Archive for the 'Science Ethics' category

Plea bargains are unsatisfying to the victims of their type of crime

Jun 11 2018 Published by under Science Ethics, Tribe of Science

Inder Verma has resigned his position at the Salk Institute before a formal conclusion was reached in their internal investigation. One can only imagine they were moving toward a finding of guilt and he was tipped to resign.

http://www.sciencemag.org/news/2018/06/leading-salk-scientist-resigns-after-allegations-harassment

5 responses so far

Ethics reminder for scientists

If the lab head tells the trainees or techs that a specific experimental outcome* must be generated by them, this is scientific misconduct.

If the lab head says a specific experimental outcome is necessary to publish the paper, this may be very close to misconduct or it may be completely aboveboard, depending on context. The best context to set is a constant mantra that any outcome teaches us more about reality and that is the real goal.

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*no we are not talking about assay validation and similar technical development stuff.

15 responses so far

Does it matter how the data are collected?

Commenter jmz4 made a fascinating comment on a prior post:


It is not the journals responsibility to mete out retractions as a form of punishment(&). Only someone that buys into papers as career accolades would accept that. The journal is there to disseminate accurate scientific information. If the journal has evidence that, despite the complaint, this information is accurate,(%) then it *absolutely* should take that into account when deciding to keep a paper out there.

(&) Otherwise we would retract papers from leches and embezzlers. We don't.

That prior post was focused on data fraud, but this set of comments suggest something a little broader.

I.e., that fact are facts and it doesn't matter how we have obtained them.

This, of course, brings up the little nagging matter of the treatment of research subjects. As you are mostly aware, Dear Readers, the conduct of biomedical experimentation that involves human or nonhuman animal subjects requires an approval process. Boards of people external to the immediate interests of the laboratory in question must review research protocols in advance and approve the use of human (Institutional Review Board; IRB) or nonhuman animal (Institutional Animal Care and Use Committee; IACUC) subjects.

The vast majority (ok, all) journals of my acquaintance require authors to assert that they have indeed conducted their research under approvals provided by IRB or IACUC as appropriate.

So what happens when and if it is determined that experiments have been conducted outside of IRB or IACUC approval?

The position expressed by jmz4 is that it shouldn't matter. The facts are as they are, the data have been collected so too bad, nothing to be done here. We may tut-tut quietly but the papers should not be retracted.

I say this is outrageous and nonsense. Of course we should apply punitive sanctions, including retracting the paper in question, if anyone is caught trying to publish research that was not collected under proper ethical approvals and procedures.

In making this decision, the evidence for whether the conclusions are likely to be correct or incorrect plays no role. The journal should retract the paper to remove the rewards and motivations for operating outside of the rules. Absolutely. Publishers are an integral part of the integrity of science.

The idea that journals are just there to report the facts as they become known is dangerous and wrong.

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Additional Reading: The whole board of Sweden's top-ranked university was just sacked because of the Macchiarini scandal

13 responses so far

Story boarding

When you "storyboard" the way a figure or figures for a scientific manuscript should look, or need to look, to make your point, you are on a very slippery slope.

It sets up a situation where you need the data to come out a particular way to fit the story you want to tell.

This leads to all kinds of bad shenanigans. From outright fakery to re-running experiments until you get it to look the way you want. 

Story boarding is for telling fictional stories. 

Science is for telling non-fiction stories. 

These are created after the fact. After the data are collected. With no need for storyboarding the narrative in advance.

32 responses so far

The Journal of Neuroscience needs to explain the author ban

I agree with the following Twitter comment

Insofar as it calls for the Editorial Board of the Journal of Neuroscience to explain why it banned three authors from future submissions. As I said on the prior post, this step is unusual and seems on the face of it to be extreme.

I also said I could see justification for the decision to retract the paper. I say that also could stand some explanation, given the public defense and local University review decision.

5 responses so far

The Journal Ban Hammer: Nastier implications

Mar 02 2015 Published by under Ethics, Science Ethics, Scientific Publication

There is one thing that concerns me about the Journal of Neuroscience banning three authors from future submission in the wake of a paper retraction.

One reason you might seek to get harsh with some authors is if they have a track record of corrigenda and errata supplied to correct mistakes in their papers. This kind of pattern would support the idea that they are pursuing an intentional strategy of sloppiness to beat other competitors to the punch and/or just don't really give a care about good science. A Journal might think either "Ok, but not in our Journal, chumpos" or "Apparently we need to do something to get their attention in a serious way".

There is another reason that is a bit worrisome.

One of the issues I struggle with is the whisper campaign about chronic data fakers. "You just can't trust anything from that lab". "Everyone knows they fake their data."

I have heard these comments frequently in my career.

On the one hand, I am a big believer in innocent-until-proven-guilty and therefore this kind of crap is totally out of bounds. If you have evidence of fraud, present it. If not, shut the hell up. It is far to easy to assassinate someone's character unfairly and we should not encourage this for a second.

Right?

I can't find anything on PubMed that is associated with the last two authors of this paper in combination with erratum or corrigendum as keywords. So, there is no (public) track record of sloppiness and therefore there should be no thought of having to bring a chronic offender to task.

On the other hand, there is a lot of undetected and unproven fraud in science. Just review the ORI notices and you can see just how long it takes to bust the scientists who were ultimately proved to be fraudsters. The public revelation of fraud to the world of science can be many years after someone first noticed a problem with a published paper. You also can see that convicted fraudsters have quite often continued to publish additional fraudulent papers (and win grants on fraudulent data) for years after they are first accused.

I am morally certain that I know at least one chronic fraudster who has, to date, kept one step ahead of the long short and ineffectual arm of the ORI law despite formal investigation. There was also a very curious case I discussed for which there were insider whispers of fraud and yet no findings that I have seen yet.

This is very frustrating. While data faking is a very high risk behavior, it is also a high reward behavior. And the risks are not inevitable. Some people get away with it.

I can see how it would be very tempting to enact a harsh penalty on an otherwise mild pretext for those authors that you suspected of being chronic fraudsters.

But I still don't see how we can reasonably support doing so, if there is no evidence of misconduct other than the rumor mill.

5 responses so far

Banning authors once a paper is retracted from the journal?

Mar 02 2015 Published by under Ethics, Science Ethics, Science Publication

A post at Retraction Watch alerts us to to a paper retraction at the Journal of Neuroscience. The J Neuro notice on this paper reads:

The Journal of Neuroscience has received notification of an investigation by the Perelman School of Medicine at the University of Pennsylvania, which supports the journal's findings of data misrepresentation in the article “Intraneuronal APP, Not Free Aβ Peptides in 3xTg-AD Mice: Implications for Tau Versus Aβ-Mediated Alzheimer Neurodegeneration” by Matthew J. Winton, Edward B. Lee, Eveline Sun, Margaret M. Wong, Susan Leight, Bin Zhang, John Q. Trojanowski, and Virginia M.-Y. Lee, which appeared on pages 7691–7699 of the May 25, 2011 issue. Because the results cannot be considered reliable, the editors of The Journal are retracting the paper.

From RetractionWatch we learn that the Journal has also issued a submission ban to three of the authors:

According to author John Trojanowski ... he and Lee have been barred from publishing in Journal for Neuroscience for several years. Senior author Edward Lee is out for a year.

This is the first time I have ever heard of a Journal issuing a ban on authors submitting papers to them. This is an interesting policy.

If this were a case of a conviction for academic fraud, the issues might be a little clearer. But as it turns out, it is a very muddy case indeed.

A quote from the last author:

In a nut shell, Dean Glen Gaulton asserted that the findings in the paper were correct despite mistakes in the figures. I suggested to J. Neuroscience that we publish a corrigendum to clarify these mistakes for the readership of J Neuroscience

The old "mistaken figures" excuse. Who, might we ask is at fault?

RetractionWatch quotes the second-senior author Trojanowski:

Last April, we got an email about an inquiry into figures that I would call erroneously used. An error was made by [first author] Matt Winton, who was leaving science and in transition between Penn and his new job. He was assembling the paper to submit it, there were several iterations of the paper. One set of figures was completely correct – I still don’t know what happened, but he got the files mixed up, and used erroneous figures

Winton has apparently landed a job as a market analyst*, providing advice to investors on therapeutics for Alzheimer's Disease. Maybe the comment from Trojanowski is true and he was in a rush to get the paper off his desk as he started the new job**. Maybe. Maybe there is all kinds of blame to go around and the other authors should have caught the problem.

Or maybe this was one of those deliberate frauds in which someone took shortcuts and represented immunohistochemical images or immunoblots as something they were not. The finding from the University's own investigation appears to confirm, however, that a legitimate mistake was made.

...so let us assume it was all an accident. Should the paper be retracted? or corrected?

I think there are two issues here that support the Journal's right to retract the paper.

We cannot ignore that publication of a finding first has tremendous currency in the world of academic publishing. So does the cachet of publishing in one Journal over another. If a set of authors are sloppy about their manuscript preparation, provide erroneous data figures and they are permitted to "correct" the figures, they gain essentially all the credit. Potentially taking credit for priority or a given Journal level away from another group that works more carefully.

Since we would like authors to take all the care they possibly can in submitting correct data in the first place, it makes some sense to take steps to discourage sloppiness. Retraction is certainly one such discouragement. A ban on future submissions does seem, on the face of it, a bit harsh for a single isolated error. I might not opt for that if it were my decision. But I can certainly see where another scientist might legitimately want to bring down the ban hammer and I would be open to argument that it is necessary.

The second issue I can think of is related. It has to do with whether the paper acceptance was unfairly won by the "mistake". This is tricky. I have seen many cases in which even to the relatively uninformed viewer, the replacement/correct figure looks a lot crappier/dirtier/equivocal than the original mistaken image. Whether right or wrong that so-called "pretty" data change the correctness of the interpretation and strength of the support, it is often interpreted this way. This raises the question of whether the paper would have gained acceptance with the real data instead of the supposedly mistaken data. We obviously can't rewind history, but this theoretical concern should be easy to appreciate. Maybe the Journal of Neuroscience review board went through all of the review materials for this paper and decided that the faked figure sealed the acceptance? For this concern it really makes no difference to the Journal whether the mistake was unintentional or not, there is a strong argument that the integrity of its process requires retraction whenever there is significant doubt the paper would have been accepted without the mistaken image(s).

Given these two issues, I see no reason that the Journal is obligated to "abide by the Penn committee’s investigation" as Trojanowski appears to think they should be. The Journal could accept that it was all just a mistake and still have good reason to retract the paper. But again, a ban on further submissions from the authors seems a bit harsh.

Now, I will point out one thing in this scenario that chaps my hide. It is a frequent excuse of the convicted data faker that they were right, so all is well. RetractionWatch further quotes the senior author, Lee:

...the findings of this paper are extremely important for the Alzheimer’s disease field because it provided convincing evidence pointing out that a previous report claiming accumulation of intracellular Abeta peptide in a mouse model (3XFAD) is wrong (Oddo et al., Neuron 2003), as evidenced by the fact that this paper has been cited by others for 62 times since publication. Subsequent to our 2011 J. Neuroscience paper, others also have found no evidence of intracellular Abeta in the 3XFAD mice (e.g. Lauritzen et al., J. Neurosci, 2012).

I disagree that whether the figures are correct and/or repeatable is an issue that affects the decision here. You either have the correct data or you do not. You either submitted the correct data for review with the manuscript or you did not. Whether you are able to obtain the right data later, whether other labs obtain the right data or whether you had the right data in a mislabeled file all along is absolutely immaterial to whether the paper should be retracted.

The system itself is what needs to be defended. Because if you don't protect the integrity of the peer review system - where authors are presumed to be honest - then it encourages more sloppiness and more outright fraud.

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*An interesting alt-career folks. One of my old grad school peeps has been in this industry for years and appears to really love it.

**I will admit, my eyebrows go up when the person being thrown under the bus for a mistake or a data fraud is someone who is no longer in the academic science publishing game and has very little to lose compared with the other authors.

26 responses so far

PSA on reporting conflicts during academic presentations

The joke about how you'd like to have some financial conflicts of interest to declare, but sadly you have none, is no longer amusing.

Knock it off.

9 responses so far

Citing review articles robs the authors of original research articles. So stop it.

Someone or other on the Twitts, or possible a blog comment, made a remark about academic citation practices that keeps eating at me.

It boils down to this.

One of the most fundamental bits of academic credit that accrues to authors are the citations of their research papers. Citations form the ballyhooed h-index (X papers with at least X cites each) go into the "Highly Cited" measure of awesomeness and are generally viewed as an important indication of your impact on science.

Consequently, when you choose to cite a review article to underline a point you are making in your own article, you are taking the credit that rightfully goes to the people who did the actual work, and handing it over to some review author.

Review authors are extracting surplus value from the people who did the actual creating. Kind of like a distributor of widgets extracts value from those people who actually made them by providing the widgets in an easy/efficient location for use. Good for them but.....

So here's the deal. If you are citing a review only as a sort of collected works, stop doing that. I can make an exception when you are citing the review for the unique theoretical or synthetic contribution made by the review authors. Fine. But when you are just doing it because you want to make a general "..it is well established that Bunnies make it to the hedgerow in 75% of baseline time when they are given amphetamine" type of point, don't do that. Cite some of the original authors!

If you really need to, you can cite (Jo et al, 1954, Blow et al 1985, Moe et al 2005; see Pig and Dog, 2013 for recent review).

Look at it this way. Would you rather your papers were cited directly? Or are you okay with the citations for something to which you contributed fundamentally being meta-cites of some review article?

53 responses so far

Another weird authorship shenanigan for your consideration

This is, vaguely, related to an ongoing argument we have around here with respect to the proper treatment of authors who are listed as contributing "co-equally" to a given published paper. My position is that if we are to take this seriously, then it is perfectly fine* for the person listed second, third or eighth in the list of allegedly equal contributors to re-order the list on his or her CV. When I say this, my dear friend and ex-coblogger Comrade PhysioProffe loses his marbles and rants about how it is falsifying the AcademicRecord to do so. This plays into the story I have for you.

Up for your consideration today is an obscure paper on muramyl peptides and sleep (80 PubMed hits).

I ran across Muramyl peptides and the functions of sleep authored by one Richard Brown from The University of Newcastle in what appears to be a special issue of Behavioural Brain Research on The Function of Sleep (Volume 69, Issues 1–2, July–August 1995, Pages 85–90). The Preface to the issue indicates these Research Reports (on the original PDFs; termed Original Research Article on the online issue list; remember that now) arise from The Ravello Symposium on 'The Function of Sleep' held May 28-31, 1994.

So far so good. I actually ran across this article by clicking on an Addendum in the Jan 1997 issue. This Addendum indicates:

In the above paper an acknowledgement of unpublished data was omitted from the text during preparation. This omission could affect the future publication of the full set of data. Thus the author, Dr. Richard Brown, has agreed to share the authorship of the paper with the following persons: J. Andren, K. Andrews, L. Brown, J. Chidgey, N. Geary, M.G. King and T.K. Roberts.

So I tried to Pubmed Brown R and a few of the co-authors to see if there was any subsequent publication of the "full set of data" and....nothing. Hmmm. Not even the original offending article? So I looked for Brown R and sleep, muramyl, etc. Nada. Wow, well maybe for some reason the journal wasn't indexed? No, because the first other article I looked for was there. Ok, weird. Next I searched for the journal date and month. Fascinatingly, PubMed lists these as "Review". When the print PDFs say "Research Report" and the journal's online materials list them as "Original Research Articles".

But it gets better....scanning down the screen and .....Whoa!

Behav Brain Res. 1995 Jul-Aug;69(1-2):85-90. Muramyl peptides and the functions of sleep. Andren J, Andrews K, Brown L, Chidgey J, Geary N, King MG, Roberts TK. Department of Psychology, University of Newcastle, Australia.

Now this Richard Brown guy has been disappeared altogether from the author line! Without any obvious indication of this on the ScienceDirect access to the journal issue or article.

The PubMed record indicates there is an Erratum in Behav Brain Res 1997 Jan;82(2):245, but this is the Addendum I quoted above. Searching ScienceDirect for "muramyl peptides pulls up the original article and Addendum but no further indication of Erratum or correction or retraction.

Wow. So speaking to PP's usual point about falsifying the academic record, this whole thing has been a clusterbork of re-arranging the "academic record".

Moving along, the Web of Science indicates that the original, credited solely to Brown has been cited 9 times. First by the Addendum and then 8 more times after the correction...including one in 2011 and one in 2012. Who knows when the PubMed record was changed but clearly the original Addendum indicating credit should be shared was ignored by ISI and these citing authors alike.

The new version, with the R. Brown-less author line, has been cited 4 times. There are ones published in Jan 2008 and Sept 2008 and they indeed cite the R. Brown-less author list. So the two and possibly three most-recent citations of the R. Brown version have minimal excuse.

Okay, okay, obviously one would have to have done a recent database search for the article (perhaps with a reference management software tool) to figure out there was something wrong. But even so, who the heck would try to figure out why EndNote wasn't finding it rather than just typing this single-author reference in by hand. After all, the pdf is right there in front of you.....clearly the damn thing exists.

This is quite possibly the weirdest thing I've seen yet. There must have been some determination of fraud or something to justify altering the Medline/PubMed record, right? There must have been some buyin from the journal Publisher (Elsevier) that this was the right thing to do.

So why didn't they bother to fix their ScienceDirect listing and the actual PDF itself with some sort of indication as to what occurred and why these folks were given author credit and why Richard Brown was removed entirely?

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*The fact that nobody seems to agree with me points to the fact that nobody really views these as equal contributions one little bit.

h/t: EvilMonkey who used to blog at Neurotopia.

22 responses so far

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