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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: Twitter: Dereklowe

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« On Conspiratorial Thinking | Main | Promise That Didn't Pan Out »

August 27, 2013

Not Sent Out For Review

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Posted by Derek

Blogger Pete over at Fragment-Based Drug Discovery has a tale to tell about trying to get a paper published. He sent in a manuscript on alkane/water partition coefficients to the Journal of Chemical Information and Modeling, only to get back the "not sent out for review" response. That's the worst, the "We're not even going to consider this one" letter. And the odd thing is that, as he rightly put it, this does sound like a JCIM sort of paper, but the editor's response was that it was inappropriate for the journal, and that they had "limited interest" in QSAR/QSPR studies.

So off the paper went to the Journal of Computer-Aided Molecular Design. But as it was going to press, what should appear in JCIM but a paper on. . .alkane/water partition coefficients. There follows some speculation on how and why this happened, and if further details show up, I'll report on them.

But the whole "not sent out for review" category is worth thinking about. I'd guess that most papers that fall into that category truly deserve to be there - junk, junk that's written impossibly and impenetrably poorly, things that should have been sent to a completely different journal. These are the scientific equivalent of Theresa Nielsen Hayden's famous Slushkiller post, about the things that show up unsolicited at a publisher's office. If you're editing a science fiction magazine, you might be surprised to get lyric poetry submissions in another language, or biographical memoirs about growing up in Nebraska - but you'd only be surprised, apparently, if you'd never edited a science fiction magazine before (or any other kind).

But a journal editor can consign all sorts of papers to the outer darkness. At some titles, just getting a manuscript sent out to the referees is an accomplishment, because the usual response is "Stop wasting our time" (albeit not in those exact words, not usually). An author isn't going to be surprised in those cases, but getting that treatment at a less selective journal is more problematic.

Comments (17) + TrackBacks (0) | Category: The Scientific Literature


1. Anonymous on August 27, 2013 7:14 AM writes...

The "not sent out for review" email is much more common than you think. I know almost everyone of my junior colleagues and a few senior colleagues has received such an email. The papers end up in another journal and a few have been JACS reject without review, followed by ACIEE accept. As I stated here in a post months ago, the journal editors have an incredible amount of power. They decide if your article goes into review and more importantly, to whom it goes. And remember, these are the same editors who let the NaH as an oxidant through review and acceptance.

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2. Virgil on August 27, 2013 9:40 AM writes...

What? A journal editor acting unilaterally and then refusing to explain their clearly corrupt actions? Never! How dare you make such wild accusations!

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3. Lyle Langley on August 27, 2013 10:42 AM writes...

Dr. Lowe...
I don't quite understand your last statement, "An author isn't going to be surprised in those cases, but getting that treatment at a less selective journal is more problematic."
Why is it "problematic" at a less selective journal? If it's okay at a higher tiered journal, why isn't it okay at a lower tier. One man's trash is another man's treasure. And sometimes, it's just trash. I've gotten many requests for review and as soon as I agreed and opened up the article and "tried" to read it, I immediately sent it back rejecting it and telling the editor to stop wasting our (reviewers) time.

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4. MDACC Grad on August 27, 2013 11:05 AM writes...

Maybe they have some sort of diversity/quota approach? Putting my business cap on, if one were to have two "alkane/water partition coefficient" papers they would be read/cited by the same population of customers. But if these two papers were on two different topics you'd have an increased consumer base?

I'm not sure if this type of thinking exists, just throwing it out there...

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5. Anonymous on August 27, 2013 11:05 AM writes...

Surely this is a circular argument:

The more selective a journal, the more selective they are. And if a journal is being more selective, then it is one of the more selective journals!

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6. newnickname on August 27, 2013 1:01 PM writes...

The explanation does sound fishy (inappropriate for the journal, only to publish a similar paper later).

I do believe I recall MANY, MANY examples of similar papers from different groups actually being published back to back to back in JACS and elsewhere. All right, I'm mostly talking about total synthesis and synthetic methods. Wouldn't it be a service to the readers to have two different treatments of the same problem in the same journal, even the same issue?

Some editors, I am told, would even facilitate back to back publication if they received mss from different groups at around the same time. (I know of one Big Guy who agreed to have his publication date delayed to the next issue to accommodate the "competitor" who needed a few more days to make revisions. Big Guy still had the earlier submission date.)

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7. Anonymous on August 27, 2013 1:39 PM writes...

I had one of these from JACS. They said it was not fit for publishing in any journal. The resultant ACIEE paper has been cited over 100 times......

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8. dearieme on August 27, 2013 2:39 PM writes...

I have had very few papers rejected, but one was rejected as a matter of doctrine: we have decided not to publish this sort of thing any more. Pity: it was lovely stuff. Anyway, after a change of editor they carried quite a bit by me but nothing, alas, remotely as elegant. Life, eh?

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9. Anonymous on August 28, 2013 8:30 AM writes...

I got a paper sent to Bioinformatics rejected within minutes along with a letter stating that our paper was selected for automatic rejection due to he extremely high volume of papers they received. Yay.

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10. Anonymous on August 28, 2013 9:33 AM writes...

When being a PhD student, I struggled with my own supervisor to submit a manuscript that basically invalidated 8 papers in J.Med.Chem where irreproducible bioactivity data had been puplished. The natural journal to go for this manuscript of course was J.Med.Chem!
They rejected without reviewing. My boss did not have the attitude to submit the manuscript somewhere else as he thought he would only have enemies in the peer scientist. So it never got published. Sad world, but at least I cited many J.Med.Chem papers, so that was definitely not the reason for rejection...
Why do we complain about chinese moral, when the most doubtful moral is represented by ACS journals?

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11. Anonymous on August 28, 2013 10:24 AM writes...

Derek - thanks for the post, we really need more influential blogs bringing attention to this important problem. I am not buying the "we are too busy" argument for not sending seemingly well-conducted studies to review. To me, it is clear that this power is abused to prevent innovative research that goes again the status quo to reach high impact journals. Nature/Science would be so different if only professional scientists had more to say than professional editors! And it is on my view a problem with easy solution by defining a new type of quick review whereby three reviewers would decide whether the paper goes to full review.

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12. Pete on August 28, 2013 11:16 AM writes...

Thanks for highlighting this and apologies for my tardiness in commenting (I was off on big road trip to the south west of Trinidad). Hopefully, we'll help get editors thinking a bit more carefully about this issue. I would like to see more accountability when journals decline to review. For example, the editor should state whether the manuscript was farmed out to a member of the editorial advisory board and what comments were made.

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13. Anonymous on August 28, 2013 4:28 PM writes...

I tried to post my comment at Pete over at Fragment-Based Drug Discovery,
but was was not able to do so, so I duly submitted the letter to
Pete here at the Pipeline.

Hi Pete,

I have no idea why people would be obsessed with JCIM.
I think its a good journal with respectable editors and co-editors.

But isnt that the first thing before a publication,
to make a list of journals where the paper would go if its rejected?

I also dont follow the argument that another paper was
published there recently about the same topic, who cares?
There are a thousand papers about PAH analysis, and they
are more or less all using the same methodology, just with
slight variations. And this is old school chemistry,
talk about proteomics or genomic sequencing of this and that.


BUT, besides not beeing able to read the article,
because it was subscription locked, I was able to
read the supplement.

And I loved the article, even I could not read it,
and whatever the outcome and quality is,
because it provided me with test data, validation data,
the values, structures, citations,
a C++ package (hear hear) with source code
(besides not having the license to it), the PDF files
for documentations, the SMARTS fragment tables, the coefficients.

Everything! Even not reading the paper I would be able to
instantly reproduce that, and implement it somewhere else,
and check and validate it. No opaqueness, just a very
good QSAR/QSPR study.

So maybe the editor-in-chief (William Jorgensen) pulled out
his golden rule table and looked at rule number one:
"The QSAR study or methodology or theory must be truly new :-)"

Then he fired up Scifinder and decided, meehh,
Toulmin A, Wood JM and Kenny PW. published an article in
2008 in our sister journal, "Toward prediction of
alkane/water partition coefficients", so it does not refer
to my rule number one! It must be *truly* new.

QSAR/QSPR and Proprietary Data;
William L. Jorgensen
Source ?J. Chem. Inf. Model., 46 (3),937 -937,2006

As an editor-in-chief (EIC) he has the little red button
with the trigger for ?the paper trash. So who could blame him?
I think because its his journal he can do whatever he wishes.
And again, who blocks you to publish in another open journal,
such as JCHEMINF ( at least its open.
And the IF is not that different, talk about Science ot Nature.

So I love your article, I have no idea how important
alkane water coefficients are, I guess they are,
and I could care less if its in Journal of Computer-Aided Molecular Design
or in JCIM, Nature, Science or in any other journal. I simply love the
supporting info, which also adhhers to WLJs nine golden
rules, or a few of them.

BUT, then again I was intrigued, so I paid $39.95 to read the article,
just kidding, I used a complicated university login and then I
did a wonderful thing. I tried to find out, where the article is
supposed to go and what William L. Jorgensen potentially did to
figure out if it fits into his journal.

I fired up the JANE Journal Estimator (
copied your HTML text (without that tables, because they are too long
and complicate and confuse the algorithm into thinking
its crystallography coordinates) and guess what?

The article fits eactly where it should be, into
Journal of computer-aided molecular design (JCAMD) in the top five.
Minus of course three chromatography journals (error bars).
So no complaining, no perplexation, the world is in
order again (I hope).

Then again, I was also able to find some errors,
with the help of your supplement table,
in the paper the coefficient "C with hydrogen and I"
SMARTS [C;X4;!H0]I is ?0.83, in the supplement its ?0.86.
Without a proper and needed supplement I would
not have stumbled upon this difference.

And frankly, even WLJs rule number two,
the most important one in my opinion,
"All used data, molecules,
descriptors must be published, to permit the
author's peers to repeat the work."
is not always observed by JCIM papers,
actually only a few of them.

So im my chemistry focused opinion, the article would have fit
into Science (journal), because guess how many articles
about genome sequencing are published in Science?
A thousand. Are they all important? No.

So why not a thousand papers about octan/water partition coefficients?
Meaning, it doesnt actually matter were the paper is published,
a good article will climb the citation letter no matter what,
of course crappy articles in Science or Nature do the same
just much faster sometimes.

I am waiting for a rebuttal from people who study the EigenFactors,
The article influence (AI) is slightly higher for JCAMD (0.786) compared
to JCIM (0.766). Science and Nature AI ranks are around 15,
PLOS Biology (open access peer-reviewed) around 10.

Comparable bioinformatics journals, Oxford Bioinformatics
and BMC Bioinformatics rank around 2 and 3 AI.
And, drum roll, Journal Cheminformatics ranks around an
AI of 0.8 (2011), besides graphs are empty
so not sure if that is correct, also the Eigenfactor is 40-times lower.
BUT the Eigenfactor grows with the number of articles in the journal,
so thats understandable 1200 articles vs. 31 tracked ones in 2011.
Still article influence is higher.

Should you wait for a mea-culpa from the EIC of JCIM?
Clearly no, its his journal and he can do as he wishes.
Also dont blame anybody for using templates, dealing with
a cload of submissions. Checking all those new articles
is already enough and of course requires seriuos
commitment and payment for the job.

PLUS, as you said: "journals can publish anything they want to."
Right! *they want to*, they. Whoever that is :-) The EIC mostly.

Pete, one final comment, "Nobody is entitled to have
their manuscripts published. Unless of course they
have paid for the service as is the case for Open Access"

That is actually (hopefully) wrong; open (OA) journals also
have editors in chief, with the same powers as closed access
(CA) journals and they have similar criteria for rejection.
Submitting to an OA journal does not protect you from
rejection by template (RbT) as you experienced. (Evidence,
I am reviewer for OA and CA journals, > 30 of them).

So if your article is so precious to you,
wouldn?t you have the 3000 Dollars to pay for Open Access?
That is of course a rethoric question, but top notch science
has its price, publication expenses are research expenses, even
in Brazil, plus Dilma Rousseff decided to put PetroDollars
into education, good goal. So that should cover any
costs for publications (the free lunch is over).


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14. Anonymous on August 29, 2013 2:12 AM writes...

I'm pretty sure ACSJournals show bias to US authors - one significant difference between the two papers in question.

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15. Pete on August 29, 2013 3:35 PM writes...

@14, I would actually be surprised if there was a bias in favor of US authors although I'd be interested to know if anybody has concrete evidence. It is possible that the manuscript was sent to a member of the editorial advisory board and it is difficult to achieve consistency there.

@13, I'm not actually blaming anyone. These days it is of less importance exactly what journal an article is in. Open access is nice to have but not accessible to authors who lack the budget provision for publication charges. There are advantages in having a blog that some people read.

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16. Anonymous on August 31, 2013 6:35 AM writes...

As an editor working in a "high impact" journal, I found this really interesting. I don't know what happened in this case, it seems odd. Submitted (not yet accepted) articles of course should not count against the novelty of new submissions. Could it have been that a different editor, with a different take on the guidelines, handled the first paper?

As for the more general points, I think it really is necessary to not send a number of manuscripts out to review - the entire system would otherwise break under the workload. Also in cases where it seems fairly clear that the manuscript will not make it past peer-review it is best for everyone to give a quick decision. I have tried giving borderline papers the benefit of the doubt, but in general referees unanimously reject it (and sometimes they are very clear that I should have not have wasted their time by sending it out...)

Regarding comment #11, depending on the journal a well carried out study is of course not enough. It has to show impact in the field, novelty, etc. And as for sending a preliminary request to 3 referees...everyone knows how busy these referees are. And finding appropriate referees, with suitable backgrounds, no conflict of interest and who have not been overloaded by the journal already takes a long time. Then of course many of these referees are travelling, not interested, or busy with research/teaching/reviews for other journals. So you start the process again. If there had to be another round, and this was done for all of the gigantic number of papers submitted a journal (and then again as the less interesting papers trickled down to lower impact titles), a lot more editors would have to be hired (with a corresponding increase in costs) and already busy referees would have to devote every free moment to reading papers.

So sure, the current system is imperfect. But I don't see a way to improve it - and I say this as someone who has had papers of my own not sent out for review.

And regarding point #12 - Pete, maybe you are right, perhaps there should be more feedback from the editors on the process.

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17. A. Postdoc on August 31, 2013 9:04 AM writes...

JCIM breaks their own editorial guidelines all the time. And ignores their reviewers. And publishes lots of articles that should have serious disclaimers attached. And continues to publish papers from 'friends' that are just totally wrong. I'm so over it, JCIM is dead.

Also, when the Editor-in-Chief (acting as editor for the paper) & Corresponding Author are both on the SAB of the same software company, isn't that enough of a conflict of interest to exclude them? You'd think so, wouldn't it? But instead, they don't seem to care at all.

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