Archive for the 'Scientific Publication' category

Repost: A nonpology for my Glamour hatred. And for PP.

I wrote this awhile ago. Seems worth reposting for new readers:

I really should apologize to my readers who get their feelings hurt when 1) I bash GlamourMag science and 2) CPP bashes society journal level science. I just couldn't figure out how to make it something other than a nonpology. So the nonpology version is, sorry dudes, sorry that your feelings are hurt if there is some implication that you are a trivial fame-chasing, probably data faking GlamourHound. also, if the ranting that I trigger from certain commenters has the effect of making you feel as though you are a trivial, meaningless speedbump who is wasting NIH dollars better spent on RealScientists who do RealGrandeWorkEleven. The fact is, CPP and I are in relatively comfortable situations compared with many of our readers. It is no secret that we have jobs and grant funding. Although it is true that both of us are not above making an exaggerated point for dramatic discussion-encouraging purposes, it is probably no surprise that we come from distinctly different points of view ForRealz on this particular issue. Speaking only for myself in this case, I've been around long enough and enjoyed enough of what I consider to be success in what I want to do as a scientist that it tends to insulate me against criticism. I get that this is not true for all of you. If my intent in raising these issues (i.e., to show that the dominant meme is not reflective of the only way to have a career) backfires for some of you, I do regret that.

One response so far

Scientific peer review is not broken, but your Glamour humping ways are

I have recently had a not-atypical publishing experience for me. Submitted a manuscript, got a set of comments back in about four weeks. Comments were informed, pointed a finger at some weak points in the paper but did not go all nonlinear about what else they'd like to see or whinge about mechanism or talk about how I could really increase the "likely impact". The AE gave a decision of minor revisions. We made them and resubmitted. The AE accepted the paper.

Boom.

The manuscript had been previously rejected from somewhere else. And we'd revised the manuscript according to those prior comments as best we could. I assume that made the subsequent submission go smoother but it is not impossible we simply would have received major revisions for the original version.

Either way, the process went as I think it should.

This brings me around to the folks who think that peer review of manuscripts is irretrievably broken and needs to be replaced with something NEW!!!!11!!!.

Try working in the normal scientific world for awhile. Say, four years. Submit to regular journals edited by actual working peer scientists. ONLY. Submit to journals of pedestrian and/or unimpressive Impact Factor (that would be the 2-4 range from my frame of reference). Submit interesting stories- whether they are "complete" or "demonstrate mechanism" or any of that bullshit. Then submit the next part of the continuing story you are working on. Repeat.

Oh, and make sure to submit to journals that don't require any page charge. Don't worry, they exist.

Give your trainees plenty of opportunity to be first author. Give them lots of experience writing and allow them to put their own thoughts into the paper..after all, there will be many more of them to go around.

See how the process works. Evaluate the quality of review. Decide whether your science has been helped or hindered by doing this.

Then revisit your prior complaints about how peer review is broken.

And figure out just how many of them have more to do with your own Glamour humping ways than they do with anything about the structure of Editor managed peer-review of scientific manuscripts.

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Also see Post-publication peer review and preprint fans

16 responses so far

A "Registered Report" with a guarantee of publication?

Mar 20 2014 Published by under Science Publication, Scientific Publication

Craziness.

From Drug and Alcohol Dependence:

Drug and Alcohol Dependence will now be offering a new submission format, Registered Reports, which offers authors the opportunity to have their research protocol reviewed before data collection begins, with acceptance of the protocol providing acceptance in principle of the eventual results, irrespective of the nature of the results.

 

and more specifically....

Manuscripts which comprise the introduction, hypotheses, methods, analysis plan (including a sample size justification, for example based on a power calculation) and pilot data if applicable can be submitted via this format, and will first be considered by Drug and Alcohol Dependence's Editor in Chief or one of its Associate Editors. Those Registered Report manuscripts considered of appropriate interest and value will be sent for peer review, and then either rejected or accepted in principle. Following acceptance in principle, the study can begin and the authors are expected to adhere to the procedures described in their initial submission. When data collection and analysis is complete, the authors are to submit their finalised full manuscript for final peer review. As long as the procedures originally described have been followed, and the results interpreted sensibly, the manuscript will be published, irrespective of the nature of the findings.

 

Yeah.... let me get right on that.

 

 

No responses yet

Open Access, possibly predatory publisher and that's just the start of the weirdness

Mar 18 2014 Published by under Open Access, Scientific Publication

I recently received a run-of-the-mill spam that I should sign up for email updates from the Journal of Experimental Neuroscience. It is described as "an open access peer reviewed journal published by Libertas Academica".

Okay, what the heck, I'll visit the journal website to find out it isn't indexed in PubMed so, no thanks. But let's check on the Editorial Board (ok, at least couple of names most everyone would know) and do a little check on the Editor in Chief to make sure he's a scientist, not a professional editor.

The bio lists Raphael Pinaud as "an Associate Professor in the Department of Neurobiology at Northwestern University, USA" so let's look at the Department listing for Core Faculty and Research Faculty. Nothing. Courtesy faculty? Emeritus?

Ok, weird. No sign of the guy. Google search seems to turn up validation that he was once there.

On to RePORTER!

Interesting. So the journal EIC bio page did mention two prior faculty appointments that I originally missed. The RePORTER record puts a grant timeline on this. Lets reconstruct.

The 7R01DC010181-03 award is the only one at Northwestern. The "7" type code indicates a switch of University and it went there for the 2012 Fiscal Year. Okay, the first year of funding was at University of Oklahoma Health Sciences Center starting from August 15, 2010. The end date for the total award is listed as July 31, 2015, your typical 5 year R01. But we're in 2014. Hmm, the latest year for this award says that it ended Feb 15, 2013. Odd.

It is odd to end in the middle of an award year to me. If someone dies or takes another job or something it is frequently the case that the University and the IC will just run out the existing award. There are usually some students, postdocs or collaborators finishing up projects or whatnot. And it is just so bloody convenient to fit into the regular University accounting.

I did notice that this guy had another institutional change code 7R21DC010033-03. The original award funded at University of Rochester which has a writeup on one of the guy's papers. The R21 originally ran from June 15, 2009 to May 31, 2011 and the jump-code award started Sept 1, 2010 and expired May 31, 2012. So a move in year 2 followed by a no-cost extension, no doubt.

Not sure exactly when Pinaud got appointed at U. Rochester but an alumni blurb from his postdoctoral lab suggests in 2007.

Hmm. "Frankland" Lab, eh? That name is on the Editorial Board list for this spammy journal. And for that matter, that oddly spelled name "Liisa" drew my attention on the Editorial Board as well, it popped up on the University of Rochester PR bit. And presumably this is the guy's spouse going from the consistent co-publication record.

Ok, now we're starting to make some sense.

The Editorial board lists Liisa Tremere as "Assistant Professor, Department of Neurobiology, Northwestern University, Evanston, IL, USA". The U. of Rochester splash on the paper as "Liisa Tremere, a research assistant professor of brain and cognitive sciences". Clearly this is a dual hire situation. A couple working their way until they both get tenure track faculty appointments. Perfectly understandable.

But what was up between Sep 2010 and Aug 2012 at University of Oklahoma Health Sciences Center?

Well, it looks like Tremere was put on some existing P20 center funding there. Aha, Google to the rescue. "In September of 2010, Dr. Tremere joined the faculty of OUHSC as a tenure-track Assistant Professor."

Ok, ok, I can see this. A couple in science plays the multiple-job search game to reach their goal of two tenure track positions. One jump moves the more-junior person up to Assistant Professor and they soon leverage this into another move- who knows, maybe for the culture or family proximity or something. Anyway, this explains the departure from University of Rochester and the brief stay in Oklahoma. Pretty understandable stuff.

But after less than two years they...disappear? With an R01 terminated in the middle of a year of funding instead of running to the end of an award interval?

That part is weird.

Why do all this academic career climbing, appear to pull off an amazing dual-career triumph and then just....bail.

I am perplexed.

Is being an Editor in Chief at a Libertas Academica title some sort of amazing paying gig?

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See predatory journal list from Jeffrey Beal. The spouse and the postdoctoral advisor of the EIC on this journal Board do not help with the impression of dodginess.

39 responses so far

Why are US Government produced "works" on the Mars Curiosity Rover locked up behind a GlamourMag paywall?

or so asketh Mike Eisen:

There’s really no excuse for this. The people in charge of the rover project clearly know that the public are intensely interested in everything they do and find. So I find it completely unfathomable that they would forgo this opportunity to connect the public directly to their science. Shame on NASA.

This whole situation is even more absurd, because US copyright law explicitly says that all works of the federal government – of which these surely must be included – are not subject to copyright. So, in the interests of helping NASA and Science Magazine comply with US law, I am making copies of these papers freely available here:

FORWARD THE REVOLUTION, COMRADE!!!!!!!

Go Read, and download the papers.

h/t: bill

4 responses so far

Rules for writing review articles

There should be a rule that you can't write a review unless you've published at least three original research papers in that topic/area of focus.

Also a rule that your total number of review articles cannot surpass your original research articles.

57 responses so far

Thought of the Day

There seems to be a sub population of people who like to do research on the practice of research. Bjoern Brembs had a recent post on a paper showing that the slowdown in publication associated with having to resubmit to another journal after rejection cost a paper citations.

Citations of a specific paper are generally thought of as a decent measure of impact, particularly if you can relate it to a subfield size.

Citations to a paper come in various qualities, however, ranging from totally incorrect (the paper has no conceivable connection to the point for which it is cited) to the motivational (paper has a highly significant role in the entire purpose of the citing work).

I speculate that a large bulk of citations are to one, or perhaps two, sub experiments. Essentially a per-Figure citation.

If this is the case, then citations roughly scale with how big and diverse the offerings in a given paper are.

On the other side, fans of "complete story" arguments for high impact journal acceptances are suggesting that the bulk of citations are to this "story" rather than for the individual experiments.

I'd like to see some analysis of the type of citations won by papers. All the way across the foodchain, from dump journals to CNS.

21 responses so far

Dodging Vaporware: In Preparation, In Submission, Under Review, Accepted Pending

As we all know, much of the evaluation of scientists for various important career purposes involves the record of published work.

More is better.

We also know that, at any given point in time, one might have work that will eventually be published that is not, quiiiiiite, actually published. And one would like to gain credit for such work.

This is most important when you have relatively few papers of "X" quality and this next bit of work will satisfy the "X" demand.

This can mean first-author papers, papers from a given training stint (like a 3-5 yr postdoc) or the first paper(s) from a new Asst Professor's lab. It may mean papers associated with a particular grant award or papers conducted in collaboration with a specific set of co-authors. It could mean the first paper(s) associated with a new research direction for the author.

Consequently, we wish to list items that are not-yet-papers in a way that implies they are inevitably going to be real papers. Published papers.

The problem is that of vaporware. Listing paper titles and authors with an indication that it is "in preparation" is the easiest thing in the world. I must have a half-dozen (10?) projects at various stages of completion that are in preparation for publication. Not all of these are going to be published papers and so it would be wrong for me to pretend that they were.

Hardliners, and the NIH biosketch rules, insist that published is published and all other manuscripts do not exist.

In this case, "published" is generally the threshold of receiving the decision letter from the journal Editor that the paper is accepted for publication. In this case the manuscript may be listed as "in press". Yes, this is a holdover term from the old days. Some people, and institutions requiring you to submit a CV, insist that this is the minimum threshold.

But there are other situations in which there are no rules and you can get away with whatever you like.

I'd suggest two rules of thumb. Try to follow the community standards for whatever the purpose and avoid looking like a big steaming hosepipe of vapor.

"In preparation" is the slipperiest of terms and is to be generally avoided. I'd say if you are anything beyond the very newest of authors with very few publications then skip this term as much as possible.

I'd suggest that "in submission" and "under review" are fine and it looks really good if that is backed up with the journal's ID number that it assigned to your submission.

Obviously, I suggest this for manuscripts that actually have been submitted somewhere and/or are out for review.

It is a really bad idea to lie. A bad idea to make up endless manuscripts in preparation, unless you have a draft of a manuscript, with figures, that you can show on demand.

Where it gets tricky is what you do after a manuscript comes back from the journal with a decision.

What if it has been rejected? Then it is right back to the in preparation category, right? But on the other hand, whatever perception of it being a real manuscript is conferred by "in submission" is still true. A manuscript good enough that you would submit it for consideration. Right? So personally I wouldn't get to fussed if it is still described as in submission, particularly if you know you are going to send it right back out essentially as-is. If it's been hammered so hard in review that you need to do a lot more work then perhaps you'd better stick it back in the in preparation stack.

What if it comes back from a journal with an invitation to revise and resubmit it? Well, I think it is totally kosher to describe it as under review, even if it is currently on your desk. This is part of the review process, right?

Next we come to a slightly less kosher thing which I see pretty frequently in the context of grant and fellowship review. Occasionally from postdoctoral applicants. It is when the manuscript is listed as "accepted, pending (minor) revision".

Oh, I do not like this Sam I Am.

The paper is not accepted for publication until it is accepted. Period. I am not familiar with any journals which have accepted pending revision as a formal decision category and even if such exist that little word pending makes my eyebrow raise. I'd rather just see "Interim decision: minor revisions" but for some reason I never see this phrasing. Weird. It would be even better to just list it as under review.

Final note is that the acceptability of listing less-than-published stuff on your CV or biosketch or Progress Report varies with your career tenure, in my view. In a fellowship application where the poor postdoc has only one middle author pub from grad school and the two first author works are just being submitted...well I have some sympathy. A senior type with several pages of PubMed results? Hmmmm, what are you trying to pull here. As I said above, maybe if there is a clear reason to have to fluff the record. Maybe it is only the third paper from a 5 yr grant and you really need to know about this to review their continuation proposal. I can see that. I have sympathies. But a list of 8 manuscripts from disparate projects in the lab that are all in preparation? Boooo-gus.

32 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

Challenging grant attribution on manuscripts

One of the little career games I hope you know about is to cite as many of your funding sources as possible for any given manuscript. This, btw, is one way that the haves and the rich of the science world keep their "fabulously productive" game rolling.

Grant reviewers may try to parse this multiple-attribution fog if they are disposed to criticize the productivity of a project up for competing renewal. This is rarely successful in dismantling the general impression of the awesome productivity of the lab, however.

Other than this, nobody ever seems to question, assess or limit this practice of misrepresentation.

Here we are in an era in which statements of contribution from each author is demanded by many journals. Perhaps we should likewise demand a brief accounting as to the contribution of each grant or funding source.

68 responses so far

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