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).


Single use website privacy in academia

It’s grad’ school admissions time again (yay!) which means I’m knee-deep in requests for letters of recommendation. Just as an example, one student has requested letters for 7 different institutions. Writing the actual letters is not a big deal (hey Nick you owe me a beer!) but the websites some Universities use for admissions are a royal P.I.T.A.

One such website (used by a mid-size college in that big metropolis near Cape Cod MA) is “LiasonCAS“.  The premise seems rather innocent and simple at first – the University uses such a site to coordinate the upload of application materials, so nothing gets lost along the way, and presumably this saves a lot of collating work that would have previously been done by a grad’ school administrator. The problem is, there are hundreds of these sites, all commercially operated, and all requiring their own User ID / Password combination.  This creates 2 problems…

Problem 1 – too many passwords

I’m a strong believer in never using the same password twice, hence my reliance on the open source KeePass application, which stores passwords (typically random strings of 20+ characters) in an encrypted file. All told, I have 200+ unique log in IDs. Just to emphasize the size of the problem here, I recently consolidated my logins for Elsevier journals into a single user ID, and it broke the portal set up to do this. It turns out I had reviewed for 37 separate Elsevier journals over the years, and some extensive ‘phone tech support was required to give me a single account to manage them all.

So the problem here is do I really want to register for yet another website, create a unique user ID, have all my contact info’ out there in the cloud?  Am I ever going to use this website again?  Probably not, which means it’ll just sit there waiting to be hacked a decade from now, resulting in a bunch of spam and junk-mail or ‘nuisance phone calls. Over the years, on top of the 200+ login UN/PW combo’s mentioned above, I would guess I’ve accumulated at least that number again in single-use website visits.  This is not good for security.  And no, it’s not as simple as me going to the trouble of making another 200+ unique UN/PW combos for all these sites. I don’t want a KeePass database filled with junk.

Problem 2 – Draconian privacy policies

Like most admissions portals, the one mentioned above requires that you agree to their privacy policy as a condition of signing up for the privilege of submitting materials.  Most people breeze through these things when signing up for a site, which is no big deal if you’re going to use it regularly and it’s a necessity for your job. Apple’s iTunes EULA is notoriously squirrely about privacy issues, but if you wanna use an iPhone, deal with it.

However, in the case of a single-use site, these policies need a bit more scrutiny. What exactly are you agreeing to, for this one-time use?  Here’s the section from LiasonCAS’ policy on what they (the site owner and the University by extension) can do with your information. There’s a bunch of guff about using your contact info’ for contests, surveys and promotions, which is worrying in itself. But then there’s this:

3.10. Other Uses. In addition to the uses specifically identified in this Section 3 (Our Uses of Your Personal Information), we may use Personal Information you submit in any other manner we reasonably deem necessary in order to provide you with the information, products and services you request from us….

Essentially what they’re saying here, is they can do what the hell they like with your data, so long as they can write it off as “necessary” for the service you request.  What you’re requesting of course, is the privilege of uploading stuff for admissions. And the price you pay is them having the freedom to shill your data out to their spammy partners under the guise of necessity.

This is not cool.

So what to do instead? In this case I found the email address of the Dean for the graduate school in question, and emailed them the letter directly. Sure, it took another 5 minutes but at least all my personal contact info isn’t sitting out there on some nondescript company’s website waiting to be sold.

New Year’s Resolution for academics – fight the requirement to create a new User ID / Password for any website that you know you’ll probably never use again.


A cluster of chlorination… our latest paper in AJP Heart

Our paper on autophagy is finally out in AJP Heart. It’s essentially the story of a follow up on a high throughput screen we did several years ago, to find molecules that protect cells (and hearts) from ischemia-reperfusion injury.

One of the hits was the molecule cloxyquin, an 8-hydroxyquinoline with striking structural resemblance to another drug, clioquinol. The latter has been proposed to stimulate autophagy, and also causes mitochondrial uncoupling (it’s also known as “chinoform” in the older literature). Notably, Roberta Gottlieb’s group has shown that stimulation of autophagy occurs in ischemic preconditioning, and it’s also known that mito’ uncoupling stimulates autophagy.

So, we hypothesized that the protective effect of cloxyquin might also be due to mito’ uncouping stimulating autophagy.  First we showed that cloxyquin, like its cousin clioquinol, does indeed uncouple mito’s. It also stimulates autophagy in cardiomyocytes (for this we made cells from GFP-LC3 mice). We also showed that cloxyquin is protective in an in-vivo model of IR injury.  Lastly we showed that protection by cloxyquin could be blocked by the autophagy inhibitor cloroquine.

Cloxyquin, clioquinol, chloroquine, what a cluster!

An important thing we learned during this work, is that combining an autophagy activator and inhibitor in-vivo is not a good idea. Apparently this is well known in the field, but not to us…. when you stimulate autophagy and inhibit it at the same time, things go downhill very fast (aka the mouse drops dead).  We learned about this verbally at a conference but I can’t find a reference in the literature for it.  I guess nobody likes to report when experiments don’t go as planned.

Another key thing we learned during the review phase was that drugs can often be had from obscure suppliers for less money.  Specifically, we had argued in early reviews that doing a complex series of experiments using Bafilomycin A1 (another autophagy inhibitor) would be prohibitively expensive, because the drug is $150 for 10 micrograms, and we would have required several thousand dollars’ worth for this experiment.  A reviewer kindly alerted us to the same drug from $198 for 5 milligrams from LC Biosciences. Literally, 500 times more drug for about the same price!  The experiment ended up not working out anyway, so is not lost to the ether (aka figures for reviewers only), but it’s always good when a reviewer offers to help out in this way with practical advice rather than just crapping on your work.

Finally, does this get us any closer to a therapy for MI?  Probably not, because the protection by cloxyquin is prophylactic – we need to guess who’s going to have a heart attack and load them up with drug. Not easy from a clinical perspective. BUT – cloxyquin does appear to be an interesting tool compound.  If you’re looking for something other than rapamycin to stimulate autophagy then give it a try (and no, we haven’t tried to see if it extends lifespan yet)!

Moving forwards, we’ve recently done another screen with a more relevant cell type and adding drugs at the moment of reperfusion (equivalent to delivery during percutaneous coronary intervention in the cardiac catheterization lab’).  This has yielded some very interesting hits which we’ll be reporting on soon.

Kudos here goes to Jimmy Zhang, MD/PhD student in the lab who led this project (and who also BTW just passed his PhD qualifier exam last month). Congratulations Jimmy!


Punching down; In defense of PubPeer

Today marked a new low in the depths to which publishing industry will sink to maintain their outdated business model.  I’m talking about a piece of literary detritus entitled “Vigilante Science” published in Plant Physiology and penned by its editor in chief Michael Blatt. It’s a classic punch-down piece from a journal editor having a hard time coming to terms with the death of the publishing industry as we know it.

Readers of this op-ed masquerading as serious discourse will rapidly learn that the popular post-publication peer review portal PubPeer (8 Ps – count em!) is a mere “by-product of the social media age”. Straight away, he starts out dissing it as side-issue, as opposed to what it really is – a potential solution to a rampant problem foisted on academia by multi-billion dollar publishing corporations (one of which he happens to work for).

Readers are then treated to (wait for it…) the two-fold problems with PubPeer…

Problem 1 is simply stated as “Most commenters take advantage of the anonymity afforded by the site in full knowledge that their posts will be available to the public at large”.  There is no further attempt to explain why this is a problem, we’re just asked to assume that it is.

Problem 2 is stated bluntly as “The vast majority of comments that are posted focus on image data (gels, blots, and micrographs) that contribute to the development of scientific ideas but are not ideas in themselves”.

After stepping back from my monitor to avoid spitting coffee at it, I read that sentence again, and have read it several times since, and I can’t even begin to understand how someone purporting (pretending) to be a scientist could think in such a way?

To borrow another of Dr. Blatt’s phrases – “Let’s not mince words”.  What we’re talking about here is the editor of a major journal, claiming that problems with data are not a big deal, as long as the underlying ideas are OK.  Hopefully I don’t need to explain how dangerously at odds with the scientific method such a viewpoint is (hint – it’s all about the data; anyone can have ideas, but without data to support them, ideas are worthless).

Taken together, the two-fold problems (anonymity and mostly petty issues with figures) pose fundamental paradox:  If PubPeer is really as unimportant as he claims it is, why bother with an editorial such as this?

The good Dr. Blatt’s justification for his tirade against commenters who have an eye for dodgy data, is that “no journal club I ever organized or contributed to was so obsessed with the minutiae of data presentation”.  My only response can be to suggest he find a better journal club!

The article moves on with a series of poorly informed opinions. Take for example this gem…

“While there is no danger of public embarrassment for the commenter, likewise there is no opportunity to gain from a personal exchange with the author.

Does Dr. Blatt even consider the possibility that many commenters on PubPeer have already exhausted the polite channels he espouses?  Does he consider the fact that when confronted with problem data, many authors simply ignore, obfuscate, or go on the offensive (often hiring lawyers)?  The opportunity to interact with authors is presented as a panacea, failing to acknowledge the reality that such interaction is often fruitless.

He continues…

What is the rationale? Given that the majority of comments show the most petty kind of scientific criticism, can there be any doubt that the intent often is to pillory”.

Does it even cross his mind that a possible motivator might be the integrity of the scientific record? Does he stop to think that commenters may be tired of trying to compete with cheats?  No, it’s far easier to write it all off as a bunch of disgruntled scientific competitors whose sole motivation is the satisfaction of tanking someone’s career!  To put it mildly – many of us have bigger fish to fry (i.e. our own science).

This little gem seeks to put pre-publication peer review (i.e. the bread-and-butter of his journal) on a podium, somehow better than post-pub…

“I accept that there is a case for anonymity as part of the peer-review process. However, the argument for anonymity in postpublication discussion fallaciously equates such discussion with prepublication peer review.”

Given that many of the cases on PubPeer have found problems that should have been discovered during pre-pub’ peer review, there is a strong argument to be made that post- review is not only equal to pre-, but better!  Considering that both exercises are conducted for free, but the only one making a profit on the back of free labor is the pre-pub’ variety, perhaps we should equate them by paying people for post-pub’ peer review?

It goes on… he sides with Hilda Bastian in espousing “the importance of assessing whether commenters are outside their areas of expertise”.  This is a classic prat-fall of the entitled.  I’ll re-phrase it into plain English – Your opinion only counts if I deem you important enough to have an opinion.  Witness this discussion between myself and a senior scientist on PubPeer, in which my scientific credentials were considered as a topic worthy of discussion, instead of the actual data in question.  Quite simply, there are no rules regarding who is qualified to comment on science. Anyone who claims otherwise is engaged in protectionism/racketeering.

He then adds this beauty…

“So, whatever the shortfalls of the peer-review process, I do not accept the argument that it is failing, that it is a threat to progress, or that, as scientists, we need to retake control of our profession. Indeed, if there is a threat to the scientific process, I would argue that, unchecked, the most serious is the brand of vigilante science currently facilitated by PubPeer.”

So let’s get this straight – the problems facing science today are not: (i) a lack of funding,  (ii) rampant fakery, (iii) politicians seeking to defund things they don’t like, (iv) inadequate teaching of the scientific method in schools, (v) proliferation of the blood-sucking profiteering publishing industry, (vi) an obsession with impact factor and other outdated metrics, (vii) a broken training to job pipeline in academia, (viii) insert your favorite #scipocalypse cause here.

No, the #1 threat to science right now is vigilantes on PubPeer! Of course… if only we could just get rid of the idiots on PubPeer, the most serious threat to science would disappear and we could all go back to living the high life!  Sign me up!

He then issues a dangerous call to action…

“I urge scientists publishing in Plant Physiology and other reputable scientific journals not to respond to comments or allegations on PubPeer”.

My only suggestion here would be to ignore this “advice”, unless of course you plan on a long and protracted series of legal challenges or online battles, resulting in an institutional investigation and your eventual firing.

The way that “real” scientists respond when their data is questioned, is to answer the damn question!  Show the data. Produce the originals.  In case you hadn’t noticed, the front page of PubPeer cycles once every 3-4 days – if there’s an innocent explanation, you WILL be vindicated and your career will not end if you engage with the commenters.

To cap it off, in the ultimate punch-down, Dr. Blatt accuses the founders of PubPeer of unmasking themselves solely for the purpose of making money. This neatly sidesteps the huge amount of personal resources they poured into the enterprise from the beginning, and of course ignores that they will not gain anything personally from this new effort, because the organization is a 501c3 non-profit foundation.

It takes an exquisite amount of hipocrisy, to speak from the bully pulpit of an entitled publication, part of a multi-billion dollar enterprise, punching down at a non-profit foundation, and accusing it of being money-hungry.  The only possible motivation I can think of for this Op-Ed, is an editor and an industry witnessing the slow decentralization of their control over information (for massive profit), seeking to discredit an upstart grass-roots organization that might disrupt the status quo.

What a sad sad display of the death throes of an empire.

Such events usually do not end in the emperor’s favor.