An open letter to PLoS ONE — a pox on your numbered references!

January 7, 2011

In most journals, in-line citations are by author and year.  So, for example, if someone writes “Haplocanthosaurus has been recovered as a non-diplodocimorph diplodocoid (Wilson 2002)”, you know that the paper that recovered Haplo in that position was, well, Wilson 2002.  And everyone who works on sauropods is familiar with Wilson 2002.

But there are some journals — our old friends Science and Nature are the most significant perpetrators here — that use numbered references instead.  So you’d read “Haplocanthosaurus has been recovered as a non-diplodocimorph diplodocoid [35]“, and then you have to flip to the end of the paper, look up number 35 in the numbered list of notes, and see that the reference is given as “J. Wilson, Zool. J. Linn. Soc. 136, 217 (2002).”  (Yes, it’s true: Science doesn’t even bother to tell you the title or end-page of the cited paper.  You just get author name, hghly abbrvted jrnl ttl, volume, start-page and publication year.)

This is completely stupid, of course, but you can just about see why the world is that way: S&N are basically print journals (albeit with online editions), and space is at a very tight premium.  So this kind of extreme compression may be worth the pain it costs in terms of space recovered.

But you want to know what’s really stupid?

PLoS ONE, and the rest of the PLoS journals, use numbered references.  Yes, PLoS ONE, the online-only journal that has no length restrictions whatsoever.  In PLoS ONE, you can have as many giant figures as you need, and as many tables, and as much text.  Yet still they niggle away at space by using the objectively inferior numbered-references format.

Why?

I can only assume it’s because they want to look like Science ‘n’ Nature.

Which is really, really, really stupid, because the whole point of the PLoS journals is that they’re not Science and Nature.  PLoS is the antidote to all the dumb diseases that the tabloids have infected us all with.  But for some reason, this particular part of the Tabloid Plague Complex — numbered references — has been picked out as worthy of promotion.  The stupid, it burns.

I’ve made no secret of the fact that when I finally get around to finishing the Archbishop description, I’ll be sending it to PLoS ONE, mostly because of its open access and its handling of figures: no limits on number, and they’re made available at original resolution.  The use of numbered references is a significant drawback to comprehensibility, but a price I’m prepared to pay in order to get those delicious figures.

But I was interested last night, when discussing journal selection with a colleague who will remain nameless, to read this [edited for punctuation only]:

Everyone loves PLoS — I can’t stand their referencing …  I just think no way would I want to have a reader of a my hypothetical longer paper suffer that.

And yes, it is an abolute deal breaker for me.

The longest paper I had to deal with was Hocknull’s “short” monograph on titanosauriforms/Australovenator.  What a nightmare for me.

I hadn’t realised how strongly the feelings run for some people.  My interlocutor was dead serious — I did check.  He’s going to be not sending his good papers to PLoS journals for this single reason.  Because of this dumb, ever-so-avoidable screwup.

Come on, PLoS people — sort it out.  (I called out Palaeontologia Electronica on their lame image resolutions, so it’s only fair that I spread the love around.)

SEE ALSO: A pox on your numbered references, redux

Acknowledgement

The very nice Lego Nebulon B Frigate that decorates this page is the “Malevolent Nova”, created by The One They Call Eric.

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56 Responses to “An open letter to PLoS ONE — a pox on your numbered references!”

  1. Mike Keesey Says:

    If I may offer a dissenting view…

    Numbered references are a bit annoying in a printed journal. But, as you point out, this is not a printed journal. Since it’s electronic, it can (and should, and does) use *hyperlinks* for references. Because of this, it makes sense to choose an unobtrusive form that gets in the way of the reading as little as possible. Really, they could just get rid of ALL the reference notation and just link the text itself! The only problem with that is that it’s useless if printed out; numbered references are backwards compatible.

    Seems like a good choice to me.

  2. Nick Gardner Says:

    I don’t find full author citations to be obtrusive to my reading, I find knowing what the sources are for statements to be absolutely essential when I’m reading a paper. =P

  3. Grant Says:

    Another option would be to have rollovers on the square-bracketed citations, so that hovering a mouse over the number would reveal what is being referenced.

    (Likewise it is possible to have text appear in the browser’s status bar, which has the mixed blessing of not obscuring the text being read, but on the other had asking that the reader track eyes to the status bar.)

  4. Mike Taylor Says:

    Mike, when I click a numeric reference in the online version of the PLoS ONE article, the whole page leaps away from where I’m reading and launches me into the middle of the reference list. Not what I wanted at all. I just want to know what paper is being cited, and continue reading.

    Grant, rollovers on the numeric references would go some way to making the online versions of PLoS ONE articles bearable, but wouldn’t help at all if you print them out. (Text in the status bar would be less useful, I think — I know that my eye completely fails to pick this up when its used.)

  5. Zen Faulkes Says:

    Gregory (1992) called the Harvard reference system “unspeakable.”

    He gives an example from the journal Gut, in which replacing “author and year” references with numbered references reduces 149 words to 22. He writes, “The original passage is unspeakable and unreadable, but neither the author nor the editor is interested in whether anyone reads the paper. Indeed, they prefer nobody reads beyond the summary, or better still, beyond the authors’ names.”

    I think people’s preferences for one system over another are quite telling about what different readers consider relevant. I may have a post of my own about this later.

    Reference

    Gregory, M. W. 1992. The infectiousness of pompous prose. Nature 360: 11-12. doi: 10.1038/360011a0


  6. I’m totally with Mike on this one. The numbered citations were one of my few real gripes with publishing in PlosOne, and I would rather absorb the citation while reading rather than flipping back and forth. If they had full text citations AND they were hyperlinked, that would be good.

  7. Bill Parker Says:

    Bravo! I am not a fan of the numbered citations either. It is a pain for the author and the reader. Like Mike I dislike immensely having to constantly flip back to the reference section in a printed version. It is bad in S & N and almost unbearable in a longer paper like PLoS ONE allows.

    As an author, the citations are not listed alphabetically, but rather by order of placement in the text. Therefore if you forget a reference or decide to add one or more you have to completely renumber all of your references through the entire paper an reference section. Not fun.

    I vote with Jeff. Hyperlinked full text citations. Please PLoS ONE…please.

  8. Zen Faulkes Says:

    Bill: Some reference manager programs can renumber things for you automatically.

    Investing in a reference manager program was probably the single best buy I ever made as an academic.

  9. Mike Keesey Says:

    Word, for one, can do automatic numbered references.

    Mike (other Mike), fair point about what the actual hyperlink is going to. Ideally it would be a rollover with the citation and an external link. But it still works printed out if the numbered references are also listed at the end.

  10. jay Says:

    Awesome that this issue to brought up. PLoS ONE can really be improved if this is addressed.

    1) Another issue is that errors in numbering can be compounded/increase with the length of the paper, especially where the authors make modifications to MS but don’t employ a reference manager.

    To illustrate, if the author cited Taylor, 2010, when he really meant Taylor et al., 2011, (hypothetical refs) i should be hazard a guess regarding the intended paper, being aware of topic & literature of that topic somewhat. Instead, it will take me a while (or not at all) to figure out that ref [34] was meant, not [46] when this mistake is made.

    This actually happened to me once, but i don’t recall the actual example ref numbers here, when i realized the actual cited ref was nothing to do with the point being made in-text, realizing the actual ref had cited numbers reversed–perhaps the author didn’t use a ref-manager at this sentence.

    2) Some of you might recall the issues on citing pneumaticity research when the paper on Aerosteon came outa few years back–could it be that number-only refs encourage misciting of works, because authors know not every single number will be checked as the paper is read? I think it unlikely, but at least if a read something like:
    “…the African species B. brancai was placed within a separate genus recently, Giraffatitan (Taylor, 2009; Upchurch et al., 2004)” should ring alarm bells, because we all know the 2nd reference made no such claim.

    3) – using ‘back’ to return to the text (from the ref list) is fine if reading online. However, most times i tend to read over a paper, i’ve downloaded the pdf. The linking/’back’ function are not available on the pdfs.

    For a couple of larger papers, i’ve printed them out (not intending to stare at a computer screen for ages). One paper, i needed to utilize while overseas as well as away from internet access. You can imagine the difficulty the number style prooved.

    Backing Jeff & Bill here, there is no reason why hyperlinked harvard-style in-text citations can’t be used in journal with no length restrictions.


  11. I totally agree with the post. I want to know what article is being cited, and end up flipping to and fro. It’s irritating.

  12. Jaime Headden Says:

    Following of what Mike Keesey said, simply observing a reference-heavy sentence, such as a paragraph citing apomorphies in a diagnosis, or a discussion of author’s opinions on a taxonomic composition of a clade, allows one to see where “(Chiappe et al., 1993)” and “[4]” come into competition, and where the flow of the text is best preserved by the latter, not the former.

    Jay commented about reading papers in paper format. In response to this, I’d aver that reading in physical form is no longer a positive option for me (for space reasons, as well as accessibilty). My computer is always available, and a downloadable reader (iPad or such) can access the digital format for reading just as well for portability. Such readers will become cheaper and more commonplace, although I ignore the doom/gloom about them replacing paper. They should (environmentally) but won’t.

    Graphically, I snapshot or download the images for full-size reading, a resolution that can often be impaired in paper as the pdf file generated uses a very small (300dpi or less) digital format for figures for print, and can be expensive to reproduce. So viewing these images on my computer and using a digital measuring tool and simple math allows a viewer to correctly scale against the provided scale and make their own measurments on the fly. This advantage outweighs the print version of a paper for analysts, and the previous point outweighs long-form referencing in the body for readers.

  13. jay Says:

    “Jay commented about reading papers in paper format. In response to this, I’d aver that reading in physical form is no longer a positive option for me (for space reasons, as well as accessibilty). My computer is always available, and a downloadable reader (iPad or such) can access the digital format for reading just as well for portability. Such readers will become cheaper and more commonplace, although I ignore the doom/gloom about them replacing paper. They should (environmentally) but won’t.

    Graphically, I snapshot or download the images for full-size reading, a resolution that can often be impaired in paper as the pdf file generated uses a very small (300dpi or less) digital format for figures for print, and can be expensive to reproduce. So viewing these images on my computer and using a digital measuring tool and simple math allows a viewer to correctly scale against the provided scale and make their own measurments on the fly. This advantage outweighs the print version of a paper for analysts, and the previous point outweighs long-form referencing in the body for readers.”

    This misses the point I make — i also noted the PDF format of PLos One papers (with out the ‘back’ function) is similar to a printed-out version — the reader still has to flick back and forth between the ref list and the body text to decipher the citations in both of these formats


  14. I agree with the post.

  15. Bill Parker Says:

    @Mike Keesey,

    A post sometime on how Word can automatically do numbered references would be greatly appreciated.

    Some of us our still in the technological stone age and neither have the money (e.g., for ipads) nor the time to learn all these tricks (e.g., screenshots, reference managers, etc…) to come out. Eventually we will be left behind (I marvel at how intuitive computer use and the internet are to my six year old kids), but for the time being we really like to read hard copy and full citations in the text ;).

  16. Mike Taylor Says:

    @Bill … I really must make the time to learn Zotero. A decent starting point is Andy Farke’s post about it over on the Open Source Paleontologist: http://openpaleo.blogspot.com/2007/12/reference-managers-on-parade-part-iii.html

  17. Lynn Cage Says:

    It’s an electronic journal: why not let the readers choose how they want the references displayed?

  18. Mike Taylor Says:

    Lynn’s right, of course — there is no technical reason at all why the PLoS journal’s online rendering of articles shouldn’t be changeable on the fly. But I’m interested, too, in how the articles appear as PDFs, and I do think the right number of PDF versions for the journal to render is one. The reason for that is so that when I cite a statement made in a PLoS paper, I can give the page number.

  19. Mike Keesey Says:

    @Bill, I’m not sure a full post would be necessary. It’s just under Insert > Footnotes. There are options for placement of the references (end of document vs. end of page) and numbering style (Arabic, Roman, etc.), and Word pretty much takes care of the rest. (The open source alternative to Word, OpenOffice‘s Writer, works pretty much the same way.)

    On Mike Taylor’s comment, that actually brings up some good points. What does a “page” mean in the digital era? And are page numbers really the best way to specify position within a document?

    It seems to me that the way nomenclatural codes handle this is better. When you cite, e.g., the draft PhyloCode, you don’t use page numbers—you use, e.g., Art. 12, Note 4.3.1, etc. What if papers simply numbered their sections? Then citations could look like (Taylor 2012 §3.1.5). Not only does this protect against confusion from formatting issues (a problem I ran into just yesterday in a project I’m collaborating on), but it’s also a much more accurate method of specifying the intended content.

  20. SamW Says:

    I’d like to add that while most of these comments mention that people would automatically know what a paper was about when seeing a Harvard reference, it is also useful for people who don’t.
    As a student, when reading up on a new topic, I prefer the Harvard system because when I see a specific author or even paper referenced often across several other papers, I know that they’re important and I should check it out. I’ll remember it for the future. Numbered references however do not allow the learning process to include authors but instead create anonymity.

  21. Jura Says:

    Mike Keesey wrote:
    “It seems to me that the way nomenclatural codes handle this is better. When you cite, e.g., the draft PhyloCode, you don’t use page numbers—you use, e.g., Art. 12, Note 4.3.1, etc. What if papers simply numbered their sections? Then citations could look like (Taylor 2012 §3.1.5).”

    That looks way too similar to a bible verse. Do not like.

    As for dynamic reference lists, I think it would be a great idea, but I wonder how much extra work it would mean for the authors (which ultimately depends on what the programmers decide on).

  22. Allen Hazen Says:

    Author and WHICH date? It may not be relevant to your work, but in my field (I have recently been writing about the history of logic) I have frequent occasion to refer to classic papers that have been reprinted, and I would really much prefer a citation to the date of original publication, not to some later reprinting. It bugs me when I see, for example, [Russell 1956]– “Mathematical logic as b ased on the theory of types” was published in 1908, dammit, and I don’t care if author of a paper i am reading got it from March’s 1956 collection of Russell papers!

    But I think at least some style manuals insist that a date in a reference should be to the edition actually consulted.

  23. Mike Keesey Says:

    “That looks way too similar to a bible verse. Do not like.”

    Actually, I think you’ve helped make my point there. Think of all the thousands of editions of the Bible printed–different translations, different layouts, different pages. And yet the chapter/verse system allows cross-referencing regardless of edition. It’s a very elegant system.

  24. Mike Taylor Says:

    Allen, what you are describing is Just Plain Wrong. When citing a published work, of course you cite the date of original publication. (Exception: when you are specifically citing a particular edition — especially in the case of books such as The Dinosauria in which consecutive editions are really completely separate books.)

    Mike K., I agree that a page-independent numbering scheme could be the answer, and that it works very well for the bible. But there’s no doubt that it’s visually cumbersome to sprinkle your work with all those §3.1.5s, whereas page numbers are pleasantly unobtrusive. I’m not sure yet what I think the best answer is.

  25. Jura Says:

    I don’t see what the big deal is with page numbers. PDFs already naturally produce standard “print” sized pages, which makes citing page numbers really easy. Even if one doesn’t ever print it out the page numbering scheme still exists, and since it is available in a universal format, the page numbers don’t change. Let’s not try and foist yet another cumbersome citation scheme on people when the current one works just fine. Besides how much better is 3.1.5 over page 7, when everyone reading it online is just going to do a ctrl/cmd+F anyway?

  26. Andy Farke Says:

    I figured I should probably chime in on this with a few notes/thoughts. Let me also be clear that although I volunteer as an editor at PLoS, I am speaking only as a private citizen here (both for points on which I agree as well as disagree with current journal practice).

    1) I too have a strong _personal_ preference for the author-year citation format. It is (for me) much more convenient to follow an author’s citations when they are right there in the text. But, see the next point. . .

    2) The author-year format is helpful primarily if you are already familiar with the relevant literature. Otherwise, you’re still in the game of flipping back and forth to the reference section. If I quote from my 2010 JVP paper on ceratopsian sinuses, “Less detailed descriptions have been published for other chasmosaurine and some centrosaurine ceratopsids (e.g., Gilmore, 1917; Lehman, 1990; Sampson, 1995; Sampson et al., 1997),” a long-time ceratopsian worker will know right off the top of her or his head that I’m talking about the Gilmore Brachyceratops monograph, Tom Lehman’s paper in the Dinosaur Systematics volume, Scott Sampson’s description of the Two Medicine centrosaurines in JVP, and the ZJLS paper with Scott, Michael, and Darren. I could almost write the citation for each of these off the top of my head. Contrast that with this example (Najman et al., 1997, Geology 25:535-538): “Why is this so, as crustal thickening and metamorphism are thought to have occurred by this time (Frank et al., 1977; P. Zeitler in Hodges and Silverberg, 1988; Inger and Harris, 1992; Searle, 1996, and references therein; Vanny and Hodges, 1996)?” Although I understand the meaning of the sentence, the names and dates have absolutely no meaning to me, other than to help me find the appropriate citation in the back.

    3) This leaves the main advantage of the author-year format in that it improves the likelihood that the authors will maintain the correct citation-reference correspondence when adding that one reference to the middle of the paper during revisions. With the rise of reference managers, that issue becomes increasingly irrelevant.

    4) I think people are giving Science and Nature a little too much credit for driving the numbered citation game. Yes, they certainly are the most visible journal to those of us in paleo/geo/gross morphological sciences, but that’s a rather myopic view. I just did a quick survey of the other 99 percent of the scientific literature, and numbered citations simply dominate. Even arXiv – the epitome of digital presentation with no real standard format – has a vast majority of papers with the [1,2,3] style (in fact, the only counterexamples I found were in a handful of biologically-oriented papers). The medical literature (medically oriented papers are the great majority of PLoS ONE submissions), computing literature, physics literature, etc., often use on numbered citations. Let’s face it – we are not the biggest fish in the sea. It doesn’t mean we’re wrong or can’t change things, just that it’s a very uphill battle.

  27. Mike Keesey Says:

    The example I gave with section 3.1.5 is deeper than most references would have to be. I want to make it clear that I’m not suggesting anything as finely-grained as Bible verses or nomenclatural code articles.

    For example if I wanted to cite the Introduction of this paper, it would simply be §1. Or, to cite the section titled, “An Endocast with Olfactory Bulbs and Cerebrum,” it would simply be §2.3. The only change needed to the paper would be that each of the headers would require a number. Mike Taylor’s right that this is more obtrusive than page numbers, but in my opinion it’s a small obtrusion and well worth the benefits.

    @Jura, I don’t think that considering the PDF to be the canonical form of the document is a good idea, at least not in all cases. I’m far more likely to read the HTML version of the paper I just linked to. Guess what–no page numbers in the HTML version! And why would there be–it’s an electronic document. Pages are an artifact of codices, and while codices have been dominant for a very, very long time (to the point that we hardly ever even use the word “codex”, and just assume it), that is beginning to change as electronic alternatives gain ground.

    (And note that “§2.3″ specifies the intended content better than a page number would.)

  28. Mike Keesey Says:

    I botched the link in my last comment. Here it is: doi:10.1371/journal.pone.0001230.

  29. Michael Richmond Says:

    The astronomical literature is still dominated by the old-fashioned (Smith 1999) notation. Thank goodness.

  30. Simon Says:

    Long time lurker, first time poster,

    I completely agree with you post Mike! Every well-informed scientist/reader knows most other authors by name (and reputation) and knows instantly whether the cited reference is any good or not…

    What’s even more irritating is that the reference list in Nature or Science isn’t alphabetical, it’s ranked according to where in the article the reference is from. Highly annoying.

    SamW made a good point with regards to students (or just about anyone) who wants to read up on a certain topic. See a name pass a few times in several articles, and you’ll instantly know “those are some important papers…” (well, they should be, anyway).

  31. Andy Farke Says:

    I just posted a lengthy tome on the citation format topic over at The Open Source Paleontologist.

  32. Nathan Myers Says:

    As an outsider, I wonder why references are still shoveled to the posterior parts of the paper. Surely, with modern page layout software, references could better be placed right at the bottom of the page, or even (in on-line formats) the paragraph. Then the numbers may start at 1 on each page, and the whole takes less space, overall, than S’n’N’s hypercompressed format, without any of the annoyance.

    Yes, sometimes exigencies of formatting would force you to consult the next or previous page, instead. Please excuse my dry eyes.


  33. Nathan,

    Classic literature (1800’s to early 1900’s) for paleo, geo, and even bio cited works as footnotes, including comments or opinions on a citations effect on the topic being discussed when used. This format Becomes extremely easy to follow as one’s eye merely flow to the bottom of the print page to catch the citation. The problem with this method is that in high-citation regions of an article (e.g., the introduction, methods, historical aspect of a more ingrained topic such as a systematic review portion, etc.) this can take up a very large portion of the page.

    This format was used as recently at the 1990s in (if I recall correctly) both editions of Paleontologicheskii Zhurnal, which featured at most on average 15 references throughout a ten-page article.

    Hyperlkinks in a digital age shortcut this, and there are ways to handle this even further in a digital only format by creating a sidebar for citations, so that one may never scroll down, then scroll back up, or jump to section, etc. In print, this is not possible, and high-citation works must contemporize by having the citations as endnotes or with short easily-recognized shorthand (Andy’s argument) embedded within the text to associate with the endnotes.

    Given the format, no one solution appears to best be suited for the way each individual wishes it were, for whatever flow they seem to enjoy. On my own blog, I use embedded numbers to associate with endnotes for the sole purpose of cleaning my text fields of citations and make them as unobtrusive as possible while preserving their position and referencing capability, but I would never claim this is the best way. That’s just how I feel it should be for me.

  34. Mike Taylor Says:

    Nathan, the problem with just putting the full reference as a footnote on each page is that it’s very common to cite the same paper over and over again. So, for example, my 2009 paper on Brachiosaurus and Giraffatitan would have ended up absolutely packed with copies of the full references to Janensch 1950a and 1961 — probably both of them on almost every page. Having a separate bibliography eliminates this repetition.

  35. Brad McFeeters Says:

    Now I want to see some Lego models of sauropod vertebrae.

  36. Mike Taylor Says:

    Brad: Waaay ahead of you …

    :-)

  37. Ilja Nieuwland Says:

    In a digital age it is no problem at all to present notes in one form on a web page (for instance as ‘hoverable’ text) and in quite another and standardised form in print or PDF.

  38. D Rordorf Says:

    “In most journals, in-line citations are by author and year [...]” but only in your humanities and social science. Medical, (natural) science and technical journals usually use the numbered references. It is more logical. It is wrong to use the “Wilson 2002″ style. It is not a unique identifier. If you have several papers from that guy in 2002 cited in the same paper, you have to go figure out which it is (or you need to add a, b, c, … labels – which is then again not far from just numbering the references!).

  39. Mike Taylor Says:

    D Roedorf, I’ve never seen a paper that cites using Author-and-Date style, that didn’t use disambiguating letters so that readers known when a citation is to Taylor 2009a and when it’s to Taylor 2009b. Such papers might exist, but I don’t think they’re in any palaeo journals.


  40. Authors at Palaeontologia Electronica have the option of publishing high-resolution images if there is need to do so. We require two levels of resolution for all authors: screen-resolution and screen size for the HTML version (i.e., 72 dpi at full screen size) and print-resolution and printed page size for the PDF/print version (i.e., 300 dpi at page width size). Most authors do not opt to publish versions of their figures at resolutions higher than that, but it is an option free to those few who have a real need for it.

  41. Mike Taylor Says:

    Thanks, David, that is good news indeed. But isn’t this a new addition? I don’t recall there being such an option in place back when I wrote this article.


  42. Palaeontologia Electronica has used the Taylor 2009a, Taylor 2009b citation system since its conception 14 years ago. We also link directly to the specific reference. If the reader is curious about the reference, the reference list can pop up for reading at the location of the specific reference with a single click – beside (or floating around) the page that is being read.

    When an author is heavy-handed with the references, I personally think the name/date does slow reading down, not naming any names here … But the benefit of knowing what reference the author is referring to seems to out-weigh the weight of a sentence full of references.

  43. Gerard Ridgway Says:

    Jennifer’s point above, “When an author is heavy-handed with the references … name/date does slow reading down”, is exactly why I prefer the name-date style! It discourages the kind of lazy writing where authors say “blah blah broad concept [1,3,5,9-27]“, and encourages authors to make specific points supported by one or a few specific references, which is almost always better for the reader (whether they’re experienced enough to recognise the author names or not).

  44. Gerard Ridgway Says:

    Having just read the article Zen Faulkes cited (Gregory, 1992), I see that Gregory’s example reduces an unreadable and useless paragraph to a much shorter, more readable, but *still largely useless* one:
    “All these measurements have wide ranges of values in both control [1-12] and coeliac [3-7,9,11-14] mucosae and the differences between the means are small [3,4,6,9,13-15]”

    I would prefer to read something like:
    “Measurements have a wide range of values in control mucosae, from 12.3 (Bloggs, 1999) to over 50 (Smith et al., 2000; Jones, 2001). Values reported for coeliac mucosae overlap these, with the largest study (Bloggs et al., 2002) reporting a mean (std) of 34.5 (12.3) …”

    Sure, it’s longer, but at least it tells you something useful without you having to go away and read all 15 of the references originally cited. For all we know from the original passage, the means and standard deviations in references 1-12 might all have been virtually identical, in which case just cite the first and/or the biggest study (and say what its values actually were!). If there are inconsistencies, why not state them explicitly? E.g. “Smith’s (2000) finding of a mean of 60 is inconsistent with all six studies reviewed by Jones (2001)”. (all numbers made up here without reference to the cited articles in the original passage).

    In my opinion, it’s very rarely helpful — even in a review article — to cite more than about three articles for a specific point, and one can easily read a sentence containing three author-year citations.

  45. Mike Taylor Says:

    Gerald, your rewritten example is ten times more informative than the original. Food for thought, there, for when I am writing my own introductions.


  46. I agree with the writer. When reading over the same subject in ad infinitum, it is really nice to see the author year on refs. to be able to say, “oh yes, I’ve read that”, or “OH! this might be something new”. Make it easier on us PluSOne, your such an excellent…. journal/site/resource/social-networking/excellent place to find information.

  47. D L Dahly Says:

    The use of full references in the text is also good for learning about your field. When you see the same references over and over, that should tell you something. Then you can revel is all your geeky academic glory at cocktail parties by casually mentioning “Pearson, 1901″ to a colleague – which sounds much better than saying, “…reference number 3 from this paper I just read.”

  48. Mike Taylor Says:

    Yes, absolutely. Author+date citation are themselves information, not merely pointers to where information can be found.


  49. Just a relativistic quibble (I like to complain, I guess):

    In connection to Dahly’s statement that when “you see the same references over and over, that should tell you something,” Mike says:

    Author+date citation are themselves information, not merely pointers to where information can be found.

    This shouldn’t differ from the repeated appearance of a [number] in place of a alphanumeric in-text citation. The difference is in how we perceive the reference. As Ridegway’s argument above goes, readability of a sentence increases when one is familiar with the topic, or some of the references, than when one has plugged only numbers in. Numbers prefer raw data entries, are shorter, and yes ultimately drier and less readable. They require you to scroll to check what you should be looking at, and this is their biggest pain. But … words for the unfamiliar require the same thing. Where words differ most strongly is that the printed word becomes more prevalent than it would otherwise be. I might even suggest that it can border on the egoistic to prefer to see one’s [name] printed over and over in the text than to see “[number]” instead. This may then be a psychological distinction that detracts from the scientific brevity desirable in citation.

    Nonetheless, I agree that PLoS ONE should switch to alphanumeric cites, as this agrees with most other journals (in bio and paleo fields, anyway), and for other reasons stated by Mike and commenters.


  50. [...] had occasion to be critical of them, I’ve also been critical of Palaeontologia Electronica, PLOS and Royal Society publishing, among others; and I have praised Elsevier when they’ve done [...]


  51. [...] am preparing a manuscript for PLOS ONE, which uses numbered references rather than author+date citations like sane journals. And I am hating it. I am taking perfectly [...]

  52. Kenneth Carpenter Says:

    PLoS An Unpleasant Experience

    I finally bit the bullet and submitted a paper to PLoS One. It will probably be my last.

    Hate the [numbered references]. Adding a new reference meant changing all the numbers of the references AND in the text. It is really easy to screw that last part up. I wasted so much time verifying references after rearranging paragraphs and adding new references in different paragraphs on the same page (“let’s see, number 17 became number 23, or was that 24? No, I think it is now 22. No, wait, I added a new number 17. I also deleted 19, so now does that make 17, which became 24, now 23? Ah shit! start all over!”). This mess certainly explains why I have caught erroneous references in PLoS papers (names withheld to protect the guilty). Name-Date will not change and in fact stays the same regardless of how much rewrite I do. I suppose you could start with name-date and change these to numbers when you have finished the manuscript as I initially did. But then came the BIG screw up during the post-review revision.

    PLoS must be cheapskates when it comes to electrons – uses more to write (Hatcher, 1901) than [4]. Anyone read a paper on sauropods is going to know that Hatcher 1901 means his osteology of Diplodocus. But what the hell does [4] mean? It is SOOOOO frustrating trying to find where you were reading when you foolishly went to check what [4] was.

    I also dislike having to shoehorn according to “set” (i.e., mandatory) headings, like “Results”. How does a description of a specimen become a “Result”???? Authors should be allowed to use appropriate headings that have meaning to colleagues reading the paper, not simply use headings dictated by someone who obviously doesn’t publish in their own journal.

    Also incredibly silly are some of the disclosure statements required. “Funding: The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript” This reads really SILLY paying for the work out of my own pocket: “Funding: The funder had a role in study design, data collection and analysis, decision to publish, and preparation of the manuscript”. Think that is somehow going to “taint” the paper? “Shocking! the funder influenced his own paper!”

    Another silly disclosure: “Competing Interests: The authors have declared that no competing interests exist” (besides, if I did, I wouldn’t admit it and you’d never both to verify, so why ask?).

    Sorry, PLoS, but the hassle and frustrations with the [references] and the added petty crap you piled on top is a deal breaker for me. There are plenty of other journals out there with fewer headaches. My time is better spent writing, not dealing with your obstacles.

  53. Mike Taylor Says:

    Well, Ken, I’m afraid I have to agree with most of that. The numbered references are really fantastically stupid in this day and age, and horribly error-prone. They’re OK for tiny papers that cite half a dozen works, but not for substantial papers.

    For the paper that Matt recently had accepted at PLOS, he submitted initially with sane (= author+date) citations, with the promise of converting the final version if accepted. That way, he was able to do the revisions without breaking all the references.

    Regarding the standard headings: yes, completely inappropriate for palaeontology. I just ignored these in my submission, and it doesn’t seem to have caused a problem.

    I don’t really see a problem with the funding or competing interests statements, though. These are pretty standard in most journals, aren’t they?

    Still and all — I hope that when the paper is out, and when it’s very widely read and cited, you’ll feel it was worth doing. Mean time, don’t forget there’s PeerJ, which does right all the things PLOS does right, and doesn’t care what format your references are in!

  54. Jim Bassuk Says:

    @Ken Carpenter: I feel your pain when you add an extra reference, but this is why I’ve used Reference Manager for 20 years…and alot of folks use EndNote — and when you get the hang of it, this pain simply goes away (of course I agree with non-numbering is the way to go)…


  55. With PLOS is really depends a lot on the editor you get.


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