self-plagiarism and JACS

April 25, 2012 at 7:52 am | | literature, science community, scientific integrity

Hi all! I’m back! Well, not exactly: I won’t be posting nearly as much as I did a few years ago, but I do hope to start posting more than once a year. Sorry for my absence. There’s no real excuse except my laziness, a new postdoc position, commuting, and a new baby. I suppose those are good excuses, really. Also, I’m sorry to say, that I’ve been cheating on you, posting on another blog. We love each other, and I won’t stop, but I want to keep you Everyday Scientist readers in my live, too. I’m just not going to pay as much attention to you as I used to. You’re cool with that, right?


Anyway, I thought I’d comment on the recent blogstorm regarding Ronald Breslow’s apparently self-plagiarized JACS paper. Read the full stories here (1, 2, 3, etc.).

I feel bad for Breslow, because I like him and I respect his work and I think his paper in JACS is valuable. However, I think he should retract his paper. Sorry, but if some no-name had been caught completely copying and pasting his or her previously published paper(s) and submitting that to JACS as an ostensibly novel manuscript, that paper would be retracted when found out. If he had just copied the intro paragraph, I’d be more forgiving, but the entire document is copied (except, that is, the name of the journal)!

That said, it might be possible to save the JACS paper, but the editors would have to label the article as an Editorial or Perspective or something, and explicitly state that the article is reprinted from previous sources. I know that might not be fair, to give Breslow special treatment, but life isn’t fair. Famous scientists might get away with more than peons. And, honestly, Breslow’s paper remaining in JACS might be good for future humanity, because JACS archive will probably be more accessible than other sources. That way, we’ll be able to look up what to do when space dinosaurs visit us!

extraordinarily repeatable data

May 3, 2011 at 5:31 pm | | crazy figure contest, literature, scientific integrity

UPDATE: My friend on Facebook pointed out that Figure S5c in the supporting info is even more fishy (click on the image below to see a zoomed-in version). Clearly, some portions of the image were pasted on top of other parts. On the right, it is obvious that the top part of the image is from a different frame as the bottom part. On the left, it looks like there’s another image hidden behind (see the strip showing through on the left top part of the image). I’ve added red arrows to aid the eye.

This could possibly be mistakes by someone who doesn’t know how to use Photoshop layers, but I’m thinking there might have been some intentional manipulation of the data. Either way, this type of slicing and stitching and Photoshopping of scientific data is totally unacceptable. I think Nature editors and referees should be more than ashamed to have let this slide.

Nature editors announced that they are investigating.

(Original post below.)

This paper in Nature contains some serious errors: some of the images that are purportedly from different samples (different mice, even) appear to be identical! Note the triangle of spots in the two images below:

Many commenters have noticed the weirdnesses in the figures. This is my favorite comment so far:

2011-04-22 09:31 AM aston panda said:
This is an excellent article shows extraordinary .. skills and amazingly repeatable data. for example
Fig.1a, 2 middle vs 3 bottom left
Fig.1c, 2 right side vs 3 left side
Fig.S4, 1 left side vs 2 right side
Fig.S5, c4 middle right vs e4 middle left
GOOD JOB

I suspect that some sloppy organizing by the authors led to them mixing up some files on their computer. That’s my optimistic view. If they were trying to fabricate data, they wouldn’t use the same region of the same image of the same sample! It must have been sloppy bookkeeping. I hope their results stand up after they correct these errors.

It just goes to show that real science can’t get accepted into Nature and Science. ;)

UPDATE 2: RetractionWatch is surprised that this paper eventually was published with only a correction!

CV of failures

December 10, 2010 at 12:34 pm | | postdoc life, science community, scientific integrity

Nature Jobs has encouraged folks to spread the word of their failures, as well as their successes. So I made a CV of my failures. I’m probably forgetting a lot of failures, but I’m not really motivated to spend a lot of time trying to remember. Anyone else want to air their dirty laundry?

man bites dog

August 14, 2009 at 9:47 am | | grad life, news, science community, scientific integrity

Former Stanford graduate student Christopher Sclimenti is suing his former PI, Prof Michele Calos, for patent infringement and plagiarism. See stories here, here, and here. The complaint can be read here.

The summary is as follows:

  • Student was originally on a patent application.
  • At some point, Stanford and/or prof removed student’s name from application, which becomes this patent. Prof Calos is the only inventor listed on the patent.
  • Prof filed a second patent, which is a continuation of the first. Prof Calos is still the only inventor listed.
  • Prof filed two other applications (here and here), still the sole inventor listed, with significant portions copied from the student’s dissertation. (Stanford Daily found about 20 paragraphs in one application that were essentially identical to paragraphs in his dissertation!)

All parties agreed to an Alternative Dispute Resolution (ADR) with a neutral party. The ADR panel concluded that the student was a co-inventor and should have been included in the patent. As a result, Stanford agreed to add him to the issued patent (but I see no evidence that that has occurred yet).

CalosAccording to Stanford’s OTL page, inventorship is different than what most scientists would consider authorship. For instance, “A person who contributed only labor and/or the supervision of routine techniques, but who did not contribute to the idea—the concept of one of the embodiments of the claimed invention—is not considered an inventor.” For the prof and the University to claim that the student was not an inventor, they implied that he was only a technician and did not contribute to conceiving any of the claims in the patent. That’s possible, but the ADR panel disagreed. It seems pretty straightforward that the student should have been on at least the first patent!

Why would Prof Calos and Stanford University fight so hard against their former student, who clearly contributed enough to the invention to appear on the original patent application? Is splitting the royalties from one patent with one extra person, a student who contributed to the work, so terribly painful? Stanford’s policy is to divide the royalties (after paying for the patenting and lawyer fees) 1/3 to the inventors, 1/3 to the department, and 1/3 to the school. So the prof loses half of her royalties by re-including her former student as an inventor, but the University loses nothing.

Is the recent patent application plagiarized from the student’s dissertation? Only if the dissertation was not first self-plagiarized from an earlier paper. Who knows. Regarding the plagiarism complaint, Stanford had this to say:

“I think we’ve really done our part at this point,” Dunkley said. “The inventorship has been corrected. He has been made whole for any amount that he would have received if he had been an inventor from the beginning. So from the University’s perspective, all necessary action has been taken to rectify any differences on the inventorship issue.” (source: Stanford Daily)

Sclimenti

That’s not really very satisfying. What if the roles were reversed and a student copied significant portions of his PI’s earlier grant proposal into his dissertation without the PI’s permission? Or submitted a paper without the PI’s knowledge? That student would probably be kicked out of Stanford at a minimum. The least the University could do is investigate this case and if Prof Calos has a history of taking credit for other peoples’ work. Maybe Prof Calos is innocent and the student is trying to steal credit, but it would be nice if the University would check into it.

All in all, the entire situation is not clear-cut. I suspect that the whole incident is the result of large egos, hurt feelings, and greed—from all parties! This is why it is very important to not burn bridges and to try to empathize with your PI or your student. I suspect this conflict could have been resolved early on if all parties had been more understanding and willing to listen and compromise.

Bottom line though, I find it unfortunate that the University would fight one of its own students.

P.S. Guess what Sclimenti is doing now?

you don’t understand how karma works

July 30, 2009 at 8:34 am | | news, scientific integrity

A former employee at SLAC intentionally destroyed thousands of protein crystals. Fortunately, only a couple hundred had not already been measured. You can read about it at C&E News or SF Chronicle.

Apparently, she claims that she wanted to reset her bad karma by harming her boss who had fired her (for not showing up to work for weeks). That’s not karma, that’s vengence.

We don’t know the entire story; maybe her boss was a real jackass. Regardless, she acheived vengence upon her boss by harming many other people—who had spent their research time crystallizing those proteins. That’s not very considerate.

They let this crazy woman in and Charles can’t even get past the gate at SLAC when he’s invited there!

UPDATE: She’s missing!

missing link?

June 16, 2009 at 7:20 am | | science and the public, science community, scientific integrity

I read this interesting editorial in Science about the media hyping of a recent archeological find. Just look at Jørn Hurum, the team leader:

hurum

The report of finding the intact skeleton of a monkey-thing was reported in PLOS One, but not before the media hype started. There is a TV documentary of the find and the research on the fossil, and the group is touting the find as the next Rosetta Stone and the “missing link” between apes and humans. For instance, here are a few quotes from the team that reported the find:

“This specimen is like finding the lost ark for archaeologists. It is the scientific equivalent of the Holy Grail.” –Jørn Hurum

“[It is] like the eighth wonder of the world.” –Jens Franzen

What douchebags. This kind of bullshit is seriously likely to undermine the credibility of science in the public eye. Going around claiming that you’ve found the missing link—not to fellow scientist but to the public at large—is very dangerous: when it turns out that your monkey-thing is not a little human, the incident will only add gasoline to the anti-evolution fire. If it really is the missing link, let your fellow paleontologists make those statements.

I find this type of grandstanding by the authors scary, and very reminiscent of the Fleischmann and Pons cold fusion debacle. In fact, I recently watched a 60 Minutes episode about cold fusion, in which Fleischmann stated that his only regrets were naming the effect he saw “fusion” and holding a press conference. In other words, if he and Pons had not overhyped their results directly to the media, then maybe they wouldn’t have been run out of science when their science turned out to have fatal flaws.

Hurum claims that he’s only hyping in this fashion in order to help get children intersted in science. But clearly, his base motivation is to make himself rich and famous. Yes, we should get children excited about real science, but not at the expense of scientific integrity.

Or maybe this little monkey-thing will end up being seen as a great scientific discovery for generations. But I doubt it.

deja boo?

June 2, 2009 at 9:53 am | | everyday science, literature, open thread, science community, scientific integrity, wild web

I’d like to know everyone’s opinion about Deja Vu, the database of “duplicate” scientific articles. Most of the articles in the database are “unverified,” meaning that they could be entirely legitimate (e.g. a reprint). Some are instances of self-plagiarism: an author recycling his or her own abstract or intro for a new paper or review. A few instances are true plagiarism: one group of authors stealing the words (entire paragraphs or papers) of other authors. You can read more in Science.

I can imagine several possible responses (see the poll below):

  1. Great! Now there’s a way for authors, journals, and institutions to better root out plagiarism and unauthorized copying.
  2. Granted, this is information in the public domain, so authors should expect their work to be scrutinized. However, it’s worrisome to have a computer algorithm put red flags on articles that may be legitimate. Deja Vu is probably a good idea, but needs to be reworked.
  3. Careers will be unfairly destroyed by this approach. Labeling a paper as a “duplicate” sounds negative, even when listed as “sanctioned” or “unverified.” This database takes a guilty-until-proven-innocent approach that has the potential to sully the reputation of good scientists.
  4. Um, haven’t these people seen Terminator 2? What is Deja Vu becomes self-aware and starts killing plagiarists.

[poll id=”2″]

Fortunately, an author can check his or her work in the eTBLAST database before submission, to see if a coauthor copied a section, or if the text will unfairly put up red flags. But I found that the results were confusing (e.g. I can’t find the meaning of the “score” or the “z-score”) and unhelpful (of course papers in the same field will have the same keywords). And the results page was really buggy (maybe just in Firefox?).

Personally, I vote #2: Deja Vu is a good idea, but needs to be more careful about the papers it lists as “duplicates,” even “unverified” or “sanctioned.” When a junior faculty member  gets a hit in the database, his or her name will be associated with plagiarism. Some people will not bother to check if it was a legitimate copy, or even who copied whom. I think that the current approach that Deja Vu takes is reckless and unfair. Even lazy.

Moreover, self-plagiarism is not necessarily bad. Copying your own abstract is different than copying your entire paper. Obviously, at some point, self-plagiarism is unacceptable (e.g. submitting the same paper or review to two journals).

I think this topic deserves more nuance than Deja Vu offers.

(Deja Vu has it’s own survey here.)

So that’s how you make a laser work

March 19, 2009 at 5:25 pm | | scientific integrity, wild web

Photoshop!

shopd

This image is from a Wired! article on a 100kW mobile laser defense system that was recently tested.  I guess they’re planning on just airbrushing out the warheads faster than the Iranians can photoshop them in.

someone told the editors

November 11, 2008 at 9:57 am | | literature, news, scientific integrity

A while back, David posted two paragraphs from two different papers with different authors; they were nearly identical. Since then, someone has alerted the editors, because they retracted the paper:

Whoa. (Thanks for the heads-up, Roberto.)

i guess this is how you comment on a JACS comm

September 29, 2008 at 11:15 am | | crazy figure contest, EDSELs, literature, science community, scientific integrity

So I guess there’s not really an official way to get a comment published in JACS. So I’ll be a jerk and complain to everyone on the AEthernet. I saw a paper in JACS which really caught my eye, an interesting title for me, who designs fluorophores:

Yamaguchi, Y.; Matsubara, Y.; Ochi, T.; Wakamiya, T.;  Yoshida, Z.-I. How the pi Conjugation Length Affects the Fluorescence Emission Efficiency. J. Am. Chem. Soc. 2008 (ASAP).

And, of course this amazing fit to data in the TOC image (scroll down to see what this plot should look like):

My first thought was, Whoa! Then I immediately thought, Wait, why do all the points fall exactly on the theory line? That’s unusual. Still, I read the paper with much interest. By the time I got to the end, I earnestly thought it might be an April Fools edition JACS.

I followed the basic theory (Marcus-Hush theory) and the mathematical manipulations. Their result was fascinating: the length of the pi conjugation should directly influence the deexcitation rates: , where Aπ is the length of the conjugation, Β is a constant (approximately 1 Å-1), c is the speed of light, ν is the emission frequency, h is Planck’s constant, and kr and knr are the radiative and nonradiative deexcitation rates, respectively. This is interesting, because fluorescence quantum yield (Φf) is defined by those same rates: . So inserting an equation that depends on conjugation length should be a simple and interesting result.

But, for some reason, the authors normalize out the leading factor. I didn’t really understand why. Anyway, the final result is a little different than I would have figured: . Now, somehow Aπ can be negative, and the authors justify that with the fact that it had become a logarithm in their mathematical gymnastics. I won’t really argue that that’s wrong, because I don’t understand why they did it in the first place.

And here comes the central problem with the paper. In order to confirm this theoretical relationship between quantum yield and pi length, they plot the theoretical equation along with data they have measured (plot above). But they never measure Aπ, they calculate it from the measured rates listed in the table; those same rates were calculated from the measured quantum yield. This is circular logic. So there’s no “correlation between absolute fluorescence quantum yield (Φf) and magnitude (Aπ) of π conjugation length,” as they claim. Instead, they simply plot the ratio of rates versus a different ratio of those same rates. The real axes of the plot are  on the ordinate and  on the abscissa. That’s totally unfair and misleading!

They claim that other independent measures of pi length also work, and that is shown in (of course) the Supporting Information. There, they do give some analysis using Δν1/2a3/2 as a value for Aπ, where Δν is the Stokes shift in a given solvent, and a is the Onsager radius of the molecule in a continuous dielectric medium (taking the relevant factors of the Lippert-Mataga equation). The authors chose not to plot this analysis—they offer only a table—so I’ll plot the real results for you:

That’s sad. Note also that the calculated values cannot be less than 0.5, because size is always positive and even zero for this Lippert-Mataga value of Aπ means that the exponential goes to 1 and the denominator of the new theoretical quantum-yield equation goes to 2.

How does Aπ scale with the Onsager radius or the Lippert-Mataga measure of size?

Well, there is a trend. Not a great trend, but a trend nonetheless. This paper would have been a lot better if they had explored these relationships more, finding a better measure or estimator of size or Aπ. Instead, the authors decided to deceive us with their beautiful plot.

Assumptions in this paper:

  1. That all the nonradiative pathways come from intramolecular charge transfer.
  2. That the emission wavelength does not change with increasing pi conjugation.
  3. For the independent test, that the charge transfer in all cases is unity, so that the change in dipole moment from ground to excited state equals the distance over which the charge transfer occurs.

Assumption 1 is fair, but not entirely applicable in the real world. Assumption 2 is patently false, which they even demonstrate in one of their figures; however, that may not be this paper’s fatal flaw. Assumption 3 is, well, fine … whatever. The real problem is that the authors do not independently test the theoretical prediction, and use circular logic to make a dazzling plot (dazzling to the reviewers, at least).

The biggest disappointment is that the approach and the concept is really interesting, but the authors fail to follow through. I think this could have been an great paper (or at an least acceptable one) if they had been able to demonstrate that the deexcitation rates (and thus the quantum yield) did depend on the size of the pi conjugation. For instance, if the authors had been able to accurately predict pi-conjugation length using the experimental deexcitation rates, then they could have then flipped that and predicted quanum yield from the size. Instead, there’s just a stupid plot that doesn’t make any sense.

So this paper wins an EDSEL Award for the worst paper I’ve read in JACS. I have no idea how that even got past the editors, saying nothing of the reviewers! That said, I am willing to admit my ability to be totally wrong. If so, I apologize to everyone. Please let me know if I made any mistakes.

Plaigiarise an American? The French would never do that!

May 21, 2008 at 11:07 am | | literature, science community, scientific integrity

I was recently doing a bit of reading and happened to have two papers on the same subject, short pulse amplification, on my desk at the same time. As I was reading the more recent paper I kept having the feeling that I had just read something very similar. Upon comparison I found that almost the entirety of the more recent paper was plaigiarised from the earlier paper. The French authors even stole a figure from the earlier paper, all without referencing. Ironically the figure that they stole happened to be figure 6 in the original and in their paper, so the text that I copied from the two manuscripts even has the same figure numbers in it! Check out the papers yourself to see just how low people can go in science.

This is excerpted from the 1998 paper by Backus et al.

materials due to the Pockels cells and polarizers can add high-order dispersion to an amplifier system, making it more difficult to recompress very short pulses. Nevertheless, regenerative amplifiers have also been used to generate pulses of 30 fs and shorter durations.102–104

A multipass preamplifier configuration differs from the regenerative amplifier in that, as its name suggests, the beam passes through the gain medium multiple times without the use of a cavity, as shown in Fig. 6(b). The particular geometry

This is excerpted from the 2001 paper by Cheriaux and Chambaret

materials due to the Pockels cells and polarizers can add high-order dispersion to an amplifier system, making the recompression more difficult for very short pulses. Nevertheless, regenerative amplifiers have also been used to
generate pulses of 30 fs and shorter duration [36, 37].

A multipass preamplifier configuration (figure 6(b)) differs from the regenerative amplifier in that, as its name suggests, the beam passes through the gain medium multiple times without the use of a cavity. The particular geometry

[UPDATE: I wanted to put in the copied figures. See my addition to David’s post below.

From the first paper:

From the later paper:

And there you have it. -Sam]

The Assault on David Baltimore

April 13, 2008 at 7:53 am | | science and the public, science community, scientific integrity

All NIH fellows have to take a course on Ethical Scientific Conduct, so I’ve become quite familiar with all the rights of lab rats. Never mind that down in the subway, just a few floors below the 24hr rat veterinary facility, they’re throwing rodenticide out like candy wrappers.

Amidst the jetsam of the course’s various “case studies” we sometimes get an interesting nugget; the David Baltimore affair was one of them.  Its a very interesting case because of the grayness of the accusations and the high level of the involved parties (Baltimore is a Nobel laureate and was president of Rockefeller at the time). Eventually, Congress and the Secret Service got involved!

If anyone is interested, checkout a New Yorker article about the case (abstract only). I’ve just ordered a book (ISBN: 0393041034) by the author of the New Yorker piece. Another excellent overview can be found in this Ethics & Behavior article.

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