The second stupidest thing in the world

If DVD region locking is the third stupidest thing in the world, then the second stupidest thing is …

The wildly differing submission formats of academic journals.

Long-time readers might remember that when I’m not programming, I am a palaeontologist specialising in the sauropod dinosaurs.  (I got my Ph.D from the University of Portsmouth in 2009, and I’m currently an honorary research associate at UCL).  One of the reasons I’ve not been writing The Reinvigorated Programmer much in recent weeks is that I have — finally — got around to working on resubmission of a couple of pretty substantial papers.  (One is the description of a new genus; the other is about the anatomy and mechanics of sauropod necks.)

Both of these papers were submitted to journals in 2009, and both were rejected.  (Needless to say, I disagree with the reasons for the rejections, but there’s no point whining about that — periodic rejections and resubmissions are just part of the game in academia, at least if you submit to good journals.)  The procedure when this happens is to update the manuscript to reflect those of the reviewers’ point that you feel are of value, then reformat it and send it off to another journal.

In theory this is a relatively quick and easy job — a lot quicker than writing the paper in the first place, anyway.  In practice, it’s a horrible demoralising slog.  One aspect of this is of course just that it’s a pain to have to revisit a manuscript that you thought you’d done with.  But a bigger deal for me is the sheer mindless drudgery of the reformatting process.

Here’s the kind of thing I’ve been doing in my evenings as I change my manuscript from one journal’s format to another:

  • Adjusting the sizes of the margins.
  • Changing the punctuation of the title.
  • Adding telephone and fax numbers to the author addresses.
  • Moving the addresses up before the abstract.
  • Rewriting the abstract from 200 to 250 words.
  • Changing the format of all the headings.
  • Changing the spacing between lines.
  • Changing the capitalisations of taxon names in the Systematic Palaeontology section.
  • Putting commas between the names and dates in all the citations (so “Hatcher, 1901” instead of “Hatcher 1901”).
  • Separating consecutive citations with semi-colons rather than commas (so “Marsh, 1878; Hatcher, 1901”) rather than (“Marsh 1878, Hatcher 1901”).
  • Removing italics from the “et al.” in citations of many-authored papers.
  • Putting the “e” back after the “e” in the “Acknowledgements” heading.
  • Changing the “Bibliography” heading to “Literature Cited”.
  • Changing the formatting of tables to have vertical lines between columns.
  • Rewriting table captions to be much shorter with the rest of the old caption repurposed as table footnotes.
  • Changing mentions of “figure 4” to “fig. 4” when part of a citation of another work, but to “Figure 4” when referring to an illustration in the current paper.
  • Obtaining formal consent, on the new journal’s mandatory form, to cite the personal communications that I had already obtained permission to use by email.

And none of this even touches on the true nightmare of reformatting — handing the references.  Everything changes between one journal’s reference format and the next.  Here are a few off the top of my head:

  • Authors listed as “Firstname Lastname” are changed to “Lastname, Firstname”.
  • First names are replaced by initials.
  • Author names are set in capitals, normal case or in some cases small caps.
  • Publication years need parentheses added.
  • Journal names need to be set in italics.
  • In many cases, journal names need to be abbreviated, using only the sanctioned abbreviations in an official (and apparently secret) list.
  • Page ranges need to be separated by en-dashes rather than hyphens, or the last-page numbers need to be removed completely.
  • Publisher names (for books) need to have publication states added as well as cities.
  • States must be written out in full/abbreviated in two letters.
  • For chapters in edited volumes, page-ranges need to be moved from the middle of the reference to the end.
  • Names of editors need to be messed about much as those of the authors are, but — need I even say? — the editor names are not formatted the same as the author names.

And so it goes on.

By the way, the manuscript that I have successfully resubmitted (one is done, the other is still in progress) has ten solid pages of references.  Each one of them needs to have all these things done to them.  Just think of the endless tedium and the huge potential for introducing error.

And do you know what the value of all this work is?

I will tell you.

None at all.

That of course is not the same thing as its cost.  (In fact, this is a great illustration of the difference between cost and value, and why those two concepts shouldn’t be confused.)  It’s costing me a lot.  I’ve spent a whole bunch of evenings on this — evenings that I could have spent watching Buffy season 6, or writing The Reinvigorated Programmer, or indeed a new palaeontology paper.  More frightening still is calculating the value of that time if I’d spent it on doing consulting work.

I gotta tell you, It really burns my badgers that journals are wasting my valuable time like this.  I would understand it (though I’d still resent it) if it had any value for them, but the truth is that no journal derives any actual benefit whatsoever from having a different mandated spelling of “acknowledgments” than some other journal.  I fully understand that each journals wants its own distinctive look, and I support that; but this can be done by typography, and most certainly doesn’t need to require all the pithering little changes that I’ve wasted the last few weeks’ evenings on.

So, when I am appointed Supremor, my first act will be to make all the journals agree on a single submission format and especially a single format for references, with instant death as the penalty for non-compliance.

You know it makes sense

But Mike, you’re whining about nothing as usual

You can use EndNote/BibTeX/whatever to reformat your references.

No I can’t — by the time a manuscript’s been submitted to one journal, the citations and references have all been resolved, and further manipulation has to be on the resolved manuscript.

But there are standard reference formats.

Yes, there are — at least eight of them (APA style, MLA style, The Chicago Manual of Style, Bluebook, ALWD Citation Manual, ASA style, Harvard referencing, and Vancouver system).  And of course that makes them all completely useless for moving from one journal to another.  (Plus it seems that in my own field, none of the journals uses any of the standards anyway.)

Surely the journal’s publisher can do all this formatting for you, as part of this “added value” they’re always going on about.

Ha ha ha ha ha.

Is it really that big a deal?

It surely is.  Suppose I spend 2% of all my palaeontology time formatting and reformatting manuscripts (and especially references).  Actually I suspect it’s more than that, maybe much more, especially once you throw in all time spent studying the submission guidelines and style guides, but that figure will do.  I doubt that I am unusual in this, so perhaps 2%-5% of all academic work is spent on formatting.  What could be done with that extra time if it were spent elsewhere?  More research, more writing, more students able to be taken on, more conferences attended?  There are plenty of options.

Or to put it another way, suppose the government came up with a new tax that would take away 2-5% of your time?  Or your income?  How would you feel?  Of if such a tax already existed, how would you feel if it were abolished?

So we need to get rid of that tax on academic work.  Bottom line, it’s just stupid.  Really, really stupid.

29 responses to “The second stupidest thing in the world

  1. Its really stupid to be underestimating stupidity by putting these things amongst the most stupid things. Or more precisely, exaggerating the stupidity in you are facing by an order of magnitude, just because you are facing it.

    PS: I find food pictures in your blogs more stupid.

  2. I must say that as a PhD student in theoretical physics I can agree with most of what you say. But for the references I think LaTeX and BIBTEX really does solve that. At least as long as you are allowed to submit your manuscript as a latex file.
    That is my experience anyway.

  3. Phillip Howell

    further manipulation has to be on the resolved manuscript.


  4. Write in TeX / LaTeX. Then you just have to redefine some macros to change layouts / switch bib styles, etc.

    This sounds an awful lot like a paper written by a colleague which my supervisor and I had to “fix.” He’d done it in Word and so we had to manually reformat the entire thing piece by piece. It was an utter nightmare and took upwards of four hours. It wasn’t even that long.

    As for your comments as to why you can’t use BiBTeX, it sounds very much like you’re either using it wrong or don’t know how it’s supposed to be used. The whole point of the TeX is that all formatting should be abstracted.

    Imagine TeX / LaTeX as a big function you feed your abstract document code into; it formats it and hands you back a PDF. Having manually applied formatting is a bit like hard-coding all the data into a program without symbolic constants, forcing you to go back and trawl through the whole code base to change anything.

    Hmm… bit of a tortured metaphor there; I think I’ll stop now.

  5. Oooh, yes, a subject near and dear to my heart.

    Can I ratchet up a level of stupidity a little for you? I work for a government lab; papers have to be approved internally before submitting to an external journal. We have a “publications department” who is supposed to keep current on the journal formats and make sure your MS meets formats. So, do they helpfully take your electronic document and edit? No. They take a red pen (not even something electronic), mark your errors, hand it back to you, half the time getting it wrong, and so (by the time the journal sends it back) you have to do it twice per each journal.

    Way to spend money on scientists’ time, there!

    Well ok, that’s a very specialized rant. Here’s a general one: I use custom software tools that make (very high resolution/quality) specific figures for my MS (I spent some time programming and fiddling to get the fine control right). It happens to output in png only.

    When I submitted it to a journal and the paper was accepted, they returned the figure saying “please submit this in an original, known format, high-quality format. You know, a gif.” So: a so-called PROFESSIONAL PUBLISHER (whom we pay for the privilege and sign over copyright, etc) couldn’t perform the basic service of converting from a png to a gif – I had to waste a couple hours per figure fiddling with a secondary converter to get it looking good enough to be “original”.

    Ugh. Just… ugh.

  6. further manipulation has to be on the resolved manuscript.


    Nearly all of the time, other changes have happened to the submitted manuscript in the process of submission, so the Most Recent Copy, which is what you want to go forward with, is the one that has the citations and references resolved and formatted (in the first journal’s preferred format). That is particularly true in co-authored manuscripts, where the co-authors don’t have the same reference management tools (and in most cases don’t even have the same word processor) as I do. In that case, I use the reference tools when putting together the initial draft, but as soon as it goes to the co-authors for their contributions, it has to be resolved so that they can work on it.

  7. Quxxy, I am perfectly familiar with what LaTeX is, in fact I did write a couple of my short computer-science papers in it. But outside of CS and maths, it’s hardly used. None of the palaeo journals, or broader biology journals, accept manuscripts in LaTeX format, and I can guarantee that no-one who I’ve co-authored a palaeo paper with has ever so much as set eyes on it. It is absolutely not an option (which is a shame, because it’s obviously The Right Thing). The bottom line is that outside of CS/maths, you have to live in a world where everyone else uses hardcoding of styles rather than separating content and presentation.

    Squidfood, I feel your pain. I have submitted PNGs to journals that have rejected them and required JPEGs.

  8. Mike: in that case, you have my condolences.


  9. LaTeX is also very common in physics.

  10. I am sure this a daft suggestion, but have you tried using Zotereo. It lets me re-define citation formats on the fly (today I even created my own) and dynamically update the same in MS Word. Yeah, I hate MS Word, but that’s what my client uses.

    For special formatting, well I used to swear by (and at) LaTeX but now I tend to use Restructured Text + rst2pdf — of course won’t be any use to you…

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  12. Peter — sorry, you’re right of course. I am used to thinking of physics as a branch of applied maths :-)

    Richard, thanks for the heads-up on PLoS ONE accepting LaTeX submissions now. For all sorts of reasons, the PLoS journals are by far my favourites, and it pains me that I don’t yet have the PLoS notch on my own bedpost, though I do have a couple of in-prep manuscripts headed their way. One of those manuscripts is sole-authored, and I will give some thought to preparing it in LaTeX. I probably won’t do it, though, because if PLoS don’t accept it, then it’ll be no use in any other relevant venue without a far more complete reformatting than I’d otherwise need. In short: we need all the journals to accept LaTeX, not just one.

    Bhasker, I’ve not used Zotero, though one of my co-authors swears by it. Does it do all those nice things with OpenOffice as well as MS-Word? If so, then I might make a semi-concerted effort to get my co-authors to use it, too, and the problem might be somewhat solved. (Of course references are only one of the aspects of manuscripts that has to be reformatted when resubmitting an article, but they are by far the most painful.)

  13. Then when your paper is finally accepted you hand over the copyright. The journal then makes it impossible for anyone outside the academic community to obtain a copy :-(

  14. John, I certainly could have included academic publication’s iniquitious copyright-retention practices among my list of stupidest things, but (A) the stupidity in this case lies with us, the scientists, for putting up with it; and (B) I’ve already written about it a couple of times before over on my other blog, Sauropod Vertebra Picture of the Week. See the articles Choosing a journal for the neck-posture paper: why open access is important and Right, that’s it — time for the revolution.

  15. I think that in order to obtain practical suggestions, you will need to supply more detail about your process. Which word processors do you and your colleagues use? What is the final format for submission in most cases (PDF, PostScript, hard copy, …)? What specifically do you mean by “resolving references” and why does this have to be done before colleagues add to the paper? (As long as they have some kind of lookup table, then they effectively have the same thing.)
    What about working from the Most Recent Unresolved Copy: would it be easier to import the changes of colleagues into that, rather than trying to edit the resolved one later?

    I think the “stupid thing” here is not separating content and presentation, as you point out. But this occurs because we have not found a way to trade off a too abstract interface with a too cluttered one: people object to “obscure” control codes and markup, they object to too many buttons on the interface instead (like a 747 flight deck), and they object to something so abstract that how it works is mysterious (i.e., uncontrollable, or, at its worst, patronizing). Part of the solution must lie in hiding such details until they are needed, but that is tricky, because one doesn’t need all of them at once.

  16. Hugh, I am not looking for practical suggestions: I want the world to change.

    “The reasonable man adapts himself to the world; the unreasonable one persists in trying to adapt the world to himself. Therefore, all progress depends on the unreasonable man.” — George Bernard Shaw

    There are for sure technological bandaids that could be applied, and separation of content and presentation is good computer science. But you will never persuade palaeontologists to mark up taxon names as “[taxon][genus]Tyrannosaurus[genus] [species]rex[/species]” when they could just write Tyrannosaurus rex in italics and have done. And I am not sure that I blame them.

  17. And my questions were about how to adapt the world. It might be that a program could detect Tyrannosaurus Rex and similarly for other species, and change the markup correctly when appropriate (not for Bolan, M; et al.). Software got us into this WYSI-not-quite-WYG-based mess, so….

    Maybe then a bolder goal can be achieved by licencing.

    23(c)(iii) By using THE SOFTWARE in the production of your journal, you agree to make the said journal OPEN ACCESS.

    Now to see what happens to my attempt at italics…

  18. Well, your italics work, but the italicised phrase was wrong: it’s Tyrannosaurus rex (lower-case “r” for the “rex“). In biological names the genus name is capitalised but the species name is not. Same for Homo sapiens, Elephas maximus, etc.

    For 90% of the people (and for the other 10% of the people 50% of the time), WYSIWYG is the right thing. Separation Of Content And Preservation (hereafter SOCAP) is a fine, lofty goal, but for most purposes you just don’t need it and it isn’t worth the extra effort. So whatever solutions we come up with, they have to be compatible with WYSIWYG.

  19. (Hadn’t noticed that about species names. Thanks.)

    If SOCAP can be achieved by a post-processing filter, the extra effort for the user is minimal and WYSIWYG is retained. The “worth” for the extra effort is reduction of the kind of pain you are talking about here. Admittedly, the programmer of the filter has much more effort. Such a filter is what I was proposing. It might have to plug in to the editor, but it’s still basically a filter.

    Once filtered to be more semantic, then further work is needed to produce the kinds of layout changes you encounter. Given their variety and complexity, a system based on Programming by Demonstration would probably be the best means to achieve that.

    That’s probably a couple of interdisciplinary Postgrad projects at least.

  20. Marco Rogers

    Interesting problem. Obviously lots of the pain points can be (and have been) solved by technology. But I think you hit on the real issue with wysiwyg. Writing content and formatting content are two completely separate brain processes. People shouldn’t really try to do them at the same time in my opinion.

    Here’s a scenario for consideration. Keep in mind I have no insight into your domain space other than what I’ve just read here.

    Consider something like this. Just write the whole paper. Then go back through with your focus switched to formatting. Your editor and filters are designed to facilitate this as much as possible. You find the first instance of “Tyrannosaurus Rex”. You highlight it and hit italics (it wasn’t italicized before because you didn’t care while you were writing). Then you hit the Taxon button that popped up contextually when you highlighted because you’ve got the nifty scientific/paleontology mode going. At this point, it finds Tyrannosaurus Rex throughout the rest of the document and tags it accordingly. Then it suggests that “Rex” should be “rex” because it looked up the proper formatting and knows that the species name shouldn’t be caps. You say “duh”, click yes and that gets changed everywhere too.

    The program would have all kinds of things like this to “enhance” wysiwyg with proper markup, but it would happen transparently and not take you out of the flow to have to worry about syntax. At the end you’d have a proper document formatted in LaTeX or whatever, and it can export to PDF or Word. But then there’s an extra filter that knows how a specific journal likes it’s formatting. It does that transformation and gives you the Word doc with 80% of the reformatting already done. Then you can go back through it and make any corrections before saving.

    This would be really hard to do well, and it would only get you so far. There would still need to manual intervention at key points. But it sounds like it might go a long way towards progress.

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  23. As it happens, I know a humanities academic who writes all his papers in LaTeX. Possibly the rest of his department thinks he’s a little weird, but it does mean he doesn’t have to re-enter all of his references!

  24. I am amazed (but impressed) that he is able to get the journals to accept his manuscripts. It would be great if you could persuade him to leave a comment here saying something about how this works out for him.

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  27. Mike, I didn’t think I would have to tell you this, but given your response re: Zotero, I thought I should.


    Point and click where you want them to be, and then it will generate them in the proper style. Want to work on the post-review version? No problem. References are embedded, and if not, it’s just point and click to put insert new ones or put them back.

    I agree, this is silly and stupid pointless stuff that no one should have to deal with, but using technology does make it a bit easier.

  28. Thanks, Mr. Gunn (or Dr. Gunn as I see you now seem to have become — congratulations!) As noted above, the real problem with using a reference management/formatting tool is with co-authors — everyone has to use the same tool, and of course share the same references. Still, I do agree that those downsides still leave it much better than the by-hand approach, and on the paper I am just starting now I will indeed be using one of these things.

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