How do you read papers? 2010 will be different

In November 2008 I wrote a blog post called How do you read papers? The blog post was actually about different strategies to find interesting papers, e.g. browsing journal tables of content (TOC), different search strategies, filtering by papers others read, or filtering by experts (e.g. Faculty of 1000). A paper by Duncan Hull et al. published around that time in PLoS Computational Biology (Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web) also talked about finding strategies and the best tools for this.

In this blog post I want to talk about the actual reading of scientific papers that you found with one of the strategies mentioned above. There are some interesting recent developments, and I think we will see some significant changes in how we read papers in 2010.

Printed journal
Holding the printed journal in your hands is probably still the most satisfying reading experience because of professional typesetting and color reproduction. But unless you have a personal journal subscription, it is not convenient as you would have to go to the library to read the paper. Plus, many journals no longer produce a printed version, or the library has only an electronic subscription.

This used to be the most common way to read papers 20 years ago. But the quality of photocopies is usually worse than a printout of an electronic version, and photocopies are far more inconvenient to obtain. Reading photocopied papers will only be necessary for the small number of journals that produce no electronic version, or for older papers.1

PDF printout
This is the way most people read scientific papers today, unless they just want to look up small parts of it. Quality color printers have become affordable, and the reading experience is similar to the printed journal with the added convenience of electronic distribution. Most people use PDF printouts for reading, and later discard the paper copy, sometimes even the same day. This is not only more expensive than reading on an electronic device, but also not very friendly to the environment.2

Reading PDFs on a computer
This approach appears to be very common for reading just parts of a paper, e.g. to look up experimental details, a figure or reference. Most people now store papers as PDF (hopefully with an intelligent program such as Papers) and not the PDF printouts. Looking at the PDF on the screen is therefore often the first step, and then the decision is made whether or not to print out the paper to read it in more detail. Reading PDFs on screen is possible, but not really convenient for longer texts. Screen sizes are often too small for the PDF format (A4 or US letter). Many people don't like the eye strain from looking at a screen for longer periods of time, although this is probably more relevant for reading books rather than reading a scientific paper.

Utopia is a PDF viewer launched in December by the University of Manchester that enhances PDF files of the Semantic Biochemical Journal with interactive content and live linking to web resources. Read more about Utopia at Duncan Hull's blog.

Reading on a mobile device
Many mobile devices such as the iPhone can open PDFs and Papers for iPhone makes this process convenient. But PDFs in an A4 or US letter format are almost impossible to read on a small screen.

The ePub format is more suitable for smaller screens found on mobile devices. ePub is usually used for e-Books, but the Open Access publisher Hindawi since 2008 provides papers also in that format. Although ePub is more suitable than PDF for mobile devices, it doesn't solve the problem that figures and tables are simply difficult to show on a small screen. Mobile devices are probably great for reading journal table of contents or the abstract of a paper (and an RSS reader such as NetNewsWire for iPhone is perfect for this), but not fulltext papers.

Reading on an e-Reader
The screen of an e-Reader uses electronic ink which not only means a much longer battery life, but also a very pleasing reading experience, including reading in direct sunlight. Electronic ink is black & white, which is not a problem for fiction books, but limits the use for scholarly papers (and scientific textbooks). Ideally an e-Reader should have a 10″ screen, similar in size to A4 or US letter paper.

The Kindle DX from Amazon was announced in May 2009 and is currently the most popular e-Reader. The Kindle uses its own file format, but a recent software update now allows the Kindle to open PDF files. Some journals (e.g. the New England Journal of Medicine) offer Kindle subscriptions, but that doesn't include early release articles and no subscriber access to the journal website. A number of similar devices were demonstrated this week at the Consumer Electronics Show in Las Vegas. The Kindle is primarily an e-Book reader, and David Crotty over on the Scholarly Kitchen blog is skeptical about dedicated e-readers, because he thinks that market is just too small.

Apple iSlate
Unless you have been on a remote island for the last three months, you will know that Apple will announce a tablet computer later this month. There is wide speculation about the technical details, but it looks like this will be a very interesting device for reading scholarly papers. In contrast to e-Readers it will not use electronic ink. This means a shorter battery life, but allows color documents and many other more traditional computer uses. Based on the iPod and iPhone experience, many people think that the iSlate will change the way we use tablet computers. One of them is Kent Anderson (Game Over, Man – Has the Disruption of Publishing Already Occurred?).

Sports Illustrated did a very nice demo of a fictional tablet computer in December, and it is obvious that many of these concepts can also be applied to scholarly publishing.

Reading Web Pages
Most examples mentioned above try to reproduce the experience of reading something printed on paper on an electronic device. An alternative approach would move beyond the traditional format of a paper and rather takes advantage of the electronic medium. And it looks like the web technologies HTML5 and Flash are best suited for this. Cell Press was experimenting with this approach in 2009, and officially launched their Article of the Future with the first 2010 issue of Cell (all papers will be available without subscription for 60 days, you can provide feedback here). The basic idea of the Article of the Future is to break away from the concept of reading a paper from beginning to end, and to make navigation between the different parts of a paper much easier.

Whereas the Article of the Future tries to make navigation with a paper easier, the PLoS article-level metrics help with navigating to related content: citations, blog posts, reader comments, etc. The Notes feature lets registered users highlight text for specific comments – very much what you would do on a printed paper (but with the added benefit that everybody can see this note).

I'm most excited about projects that enhance the scientific paper instead of recreating an exact electronic version of the traditional paper. And HTML is a more promising format than PDF for these approaches. Michael Clarke (with whom I had the pleasure to do a session at SciFoo 2009) reminded us that Tim Berners-Lee invented the WWW in 1991 to facilitate scientific communication (with HTML and navigation both within and between documents as central concepts), but papers and journals have changed surprisingly little in the last 18 years (Why Hasn’t Scientific Publishing Been Disrupted Already?).

fn1. Many journals are scanning their older papers and make them available in electronic form, e.g. Nature. The first issue of Nature from 1869 can be seen here.

fn2. We all know that computers haven't brought us the paperless office, but that we all use more paper than 10 years ago.

Related Posts Plugin for WordPress, Blogger...
This entry was posted in Snippets. Bookmark the permalink.

28 Responses to How do you read papers? 2010 will be different

  1. Bob O'Hara says:

    bq. A number of similar devices were demonstrated this week at the Consumer Electronics Show in Las Vegas.
    There were several being demonstrated at the Frankfurt Book Fair as well. They looked good, but I couldn’t work out if I’d use one. I guess I’m not an early adopter.

  2. Martin Fenner says:

    I would be very interested in the Kindle or similar e-Reader if I were reading more books. But I read mostly papers, blogs and similar shorter stuff. The iSlate sounds really interesting, especially if it also works for web and email – and if it connects to a projector for presentations.

  3. William Gunn says:

    I think the latter approach is the one that makes the most sense. On the web, objects can be connected, such that all the value doesn’t have to be contained within the object itself. Joe Dunckley said something smart along those lines recently. “It is the literature as a whole — hundreds of dull papers put together — which tells a complete and exciting story.”:
    Forget all the hoopla about tablets and e-readers and so on. It’s the connection to the greater context that’s where the value lies, no matter what device it’s displayed on.
    Not connected to anything, but Martin, I’d like to nominate “Mendeley”: as a contender in the “intelligent PDF storage” category along with Papers. After all, not everyone can *or should* use a Mac.

  4. Duncan Hull says:

    Hi Martin, thanks for the links. I’m looking forward to less paper-based journal publishing, but “for books you just can’t beat paper”:

  5. Martin Fenner says:

    William, you are of course right. But I still think it makes a difference how you read your papers, and I’m looking forward to some of the alternatives mentioned above.
    Duncan, books are obviously different from papers or other short texts. But for every article or blog post telling us that the time for e-Readers has finally come, there is another one saying that electronic devices will never replace books. I’m not so sure about this.
    BTW, my first electronic book was *Hitchiker’s Guide to the Galaxy*, produced by “Voyager”: in 1992 using HyperCard for the first Macintosh PowerBooks. It was a very nice reading experience,

  6. David Crotty says:

    Somehow I thought the “article of the future” would not entail going to 10 different web pages just to read the whole thing….

  7. Maxine Clarke says:

    Not particularly a science-oriented point, but I think in these discussions it is often assumed that a person will always read (or archive) content in the same way. I think that it will become more and more standard for one individual to read in a variety of ways, depending on circumstances – eg one might read electronically on the plane but not in the bath.
    I agree that the market might be too small for dedicated e-readers, but it won’t be long before dedicated e-readers seem a bit old fashioned. Even so, they’ll still suit some people/circumstances.

  8. Roderic Page says:

    I particularly like the final section *Reading Web Pages*. It seems ironic that the focus on publishing online seems to be “how can we replicate the experience of reading a physical publication?”, PDF being the culmination of this. I have considerable sympathy with “Ted Nelson’s”: view that replicating paper on a screen is huge wasted opportunity (Nelson calls it “insane” “here”: ).

  9. Martin Fenner says:

    Maxine, I agree that we read content in many different ways. One way to think about e-Readers is not as little computers that display eBooks, etc., but to use them instead of a printer for the many small pieces of paper you produce every day just to read them. The “IREX Reader”: is taking this approach.
    Roderic, thanks for the link to Xanadu Spaces – that is a much deeper look at the same problem. It is obvious to me that we are still at the very beginning of finding the best way to publish a scientific paper online. One interesting question: why haven’t we made more progress in the last 18 years? Is it because publishers weren’t really interested in moving beyond the printed paper? Were authors and readers not interested? Technology is probably not the reason.

  10. Henry Gee says:

    Thanks for this post, Martin – insightful as ever. Like you, I’m intrigued by the iSlate as its possible use as a mobile office. I can honestly say that the iPhone has changed my life. As an editor, I have used it repeatedly for emailing, surfing and doing my job as a _Nature_ editor. As a test, I used the iPhone as my sole work interface to see how long I lasted – about three hours. So, good for when you are between here and there, and no substitute for the 24″ iMac I have at home. But if the iSlate has a bigger screen, and the virtual keyboard is as good as it is on the iPhone (well, _I_ like it) I could be using mobile computing much more than I already am.
    Mrs Gee is dreading it, by the way.

  11. Ken Doyle says:

    I’m also looking forward to the rumored iTablet/iSlate/iWhatever (although I risk incurring my wife’s wrath by getting one). Like Henry, the iPhone has made it possible for me to carry around far less gadgetry. I even like reading e-books using “Stanza”: , something I never did before. I don’t see the point of having an extra, dedicated e-book reader, other than the screen size. A WiFi and 3G-connected tablet would do the job nicely.
    Speaking of which, MacWorld has an interesting commentary regarding “text input”: on such a device.

  12. Maxine Clarke says:

    I don’t have an iPhone, nor do I carry around gadgetry 😉
    Screens are one thing, but accessing systems is another. I think these screen readers are fine for casual stuff, but for work experience shows that they aren’t great for many tasks that require interface with other systems, particularly where large files are involved. Sometimes, there is no substitute for being in the same place as everything else.

  13. Nicolas Fanget says:

    I think we could maybe move everything over to HTML5 once it has matured. It will have tags for audio/videos, so those can be integrated in the original paper, and any smart browser-based system can open the files and adapt them to the medium used. So say I open the paper on my phone, it would show me the text only in single column with appropriate font size and links to the figures/tables/extra material. On the desktop/laptop I would get something similar to what we have now, which works quite well, although I would like to see more pop-up on hover for figures/tables. And finally if you tell your browser to print it, it would automatically be formatted to double column/small font/copy of printed journal, if only to save paper. One file, with tags, many uses. Isn’t that what HTML and XML were designed for anyway?

  14. Roderic Page says:

    Change (if we define that as moving away from mimicking printed papers) is likely to be very uneven. I suspect that data-rich subjects with lots of links out (to things others will link to) will be where the action is (biology is an obvious example). Publications where people actually “read” and digest will have less incentive to change.
    Perhaps this is part of the problem for publishers. If a “paper” is a richly linked hypertext document, I might not hang around on the publisher’s site, instead I’m off following links. But, presumably this argument was raised when publishers first started hyperlinking the literature cited section of a paper. I guess the assumption was that linking would bring people to a publisher’s content, as well as take them away. So, perhaps one way to encourage the evolution of the paper is to have external sources link back to the paper, so publishers will gain new traffic.

  15. Richard Wintle says:

    Honestly, I can’t imagine changing anything. My standard M.O. is to download PDFs of papers I’m interested in, then print them out for reading on the train/at my desk/in bed (sad but true). Less frequently, I’ll read them on-screen. I am definitely not interested in (a) reading on the mobile devices I own (two iPods and a Blackberry Bold – screens waaaaaaaaay too small) or (b) purchasing another reader (Kindle, Sony thingummy, iBook or whatnot).
    I almost never read paper journals any more. Not surprisingly.

  16. Martin Fenner says:

    Henry, we both want to see the _Nature_ issue of March 17, 2011 in that slick “Sports Illustrated-like”: enhanced version on our iSlate Pros, dont we?
    Nicolas, I like HTML5. Not everybody is a fan of “Google Wave”:, but it certainly is a cool demonstration of HTML5. It will be interesting to see if every publisher develops his own way for displaying papers in HTML – or will we see an evolving standard, e.g. using tools provided by a third party?
    Roderic, _Cell Press_ held two contests before they launched the “Article of the Future”: The “Article 2.0 contest”: was looking at new concepts for navigation within a paper (among other things), whereas “Reflect”:, winner of the “Elsevier Grand Challenge”:, enhances navigation to information outside the paper:
    _identifies the proteins, genes and small molecules mentioned in the Cell articles, and generates pop-up windows containing relevant contextual information, with additional links, about those entities._
    Richard, I also print those PDFs for later reading, especially since we bought this nice color laser printer for our home office last year. But I expect this to change. Did you imagine just a few years ago that you would carry around all your favorite music in your pocket, or look up even the obscurest encyclopedic information with your telephone?

  17. Nicolas Fanget says:

    Martin, I think _Cell_ are onto something, but the problem is that I can’t yet download those paper 2.0 to have with me in my database, whether on a phone/laptop or other. We have to be connected to the net, and sometimes we just can’t be (out in the field, tunnels, power cuts, O2 3G outside London…). That format they have would be great to read on a small screen, it’s certainly OK on my netbook (10″), and the outlinks are great for gene/protein info. I don’t know about iPhones and the like, I haven’t made the upgrade yet. I think an interesting addition to our paper reading would be if Zotero could be ported to Fennec, the Firefox mobile equivalent that is due out soon. Alternatively, Mendeley runs on Linux, so could possibly be added to Android phones and the iPhone.
    Of course the iPhone already has Papers, but it’s not cross-platform so the not-all-Mac among us would get a bit stuck. Also, I’m not sure it can handle anything but PDFs, that I hope we will move away from them as an industry. I have a love-hate relationship with PDFs, they’re great for print publishing, which they were designed for, but not so great for web-publishing.
    With mobile phone memory going up to 32GB, it should be possible to have your bibliography and the data you’re working on synced over the air and in your pocket all the time, I’d love that, now to look for a mobile that I can compile CLC Bio or EMBOSS on…

  18. Henry Gee says:

    @ Martin: _Henry, we both want to see the Nature issue of March 17, 2011 in that slick Sports Illustrated-like enhanced version on our iSlate Pros, dont we?_
    We do! We do!
    @ Ken: _I’m also looking forward to the rumored iTablet/iSlate/iWhatever (although I risk incurring my wife’s wrath by getting one)_
    Mrs Gee said that if I got one I’d have to move out and go live in our beach hut.

  19. Alejandro Correa says:

    @Martin – very good your post is a great thing to know about the current programs for writing and reading, the truth is that I have not updated may be the occasion to know more about these programs useful.
    Is impressive but you really I confused on which program will best print quality for text, the only really used by me is the PDF. Maybe someone could explain that exist a better program from realize a text.

  20. Nicolas Fanget says:

    I’ve found it! Obviously you need net connection to use it (although maybe I can get ClustalW to run on an Android), but “SeWeR”: should fulfil all my nerdy sequence analysis needs on the go. Now I need to borrow that Android phone from my sis in law to see if it works on it…

  21. Richard Wintle says:

    _Did you imagine just a few years ago that you would carry around all your favorite music in your pocket, or look up even the obscurest encyclopedic information with your telephone?_
    I do neither of these things. It’s too much of a faffle to get music onto the iPod (and yes I have two) or the Blackberry, so I seldom update the stuff on there and am not interested in taking the time to get all of it organized. CDs in the car for me, still. As for using the Blackberry’s web browser – no thanks. I can wait until I’m in front of something with a real screen.

  22. Alejandro Correa says:

    Seems that the frog went insane!

  23. Ken Doyle says:

    I don’t blame you for ditching the Blackberry at all, but the iPod should be easy. Connect and sync. Or, if you’re picky like me, turn off automatic syncing and manually drag/drop playlists onto said iPod’s icon in the iTunes sidebar.

  24. Richard Wintle says:

    Oh, it’s easy enough. Getting all the tunes off CD and onto the iPod is a faffle though (CDs take too long to spin up and spin down just for one song at a time). And I don’t like the sync feature, I’d rather manage my playlists manually. There’s no need for playlists on my computer to be identical to those on my iPod.

  25. Alejandro Correa says:

    Oh! is a deep reflection!, Bah H…….G

  26. Alejandro Correa says:

    Sir Gee should be considered in Nature, and not renew the contract to other, For example:
    @Frog, should be in an aquarium on swampy waters @ Ken (is a drawing) and @Wintlito, he has a very deep reflection!
    I am impressed with such wisdom.

  27. Pingback: Beyond the PDF – it is time for a workshop | Gobbledygook

  28. Pingback: Beyond the PDF … is ePub | Gobbledygook