Tetrapod Zoology

The literature

Even in this day and age – when anyone who’s anyone has a huge personal pdf archive – ‘dead tree’ libraries are still used by many (or most?) of us.

i-3315b12e21e5867c319df0c9c4b191f8-boxfiles-1-Mar-2010.jpg

Partly because I’ve never worked on a computer that can do more than three things at once, partly because I spend 90% of my waking life staring at screens anyway, and partly because I really prefer to hold literature in my hands and have it scattered about the desk while writing, I hate using pdfs and will always use hard-copy when possible. I even find myself wasting time hunting down a printed-out copy of a paper when I know full well that a digital version is just a few clicks away on a hard-drive. I blame the few billion years my ancestors spent in three-dimensional space for all this. Relying on dead-tree literature has its drawbacks, of course: I refer to the space you need for all that paper. But, come on, paper libraries are surely a thing of beauty. Feast your eyes on my collection of bird literature… (and this isn’t all of it)

i-28c2ead3007fbb6d91e3557d509a535f-boxfiles-2-Mar-2010.jpg

i-06c965c07ee625b6038a5cf670b1097a-boxfiles-3-Mar-2010.jpg

Pretty, no?

Comments

  1. #1 David Marjanović
    March 9, 2010

    Pretty indeed. I’m used to working with less pretty ones…

  2. #2 Dartian
    March 9, 2010

    anyone who’s anyone has a huge personal pdf archive

    Hey! It’s not the size of your pdf archive that matters, it’s how you use it!

    I totally agree with you about preferring to read hard-copies, though. I’m hopelessly old-school in that regard myself.

    Relying on dead-tree literature has its drawbacks, of course: I refer to the space you need for all that paper.

    So true, so true…

    Are those pictures from your home, btw? Have you run out of space on the bookshelves, or are the bird paper folders only temporarily on the floor?

    Feast your eyes on my collection of bird literature… (and this isn’t all of it)

    Impressive indeed. How many books about birds do you have? A three-digit number?

  3. #3 R. S. Sahsi
    March 9, 2010

    I completely understand the sentiment, as it’s pretty much the way I have approached literature over the years… but the problem is that I never took the time to organize the mountains of paper as well as you have. After a while, paper begets paper… I make sure I know where my snowboard is if the piles get too high.

    I mean, I’ve had my various systems, but they were all fairly piecemeal or task-specific That, and as you pointed out, it still starts to take up a LOT of space.

    In the last year I’ve broken down and purchased a Fujitsu ScanSnap, and between the Mac apps DevonThink and Papers, have managed to get things much more organized. Sure, I still periodically print out articles to read on-the-go, or so I can scribble comments all over the pages. But now I’ve have realized the tremendous organizational and uncluttering benefits of this hardware-software combination.

    It’ll be hard to go back to piles o’ paper, but I retain the ability to print what I need when it suits me.

    (I just make sure I recycle when I’m done or the eco-terroists will eat me!)

  4. #4 Donald Prothero
    March 9, 2010

    There’s another major reason a paleontologist cannot rely on PDFs–most of our literature is pretty old and not yet scanned into digital form (if it will ever be). We’re one of the few sciences that routinely reads and cites century-old systematic literature. My collection began when I was in grad school at the AMNH and got free copies of nearly every old AMNH Bulletin and Novitates, and expanded as I published papers and made sure to send out reprints to over 200 VPs just so they’d send me their reprints. Now my collection stretches across the top of every shelf in my lab, at least 100 feet of shelf space, and is constantly expanding. That leads to another drawback of PDFs: if you print them, you nearly always end up with thick documents of one-sided pages, a much less efficient (and larger volume) method than the old double-sided printed literature. PLUS you have to have an extraordinary printer to get the grayscale quality of the original published journal photos.
    For me, the biggest consideration is convenience. I can tote paper offprints around and work on them or read them anywhere, and not require a power supply, wifi, and a dark enough room that I can see my screen. Like Darren, I spread them out, leaving them open to the key pages when I’m writing so I can quickly scan between one and another–it’s very clumsy to do this on a computer, especially when you have a lot of windows open at once. I’d rather have my computer open to my Word document I’m writing, and not have to flip between lots of windows (and my Powermac manages these better than most computers).
    But I’m definitely old school–I was the last Ph.D. student at the AMNH DVP to hand-type his dissertation in the age before Macs and PCs and word processing, and I can still do math on a slide rule. I’m just amazed that the younger generation (Darren included) still does things the old-fashioned way, even though they are computer-fluent. Maybe it says something about the ease of working in this manner, no matter how much better the computers become.
    Just be glad you didn’t have to hand type every report through your school years, or use carbon paper to make copies! And I’ll bet most of the readers of this blog are too young to remember the smell of the old mimeograph machines in the days before cheap efficient photocopying…

  5. #5 Brian
    March 9, 2010

    I will add, however, that a major advantage for my purposes is the ability to search for key terms throughout my entire pdf library (at least, those pdfs that support ocr) fairly quickly.

  6. #6 Nick Gardner
    March 9, 2010

    “There’s another major reason a paleontologist cannot rely on PDFs–most of our literature is pretty old and not yet scanned into digital form (if it will ever be). We’re one of the few sciences that routinely reads and cites century-old systematic literature.”

    Not necessarily true for dinosaur and pterosaur paleontologists, much of that literature has been transmogrified into PDF form. Though for non-ornithodiran archosaurs and many other reptiles (and probably for your clade, mammals, as well) remains locked in hard copy (or behind JSTOR’s subscription wall).

    Most of my hard copies are the result of photocopying other people’s books or non-‘avian-line archosaur’ reptile papers. =)

  7. #7 TheBrummell
    March 9, 2010

    I’m more impressed by the level of organization than by the volume. My in-silico PDF collection is organized by citation (author, year), and as Brian pointed out, I can search through most of those files for key words pretty quickly.

    My dead-tree collection of papers is not nearly so well organized – mostly it consists of papers stuffed into a series of file boxes and folders, roughly by last name of first author. Much more difficult to find relevant bits inside that.

  8. #8 MikeW
    March 9, 2010

    You guys don’t have multiple monitors? Two monitor systems are common and I have seen pictures of three monitor systems. A good video card would seem to be called for (and they are rather inexpensive if that matters). Harder to do on a laptop, I guess.

    Well, that said, hard copy is just more satisfying in many ways.

  9. #9 Jerry D. Harris
    March 9, 2010

    I also have a huge (primarily paleo) library of hard copies, so big that it no longer fits well into my office. Over the years, though, I have become increasingly used to reading PDFs on a screen — I blame having to do dozens of manuscript reviews that way. I no longer collect hard copies of papers (though I will happily keep actual reprints if I get them, and books are, of course, a must), but have a massive and ever-growing library of PDFs (closing in on 13,500 individual files), both recent and old (including PDFs of things from the 1700s and 1800s), and it’s a tremendous boon when reviewing papers, particularly when I’m not in my office! It definitely takes some getting used to, and it doesn’t replace the nice feel of a hard copy…and yes, it’s not as nice as having a bunch of papers scattered about that can be reached for at any one moment, but it can be cone and is exceptionally helpful! I love being able to tote an entire research library around with me anywhere I go!

  10. #10 ginasketch
    March 9, 2010

    Hell yes.

    As an illustrator I find having hard copy reference to study is more useful than trawling google.

  11. #11 Boesse
    March 9, 2010

    Haha, when I read this, I felt like I was listening to my own voice in conversations past (minus the whole bird thing; my bird literature is restricted to a thin folder on Neogene marine birds).

    Marine mammal paleontology is a small enough field that I can fit much of the known literature into only a few file cabinets (2 and a half?). Anyway… I prefer paper for several reasons: I simply get a headache if I stare at a computer screen for so long, and I hate laptops, so I can’t take those around with me, or read a short paper on my way to class (or in the bathtub for that matter; unfortunately reading in the tub often leads to me passing out, or sometimes dropping my printed version in the tub – oops). Also… with a pdf, you can’t scribble all over it (I understand you can in some cases, but I prefer a pencil), or better yet, tear it up or crumple it into a little ball if you get angry at it.

  12. #12 John Harshman
    March 9, 2010

    Yeah, I get almost all my scientific literature in pdf form. But when it comes time to read anything, I usually print it out. When digital displays have as much contrast and resolution as ink on paper, and are as cheap, then maybe we’ll talk. Then again, the pdfs are searchable, which is nice. So I keep both forms, and use both on occasion.

    When do we get to have the smart paper, like on Caprica?

    By the way, I’m fanatical enough to have a complete set (so far) of HBBW. It looks very impressive, but I don’t have a single bookshelf that will contain the whole thing.

  13. #13 John Harshman
    March 9, 2010

    By the way, do all those binders (which seem to be organized roughly by family) have anything to do with your secret bird project?

  14. #14 Kelly Clowers
    March 9, 2010

    @MikeW – I have seen 3 monitor systems, and seen pictures of up to 6 monitor systems. Anything above 4 monitors (2 monitors per card, 2 cards) used to require really expensive custom setups, but with DisplayPort and the Radeon 5000 series Eyefinity, up to six monitors is easy. Of course, I think more than tree monitors isn’t useful to most, outside of gaming demos and things like network monitoring centers.

  15. #15 David Marjanović
    March 9, 2010

    Here in the lab, I have two screens. Mwahah. I can have a pdf open on one screen and my “manu”script on the other…

    Also, I have no problems with reading on a screen all day. =8-) Paper just has the advantage that I don’t need to carry a computer around to read it.

    And I’ll bet most of the readers of this blog are too young to remember the smell of the old mimeograph machines in the days before cheap efficient photocopying…

    Oooooh no. I got that a lot in elementary school (late 80s, early 90s). The smell is utterly unforgettable.

    or better yet, tear it up or crumple it into a little ball if you get angry at it.

    :-D

  16. #16 Darren Naish
    March 9, 2010

    Thanks to all for comments. Let me say at the outset that I’m not in any way down-playing the value or user-friendliness of pdfs (I use them as much as anyone else): I’m just saying that, when it comes to reading a paper (rather than just searching it for key words or phrases), or having it available for easy reference, pdfs fail and hard-copy wins. As Nick noted (comment 6), in some of the subject areas I deal with (I’m thinking dinosaurs and pterosaurs), virtually _all_ of the literature (as in, from the whole of time) now exists in pdf form thanks to the sterling efforts of a few stellar individuals (mentioning no names). So, we all carry around with us a significant percentage of the global literature on the subject, and as Jerry says (comment 9), this is awesome. But for other subjects the process of pdf-ing has only just started.

    Dartian (comment 2): yes, those photos are of the work-space in my house. The shelves are all full, so files cover the floor when I’m working on something. And, yes (comment 13), these bird files are out because I’ve been working on a bird project: it’s a book chapter. Comment 7 brings up the subject of organisation. As it happens, I have a very efficient system of keeping track of my dead tree papers: each boxfile has a code, and a paper is labelled with the same code. This is all cross-linked in a large bibliography (currently exceeding 630 pp. at 10 pt text), but to keep on top of it, I have to make sure that the references for new entries are typed up for the bibliography. That can be tedious and hard to keep up with when you acquire 100 new reprints in one go, but at least it means I never have to type the reference out more than once.

    We like to think that, one day, paper literature will become redundant, and indeed I have colleagues who have transferred to 100% digital libraries. But will paper references ever completely disappear? We are a long way off this yet, and so long as there are people (like me) who really don’t like reading from pdfs, boxfiles and reprints and photocopies will remain.

  17. #17 John Conway
    March 9, 2010

    I feel like holding on to wanting physical copies of papers is a fault. They take up a huge amount of space, and are hard to search effectively (unless you keep pretty much everything in you head, AND have your collection well organised). I’ve tried to train myself to like reading from a computer screen, dammit! — just how I trained myself to like painting in Photoshop.

  18. #18 AnJaCo
    March 9, 2010

    OK, so how do y’all organize your PDFs?

    Renaming the files is always necessary, and then placing them into a cascade of folders. My own system (which I am not 100% satisfied with) is:
    Folder system: Mostly a taxonomic tree, with parallel trees of other subjects like ecology etc. if the subject[s] span multiple taxa.
    File naming: [Year]-[New taxon name{s}, if applicable]-[Actual title of paper, or most of it or its key words]. Once in a while an authors name creeps in.
    e.g.:
    2008-[Wulagasaurus ngen]-Most basal hadrosaurine from the uppermost Cretaceous of China.pdf

    Its probably too late for me to change my system but I’d be curious to hear how others do it.

  19. #19 Rob
    March 9, 2010

    @AnJaCo

    Papers is the answer to organising your pdfs. It’s brilliant, and very cheap.

    Of course, if you don’t use a Mac then that road isn’t open to you. There’s a similar thing called Mendelev that’s out as shareware and runs on Linux (and also on Windows if you use that) but it isn’t yet as fabulously wondrous as papers.

  20. #20 Owlmirror
    March 9, 2010

    Mendelev

    Actually, Mendeley.

    http://www.mendeley.com/

  21. #21 Hans Sues
    March 9, 2010

    I am not against pdfs, but print copies are so much more user-friendly than cluttering up one’s screen (or, in my case, two large screens) with layers of open pdfs. For the old literature, the original illustrations are much better than what is currently offered online (e.g., BHL).

  22. #22 Jim Thomeson
    March 9, 2010

    Before xeroxing became common, I had no need to organize my reprints because I could sight recognize them, each and every one. Later I used an author card system with my catalog number and the date for each publication written on it.

  23. #23 John Harshman
    March 9, 2010

    Since you asked. My organizational system is pretty simple. I assign every paper a unique index number, sequential in the order I happen to input them, indexed in EndNote. PDFs get named with the index number first, followed by author & year. Hard copies get the index number written on the front page, and are stored in files folders, in numerical order. And anything I want to work with frequently gets removed from the main file and stuffed into a big folder organized around a particular subject. So right now I have separate folders for Anseriformes, Palaeognathae, Crocodylia, Galloanserae, Neoaves, Oscines, Suboscines, Aves, Dinosauria, genome evolution, and, oddly, Cambrian explosion. In theory, anything I want to find is in one of two places.

  24. #24 Jorge Velez-Juarbe
    March 9, 2010

    I hate using pdfs and will always use hard-copy when possible.

    I feel the same way. BTW, Darren, that is one amazingly large collection of bird literature!! As for organization of printed references, I organize them in binders by subject: sirenia, crocodylia, cetacea, elasmobranches, Caribbean etc. Same with the pdfs. A couple of computers ago when I had Endnote, I not only entered the references but also where I had them stored and wether it was paper or pdf. It was sooo much easier to find stuff!

  25. #25 Will Cathey
    March 9, 2010

    When we get “EMP’d”, you’ll have a source of comfort and study!

  26. #26 Vladimír Socha
    March 10, 2010

    Hi Darren, just finished reading your book “The Great Dinosaur Discoveries” and I really enjoyed it. So keep up good work in whatever you do :-)

  27. #27 Jerry D. Harris
    March 10, 2010

    I’ve got my entire library (both paper and PDF) cataloged into EndNote, which serves not only its designed bibliographic function in MS Word when I’m writing papers (thus alleviating the need to double-check bibliography vs. paper and vice-versa, as well as worrying about formatting) but also as a searchable database for words in titles, abstracts, and the custom keyword fields. So I can rapidly pull up lists of papers that mention various subjects!

  28. #28 Robert
    March 10, 2010

    I agree with you fully. Vast amounts of information are available online, but I don’t feel as if I actually possess that information unless I have it to hand in a book.

  29. #29 Bob Michaels
    March 10, 2010

    The valuable Museum collections will have to be digitized if they are to survive. Perhaps the Google`s , Microsoft`s and Apple`s can donate some time and dollars to the project.

  30. #30 Scale
    March 10, 2010

    For some tasks paper copies are still priceless, especially when browsing complex reference material… the screen can never fit enough PDFs neatly at one time.

    The bird stickers are a nice touch, do you use them as a quick clue to identify the binders too?

  31. #31 Nima
    March 10, 2010

    I gotta agree here, I love reading actual books rather than PDFs. No waiting for the things to load, no zooming necessary, no clogging up my already antiquated pentium 4 CPU and 512MB RAM (hey, it WAS considered high-end back in 2003…) Even though I’m technically part of the “Internet Generation”, I still prefer grabbing a book off the shelf than double clicking through folders and files.

    But I do like the fact that there are PDF versions of paleontology papers, I don’t subscribe to journals and I just graduated college, so I don’t have access to paper databases and open source papers are pretty essential for my art.

  32. #32 Christopher Taylor
    March 10, 2010

    I’ve got my entire library (both paper and PDF) cataloged into EndNote, which serves not only its designed bibliographic function in MS Word when I’m writing papers (thus alleviating the need to double-check bibliography vs. paper and vice-versa, as well as worrying about formatting) but also as a searchable database for words in titles, abstracts, and the custom keyword fields.

    I actually find EndNote a complete pain in the khyber when it comes to entering references into manuscripts and still prefer to do so manually (because I use a lot of old, non-English references, I’m often dealing with non-standard orthographies that EndNote has a lot of trouble with). However, my EndNote library is invaluable as my index for what references I have on hand.

    And for the record, my separate articles are simply filed alphabetically by author. Journal issues are on the shelf alphabetically according to journal. Individual books are still sitting on the shelf randomly, while photocopied references too long to fit in the filing cabinet are sitting randomly in boxes with the title on the box, but I don’t have too many of those at the moment to be be able to find things.

  33. #33 Dartian
    March 11, 2010

    Christopher:

    a complete pain in the khyber

    Now that’s an original simile!

    Since we’re sharing filing practices… I sort my hard copies of reprints by taxonomy (‘Mammals in general’, ‘Primates’, ‘Cetartiodactyla’, ‘Birds’, etc.), or by topic (‘Ecology’, ‘Physiology’, ‘Cryptozoology’, etc.), and arrange them alphabetically by first author. At one point I tried to follow a colour code system where I put papers on different subjects into differently coloured folders (e.g., I had all my papers on chiropterans in blue folders). But I very quickly run out of different colours, so nowadays I no longer bother with that. Like Darren, I also have all the references listed in a bibliography (although my bibliography is currently just a puny 450 pp. long). I also have the references catalogued separately in RefWorks.

    As for my books, I used to follow a similar sort-by-topic system, but I’ve had to largely abandon it. I’ve found out that large, heavy books really need the support of other large, heavy books on the bookshelf, so nowadays I sort my books by size first, topic second.

  34. #34 Mu
    March 11, 2010

    While I still have several cubic yards of paper around, if it’s not in electronic form, it’s pretty much lost. I guess I should have indexed all the paper at some point …

  35. #35 David Marjanović
    March 11, 2010

    I’m often dealing with non-standard orthographies that EndNote has a lot of trouble with

    EndNote X for Mac can deal with all that. EndNote X for Windows, however, can’t.

  36. #36 Zach Miller
    March 11, 2010

    Indeed, I much prefer reading a physical piece of paper than a computer screen. Strains the eyes. My own papers are locked up in a big filing cabinet, and are arranged by general category, year, and senior author’s last name. Even though I’ve been getting PDF copies of papers now for years, I print most of them out for reading.

  37. #37 Sven DiMilo
    March 12, 2010

    Also, it’s much more fun to hand a grad student a big fat manilla folder of papers, saying “you need to read these!,” than it is to e-mail pdfs.

  38. #38 AnJaCo
    March 15, 2010

    Thanks all for your feedback.

    And thanks to Rob and Owlmirror for the Mendeley link. It seems to have some use.

  39. #39 Rory
    March 20, 2010

    I like the stickers from kids books. I recognise some of them from my childhood (:

  40. #40 Nick Gardner
    April 1, 2010

    I think electronic libraries are more environmentally friendly than having large “dead tree” libraries. :/

The site is currently under maintenance and will be back shortly. New comments have been disabled during this time, please check back soon.