Citation Format Wars

Over at SV-POW!, Mike Taylor recently addressed the issue of how to format in-text citations. Writing in his inimitable style, he makes the case that PLoS ONE is simply doing it all wrong; the majority of commenters there have agreed. I posted a lengthy comment there, but realized that it would be appropriate to revise and republish those thoughts here too.

First off, let's have a quick recap of the issue. When writing a scientific paper (or any paper, for that matter), it is essential to credit the sources of information and ideas. Not only does it allow the reader to learn more about the topic, it's the ethical thing to do. Rather than a simple reference listing at the end of the paper, most scholarly works also reference the relevant works within the text. This is called an in-text citation, and allows the reader to know precisely which information was associated with which author.

Two Worlds
Two styles of in-text citation dominate the scientific literature. The first of these is author-year, which looks something like this: (Farke, 2010). The second is numbered, which looks like this: [1]. This number then refers to a specific bibliographic entry at the end of the paper. Many variants of each style exist.

PLoS ONE uses numbered citations, in common with many other high profile journals (such as Nature), and in marked contrast to most of the paleontological, geological, and anatomical literature (such as Journal of Vertebrate Paleontology, The Anatomical Record, Geology, and others). The SV-PoW! post, of course, argues that the numbered format is vastly inferior to the author-year format. Let's boil the argument down to its essentials, and delve into the pros and cons of both formats in more detail.

Two essential reasons are given for why the author-date format are preferable: 1) ease of reading for authors familiar with the literature; 2) paleontologists don't like it. PLoS ONE thus chose a numbered reference format simply because they wanted to copy the glamour magazines. Do any of these arguments hold up?

Advantages of Author-Year (and disadvantages of Numbered)
Of course, there are some significant advantages to the author-year format. These include:

1. It's easy for readers who are familiar with the literature to know exactly what's being discussed. 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 see pages from those papers when I close my eyes, and I could almost write the citation for each of them off the top of my head.
2. You don't have to flip back and forth between the main text and the reference list. For the ceratopsian expert described above, there's no need to waste time skipping around the paper (or PDF). It's just easier.
   
3. It helps readers new to the field to become familiar with the major names and papers. See the names "Wedel," "Taylor," "Wilson," "Curry-Rogers," and others often enough, and you probably have a good picture of a few of the major recent workers in sauropods.
   
4. It's easier for authors to keep their references straight. When writing and revising without use of a citation manager, the numbered system can get very unwieldy. If you add a reference in the middle of the paper, you not only have to renumber the entire bibliography after that reference, you also have to change the numbers within the manuscript itself. Miss one, and your readers are going to be grumpy when the number and citation don't match up.
5. It's familiar to the paleontological community. As mentioned above, "It's Got What Paleontologists Crave."
   

Disadvantages of Author-Year (and Advantages of Numbered References)
As you might have guessed, there are some disadvantages, too:

1. The author-year format is helpful only 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. Anticipating that most of my readers are savvy to vertebrate paleontology, but not to the latest in tectonics, contrast my above example in point 1 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. I'm not familiar with that literature, so I'm annoyed by the extra text.
   
2. Not every reader wants to become an expert on a given subspecialty. Believe it or not, I may not be reading a plate on Indian tectonics (or sauropod vertebrae) because I want to become an expert on said subject. Let's say that I'm chasing the above-mentioned example from Najman because I want to know the context for some fossils I found in a format described in that paper. I just want the bare minimum of info, and I don't care about Frank, or Zeitler, or Hodges, or Silverberg, or Inger, or Harris, or Searle, or Vanny. Sure, maybe I'll chase some of those references for alternate opinions, but once that's done the names will probably never cross my mind again. This leads to the next point. . .
3. The author-year format clutters the text. I'm not the first person to state this, and I'm not the last. By editing my ceratopsian quote above, you now get: "Less detailed descriptions have been published for other chasmosaurine and some centrosaurine ceratopsids [1-4]." Try the same with the Najman quote. Much shorter and more easily readable. A comment on the SV-POW! post by Zen Faulkes gives some more nice supporting opinions.
4. Most of the rest of the scientific world uses numbered citations. 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 journals to those of us in paleo/geo/zoological sciences, but that's a rather myopic view. I 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., most often use numbered citations. Let's face it - paleontologists 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.

Closing Words
So, I have to say that the arguments for author-year and against numbered references are not as simple as one might hope. Major advantages and disadvantages characterize both formats. In the end, I suspect much of it comes down to "what we were born into." I like the author-year format because that's all I've ever known. My spouse, who is a physicist, surely thinks otherwise, but then again all she has ever known is the numbered format. She also thinks paleontologists are silly because we don't use LaTeX (and good luck getting that instituted, no matter how easy it would make things for us).

Interestingly, I came into this with a strong preference towards the author-year citation format, but after thinking about it I'm not sure that numbered citations are the Great Evil that they have been made out to be. What are your thoughts?

Update: The above-mentioned Zen Faulkes has a post strongly coming down on the side of numbered references. He argues that numbered references decrease overall manuscript length, greatly improve readability, and level the playing field for both readers and cited authors. The last argument is particularly novel, and strikes at the heart of the true purposes of citations. I'm not sure I totally agree, but it's definitely food for thought. [12 January 2011]

(As an interesting side-note, the author-year referencing style may be so common in the paleontological and zoological literature because of a historical accident - the format was apparently invented by a Harvard zoologist, and spread throughout the zoological part of the literature. I suspect the weight of the Harvard name didn't hurt.)

Disclaimer: Although I am a volunteer editor at PLoS ONE, this posting is written strictly as my private opinion.

Thank you to the many commenters at the SV-POW! blog, whose thoughts inspired this post.