Open Letter to PLoS Biology – [UPDATE – Plagiarism too!]

Dear editors,

I’m writing to demand that you immediately retract this paper by Mario Saad and colleagues (PLoS Biol. 2011 9: e1001212. doi: 10.1371/journal.pbio.1001212.) due to overwhelming evidence of data manipulation that has been known to you for almost 3 years.

The paper was originally criticized in comments on the journal website in July 2013. In February 2014 I posted these and more problems to PubPeer and PubMedCommons, and forwarded allegations directly to the journal by email. The case was featured in an article in The Scientist in August 2014, and has been widely discussed in comment threads relating to other papers by Mario Saad on the Retraction Watch website. In March 2015, while reporting on a different Saad paper in PLoS One, Retraction Watch asked someone at PLoS Biology to comment. They responded…

The paper you’ve asked about is one that the PLOS Biology team is currently looking into. We can’t share any details and, as is standard, we are not willing to discuss this externally. As you are likely aware, journals have to follow a clear process when investigating issues on papers and at all the PLOS journals we follow the COPE guidelines. Out of respect for both the scientific process, and for all involved, these things take time.

That was over a year ago. Today, 4 more papers by Saad were retracted, thereby disavowing the findings of an internal University investigation, and rebutting a lawsuit between Saad and the American Diabetes Association.

Your continued inaction on this paper is beginning to border on gross negligence. According to ISI Web of Science the paper has been cited 96 times, with more than two-thirds of these citations coming after the initial concerns were raised in June 2013. This is bad for science, and very bad indeed for your journal’s reputation.


Paul S. Brookes, PhD.

P.S. I should note this is not the first time I’ve had problems getting your journal to take action on a problematic paper! That one only took 8 months to fix.

P.P.S. I recently had the good fortune to teach a class on scientific communication, which included a session on how to critique a paper (journal club style). I used this as an example of a spectacularly bad paper riddled with data problems. In publishing this letter, I’m now making my powerpoint slides freely available for teachers in science ethics and other classes to use as an example. I’m not sure this is what you envisaged for this paper, but I think we can agree this was a preventable outcome.

[UPDATE 3/28/2016]

It has just been bought to my attention that, in addition to all of the above figure problems, large sections of the text in this paper are plagiarized from another publication!  The paper in question is this one, and the two images below detail the extent of the copied passages based on a quick look.  There may be more to be revealed, via the use of software…

saad plos plagiat 2 - Copy

saad plos plagiat 1 - Copy

The journal has been informed, although I do not have high hopes, based on zero response whatsoever to tweeting the above letter to both the @PLoS and @PLoSBiology twitter accounts last week.


The self-fulfilling prophecy of a downward trend in retraction delays

As reported on Retraction Watch today, folks interested in the field of publications and retractions are “geeking out” at a new study from authors at Thomson Reuters, who mined the ISI Web of Science database to learn some new things.

Among their key conclusions, based on Figure 1c of the paper, is a downward trend in the time delay between publication and retraction…. ret tend orig

The problem is, such a conclusion is a self-fulfilling prophecy. The study was based on a 2014 version of the database, so for example there cannot possibly be any papers published in 2012 that would have more than a 2 year delay in retraction, because it hasn’t been long enough yet!  Here’s another way to look at the data, with the red line indicating the maximum possible retraction delay for a paper published in that year….

ret trend annotated

Are we to believe that in the coming years, papers from 2005 onward which take 10 years to retract, will simply not arise?  No, of course those papers are out there, and over time they will of course raise the average delay to retraction, of their year’s cohort of papers.

TL/DR – it’s too early to conclude a downward trend.


But, what could be done differently?  Well, they could have taken the average delay for the whole data set (it looks to be about 7-8 years) and just set that as the cut-off, ignoring any data between 2006 and 2014.  In my estimation, doing so would have nullified the conclusion of a downward trend.


The other major issue that impinges on this outcome, is the authors being based at Thomson Reuters, a large publishing conglomerate.  The paper contains no conflict-of-interest statement, but I do find it rather “convenient” that a group of people paid by the publishing industry found a favorable trend in the speed at which the industry deals with problems as they arise.  In my own experience (N=1 anecdote), the delay for publishers to deal with problem papers is either static or has risen recently due to increased workload of this kind.

Spring lab update & musings

First, lots of modifications to the lab website…

  • The personnel page finally got edited to include all the changes we underwent last summer.
  • The publications page is now up to date with all our latest papers (including the Slo2.1 paper that is finally out!)
  • The research page has been edited to provide some more recent details on directions that different projects are going in, and to list our funding sources more accurately.

It’s also been a busy couple of months for travel and other lab’ happenings…

  • Paul spoke at the Gaming Metrics conference at UC Davis, outlining some more recent data from the ongoing study of the impact of internet publicity on retractions/corrections of literature problems.
  • Paul was also at the Oxygen Radicals Gordon Conference, talking about our work on Sirtuins and mitochondrial metabolism.
  • We finally got our new custom antibodies against Slo2.x channel variants, from Aves labs, and are now testing them.
  • A bunch of metabolomics samples went off to Metabolon, so now we’re waiting for a flood of data!
  • Owen is off to the Biophysical Society meeting in Los Angeles.
  • 3 other papers currently in the pipeline, so it should be a good year for publications. (It had better be – we have an R01 renewal going out the door in October!

Coming up…

  • Raul Mostoslavsky (SIRT6 guru) is visiting Rochester next week for a seminar/visit in the cancer center.
  • Steven P. Jones from the Cardiovascular Center at Univ. Louisville is visiting us on April 28th.
  • There’s a new Mitochondrial Meeting announced at NIH campus, this May (these are usually great meetings, and free to register!)
  • Paul’s final (?) stint on the MIM study section this June. Also there’s UMDF grant reviewing in May (we’re always looking for more panel members!)

Finally, there have been quite a few interesting happenings around the web/twitter of late, which deserve to be highlighted…

  • The “Jingmai O’Connor” affair. For the uninitiated, this started out as an interview in Current Biology, in which Dr. O’Connor (a rising star in paleontology) made some disparaging remarks about blogging, along the lines of “those who can’t do science, blog about it“). The ensuing social media melt-down is nicely documented on Leonid Schneider’s blog post, in which Dr. O’Connor was found to have behaved in a totally unprofessional manner, sparking considerable general mockery and a parody twitter account.
  • The Talia Jane incident, in which a millenial English Major wrote a whiny letter to her boss about shitty wages in the SF Bay Area, including not being able to buy bread. She was subsequently revealed on Instagram as a total foodie, with expensive habits such as having bourbon delivered by courier. The responses have been appropriately worded. If you haven’t read Jean Twenge’s book “Generation Me” for a deeper understanding of the millennial phenomenon, it’s a good read.
  • The ASAPBio hashtag on Twitter provided updates on the eponymously named conference, where “influence makers” tried to sell the rest of the life-sciences community on the idea that we should all ignore glamour journals (Cell/Nature/Science et al.) and publish our work instantly as pre-prints. Part of the resistance to this idea is some of its proponents have built careers to date on glam-humping, so who are they to tell the rest of us to give up chasing high impact journals and just do everything open access / pre-print from now on?  Back in the real world, we’re unlikely to find success any time soon in convincing tenure/promotion committees to ignore publication venue as a factor in assessing a candidate’s CV. That’s not to say I’m anti-open access (we have plenty of papers in OA journals), I just think there are currently a lot of barriers to non-BSD labs going full-OA without career consequences for the PI and the trainees.


2016 update – effect of InterNet publicity on correction of the scientific literature

Some of you may recall the events of late 2012 / early 2013, in which an anonymous blog I was running to highlight data problems in the life sciences literature, was rather unceremoniously shuttered by legal threats.

In late 2013, to try and salvage something of lasting benefit to the scientific community out of these unfortunate events, I conducted a post-hoc’ study to see what happened to the 274 papers I had blogged about – i.e., were they corrected or retracted from journals?  As a control group for the study I used a set of 223 papers I had acquired during the course of running the blog, but not yet got around to writing about.

The results, which were published in April 2014 in this PeerJ paper, showed that papers blogged about were acted upon at a significantly greater rate than those whose data problems were kept private.  Specifically, the blogged papers were retracted 6.5-fold more, and corrected 7.5-fold more. Thus, the overall conclusion was that exposure of problem data in a public forum had a large impact on whether the journals/institutions/authors actually chose to do anything about it.

So, why the update?

One of my lingering doubts about this study, was that the private papers were received across an ever-so-slightly later time window than the blogged ones. Specifically, the blogged papers were received June ’12 – December ’12, while the private papers were received November ’12 – January ’13.  Even though the data for the study were collected right up until final submission of the paper in February 2014, there was always the nagging possibility that the private papers may have been acted on less, because less time had elapsed for them. Given sufficient time, would the private papers catch up with the blogged ones?

I think it can now be argued that sufficient time has elapsed.  In addition, the dramatic rise of PubPeer, PubMedCommons, and post-publication peer review in general, means there have been multiple other opportunities for the people who sent me these papers to criticize them on-line by now. So, knowing (as I do) that several of the private papers have indeed appeared on PubPeer, one might predict they’d catch up with the blogged ones?

However, it turns out that my nagging self-doubt was ill-founded. As of today (January 2016) the blogged papers have continued to be retracted and corrected at a much greater level than the private ones!

Specifically, the blogged papers have racked up another 14 errata and 10 retractions in the intervening 2 years, bringing their totals to 61 errata and and 26 retractions (an almost 32% overall rate of action). In contrast during the same period the private papers have garnered another 2 errata and 1 retraction, for respective totals of 7 and 3, or a 4.5% overall action rate.

In other words, over 3 years since the shuttering of the blog, the blogged papers continue to be acted on at a compounded rate that is 7-fold greater than the private papers.

So, the previous advantage (?) conferred to a paper by having been blogged about, seems to have held up over the intervening period.  The private papers didn’t catch up, and while I’ll hesitate to predict they never will, the overall pattern doesn’t show any signs of changing.  Bottom line – exposure works, and perhaps even some kinds of exposure (the snarky blog variety) work better than others.

FYI, I’ll be speaking about these data at the upcoming “Gaming Metrics” conference at UC Davis, next month.

It’s Slo2.1 baby!

We’ve been struggling for more than a couple of years, to find a publication home for our finding that the potassium channel Slo2.1 (aka Slick, KCNT2) is the one in the mitochondrion required for anesthetic preconditioning (APC).  Finally it was accepted last week in Anesthesiology, and should be in press fairly soon. Here are a few key points…

1) Slo2.1 is required for APC. Knockout mice can’t be protected by volatile anesthetics. This establishes Slo2.1 as a novel drug target to protect the heart against ischemic injury.

2) This lays to rest once-and-for-all the cacophony regarding a potential role for Slo1 in APC. There were a LOT of papers linking Slo1 to APC based on problematic pharmacology and the fact that it’s a KCa channel. Slo2.1 is a KNa channel.

3) We can’t rule out that there might still be Slo1 in mitochondria. I do have some issues with the papers published in this area, but even if mito’ Slo1 does exist, it’s not important for APC, as we showed in 2011 (and people still don’t seem to get).