October 21, 2014
In light of yesterday’s tutorial on choosing titles, here are the titles of all my own published papers (including co-authored ones), in chronological order, with my own sense of whether I’m happy with them now I look back. All the full references are on my publications page (along with the PDFs). I’ll mark the good ones in green, the bad ones in red and the merely OK in blue.
The Phylogenetic Taxonomy of Diplodocoidea (Dinosauria: Sauropoda).
OK, I suppose. It does at least clearly state what the paper is about. I’ll give myself a pass on this since it was my very first paper.
Dinosaur diversity analysed by clade, age, place and year of description.
NOT BAD, since the paper was basically a list of many, many results that could hardly have been summarised in the title. I give myself some points for listing the ways I analysed the data, rather than just saying “An analysis of dinosaur diversity” or something equally uninformative.
Phylogenetic definitions in the pre-PhyloCode era; implications for naming clades under the PhyloCode.
NOT BAD again, I suppose, since it was a discussion paper that couldn’t be summarised in a short title. Could I have said what the alluded-to implications are? I think probably not, in a reasonably concise title.
An unusual new neosauropod dinosaur from the Lower Cretaceous Hastings Beds Group of East Sussex, England.
RUBBISH, since it doesn’t name the new dinosaur (which was of course Xenoposeidon). I was young and stupid back then, and just followed convention. In mitigation, it does at least say when and where the specimen is from.
Case 3472: Cetiosaurus Owen, 1841 (Dinosauria, Sauropoda): proposed conservation of usage by designation of Cetiosaurus oxoniensis Phillips, 1871 as the type species.
DOUBLE-PLUS UGLY. But I am going to blame the journal on this one — they have a very firmly defined format for petition titles.
Head and neck posture in sauropod dinosaurs inferred from extant animals.
RUBBISH. What was I thinking, and why did my SV-POW!sketeer co-authors let me choose such an uninformative title? We should of course have gone with a title that says what posture we inferred. The associated blog-post had a much better title: Sauropods held their necks erect … just like rabbits.
A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914).
ADEQUATE, since the title strongly implies the conclusion (generic separation) even if doesn’t quite come out and say it.
Electronic publication of nomenclatural acts is inevitable, and will be accepted by the taxonomic community with or without the endorsement of the Code.
BRILLIANT. The best title in my CV. You hardly even need to read the paper once you’ve read the title. The only downside: it’s 12 characters too long to tweet.
Sharing: public databases combat mistrust and secrecy.
GOOD, but I can’t take the credit for that (A) because I was third author behind Andy Farke and Matt, and (B) because the journal chose the title.
The Open Dinosaur Project.
OK, but we should have done better. Something like “The Open Dinosaur Project recruits volunteer effort to analyse dinosaur evolution”. Or, if we were being honest (and prescient), “The Open Dinosaur Project will lie embarrassingly moribund for more than two years”.
Sauropod dinosaur research: a historical review.
OK, since it does say what the paper is. But this title is not as good as that of the talk it was based on, “The evolution of sauropod dinosaurs from 1841 to 2008″. (I notice that Mark Witton nicked my title for his talk at TetZooCon.)
Running a question-and-answer website for science education: first hand experiences.
UNOBJECTIONABLE, but not my choice anyway — lead author Dave Hone presumably picked it. Could have done better by stating what at least one of those experiences was.
A new sauropod dinosaur from the Lower Cretaceous Cedar Mountain Formation, Utah, USA.
RUBBISH. At least this time it wasn’t entirely my fault. When we submitted this to Acta Palaeontologica Polonica, it was called “Brontomerus mcintoshi, a new sauropod dinosaur from the Lower Cretaceous Cedar Mountain Formation, Utah, USA”, but the journal made us take the taxon name out of the title. Why? Why why WHY?
The long necks of sauropods did not evolve primarily through sexual selection.
Why sauropods had long necks; and why giraffes have short necks.
EXCELLENT. Short, appealing and (hopefully) funny. When I give talks based on this paper, I use the even better short version, just “Why giraffes have short necks”. But that seemed a bit too cute for an academic setting.
Neural spine bifurcation in sauropod dinosaurs of the Morrison Formation: ontogenetic and phylogenetic implications.
WEAK. We should have stated the conclusion: a title like “Neural spine bifurcation in sauropods of the Morrison Formation is not an ontogenetic feature, but is phylogenetically significant” would have been better.
The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines.
GOOD. Not particularly exciting, but explicit.
Caudal pneumaticity and pneumatic hiatuses in the sauropod dinosaurs Giraffatitan and Apatosaurus.
NOT GOOD ENOUGH. We should have stated the main finding: “Caudal pneumaticity and pneumatic hiatuses reveal cryptic diverticula in the sauropod dinosaurs Giraffatitan and Apatosaurus“.
The effect of intervertebral cartilage on neutral posture and range of motion in the necks of sauropod dinosaurs.
UGH, rubbish. What the heck was I thinking? I should have written this post a couple of years ago, and used it to make me choose a much better title. As it is, it just leaves the reader assuming intervertebral cartilage probably has some effect, but they have no idea what.
I make that six good titles, seven bad ones and six indifferent. Awarding two points per good title and one per adequate title, I give myself 18 points out of a possible 38 — slightly less than half, at 47%. More worryingly, there’s no apparent trend towards choosing better titles.
Must do better.
October 20, 2014
Over on his (excellent) Better Posters blog, Zen Faulks has been critiquing a poster on affective feedback. The full title of the poster is “Studying the effects of affective feedback in embodied tutors”. Among other points, Zen makes this one:
As a browser, I often want a take home message. This isn’t helped by the weak title, which represents most of your communication effort. “Studying the effect of” in a title is bland and uninformative. Every academic thing is “studying the effect of” something. A question would be better, and an answer would be better still.
I think that’s right on target. Unfortunately, we in palaeo are mired in an ancient tradition of uninformative paper titles. We look at Cope’s three indistinguishable 1877 titles “On a dinosaurian from the Trias of Utah”, “On a gigantic saurian from the Dakota epoch of Colorado” and “On Amphicoelias, a genus of saurian from the Dakota epoch of Colorado” and assume that’s the way to do it. Or his 1878 titles, “On the Vertebrata of the Dakota Epoch of Colorado” and “On the saurians recently discovered in the Dakota Beds of Colorado”.
And so we end up with uninformative titles like (to pick one at random from the most recent JVP) “Tilefish (Teleostei, Malacanthidae) remains from the Miocene Calvert Formation, Maryland and Virginia: taxonomical and paleoecological remarks” (what remarks? What did you discover about tilefish?) Or “Latest evidence of Palaeoamasia (Mammalia, Embrithopoda) in Turkish Anatolia” (what evidence? What does it tell you?) Or “On the skull of Radinskya (Mammalia) and its phylogenetic position” (what is its phylogenetic position?). [Apologies to the authors of these papers, whose titles are no worse than many, many others. I needed examples, and they drew the short straws.]
It’s in tribute to uninformative titles such as these that I stupidly titled my dissertation “Aspects of the history, anatomy, taxonomy and palaeobiology of sauropod dinosaurs”.
So what makes a good title? Here’s a rather random list of thoughts. Feel free to chip in with others that I missed.
Give the name of the taxon under study. Stupidly, lots of journals have a rule that says a paper naming a new taxon can’t use the new name in the title. I can’t begin to imagine why anyone thinks it’s a good idea to make sure that the title is missing the Single. Most. Important word, but there it is.
Avoid vague words like “study”, “aspects”, “observations”, etc. Instead, choose a title that tells us what you studied, what aspects were of interest, and what you observed.
Avoid weak puns. Don Henderson’s paper on sauropod step sequences got away with being called “Burly Gaits” because it was a clever double pun; but only just, as it had nothing to do with the Pearly Gates. It’s best not to attempt this unless you have something really smart.
In fact avoid all jocular references to well-known phrases, because they’re lame. Really, how does the introductory phrase improve titles like “Not just a pretty face: anatomical peculiarities in the postcranium of Rebbachisaurids (Sauropoda: Diplodocoidea)” or “The eyes have it: the sizes, shapes, and orientations of theropod orbits as indicators of skull strength and bite force”?
Don’t use a nounal phrase as the title. This is a amazingly common — titles like “The nature of Mauisaurus haasti Hector, 1874 (Reptilia: Plesiosauria)”. It doesn’t tell us what the paper is going to say, only what it’s going to say it about. Much better to choose a title that tells us what the nature of Mauisaurus is. (We’re guilty, too: the only paper co-written by all three of us SV-POW!er Rangers is called “Head and neck posture in sauropod dinosaurs inferred from extant animals”. Yes, sauropods have a head and neck posture, and yes we inferred it from extant animals. But we didn’t say what it actually is.)
Ask a question. For example, Roland T. Bird’s 1944 paper on the terrestrial/aquatic sauropod controversy was called “Did Brontosaurus ever walk on land?” More recently, Bonnan and Senter asked in 2007, “Were the basal sauropodomorph dinosaurs Plateosaurus and Massospondylus habitual quadrupeds?” A question draws people in.
Better yet, make a statement. Summarise the paper’s principal finding, if you can do it in a single short sentence. Bonaparte wrote an abstract in 1999 entitled “Rebbachisaurus tessonei Calvo and Salgado 1996 is not Rebbachisaurus Lavocat 1954.” Mitchell et al. (2009) called their paper “Sexual selection is not the origin of long necks in giraffes”. (I guess we had that in mind when we named our 2011 paper.)
The underlying principle here is this: for many people, the title will be the only part of your paper that they ever read. For many more, it will be the part that draws them in to read more — something they won’t do if the title doesn’t draw them in.
So, for the benefit for the first group, you want to write a title that will stand as a not-completely-inadequate surrogate for the whole paper. And you also want that title to provoke the interest of the second group.
September 23, 2014
Here’s a thing I put together to help my students understand the many branches of the internal iliac artery in humans. In the image above, we’re looking in superomedial view into the right half of the sacrum and pelvis. Bones are white, ligaments blue, the piriformis muscle sort of meat-colored, and arteries red (for a tour of the pelvis identifying all of this stuff, see my pelvic foramina slideshow). At the top is a big inverted Y-shape: the common iliac arteries branching from the abdominal aorta, which continues on, much reduced, as the median sacral artery. The right common iliac artery is shown bifurcating into the external iliac artery, which continues on out of the pelvis to become the femoral artery, and the internal iliac artery, source of much fear and doubt.
The first thing to understand is that any particular branching pattern of the internal iliac arteries, whether in an anatomical altas, a lecture, revealed in a dream, or even in your own body, will probably have no bearing whatsoever on the branching pattern in the next person you encounter, alive or dead. Furthermore, the variation between right and left in a single person can be as great as that among different people. The branches to pelvic viscera are particularly fiendish; they sometimes travel far into the pelvis as a common trunk and then “starburst” near their target organs, making identification almost impossible. Do not waste your time trying to memorize any particular branching sequence. Instead, concentrate on matching the arteries to their targets; you will discover the identities of the branches by seeing where they are going, not the order in which they branch.
There are typically 10 named branches of the internal iliac artery. Authorities quibble on the details, as we’ll see in a moment, but if you know these 10, you’ll be fine for almost any conceivable purpose. A simple scheme of my own devising for remembering them is 2-4-4:
TWO to the back body wall:
- iliolumbar A—may arise from external or common iliac AA; sometimes double
- lateral sacral A—note branches to anterior sacral foramina and anastomoses with median sacral A
FOUR leaving the pelvis entirely:
- obturator A—often arises from the external iliac A instead, exits pelvis through obturator canal
- superior gluteal A—exits pelvis through suprapiriform foramen
- inferior gluteal A—exits pelvis through infrapiriform foramen, with internal pudendal A
- internal pudendal A—exits pelvis through infrapiriform foramen, with inferior gluteal A
FOUR to pelvic viscera:
- superior vesical A—usually the dominant artery of the anterior trunk, this is the patent part of the obliterated umbilical artery, which survives as the medial umbilical ligament
- inferior vesical A (males) / vaginal A (females)—may branch off uterine A (females) or superior vesical A (both)
- uterine A (females)—major artery to uterus, approaches laterally within the broad ligament
A to ductus deferens (males)—extremely small and difficult to trace
- middle rectal A—usually the most inferior branch of the entire internal iliac tree (at least inside the pelvis)
My way to explain those last four is to extend my index finger and say, “Everybody has to pee, so up front we have superior vesical.” Then extend my pinky and say, “And everyone has to poop, so in back we have middle rectal.” Then extend digits three and four and explain that the identity of the middle two arteries varies between the sexes (but that the inferior vesical artery of males and the vaginal artery of females are basically the same vessel).
There is a LOT of variation in the descriptions of the internal iliac artery branches among different sources — almost as much variation as there is in the arteries themselves.
- The Thieme Atlas of Anatomy, 2nd Ed (Gilroy et al. 2009), Table 19.1 on p. 254, includes the inferior vesical artery for both sexes. The artery to ductus deferens is listed as a branch of the superior vesical artery, and the uterine and vaginal arteries are listed separately, bringing the total for females to 11.
- Clinically Oriented Anatomy, 7th Ed (Moore et al. 2013), Table 3.4 and pp. 350-355, lists the 10 branches I went through above. Moore et al. explicitly say that the vaginal artery is the female homolog of the inferior vesical artery (p. 351).
- Gray’s Anatomy, 40th Ed (Standring et al. 2008), pp. 1085-1089, splits the difference. The artery to ductus deferens is not listed; instead, the ductus deferens is said to be supplied by the inferior vesical A (in contrast to Thieme, which has it is supplied by the superior vesical A). Both the vaginal and inferior vesical arteries are listed, but the vaginal artery is said to frequently replace the inferior vesical artery.
The upshot is that pretty much all of these sources agree on how the blood is getting distributed, there are just some minor differences over what we call certain vessels. I have never personally seen a dissection detailed enough to allow an interior vesical artery to be recognized separately from the vaginal artery — the vagina lies so close behind the bladder that whatever you call the artery that runs lateral to them, it could easily be supplying both structures, and probably does. As far as I’m concerned, the inferior vesical artery in males and the vaginal artery in females are the same artery, in that they both supply the inferior portion of the bladder. I think it’s just a historical hiccup that we call them by different names, possibly perpetrated by smelly, lonely, vagina-obsessed men of centuries past.
A final note, added in revision: some sources refer to two trunks or divisions of the internal iliac artery: a posterior trunk that gives rise to the iliolumbar, lateral sacral, and superior gluteal arteries, and an anterior trunk that gives rise to everything else. If that’s what your professor tells you, smile and nod and keep your heretical thoughts to yourself. Personally, I regard the notion of trunks of the internal iliac artery alongside phlogiston, luminiferous aether, and snorkeling sauropods, as romantic nonsense at best. I have seen an obturator artery arise from a superior gluteal artery and a pudendal artery arise from a superior vesical artery. In a world where variants like those can and do turn up frequently, the stability and reason implied by regular trunks is illusory.
- Gilroy, A., MacPherson, B., and Ross, L. (eds.) 2009. Atlas of Anatomy, 2nd ed. Thieme, Stuttgart.
- Moore, K.L., Dalley, A.F., and Agur, A.M. 2013. Clincially Oriented Anatomy, 7th ed. Lippincott Williams & Wilkins, Philadelphia.
- Standring, S. 2008. Gray’s Anatomy, 40 ed. Churchill Livingstone, London.
I got in a conversation recently with a friend who is about to have his first paper published. It’s been through review and is now accepted at a well-respected old-school journal owned by a legacy publisher. It’s not an open-access journal, and he asked my advice on how he could make the paper open access.
We had a fruitful discussion, and we agreed that I’d write up the conclusions for this blog.
First, you can pay the publisher to open-access your paper. That’s a legitimate option at “hybrid OA” journals, which by this point is pretty much all paywalled journals. But even when the journal invites it, that’s not always possible. In this case, my friend has no institutional funds available, and really isn’t in a position to bung the publisher $3000 out of his own pocket.
The second option is to write to the journal saying that you select the OA option, but that since you have no institutional support you have to ask for a waiver. Will this work? It’s impossible to tell unless you try it. Some journals might have an absolutely-no-waiver policy; heck, some might have a “we always give waivers but don’t advertise the fact” policy. My guess is that most have no policy at all, but that editors (who are nearly all researchers themselves) will tend to be sympathetic, and support your case. Anyway, it can’t hurt to politely ask.
If that fails, the the third approach is to use the SPARC Author Addendum. Using this legal instrument (which is freely available), you do not transfer copyright to the publisher, as they usually request, but instead give them a non-exclusive right to publish — which of course is all they actually need. That leaves you legally free to post the accepted (peer-reviewed) version of the manuscript elsewhere: in an institutional repository, your own web-site or wherever. (I’ve never used this myself, but I hear it’s widely accepted.)
If the publisher is intransigent enough to reject the SPARC Addendum, the fourth approach is to dedicate your manuscript to the public domain (for example by posting it on arXiv with the CC Public Domain Declaration). Then return the copyright transfer form to the publisher, saying truthfully that there is no copyright to transfer. Publishers are used to dealing with submissions that have no copyright: for example, everything authored by U.S. federal employees is in the public domain. Their copyright forms usually already have a section for declaring public domain.
Finally if somehow all of the above tactics fail — if the journal flatly refuses to give an APC waiver, won’t accept the SPARC addendum, and rejects works that are in the public domain though not written by US Government employees — and if despite their evident hostility to science you still want to stick with the journal that accepted your paper — then you have one final option. You can just go ahead and give them the copyright, but then post the final PDF on your own web-site anyway. Of course, you are not technically allowed to do that, but historically it’s never been a problem. It’s very widely done — especially by old-school professors, because it would never even occur to them that sharing their own work could be a problem.
To be clear, I am not advocating the last of these. The four preceding approaches are better because they are fully in compliance with copyright law. But when dealing with a publisher that is simply determined to prevent your work from being read, then you have to weigh for yourself whether you’re more interested in respecting copyright, or doing what’s right.
This is the situation with several of my own old papers, which in my young and stupid days I signed over to publishers without giving it any thought at all. Having got myself into that situation, it seems to me that making those papers available anyway is the least bad of several bad options. But I would never choose that approach now, since I publish exclusively in open-access venues.
Option zero (not discussed here) is to use an open-access venue to start with: then none of these issues even arise. But failing that:
- If you have funds, use them to pay the publisher an APC to make the article open access.
- Ask the journal for an APC waiver.
- Use the SPARC Author Addendum to retain copyright and give the journal a licence to publish.
- Dedicate the manuscript to the public domain and tell the publisher there is no copyright to transfer.
- If all else fails, just post the paper publicly anyway.
In his post on Vicki’s new book Broken Bones, Matt told us his twelve-step process for producing stippled illustrations like this one of a crushed skull, which became the cover image of the book:
As soon as I saw that, I found myself thinking that it would look nice with some shading of the bone. Of course the existing stippling is a perfect guide to how dense the shading should be at each point, so I figured there had to be an easy way to do this automatically. There is, and this is what I whipped up in five minutes:
Here’s how I did it.
- I loaded Matt’s image into the GIMP, my image editor of choice.
- For some reason the crucial next step doesn’t work with greyscale images, so I converted it to RGB (Image → Mode → RGB)
- I removed the white background, leaving it transparent (Colours → Colour to Alpha… and click OK on the default colour, white)
- I added a new all-white background layer.
- I duplicated the skull layer, and named it “shading”
- I blurred the shading layer by 50 pixels (Filters → Blur → Gaussian Blur…, set the blur radius to 50 pixels and hit OK.) That gives you the shading you want, but it smudges out past the outline of the skull, hence the last two steps:
- I went back to the skull layer, and using the Fuzzy Select Tool (magic wand) selected the contiguous transparent area outside the skull parts.
- I went back to the shading layer and cut the selected area, leaving only that shading that’s inside the boundary of the skull.
As always with Gimp tutorials, it takes about ten times as long to explain as to actually do.
When I showed this to Matt, I rather immodestly said I was “super-happy with it”. Matt said he was “super-happy with the idea, but only regular happy with this specific execution”. He felt that the blurring was too strong, and that it should be backed off by 30-40%. So I made a new shading layer in the same way as above, but this time blurring by only 30 pixels. Here’s the resulting image:
It’s quite a subtle difference, but clear if you flip back and forth between the images (which you can most easily do by putting them in adjacent tabs of your browser). Personally, I think I prefer the 50-pixel version, since I think the shading clings rather too closely to the lines in this one, but YMMV.
Since I had both blur layers right there in the image, I thought it might be interesting to see how they look together. Here’s the result:
I’m actually rather fond of this version, but it’s a long way from the crisp, clinical feel of the original.
You can thicken up the shading by duplicating one or both of the shading layers as many times as you wish (or or course thin it out by sliding down the opacity level). Its also easy to make the shading coloured: just use Colours → Levels, select the individual colour channels, and bring up their bottom levels to taste.
Putting all that together, here’s one I made with very dense, yellowish (bone-coloured) shading. I did it starting with the 50-pixel shading layer, upping the red output level to 200 and the green to 150, then duplicating that layer, and reducing the 30-pixel shading layer to 50% opacity.
You can play for hours with all these sliders, tweaking as you wish, thanks to the magic of layers. It’s well worth investing a bit of time to learn some of the capabilities of a program like GIMP. Matt and I are very far from wizards, but we have at least got a bit past just using it to cut out backgrounds, and it opens up possibilities.
October 16, 2013
If the internet has any underlying monomyth, or universally shared common ground, or absolute rule, it is this:
People love to see the underdog win.
This rule has a corollary:
When you try to censor someone, they automatically become the underdog.
I say “try to censor” someone, because on the internet that is remarkably difficult to achieve. I’m not going to argue that the attention paid to the range of stories told on the internet is fairly distributed–being published is not the same as being read, and people seem to prefer cat pictures to reading about genocide. But it’s awfully hard to shut someone up, and any attempt to do so may backfire spectacularly.
If you work for an organization of any size, or have amassed any considerable power, reputation, or influence personally, you need to keep that at the forefront of your mind in every interaction you ever have with anyone, anywhere, ever. The reason for this constant attention is to keep you from becoming the overdog and thereby making an ass of yourself (and your organization, if you belong to one). Go read about the Streisand Effect and think proactively about how to keep that from happening to you.
Now, for the purposes of this tutorial I am going to arbitrarily sort the full range of possible messages into four bins:
- Those that make the teller look good.
- Those that make the teller look bad.
- Those that make someone else look good.
- Those that make someone else look bad.
Two and three are dead easy and often go hand in hand. If you want to spread messages of that type, all you have to do is find someone with less power, reputation, or influence–a prospective underdog, in other words–and be a jerk to them, thus turning them into an actual underdog. Coercion, threats, employment termination–these are all pretty good and may eventually pay off. But if you really want to look like a complete tit, and make the other party an instant hero, you gotta go for censorship. Out here in bitspace, it is the ne plus ultra of suicidal moves. It’s like Chuck Norris winding up for a roundhouse kick to someone’s face, only somehow his foot misses the other person’s face and hits him right in the junk instead. We will click and tap on that until they pry the mice and touchscreens from our cold, dead hands.
The first one–positive messages about yourself–is tricky. You can’t just go around telling people that you’re awesome. Anyone with any sense will suspect advertising. The only sure-fire method I know of is to do good work where people can see it. One thing you will just have to accept is that reputations are slow-growing but fast-burning. So, again, try to avoid burning yours down.
The last one–making someone else look bad–is also surprisingly tricky. If you just broadcast negatives to the world, that will probably backfire. At the very least, people start thinking of you as a negative force rather than a positive one. If the person you want to make look bad has ever lied or falsified data or oppressed anyone, use that. If they’ve ever tried to censor someone, or are actively trying to censor you, rejoice, they’ve done most of the work for you.
The upside of that last one is that, provided you’re not actively nasty, it is hard for others to hurt your reputation. If they just spew vitriol, it will probably backfire. If they lie about you, it will definitely backfire. About the only way to really trash your reputation is through your own actions. Your fate is in your own hands.
So, this is transparently a meditation on the DNLee/Biology Online/Scientific American story.
I would really like to know the backstory. Did someone at Biology Online contact SciAm and ask them to take down DNLee’s post? If so, well, geez, that was stupid. Why does anyone ever expect this to work anymore? I mean, the actual event from which the Streisand Effect got its name happened a decade ago, which may seem short in human terms but is an eternity online (it’s two-thirds of the lifespan to date of Google, for example).
If someone at SciAm did it unilaterally to protect their valued financial partner, it was doubly stupid, because not only did the censorship act itself fail, but now people like me are wondering if Biology Online asked for that “protection”. In other words, people are now suspecting Biology Online of something they might not have even done (although what they did do–what their employee did on their behalf, which amounts to the same thing–was bad enough).
So all in all the affair is like a tutorial on how to royally cock things up on the internet. And in fact it continues to be–Mariette DiChristina’s “apology” is a classic non-apology, that uses a torrent of words to say very little. Her self-contradictory tweets are much more revealing, despite being under 140 characters each. And in fact her loudest message is the complete lack of communication with DNLee before she pulled the post. So meaning scales inversely with message length for DiChristina–not a great quality in an Editor-In-Chief. And, OMG does she need to learn about the Asoh defense.
In the end, the whole thing just saddens me. I’m sad that SciAm made the wrong call immediately and reflexively. It says to me that they don’t care about transparency or integrity. They may say otherwise, but they are belied by their actions.
I’m sad that, having not even known that Biology Online exists, my perception of them now starts from a position of, “Oh, the ones that called that science writer a whore.” (If you’re a BO fan, please don’t write in to tell me how wonderful BO actually is; doing so is just admitting that you didn’t read this post.)
I’m sad that this happened to DNLee. I hope that going forward her reputation is determined by the quality of her work and the integrity of her actions, and not by words and circumstances inflicted on her by others.
… I wonder if I could make it as a corporate consultant if I put on a suit, walked into rooms full of pointy-haired bosses, and just explained the Streisand Effect and the Asoh Defense as if they were novel insights. I’ll bet I could make a killing.
October 7, 2013
Suppose, hypothetically, that you worked for an organisation whose nominal goal is the advancement of science, but which has mutated into a highly profitable subscription-based publisher. And suppose you wanted to construct a study that showed the alternative — open-access publishing — is inferior.
What would you do?
You might decide that a good way to test publishers is by sending them an obviously flawed paper and seeing whether their peer-review weeds it out.
But you wouldn’t want to risk showing up subscription publishers. So the first thing you’d do is decide up front not to send your flawed paper to any subscription journals. You might justify this by saying something like “the turnaround time for traditional journals is usually months and sometimes more than a year. How could I ever pull off a representative sample?“.
Next, you’d need to choose a set of open-access journals to send it to. At this point, you would carefully avoid consulting the membership list of the Open Access Scholarly Publishers Association, since that list has specific criteria and members have to adhere to a code of conduct. You don’t want the good open-access journals — they won’t give you the result you want.
Instead, you would draw your list of publishers from the much broader Directory of Open Access Journals, since that started out as a catalogue rather than a whitelist. (That’s changing, and journals are now being cut from the list faster than they’re being added, but lots of old entries are still in place.)
Then, to help remove many of the publishers that are in the game only to advance research, you’d trim out all the journals that don’t levy an article processing charge.
But the resulting list might still have an inconveniently high proportion of quality journals. So you would bring down the quality by adding in known-bad publishers from Beall’s list of predatory open-access publishers.
Having established your sample, you’d then send the fake papers, wait for the journals’ responses, and gather your results.
To make sure you get a good, impressive result that will have a lot of “impact”, you might find it necessary to discard some inconvenient data points, omitting from the results some open-access journals that rejected the paper.
Now you have your results, it’s time to spin them. Use sweeping, unsupported generalisations like “Most of the players are murky. The identity and location of the journals’ editors, as well as the financial workings of their publishers, are often purposefully obscured.”
Suppose you have a quote from the scientist whose experiences triggered the whole project, and he said something inconvenient like “If [you] had targeted traditional, subscription-based journals, I strongly suspect you would get the same result”. Just rewrite it to say “if you had targeted the bottom tier of traditional, subscription-based journals”.
Now you have the results you want — but how will you ever get through through peer-review, when your bias is so obvious? Simple: don’t submit your article for peer-review at all. Classify it as journalism, so you don’t need to go through review, nor to get ethical approval for the enormous amount of editors’ and reviewers’ time you’ve wasted — but publish it in a journal that’s known internationally for peer-reviewed research, so that uncritical journalists will leap to your favoured conclusion.
Last but not least, write a press-release that casts the whole study as being about the “Wild West” of Open-Access Publishing.
Everyone reading this will, I am sure, have recognised that I’m talking about John Bohannon’s “sting operation” in Science. Bohannon has a Ph.D. in molecular biology from Oxford University, so we would hope he’d know what actual science looks like, and that this study is not it.
Of course, the problem is that he does know what science looks like, and he’s made the “sting” operation look like it. It has that sciencey quality. It discusses methods. It has supplementary information. It talks a lot about peer-review, that staple of science. But none of that makes it science. It’s a maze of preordained outcomes, multiple levels of biased selection, cherry-picked data and spin-ridden conclusions. What it shows is: predatory journals are predatory. That’s not news.
Speculating about motives is always error-prone, of course, but it it’s hard not to think that Science‘s goal in all this was to discredit open-access publishing — just as legacy publishers have been doing ever since they realised OA was real competition. If that was their goal, it’s misfired badly. It’s Science‘s credibility that’s been compromised.
Update (9 October)
Akbar Khan points out yet more problems with Bohannon’s work: mistakes in attributing where given journals were listed, DOAJ or Beall’s list. As a result, the sample may be more, or less, biased than Bohannon reported.