Showing posts with label plagiarism. Show all posts
Showing posts with label plagiarism. Show all posts

Wednesday, July 23, 2014

"Cantrill-ing" Hits the NY Times

Apparently, U.S. Senator John Walsh has been accused of plagiarising a final assignment for his Master's degree. And how did the New York Times cover this story? Why, by literally "cantrilling" the paper!

Source: NY Times
Remember us all when you're famous, Stu.

Tuesday, August 13, 2013

Podcast: Chemjobber, Stu, and SAO Discuss Plagiarism (Part 1)

Way back in February, Chemjobber and I sat down with Stuart Cantrill, Chief Editor of Nature Chemistry, for a chat about plagiarism in scientific publishing. We had so much fun talking that the recording ballooned into a 2-h epic podcast; I didn't know where to start editing!
Mea culpa - the conversation languished on my desktop, and I made excuses each week not to get it done.

Finally, Part 1 of the CJ / SC / SAO "Epic Podcast" arrives!



0:07 - Special guests
1:29 - Stu's day job: What happens to papers submitted to Nature Chem?
4:29 - How do you define #1?
8:19 - "Actually, actually, actually..."
10:42 - Journals already use plagiarism-checking software!?!
12:10 - (and get way too many submissions)
16:22 - Cantrill, automated.
18:47 - Who bears the cost of plagiarized papers?
22:50 - CJ's curious: What happens to the person caught copying?
28:12 - The self-correcting scientific literature
28:58 - Bloggers: A small group of people who care too much...
30:17 - Why publish or perish? Shouldn't it be quality, not quantity?
32:09 - Indexes (Indices?)
33:18 - Opening the door to Hour 2...

P.S. - If you need a primer, the earlier podcast CJ and I refer to is here.

Wednesday, August 7, 2013

Valleytronics? More 'Borrowed' Phrasing...

Update: 8/9/13: Editors respond...

***

Tonight must be "Twitter tipster" and "authors behaving badly" night!

From the 'News & Views' pages of two vaunted Nature publishing journals come the latest chunks of potentially plagiarized text. Please open your browsers to this 2012 Nature Nanotech article, and then this 2013 Nature Materials piece. Now, I'm not going to pretend I'm a p-chem or 'valleytronics' expert, but I can certainly spot duped text on command:

NN paragraph 2:
"Electrons travel through a crystal as waves, which are described by a momentum (which is a continuous variable) and a spin (which is a discrete index). It is possible for a crystal to have two or more crystal axes that differ in their orientation, but are otherwise identical: such axes can support electron waves that are also identical apart from their direction (or, more precisely, their momentum)."
NM paragraph 2:
"Electrons travel through a crystal as waves, which are described by a momentum (which is a continuous variable) and a spin (which is a discrete index). It is possible for a crystal to have two or more crystal axes that differ in their orientation, but are otherwise identical: such axes can support electron waves that are also identical apart from their direction (or, more precisely, their momentum)."
Missed the changes? There are none; this is lifted word-for-word.

Another, perhaps?

NN graf 3:
"As in spintronics, there are two main challenges facing researchers trying to make valleytronic devices. The first is restricting electrons to one quantum number, which for valleytronics means localizing them to one momentum valley. This is also referred to as achieving valley polarization. The second challenge is to detect the valley-polarized current."
NM graf 3:
"As in spintronics, there are two main challenges facing researchers trying to make valleytronic devices. The first is restricting electrons to one quantum number, which for valleytronics means localizing them to one momentum valley. This is also referred to as achieving valley polarization. The second challenge is to detect the valley-polarized current."
Hope you didn't blink much, 'cause that one's identical, too.

Although I don't excuse it, I can understand the pressure to grab text under a research deadline, or to emulate a master author. But for news write-ups?!? Looks like someone's got some 'splaining to do...

Friday, June 7, 2013

Friday Fun: A Modest Proposal

What should happen to serial plagiarists?

Retraction of offending publications springs immediately to mind. Perhaps a ban on publishing in a certain journal for a period of time?

I have a different take on the matter: keep the paper, but stain it with a scarlet "P" that marks the work for posterity.


Hawthorne would be proud.

Happy Friday,
SAO

Monday, May 6, 2013

Justice = Served

Friend of the blog Stu Cantrill sends along a long-awaited decision, courtesy of our pals over at Retraction Watch. Blogizens may recall I wrote (strongly) in favor of this outcome back in February.

I applaud the editors of Chemistry: A European Journal for righting this ship. Well done.

Did you see how that worked out, Dalton Transactions?
Hope you reconsider for next time.

Thanks,
SAO

Wednesday, February 20, 2013

Podcast: CJ and SAO Talk Plagiarism



After the latest Xi Yan / Dalton story broke, Chemjobber was gracious enough to sit down with me to hash out our feelings about plagiarism, peer review, and what we hoped might happen when the next batch of purloined text comes around.

Timepoints:

0:02 - Introduction
0:56 - You say "incensed," I say "attracted"
2:29 - Bogus!
3:09 - CJ steals my Great Idea
3:40 - Playing 'Editor' with SAO
5:32 - Is it true? Is it new?
7:01 - Entering the 'gray area'
8:12 - Azaspiracids: Three papers, three different intros
9:30 - Doris Kearns Goodwin
10:44 - Please don't copy word-for-word!
12:23 - Being an Asst. Professor is hard
13:55 - We need a cultural context guidebook...
15:05 - World Science - Impact Factor 35.0
16:20 - Language / Science Barriers
18:09 - Peer Review - Get 'em while they're young!
19:57 - $$ Entrepreneurial Idea! $$
21:33 - How much time do you spend reviewing?
22:45 - CJ's Dangerous Game
23:07 - Conclusions

24:32 - Bonus track

Thanks, as always, to CJ for some stimulating conversation!

Saturday, February 16, 2013

Was Justice Served?

Source: PrariePastor, Wordpress
What should happen to serial plagiarists?*

Regular readers may recall that I posted back-to-back on suspicious swaths of text in two peer-reviewed papers by Xi Yan, a chemistry professor at Beijing Normal University. Along with others (including the authors of both original papers), I concluded that the huge blocks of essentially unchanged text in Yan's papers merited action by the respective Editors of Chemistry and Dalton Transactions.

So, what happened?

Check out the Dalton paper - there's now an "Addition" listed, off to the bottom right of your screen. It reads (emphasis mine):
"After the publication of our article, it was brought to our attention that an earlier publication containing related work to that described in the article should have been referenced:  'Dynamic copper(I) imaging in mammalian cells with a genetically encoded fluorescent copper(I) sensor', Seraphine V Wegner, Hasan Arslan, Murat Sunbul, Jun Yin and Chuan He, Journal of the American Chemical Society, 2010, 132, 2567-2569. 
The authors apologise for this oversight."
Oversight? "Related work?!" A cowardly, measly, long-overdue REFERENCE?!?!?

Fact: Xi Yan has been caught twice with duplicated text and re-hashed science.
Fact: He has now been given a "pass" for bad behavior by RSC Editors.

I cannot accept this decision. Simply put, it flies in the face of everything I know as an honest scientist. Papers are hard to write! Original science doesn't come easy! I sympathize, but that doesn't condone taking another person's work as your own. This failure to discipline permits not just Xi Yan's folly, but opens the door for future plagiarism.

Hypothetical: Playing under these rules, what's to stop me from re-publishing all of E.J. Corey's papers under my name? I'll just subtly alter the substrates, and make sure to bury his name is my References section! Does anyone else realize how ridiculous that sounds???

Another wrinkle: a friend of the blog mentions that the RSC, along with several other publishers, belong to COPE, a publication ethics group. From COPE's own Code of Conduct (emphasis mine):
"Best practice for editors would include: 
• adopting systems for detecting plagiarism (e.g. software, searching for similar titles) in submitted items (either routinely or when suspicions are raised) 
• supporting authors whose copyright has been breached or who have been the victims of plagiarism 
• being prepared to work with their publisher to defend authors’ rights and pursue offenders (e.g. by requesting retractions or removal of material from websites) irrespective of whether their journal holds the copyright"
Following ChemBark's example, I'll lay out my recommendations:

1. The half-hearted "Addition" should be taken down, and Yan's paper retracted.
2. Xi Yan should issue a massive mea culpa to his university, Dalton, and its Editors.
3. Dalton should take steps to ensure that future plagiarised papers are screened out prior to publication.

Failure to take these steps will result in a severe lack of confidence for all future journal publications. I have reached out to the Editorial staff at Dalton for comment, and will update this post if/when I receive a response.

Update (2/17/13) - Try this at home: Friend of the blog S.C. passes along DOC Cop, an online manuscript comparison tool. I uploaded the two texts, and received a match report of 19%. Although, a quick look-down indicates it's likely much higher than that (the software misses one-off substitutions and different reference numbering). I would estimate ~35% duped text.

*To everyone who comes here for fun chemical adventures and light-hearted content: I'm sorry. I don't mean to be the chemistry Internet Police, but I strongly, strongly believe that science needs a level playing field. More fun to come, I promise.

Wednesday, January 23, 2013

Here We Go Again!

Well, it's been about 12 hours, and the internet 'done blown up' over allegations of plagiarism between a 2013 Chem. Eur.J. and a 2009 JACS. Now, let's say that all this blog coverage brings a lot of otherwise-unwanted attention to your group, and people start to notice other similarities...

...such as the ones between a 2012 Dalton Trans. (same gentleman) and a 2010 JACS, this time from Chuan He's group over at the University of Chicago. Holding these up face-to-face, there sure are a bunch of similarities (again!).

He (p. 2): "In this study an Amt1-based copper(I) fluorescent reporter, Amt1-FRET, was constructed by subcloning the copper-binding domain of Amt1 (residues 36-110) between a cyan fluorescent protein (CFP) and a yellow fluorescent protein (YFP), taking advantage of the copper(I)-binding-induced conformational change of Amt1 (Figure 1b). This strategy, pioneered by Tsien and co-workers, produces a genetically encoded fluorescent reporter by inserting a sensing domain, which undergoes a conformational change upon target binding, between two fluorescent proteins that are fluorescence resonance energy transfer (FRET) pairs.10,11,21 Amt1-FRET was expressed in E. coli in the presence of 1.4 mM CuSO4 and purified to yield the copper(I)-bound Amt1-FRET (Amt1-FRET-Cu) (Figure S2, Supporting Information). The fluorescence spectra of both copper(I)-bound and apo-Amt1-FRET were taken by exciting the FRET donor CFP (433 nm) and recording the fluorescence intensities of the YFP (527 nm) and CFP (477 nm) emissions. An increase in FRET between YFP and CFP in Amt1-FRET in the presence of Cu+ was observed through the increase of the peak ratios (I527/I477) from 1.95 to 2.26 as soon as metal was added (Figure 1c), supporting the proposed copper(I)-binding-induced conformational change of Amt1"

Yan (p. 2): "In this paper a PMtb-based copper(I) fluorescent reporter, PMtb-FRET, was constructed by subcloning the copper(I)- binding domain of Mtb CDC 1551 (residues 1–162) between cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP), taking advantage of the copper(I)-binding induced conformation change of PMtb (Fig. 1) to determine the free concentration of the copper(I) in Mtb protein. This strategy, pioneered by Tsien and coworkers,31 33 produced a genetically encoded fluorescent reporter by inserting a sensing protein domain, which went through a conformational change upon target binding, between two fluorescent proteins that were FRET (fluorescence resonance energy transfer) pairs.31–34 PMtb-FRET was expressed in E. coli in the presence of 1.5 mM CuSO4 and purified to yield the copper(I)-bound PMtb-FRET (PMtb-FRET-Cu) (Fig. S2, ESI†). The fluorescence spectra of both PMtb-FRET-Cu and PMtb- FRET without copper(I) were taken by exciting the FRET donor CFP (433 nm) and recording the fluorescence intensities of the YFP (527 nm) and CFP (477 nm) emissions. An increase in FRET between YFP and CFP in PMtb-FRET in the presence of Cu(I) was observed through the increase of the peak ratios (I527/I477) from 2.01 to 2.45, supporting the proposed copper(I)- binding induced the conformational change of PMtb-FRET (Fig. 1)."

Or how about this swatch?

He (p. 2): "To further investigate if different metal ions interfere with the Cu+ binding, the copper(I)-binding-induced FRET changes were measured in the presence of an equal amount of other metal ions. First, the signal for other metal ions after the addition of 5 equiv of metal to Amt1-FRET was measured, followed by the addition of an equal amount of Cu+ (Figure 2b). In all cases, 100% of the signal was recovered, showing that Cu+ binding is tighter compared to that of other metal ions tested and that the presence of other metal ions does not interfere with copper(I) binding to Amt1-FRET. Also, common anions were shown not to interfere with copper(I) binding"

Yan (p. 3): "To further investigate whether different metal ions would interfere with the Cu(I) binding, the copper(I)-binding-induced FRET changes were measured in the presence of an equal amount of othermetal ions. Firstly, the signal for other metal ions after the addition of 5 equiv ofmetal to PMtb-FRET was measured, followed by the addition of an equal amount of Cu(I) (Fig. 5). In all cases, 100% of the signal was recovered, showing that Cu(I) binding was tighter compared to that of other metal ions tested and that the presence of other metal ions does not interfere with copper(I) binding..."

*Even worse? This time, the forgers couldn't even manage a citation!

I didn't have time today to cantrill the whole thing, but look forward to a lively (continuing!) debate in the Comments. Thanks again to Shawn at WPI for alerting me to the later papers.

Update (1/23/13) - Thanks also to Prof. Chris Goldsmith for the initial hat-tip on this round!

Tuesday, January 22, 2013

Open-and-Shut Case

Dr. Shawn Burdette tweeted up the chem-blognoscenti earlier tonight to ask about some "funny business" between two papers. The first (JACS 2009, Pierre) predates the second (Chem. Eur. J. 2013, Yan) by about 4 years, and yet their "Figures 1" both look strangely, well, similar...
Well, OK, folks who play in the same sandbox sometimes use the same shovel, right? Maybe the 2013 paper became so enamored of its predecessor that it couldn't help itself.

But then, I started through the text. Since I didn't have my pink highlighter handy to cantrill them (sorry, Stu!), I decided just to clip out phrases I thought sounded Déjà vu-ish:

Pierre (p. 1): "Time-gated luminescence imaging presents an elegant solution to the problem of background luminescence by setting a time delay between the excitation pulse and the luminescence detection, thereby allowing the luminescence of the media to decay before measuring that of the probe. This technique, however, requires chemical probes with luminescence lifetimes significantly longer than that of the biological medium."


Yan (p. 1): "Time-gated luminescence imaging presents an elegant solution to the problem of background luminescence by setting a time delay between the excitation pulse and luminescence detection; this allows the luminescence of the media to decay before that of the probe is measured. However, this technique requires chemical probes with luminescence lifetimes significantly longer than that of the biological medium."

Or how about this?

Pierre (p. 2): "Notably, the observed selectivity cannot result solely from selective binding of K+ by the diaza-18-crown-6. The selectivities of the lariat ether for K+ over Na+ and Ca2+ in anhydrous alcohol are barely 5- to 10-fold.(7) Tb derivatives of these ethers also demonstrate poor selectivity (4-fold)."

Yan (p. 3): "Notably, the observed selectivity cannot result solely from selective binding of potassium(I) by the diaza-18-crown-6. The selectivities of the lariat ether for potassium(I) over sodium(I) and calcium(II) in solution are barely five- to tenfold.[16] Tb derivatives of these ethers also demonstrate poor selectivity (fourfold)."

One more for posterity:

Pierre (p. 1): "...the flexible structure of the ligand results in an overall large separation between the Tb ion and its sensitizing azaxanthone, resulting in weak Tb luminescence the aryl ether, thereby locking the complex in a conformation where the antenna is significantly closer to the Tb center. Consequently, the efficiency of energy transfer from the azaxanthone to the Tb and the resulting luminescence from the complex are increased."

Yan (buried in the Figure 1 legend!): "...The flexible structure of the ligand results in an overall large separation between the Tb center and its sensitizing antenna, BP, resulting in weak Tb luminescence [snip] The locking conformation causes the antenna to be significantly closer to the Tb center. Consequently, the efficiency of energy transfer from BP to Tb and the luminescence from the complex are increased..."

Cherry on top? The 2013 authors bury the 2009 authors' paper in Ref. 14d. Sigh.

Well, kids, I think we have our answers. While I don't have any skin in the "fluorescent K+ sensors" game, I also abhor unfair play. To this end, I've sent a cheerful email to the Editorial staff of both journals, and will print here any response I obtain.

Thanks for playing!
-SAO

Update (1/23/13): CJ adds his thoughts and a pretty (damning) picture.