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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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In the Pipeline

« Outcomes, Expensive Outcomes | Main | Low Energy Records »

December 6, 2013

Shop Up Some Gels For the Paper

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Posted by Derek

There have been many accusations over the years of people duplicating and fudging gels in biology papers. The Science-Fraud.org site made quite an impression with some of these, and there are others. But as in so many other fields, manual labor is giving way to software and automation.

Nature News has the story of an Italian company that has come up with an automated way of searching images in scientific papers for duplication. The first scalp has already been claimed, but how bad is the problem?

Now midway through the analysis, he estimates that around one-quarter of the thousands of papers featuring gels that he has analysed so far potentially breached widely accepted guidelines on reproducing gel images. And around 10% seem to include very obvious breaches, such as cutting and pasting of gel bands. Some journals were more affected than others, he says. Those with a high impact factor tended to be slightly less affected. He plans to publish his results.

I'll be happy to see the paper, and glad to see this sort of technique applied more broadly. I wonder if it can be adapted to published NMR spectra?

Comments (21) + TrackBacks (0) | Category: The Dark Side | The Scientific Literature


COMMENTS

1. a. nonymaus on December 6, 2013 11:56 AM writes...

This could explain a lot of the irreproducibility that has been previously commented on if the literature is this full of "making it up". However, I am curious to see what tests have been done on Bucci's algorithm to determine its false positive (and false negative) rate.

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2. Piacere on December 6, 2013 12:31 PM writes...

Here is a link to gels in 2 papers. Color coded arrows show identical bands in the two.
http://www.giornalettismo.com/wp-content/uploads/2013/10/test-truccato-cellule-cancro.jpg

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3. Kazoo Chemist on December 6, 2013 1:04 PM writes...

Reverse image searching works pretty well on the internet. This wouldn't identify cases where an image was "cut up and rearranged" in Photoshop, but it should find duplicates.

TinEye is a pretty good reverse search engine.

http://www.tineye.com/

For example, if you search on the "2002 Model" picture of Derek it returns hits for this site, as well as links to articles in The Laszlo Letter and ar seekingalpha where Derek's picture appears.

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4. Dietmar on December 6, 2013 1:33 PM writes...

How hard would it be to write a piece of software that can produce an NMR spectrum or a gel with desired characteristics from scratch? Experimental noise is not that hard to reproduce.

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5. Anonymous on December 6, 2013 1:57 PM writes...

Soon the world will be driven by two kinds of software in an evolutionary arms race: one that makes up results, and the other that detects them.

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6. lazybratsche on December 6, 2013 2:28 PM writes...

If I'm reading the Nature News article correctly, the quote that Derek posted isn't quite as horrifying as it seems at first glance. The news piece seems to say that this analysis was done on a subset of papers published by Italian scientists that have collaborated with scientists with retracted papers.

In other words, it's not as bad as "25% of all blots are fraudulent".

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7. dave w on December 6, 2013 5:00 PM writes...

Seems like high schools have been doing something like this for a while now: it's my understanding that many now require students to submit their term papers electronically via online services such as "turnitin.com", which purport to automatically check for things like text duplicated from "stock" papers available on the internet.

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8. Wow chemist on December 7, 2013 9:54 AM writes...

@4 you don't even need to do that. Seems when looking at the image one could just make a gel with different amounts of the protein loaded in the different wells and claim that's the cell/binding data. I have never really understood the whole photoshop manipulation thing when low tech cheating is likely easier. In science it's about trust and it amazes me people do stuff like this that is immoral and so easy to detect

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9. eugene on December 8, 2013 11:51 AM writes...

"If I'm reading the Nature News article correctly, the quote that Derek posted isn't quite as horrifying as it seems at first glance. The news piece seems to say that this analysis was done on a subset of papers published by Italian scientists that have collaborated with scientists with retracted papers"

I don't think you're reading it correctly. What I got from the article is that he decided to focus on Italian scientists because there were too many problematic images from all over the place and he needed to narrow things down to minimize the workload. Probably, 'Italian' is a good criteria as any since he could correspond with the authors in their native language and he has Italian citizenship so he could always claim a degree of patriotism by wanting to see the Italian academy do good science. It would have looked really strange, on the other hand, if he decided to narrow the problematic papers that his software identified, by focusing only on the French problematic gels.

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10. eugene on December 8, 2013 11:55 AM writes...

Some other selection criteria could be 'top 10 universities' or 'specific journal', but I think it's less problematic to focus on your national group. Plus, if Italy is representative of the wider world, with some researchers being high-fliers, some publishing lots in low impact journals, the results can easily be extrapolated.

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11. Chris Croy on December 9, 2013 3:04 AM writes...

@3: Google's reverse image search works much better than TinEye. To use it, go to images.google and click the camera icon on the search bar.

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12. SAR Screener on December 9, 2013 4:27 AM writes...

@ Eugene
I think post no 6 was referring to the fact that these scientists had already been linked to a scientist with retracted papers and so 1/4 of gels in a subset of scientists who collaborate with people that have retracted papers is not necessarily going to translate into '1/4 of all papers contain dodgy gels'.

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13. ljote on December 9, 2013 4:49 AM writes...

oh no, not more of this... "shop up some gels" clearly means "go to the workshop [i.e., the lab] and run some gels".

what's the problem? nothing to see here...

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14. cliffintokyo on December 9, 2013 8:09 AM writes...

How about taking a break from the polemics for the holidays? Then after a refresh, redouble the efforts.

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15. Kazoo Chemist on December 9, 2013 8:11 AM writes...

@11: Thanks for the tip. I have used both. With TinEye there is a Browser plug-in. With that installed all you need to do is right click on the image and select the search function from the pull down menu. There is probably something similar for Google, but I don't have it installed.

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16. Iridium on December 9, 2013 8:16 AM writes...

@5

That is pretty much what is happaning for professional sport and doping.

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17. Kazoo Chemist on December 9, 2013 8:18 AM writes...

@15: Doh!! I was using IE as the browser. I forgot that the image search is built into Chrome with the right click function. It does give better results presented in the typical Google format. I'll stick with that.

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18. Christian on December 9, 2013 10:11 AM writes...

Does someone know whether changing the dimensions of gels is considered a breach of the guidelines? I haven't been able to find any information on this. I am talking about the practice of making the gel "shorter" so that the lanes are wider and shorter than normally.

This makes it take up less space in the manuscript and (in my personal opinion) makes it easier to see separate bands that are close together. I have seen several groups do it, however it is not mentioned in most journal guidelines.

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19. eugene on December 9, 2013 12:28 PM writes...

@ SAR screener

You're right, but I think I'm also partly right on my point too:

"Bucci and his team created a database hosting all accessible biomedical papers published since 2000. But cleaning it of scientific contamination was not the quick job he had imagined. First he removed retracted papers; then he created a network of scientists who had been co-authors at least three times with authors of the retractions.

The list ran to more than one million..."

One million might not be 1/4 of all people (or articles, the link is not quite clear) who published something related to gels, and it might not mean 1/4 of all papers, but it is not an easy to dismiss number.

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20. Anon on December 9, 2013 12:54 PM writes...

@18 Christian
That likely is not acceptable.
If one was to be "looking" for a band in a certain area, they could just as well lengthen the gel to make it appear more obvious. One could also hide unfavorable bands, whether that be light chain/heavy chain bands or a protein-protein interaction.

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21. schinderhannes on December 10, 2013 8:18 AM writes...

This what it lead to with MDs beeing trained like this:

http://pharmagossip.blogspot.de/2013/12/monday-humor.html

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