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About this Author
DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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August 25, 2014

Citable Garbage

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Posted by Derek

Experimental and Clinical Cardiology used to be a reputable journal. Now it's a trash heap piled with crap. No, literally - the Ottawa Citizen newspaper has proof, thanks to reporter Tom Spears (who's an experienced hand at this). The journal was sold last year, and the new owners will publish absolutely anything you send them, as long as you send them $1200 to their bank account in the Turks and Caicos Islands. I wish I were making all that up, but that is exactly how it goes, offshore banking and all.

Spears whipped together a gibberish cardiology paper by taking one about HIV and doing a find-and-replace to substitute "cardiology" for "HIV" wherever it occurred. I'm sure it reads just fine, if you're high on crack. He stripped out all the graphics, wrote up some captions for new ones, but didn't send any graphs or figures with his submission. No problemo, dude! Paper accepted! As soon as the money shows up under that palm tree in the Caribbean, this junk will become the latest contribution to the medical literature.

The "journal" lists an affiliation with the International Academy of Cardiovascular Sciences in Winnipeg, which organization is pretty upset about that, since there's no connection at all any more. But how to get that fixed? The phone number listed for the editorial office doesn't work. And they don't respond to any emails that they don't feel like responding to, which I'd guess are all the ones that don't involve the possibility of $1200 wire transfers.

The wonderful people behind this scam will ride it as long as a shred of reputation clings to the journal's name, or as long as people send them money, whichever comes first. The journal's web site, which I will consider linking to if they pay me twelve hundred dollars, looks legit, except for the slightly-shaky-English-style notice that "Starting from Jan 1, 2013, Experimental and Clinical Cardiology Journal will operate under new publishing group". If you click "Editorial Board", it tells you that a new one is coming soon. And this part is pretty interesting, too - they say that they provide:

. . .outstanding service to authors through a clear and fast editorial process. Review and decision will be fast and our editorial policy is clear: we will either accept your manuscript for publication or not, our editors will not ask for additional research.

All submissions will be peer reviewed, and our reviewers are asked to focus their attention to data presented in the article. Your manuscript, after the review process can be or accepted or declined. Three independent reviewers are reviewing each manuscript and if two of them accept the manuscript then your work will be published without any further corrections. Note that we will not reject a manuscript because it is out of scope or for its perceived importance, novelty or ability to attract citations: we will publish any study that is scientifically sound.

Yeah boy! But as it says under "Publication Fees", "Open access publishing is not without its costs". One of those costs should be the scientific credibility of anyone who sends a paper in to the place these days. I've looked over the most recent papers listed on the web site - there's one from a hospital in Barcelona, a university in Turkey, an institute in China, some group from Italy whose paper doesn't load well, and a bunch of people with German-sounding names whose paper appears to be two pages long and consists of one figure and no text. An erratum? Who can tell? And who would bother? You might as well copy-and-paste some old Star Wars fan-fiction; no one's going to notice. Every single one of these lead authors probably had their paper turn around within a couple of days, and sent $1200 to the flipping Turks and Caicos without batting an eye, for a journal that's supposedly based in Switzerland. For shame.

No getting around it: if you send money to any of the publishers on Beall's List, you are funding a bunch of scam artists. And if you use such a paper to pad your own c.v., then you've decided to become a scam artist yourself.

Comments (6) + TrackBacks (0) | Category: The Dark Side | The Scientific Literature

July 7, 2014

That Retracted Stressed Stem Cell Work

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Posted by Derek

This article from David Cyranoski at Nature News is an excellent behind-the-scenes look at all the problems with the "STAP" stem-cell work, now retracted and apparently without any foundation at all. There were indeed problems with all of it from the start, and one of the key questions is whether these things could have been caught:

The committee was more vexed by instances of manipulated and duplicated images in the STAP papers. Obokata had spliced together gel lanes from different experiments to appear as one. And she had used an image of cells in a teratoma — a tumorous growth that includes multiple types of tissue — that had also appeared in her PhD dissertation. The captions indicated that the image was being used to represent different types of cell in each case. The committee judged that in both instances, although she might not have intended to mislead, she should have been “aware of the danger” and therefore found her guilty of misconduct. Obokata claimed that they were mistakes and has denied wrongdoing. . .

. . .Philip Campbell, editor-in-chief of Nature, says: “We have concluded that we and the referees could not have detected the problems that fatally undermined the papers.” But scientists and publishers say that catching even the less egregious mistakes raises alarm bells that, on further investigation, can lead to more serious problems being discovered.

Many say that the tests should be carried out on all papers. Christopher says that it takes about one-third of her working week to check all accepted manuscripts for the four journals published by EMBO Press. At Nature and the Nature research journals, papers are subjected to random spot-checking of images during the production process. Alice Henchley, a spokeswoman for Nature, says that the journal does not check the images in all papers because of limitations in resources, and that the STAP papers were not checked. But she adds that as one outcome of this episode, editors “have decided to increase the number of checks that we undertake on Nature’s papers. The exact number or proportion of papers that will be checked is still being decided.”

A complication is that some of the common image manipulations (splicing gel lanes, for example) are done in honest attempts to present the data more clearly, or just to save space in a figure. My guess is that admitting this up front, along with submitting copies of the original figures to the editors (and for inclusion in the Supplementary Material?) would help to clear that up. The article raises another good point - that editors are actually worried about confronting every example of image manipulation that they see, for fear of raising the competence of the average image manipulator. There's an evolutionary-arms-race aspect to all this that can't be ignored.

In the end, one gets the impression that Nature's editorial staff (a separate organization from the News people) very much regret ever having accepted the work, as well they might. Opinion seems divided about whether they could have caught the problems with the papers themselves - this was one of those cases where a number of reputable co-authors, at reputable institutions, all screwed up simultaneously when it came to cross-checking and verification. What remains is a portrait of how eager people can be to send in groundbreaking results for publication, and how eager editors can be to publish it. Neither of those are going to change any time soon, are they?

Update: from the comments, see also this timeline of events for a look at the whole story.

Comments (14) + TrackBacks (0) | Category: The Dark Side | The Scientific Literature

June 30, 2014

The GSK-China Situation Gets Even Weirder

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Posted by Derek

OK, the GlaxoSmithKline/China business has officially crossed over into new territory. Over the weekend, the company confirmed reports that Mark Reilly, the GSK executive in the country who's been in the middle of this affair from the beginning, was the object of a blackmail attempt by unknown parties. (The story was broken by the Sunday Times, and it's behind a paywall, but it's been picked up by every major news outlet).

Someone shot extensive footage of Reilly alone with his Chinese girlfriend, and mailed the resulting file to higher-ups at the company. The connection between all this and the corruption allegations has not been made clear, but the footage apparently accompanied some of the emails accusing the company of bribery. We may never know quite what's going on here, but I'll bet it's very interesting indeed. More on surveillance in China here.

Update: an excellent overview from the BBC.

Comments (36) + TrackBacks (0) | Category: Business and Markets | The Dark Side

June 27, 2014

Varieties of Scientific Deception

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Posted by Derek

Some may remember a paper from 2011 on the "reverse click" reaction, an interesting one where triazoles were pulled apart with mechanical force. This was an interesting system, because we really know surprisingly little, down on the molecular level, about what happens when bonds are physically stressed in this way. What do molecular orbitals look like when you grab both ends of the molecule and tug hard? Which bonds break first, and why? Do you get the reverse of the forward reaction, or do different mechanisms kick in (free radical intermediates, etc.)? (Note that the principle of microscopic reversibility doesn't necessarily apply when the conditions change like this).

Unfortunately, there seems to be trouble associated with this example. Science has an editorial "expression of concern" on the paper now, and it appears that much of it is not, in fact, reproducible (see this report in C&E News).

The paper was from the Bielawski lab at UT-Austin, and Bielawski is reported as saying that a former group member has confessed to manipulating data. But he also says that the conclusions of the paper are unchanged, which is interesting. My guess is that the "unclick" does happen, then, but nowhere as smoothly as reported. Someone may have sweetened things to make it all look better. At any rate, a correction is coming soon in Science, so we should get more information at that point.

This reminds me of the scheme I use to rate political and economic corruption. Stage I is paying someone off to do something they wouldn't normally do (or aren't authorized to do) for you. This happens everywhere, to some extent. Stage II is when you're bribing them just to do the job they're supposed to be doing in the first place. Many countries suffer from institutional cases of this, and it's supremely annoying, and a terrible drag on the economy. And Stage III, the worst, is when you're paying them not to harm you - a protection racket with the force of law behind it. Cynics may adduce examples from the US, but I'm thinking about countries (Russia, among others) where the problem is far worse.

Similar levels apply to fakery in the scientific literature. Here's how I break it down:

Stage I is what we may have in this case: actual conclusions and effects are made to look cleaner and better than reality. Zapping solvent peaks in the NMR is a perfect small-scale example of this - for organic chemists, solvent peaks are sometimes the training wheels of fakery. The problem is, once you're used to altering data, at what point do you find it convenient to stop? It's far better not to take that first step into matters-of-degree territory.

Stage II is unfortunately common as well, and there's a nice slippery path from Stage I that can land you here. This is when you're convinced that your results are correct, but you're having such a hard time getting things to work that you decide to "fake it until you make it". That's a stupendously bad idea, of course, because a lot of great results were never real in the first place, which leaves you hung out to dry, and even the ones that can be finally filled in don't have to do so in the way that you were faking them to happen. So now a real result is tainted by deception, which will call the whole thing into doubt when the inconsistencies become clear. And faked results are faked results, even if they're done in what you might think is a good cause. Many big cases of scientific fraud have started off this way, with someone just trying to fill in that one little gap, just for now.

Stage III, the bottom, is when something is faked from beginning to end. There was no question of it even working in the first place - it never did. Someone's just trying to get a paper, or a degree, or tenure, or fame, or something, and they're taking the shortcut. I think that there are two main classes of fakery in this category. In one group (IIIa?), you have people whipping up bogus results in low-profile cases where no one may notice for years, if ever, because no one cares. And you have IIIb, the famous high-profile cases (see Jan-Hendrik Schön, among too many others) where impressive, splashy, look-at-that stuff turns out to have been totally faked as well. Those cases are a study in human psychology. If you report a big result in superconductors, stem cells, cancer therapy or any other field where a lot of smart, competent people are paying very close attention, you will be found out at some point. How can you not be? We're in Bernie Madoff territory here, where someone comes into work every day of every week knowing that their whole reputation is a spray-painted scrim of deception that could have a hole punched through it any minute. How people can possibly live this way I don't really know, but people do. The self-confidence displayed by this sort of personality is a wonder of nature, in its way. IIIa cases are initiated by the desperate, stupid, and/or venal. IIIb cases, though, are brought on by people born to their task.

Update: as pointed out by several good comments, there are plenty of not-quite-fraud sins that neighbor these. Those are worth a separate post, partly because they're even more common than straight-up fraud.

Comments (53) + TrackBacks (0) | Category: The Dark Side | The Scientific Literature

June 2, 2014

No More Acid Stem Cells

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Posted by Derek

In case you hadn't seen it, the "acid-washed stem cells" business has gone as far into the dumper as it can possibly go. It now appears that the whole thing was a fraud, from start to finish - if that's not the case, I'll be quite surprised, anyway. The most senior author of the (now retracted) second paper, Teruhiko Wakayama, has said that he doesn't believe its results:

The trigger, he told Bioscience, was his discovery—which he reported to Riken a few weeks ago--that two key photos in the second paper were wrong. Obokata, lead author on both papers, had in April been found by Riken guilty of misconduct on the first paper: the falsification of a gel electrophoresis image proving her starting cells were mature cells, and the fabrication of images proving resulting STAP stem cells could form the three major tissue types of the body.

But Riken had not yet announced serious problems with the second paper.

Last week, however, there was a flurry of activity in the Japanese press, as papers reported that two photos—supposed to show placenta made from STAP cells, next to placenta made from embryonic stem (ES) cells—were actually photos of the same mouse placenta.

As with so many cases before this one, we now move on (as one of Doris Lessing's characters once put it) to having interesting thoughts about the psychology of lying. How and why someone does this sort of thing is, I'm relieved to say, apparently beyond me. The only way I can remotely see it is if these results were something that a person thought were really correct, but just needed a bit more work, which would be filled in in time to salvage everything. But how many times have people thought that? And how does it always seem to work out? I'm back to being baffled. The stem cell field has attracted its share of mentally unstable people, and more.

Comments (12) + TrackBacks (0) | Category: Biological News | The Dark Side | The Scientific Literature

May 14, 2014

China Raises the Stakes in the GSK Scandal

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Posted by Derek

GSK's troubles in China have just gotten even more serious. The government has formally charged Mark Reilly, former head of the company's operations in China, of organizing and participating in a bribery scheme. This seems to have been a stronger step than people were expecting - we'll see what happens. Reilly's whereabouts do not seem to be clear to anyone - I would assume that he left China some time ago, but if he hasn't, then he's not leaving for some time to come.

Comments (11) + TrackBacks (0) | Category: Business and Markets | The Dark Side