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Nonsense article

Asked by [ Editor ] , Edited by Vladimir Chupakhin [ Editor ]

Dear colleagues, 


I need you advice: I have saw an accepted article in the journal about molecular modeling – QSAR, homology modeling, no wet-lab experiments. And I definitely can say that the article is total nonsense – the binding site is absolutely incorrect and QSAR data and interpretation treated terribly!

So, the question: what to do? write a letter to the editor?

And general question to discussion – What to do if you think that the article is incorrect not in terms of science hypothesis, but in terms of general sense? Authors have used incorrect data, or interpret results absolutely incorrectly.

Update: Wrote a letter to editor-in-chief of the journal. Will keep you with updates.

Update2: So, I don't really know is my letter to editor have been read or not, but the article was published. So, here is the article in Chemical Biology & Drug Design: A Structure-based QSAR and Docking Study on Imidazo[1,5-a][1,2,4]-triazolo[1,5-d][1,4,]benzodiazepines as Selective GABAAα5 Inverse Agonists. Here is my discussion.

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9 answers

4

rich apodaca [ Editor ]

Before doing anything, you should ask yourself some key questions:


  • How much do I care about this paper?
  • How much are others likely to care about this paper?
  • How likely are others to rely on the data and/or conclusions of this paper for external reasons such as the reputation of the journal or authors?
  • How likely is it that I’ve missed something in the paper or otherwise misinterpreted the authors' work?
Every year sees the publication of many scientific papers, and the vast majority of them are destined for obscurity. A lot of it is, frankly, crap. Doing anything about the situation you describe will take huge amounts of time, courage, determination, and energy. I wouldn’t touch this paper unless there were something serious at stake.

Let’s say you believe strongly that the paper is important enough to spend valuable time and energy on. You should treat this just like any other piece of science you would conduct. Formulate a hypothesis and develop a plan that takes your own weaknesses into account in testing it.

Here’s one plan you might follow:

Your first goal should be to gather as much feedback from your peers as possible. The reason is simple: we’re all fallible, and you could be missing something obvious or your own biases could be preventing you from seeing the paper in the proper light. If possible, you want someone else to be able to point out your own errors quickly.

Step 1.

Choose three people whose scientific opinions you value. Show them the paper and briefly outline your concerns. How does what they see compare to what you see? If they don’t see something that needs fixing, you’re likely to have a very tough time getting anyone else to give a hoot. Keep iterating on Step 1 until you strike a nerve or run out of time/energy.

Step 2

Write a short blog post about the problem as you see it. Be clear about the problem and its significance. Provide the right context so your audience can see why your concerns matter to them.

Step 3

Publicize your blog post. Write to the corresponding author, giving him/her a link to your post. Use social media to spread the word to your followers, friends, etc. Media that might be useful include: Mendeley; FriendFeed; LinkedIn; Twitter; Reddit; and Google+. Email a few key scientists in your field, giving them a link to your post. Contact other bloggers or reporters in your field about your post. Write to 3 or more scientists in your field who you respect but may not know.

You’re likely to receive much more private correspondence than public. Make sure to keep track of all of it. Get back to people quickly if they have questions or concerns.

What kind of response did your post generate? If few cared or bothered to write back to you, go back to Step 2 and keep iterating until you run out of time/energy. If few agree with you but response was good, go back to Step 2 and iterate, or call it quits.

Step 4

By now, you’ve received a number of responses that share your views on the paper. You now have leverage with the editor of the journal in question. Write a letter summarizing the problem with the paper and the responses you’ve received to your criticism. Provide a link to all relevant blog posts, tweets, articles, online discussions, or other references on the web. Address any criticisms your post may have drawn. If you’ve received permission from those who have privately corresponded, quote them in your letter.

Make sure to be clear about the action you’re proposing. Do you seek a retraction? Do you want your letter published in the journal? Something else? Whatever it is, be clear and up-front.

As you can see, this approach is iterative and is designed to build consensus about the position you’ve taken on the paper. Many other approaches could be effective, but this is one that can be done by any scientist, regardless of rank, title, or standing in the scientific community.

Also notice the prerequisites (e.g.: a blog; a network of peers, readers, and followers; persuasive writing skills). Now is the time to get started on them if you haven’t already, if not for this case, then for one that you’ll come across in the future.
NN comments
chupvl
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Thanks for detailed reply. It’s not a really big journal impact factor is around 2. But for me is really matter that incorrect articles are published. Seems that editor is not much into molecular modeling, and from the first point the article seems to be “more-or-less” ok, but in reality it contains a lot of mistakes.

Trying to make a comparison: you came to restaurant and ordered some expensive food you never tried before – you tried it and it seems more or less ok, you paid but…it’s not what you paid for, because this food should contain some ingredients that was replaced by really simple and cheap ingredients and even cooked not in the same manner as it should.

Later I will provide the link to the article.

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3

baoilleach [ Admin ]

Just concentrate on doing your own work well. Our job as scientists is not to police the chemical literature. Weak, or wrong, papers are their own reward.

And regarding specifics of software, I think the reader is always a sceptic and will only trust an independent test.

NN comments
chem-bla-ics
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I agree to some extend, but bad literature also leads to a bad image, and that affects my work… people are not so eager to fund a field which is 1. trivial, and 2. results in (many) bad papers.

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3

tony27587 [ Editor ]

Twice in my career I have seen publications published that totally misstated facts about software I was involved with developing. I contacted the authors and they were rather defensive. I contacted the editors and they were unwilling to be involved. I wrote a letter to the editor in one case and they refused it. Today I would go to the blogosphere at that point. I am more than willing to discuss in the public eye. It's far better that way as other people can participate.

I have reviewed papers and had them rejected as they were junk science. Then they were published elsewhere untouched in fringe Open Access journals. I would take that to the blogosphere today also. Science should be objectively discussed in all cases...and in the public eye is a fine place to do it.

NN comments
chem-bla-ics
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Did you send the same letter to that fringe journal too?

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2

chem-bla-ics [ Admin ]

Well, the proper thing to do is indeed write a letter to the editor, and make sure they publish that. You’ll have to make absolutely sure you show evidence showing their arguments are wrong, effectively redoing their work. In fact, in one such study I did with Harm, we showed that a method published in the JCIM has limited applicability, to put it mildly.

Alternatively, you just blog about it, raising awareness of the problems, and let the larger community take care of that. This was done recently in organic chemistry around sodium hydride, if not mistaken. I also did this previously.

I wrote up a lengthier discussion in my blog.

NN comments
kml
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Another good example is the recent discussion about arsenic substitution in nucleic acids, much of which happened outside of research journals.

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1

kml [ Editor ]

In the end it is always the editor that decides whether to accept and publish or not, and since editors are human beings they make decisions of various quality. That being said, I don't think it is normal to withdraw an article after it is accepted, so these decisions are usually final and don't expect that to happen.

You can always write to the editor. But you'll need to be diligent, as Egon already said. It is not uncommon to see comments to articles being published when there is disagreement, although the specific format depends on the journal. Usually these comments contain criticisms of various degrees, which are then often countered by the original authors. A recent example from J. Chem. Phys.:
Or you can blog about it as Egon suggests :) ... the final say in science is hopefully the result of a consensus, and communication is how things get (un)done.



P.S. By chance I stumbled upon an interesting article in Ars Technica today related to this topic.
NN comments
kml
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Of course, it’s just meant to be a recent example of commenting that I’ve read.

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1

wdiwdi [ Editor ]

Not an answer, but I am also very interested in what the community thinks about addressing such problems.


I have right now the problem that there is a publication out there which compares a structure key algorithm with our software – except that almost everything they claim to be superior in their algorithm is complete BS.

After initial pouting communication, the main author has gone silent and refuses to issue a correction – but from what I learned during this conversation, he even went so far to modify (without any indication in the paper) the cited test data (which in its original form our software processes without any problems) to contain a syntactically incorrect header. And then he  claims that his SW is superior because it simply and incorrectly ignores the header, yielding consistent results, while ours gets confused by actually trying to interpret its broken contents.

And this is not the only problem – incorrectly flat out stating that our software cannot do things which are documented in the freely downloadable manual, or bizarrely  claiming that it is a feature that his SW distinguishes two Pt/N complexes which different localized formal charges which our software merges (that is the same problem as ionic vs. pentavalent nitro groups) etc. are other really obvious problems.

Short of suing this guy for malicious misrepresentation, what are the recommendations of this forum to handle this type of incident?



NN comments
wdiwdi
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No, not open source, but free for academic/educational use. The author in question had downloaded the academic version (in compiled form, and I have absolutely no problem with its use for comparison purposes, if done properly) and he did actually run the software, i.e. cited numerical results are correct, if you manipulate the data as he did, the results were just totally spun and maliciously misinterpreted.

chem-bla-ics
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Sounds serious indeed. I would certainly try to write a commentary in the same journal, as Tony tried (see his answer).

wdiwdi
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-bla-ics Just wrote a letter to the editors – I will keep you posted here.

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0

tony27587 [ Editor ]

In a realted vein I recently coauthored a publication about Quality in Public Domain Databases. I will tell the full story on the ChemConnector Blog when the manuscript is finally published (proofs arrive this week) but it was an interesting process. We had reviewers saying important and publish with minor tweaks but rejected by editors. We had other editors saying that it would not be of interest but a supporting letter from 3 scientists saying that it was. It was a “hot potato” article since the quality issues in public domain databases is one of those dirty things that gets ignored and this focused on US based databases. Talk to people like Markus Sitzmann and he’s one of the people working hard, as we do, to ensure that data is as high quality as possible. We took the article outside and it was accepted as is. It will be free access.  

NN comments
chem-bla-ics
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You mean this paper was submitted to scholarly journals first, and rejected there?

tony27587
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-bla-ics What I meant to say was we took the article outside the USA and it was accepted as is. I am not saying there is a correlation but there may be. Hard to prove but an observation.

Yes Egon, the paper was first submitted to scholarly journals as a commentary.

chupvl
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You mean the article in Drug Discovery Today – A Quality Alert and Call for Improved Curation of Public Chemistry Databases? That should be very interesting topic (but I think most of the users know that the data in these databases is not 100% correct).

chem-bla-ics
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that’s the thing: if we all know not all data is correct, why to the database not have a mechanism to report and indicate those errors then? Is that laziness, being scared of showing you are wrong, or just ignorance… none sound good to me.

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0

chupvl [ Editor ] from Strasbourg, France

I have posted an update, here is just and copy-paste to inform you.


Update2: So, I don’t really know is my letter to editor have been read or not, but the article was published. So, here is the article in Chemical Biology & Drug Design: A Structure-based QSAR and Docking Study on Imidazo[1,5-a][1,2,4]-triazolo[1,5-d][1,4,]benzodiazepines as Selective GABAAα5 Inverse Agonists. Here is my discussion.

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