The horizontal PDF and other suggestions re:papers

Mar 29 2012 Published by under Uncategorized

8 1/2 x 11 paper can be oriented in two directions, portrait and landscape. As best as I can tell, all papers in all journals are published in the portrait orientation. This made sense in 2000, when the PDF was just a brief waystation between the journal's website and the printer.

But now, I read papers on the computer most of the time. So do you, I bet, web-savvy blog reader. Most computer monitors are in the landscape direction. Don't you want to see papers oriented 90 degrees offset?

I still do read printouts, so papers should come published in both directions. Preview and (ugh) Adobe Reader, and the other viewing programs should bring up a paper, as a default, in landscape mode and then, if you hit "print" ask if you want it in portrait.

I doubt this can be done without doing all the fancy-pants type-setting stuff twice. You'd have to rearrange the text into 3 or 4 columns, move the figures around, probably resize them a little bit. All that hassle will need to be done twice. It may double the size of the document. It's worth it.

While I am on the topic, it's time to get rid of numbered citations forever. It's time to replace them with real in-text citations. It's seriously ungainly to shift back and forth between page 2 and page 17 to find out that [6] means Smith et al. 2004. I often literally ⌘C-⌘V a paper I am reading and open both copies, one to where I am reading and one to the ref list. If logic were king, you should be able to hover the mouse over the citation and your PDF reader will bring up a box with the full citation, including full article title. I can think of how to do this with a very little intelligence in the PDF reader and two bytes per citation, so it's cheap, space-wise.

When you download a PDF, the name should be "Neuropolarbear_etal_JON_2010.pdf." This naming scheme makes them obvious for someone looking at the title, and also compatible with the search engine on my computer. Instead papers are usually called "science.pdf", "1-s2.0-S0006322310010103-main.pdf", and "3726.full.pdf" to name 3 papers currently on my desktop. I realize commenters will point out the beauty of Mendeley right here, and I agree, but there is no reason to not also give your PDF a reasonable name. This can be solved by the journal in less than a minute per paper!

Authors submitting a paper for review should be pasting the text for each section (Methods, Results, Discussion, etc) into a box on the website and at no point should upload a word document. Then the website would create a PDF. Think of the numerous advantages:
(1) Reviewers could request a single- or a double-spaced version of the paper, depending on their preference.
(2) No need to for authors count words in each section. The server does it for you. No need to reviewers to estimate words when authors don't provide this info. Why does Frontiers ask its reviewers whether the paper violates word length policies? Computers can do that.
(3) When the server creates the PDF, it inserts line numbers. As a reviewer, I love line numbers. Of course, if for some reason, you dislike them, you can request the server to make version without line numbers.
(4) No need to submitters as PNAS to insert weird markups into their paper anymore. In fact, doing it this way would make it much easier for editors to guess at page length at all journals. And I take it that page length is something editors care a lot about.
(5) Figures could be placed in-line. Much easier to read that way.
(6) Reviewer wouldn't have to pedantically point out that Neuron has a Summary instead of an Abstract and an Experimental Procedures instead of Materials and Methods. The program would take care of it.
(7) The program could provide rudimentary typesetting to make the review copy look a little nicer.
(8) Spell checking!
(9) No more realizing that track changes was on, but not visible on the screen, and you accidentally inserted comments into your review manuscript saying "reviewer 2 is a fucking asshole. change this so that you cite their latest stupid paper."

Neuropolardog, in portrait mode

19 responses so far

  • scicurious says:

    What we REALLY need to get rid of is the dang two column format in portrait. Scrolling up and down and up and down.

    And I wouldn't mind landscape except it always shows up SIDEWAYS for the tables. Then you end up reading things on your monitor like this:

    • neuropolarbear says:

      Yes! PDF layout should at least acknowledge the existence of computers, and also, the fact that this is the 21st century!

  • Dr Becca says:

    What we REALLY REALLY need are portrait-oriented computer screens. Most people with iPads hold them portrait-wise when reading, so perhaps this is the way our eyes actually want to move?

    • I note that my monitor at work can rotate 90 degrees. It is widescreen though, so the ratio isn't quite 4/3 like iPads. And I have tried to rotate my netbook 90 degs but it was rubbish.

      Not sure that's the way our eyes want to move, some writing is vertical rather than horizontal, and scrolls, that were popular before Gutenberg invented his devilish machine, could be unfurled up-down or left-right. My guess is that it is more about habit/culture.

  • Alma Dzib Goodin says:

    It's very interesting, because even if it sounds simple, reading on screen so usual,
    But extra when you read and write.
    I have two screens now, and makes my life easier, but some days I have so many articles open than I'm thinking about three screen, but the thing is, this option will be great, for reading and writing!.
    Thanks for share it!

  • fizzchick says:

    LaTeX. LaTeX, LaTeX, LaTeX. It solves 1,2,3, 5, 7, and would probably help with several of the others. Good compilers will do 8. Most physics and math journals already accept documents in .tex format, and they issue their own style files, so that if you decide to resubmit to another journal, all you do is recompile under the new style file. Setting up options for reviewers to compile in single column, double-spaced, landscape mode, etc. before downloading a pdf would be trivially easy for a journal website. And best of all, it makes your equations look far more nice than Word's annoying equation editor.

    • neuropolarbear says:

      Very good points. But I doubt that 30,000 neuroscientists can be forced to learn LaTeX. Any journal that goes this way will suffer in submission rate.

      • ecologist says:

        Maybe. On the other hand, I can remember a time when it would have been doubtful that 30,000 neuroscientists could be forced to change from typewriters to computers, or to using this new "internet" thing, or from submitting on paper to submitting online, or to adopting a universally recognized document format, or ...

        And any journal that says "if you send LaTeX files they will go directly to production and speed up the appearance of your accepted paper by a factor of X" will not suffer in submission rate.

  • ecologist says:

    What fizzchick said. LaTeX.

  • Crystal Voodoo says:

    I share your strong feelings about journals not adapting to the digital age. In my case it's my strong aversion to paying for color figures which makes sense if the journal is paying to print it in color rather than the end reader. I will mention that if you look at the html versions of paper they often have the reference boxes or at least a link to the reference list and you can hit the back button to return to your place.

    In reference to your advantages to submitting a paper numbers 2, 3, 6, 8, and 9 can be circumvented by actually reading the Guidelines for Authors before drafting the manuscript and utilizing tools available in every word processing software. It takes an hour or two at most to ensure that your manuscript is formatted correctly and there are usually ample people around (even undergrads and lab techs) to review it before hitting the submit button. I apologize if this comes across rudely but I have very little patience when there are instructions and examples to ensure that what you present is publication ready especially when it involves investing so little energy.

    • neuropolarbear says:

      True that it takes very little energy to follow the guidelines, but it takes even less energy to let the software do it for you.

  • odyssey says:


    Ah yes, the "added value" of Elsevier...

    • neuropolarbear says:

      Hahaha. I always wondered if calling it science.pdf was wishful thinking.
      Elsevier only wishes it had the IF of Science.

  • le says:

    I rather have portrait single column layout on my monitor. This way I can have a paper and my draft open and visible simultaneously. It also allows for larger text and I dont have to go up to the top of the page when I finish column one as alluded above.

    • le says:

      Hmm. I need to add that the single columns should no longer be letter sized. It should be the equivalent of a single column of words on a portrait oriented letter paper. Not sure how the figures would be handled.

  • Ah, a post about the nerdy business of the back office of science publishing, allow me to pontificate!

    It would be interesting to see landscape papers, but really I wish we moved away from PDFs altogether. They're great for print, but lousy for electronic devices. I am more interested in using things like HTML and ePub. Resizing on the fly, fonts can be adjusted easily (also allows sight-deficient people better access)...

    Pasting text in predefined boxes: although I like the idea because it allows us great input control we'll get no end of problems with specials characters, characters that were poorly encoded, odd breaks, equations, tables (tables are ALWAYS a pain), citations that will be encoded differently by EndNote, Zotero, Mendeley... But that's OK, it's our job to make your life easier, not the other way around. Worse than all that is that we will get a neverending flow of complaints that authors can't "just upload the paper", insert whatever they want, or the one symbol they need isn't available... I could see this happening with, say, the online version of LibreOffice that is due out next month, but at the time being it is not worth the hassle.

    LaTeX: it's great. Really, it is. Unfortunately the massive bulk of scientist do not know how, or want, to use it. This is reinforced by the fact that most journals accept only .doc submissions, therefore scientists do not use LaTeX, etc. It is the same cycle that keeps MicroSoft in business vs Linux. I'd be happy to switch to LaTeX/eMacs/Vi/LibreOffice, but there is much inertia in the system. Who will change first? We won't make the first move because it would be expensive, and authors won't because they want to get published. I can't see the the stalemate changing anytime soon. I'll have to ask physics/maths journals what their workflow is like though, I'll learn useful tricks.

    Finally about the hovering mouse over citations: NPG (and other publishers, but I'll plug my employer) do that with the web version. If you don't mind installing a bit of software, ReadCube ( will provide similar functionality and more (think "Papers"), but the PDFs have to be of the "improved" variety.

  • joseph says:

    Use dual-page views. IT Works wonderfully on wird screens.

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  • Janne says:

    Any solution you think of needs to handle in-line math (and some chemical typesetting, I guess, for people on the *sniff* wet side of the lab *sniff*). So, submitting plain text is right out. You can basically ask people to submit:

    * PDF
    * Word
    * ODF
    * RTF (good luck with that one)
    * LaTeX

    Only one of these actually correspond closely to plain text. And if your submission system has a default LaTeX template and header, people that have no fancy stuff in their text can pretty much dispense with the LaTeX markup altogether.

    The problem with PDF isn't the format, it's that it's made for printing so it can't reflow for your device. Whatever PLoS and similar journals do online for markup, we should do the same. A version of ePub that can handle the formatting needed for science papers.