand molecules.” The article was submitted in May 2014 and published in July (PubPeer); it does not cite Cesbron et al nor Stirling et al. This is not an isolated slip of the peer review system: there is also this one in ACS Nano with a nice stripes cartoon in the TOC graphic, accepted in May 2014… and this one in Nanoscale, accepted in April 2014 (PubPeer). Maybe the PloS One publication will carry more weight than the arXiv preprint?

I do hope that this will be not a major turn, but the beginning of the closing of the stripy controversy, 10 years, 35+ papers, and significant public funding, after the publication of Spontaneous assembly of subnanometre-ordered domains in the ligand shell of monolayer-protected nanoparticles. Francesco Stellacci has been given the opportunity to provide a referee’s report on Stirling et al and while he has not allowed us to reproduce his report, we understand that he has submitted a ms to PloS One too. I am today uploading comments and links onto PubMed Commons so that scientists interested by these 35+ articles can easily find relevant post-publication peer review information.

Shocking: France spends money to access the research produced by its researchers

That is pretty much the title of an news article published today in L’OBS avec Rue 89

La France préfère payer (deux fois) pour les articles de ses chercheurs

Au lieu de donner à tous l’accès aux travaux de ses scientifiques – qu’elle a financés –, la France choisit de verser 172 millions d’euros à un éditeur néerlandais. Rue89 dévoile le texte de cet incroyable marché.

The article has a few flaws, but over all, it is good. It clearly points out the incredible margins of publishers and the absurdities of the system in a way not too dissimilar to my recent blog post “Where to publish our next paper? Letter to a group member“.

Now this article has a few flaws. In particular, it puts all the blame on the state and suggests that other countries, in particular the UK, are doing much better. That is far from being the case. In fact, in many countries, including the US and the UK, negotiations with publishers do not happen at a national level which gives more power to the publishers to secure advantageous deals (and there was no transparency until some data were released thanks to freedom of information requests). [Update 11/11/2004: one of the author commenting below notes that their article did not cite the US or UK as positive examples, but the German and the Dutch]

The main error of the article though is in putting the blame squarely on ministers and politicians when researchers themselves have a huge responsibility for the continuation of this system.  This was immediately seen in the responses on twitter as illustrated on this thread (click to see the conversation, many more tweets) where colleagues appeared to rush to the defence of Elsevier’s profits [slight exaggeration/bait, which I hope may lead them to post some comments below].