Another picture from the recent ostrich dissection (click for full-size, unlabeled version). Last time we were in the middle of the neck, looking from anterior to posterior. This shot is from closer to the base of the neck, looking from posterior to anterior. A lot of the stuff is the same: the ragged cut from the saw at the meat processing plant where the ostrich was cut up; the spinal cord with the supramedullary airways above it in the neural canal; and the large interspinous ligament with diverticula on either side. We’ll have reason to refer back to some of those things in the not-too-distant future, but right now I want to draw your attention to something else: the tendons of the paired longus colli dorsalis muscles toward the top of the photo.

Here’s a modified version of Wedel and Sander (2002: fig. 2) with the course of the longus colli dorsalis highlighted in red (anterior is to the left). It is a curious aspect of bird necks that the large dorsal muscles do not insert on the neural spines but on the epipophyses (or dorsal tori or dorsal tubercles) above the postzygs. A naive approach based on beam theory would suggest that inserting on the neural spines would give those muscles more leverage, but necks are tricky and often defy such a priori predictions.

Instead of inserting on the neural spines, the longus colli dorsalis muscles originate from them, especially in the posterior part of the neck, and that’s what the photo at the top shows. From the reader’s point of view, the big interspinous ligament runs forward to attach to the posterior side of the neural spine (not visible because it’s buried in gloop, but it’s about a third of the way down from the top). The longus colli dorsalis tendons are running forward from the anterior side of the neural spine.

Fig. 20. An MRI of the mid-cervical series of an ostrich (Struthio camelus). In sagittal section, the interspinous ligaments are lighter than the surrounding muscle because of their high fat content. The neural canal is occupied by the spinal cord and supramedullary pneumatic airways. Also apparent in this image are the tendons of the longus colli dorsalis muscle originating from the neural spine. Scale bar is 4 cm.

Here’s the same thing again, also in an ostrich, but in an MRI this time (and with anterior to the right; Wedel et al. 2000: fig. 20). The dark streaks running forward from the neural spines are those longus colli dorsalis tendons. The interspinous ligament also shows up nicely as a series of white bands connecting adjacent neural spines.

References

Those ostrich necks I went to Oro Grande to get last Thursday? Vanessa and I started dissecting them last Friday. The necks came to us pre-cut into segments with two to three vertebrae per segment. The transverse cuts were made without regard for joints so we got a bunch of cross sections at varying points through the vertebrae. This was fortuitous; we got to see a bunch of cool stuff at the cut faces, and those cut faces gave us convenient avenues for picking up structures and dissecting them out further.

In particular, the pneumatic diverticula in the neck of this ostrich were really prominent and not hard at all to see and to follow. The photo above shows most of the external diverticula; click through for the full-resolution, unlabeled version. The only ones that aren’t shown or labeled are the diverticula around the esophagus and trachea (which had already been stripped off the neck segments, so those diverticula were simply gone), those around carotid arteries, which are probably buried in the gloop toward the bottom of the photo, and the intermuscular diverticula, of which we found a few in parting out the dorsal and lateral neck muscles.

There is one final group of diverticula that are shown in the photo but not labeled: the interosseous diverticula that fill the air spaces inside the bone.

We have tons of cool photos from this dissection, so expect more posts on this stuff in the future.

For previous posts showing diverticula in bird neck dissections, see:

Things to Make and Do, part 7: fun with rhea necks

Things to Make and Do, part 7b: more fun with rhea necks (admittedly, not the most creative title ever)

Here at SV-POW! we are ardently pro-turkey. As the largest extant saurischians that one can find at most butchers and grocery stores, turkeys (Meleagris gallopavo) are an important source of delicious, succulent data. With Thanksgiving upon us and Christmas just around the corner, here’s an SV-POW!-centric roundup of turkey-based geekery.

The picture at the top of the post shows a couple of wild turkeys that frequented our campsite in Big Bend in the winter of 2007. Full story here.

If you’re wondering what to do with your turkey, the answer is GRILL IT. I use the recipe (available on Facebook) of my good friend and colleague, Brian Kraatz, who has fallen to the Dark Side and works on mammals–rabbit tooth homology, even (Kraatz et al. 2010)–but still grills a mean theropod. (In his defense, Kraatz has published on extinct saurischians–see Bibi et al. 2006.) My own adventures in turkey grilling are chronicled in this post, which will show you the steps to attaining enlightenment, or at least a larger circumference.

While you’re cooking and eating, you might as well learn something about muscles. This shot of the fanned-out longus colli dorsalis muscles in a turkey neck was the raison d’etre for this post, and turned up again with different muscles labeled in one of the recent Apatosaurus maquette review posts. Mike and I ate those muscles, by the way.

After the meal, you’ll have most of a turkey skeleton to play with. This diagram is from my other ‘holiday dinosaur’ page, which I put together for the Lawrence Hall of Science and UCMP back in 2005. That page has instructions on how to turn your pile of greasy leftovers into a nice set of clean white bones. Tom Holtz is widely acknowledged as King of the Dino-Geeks, and in kingly fashion he took the above diagram and turned the geek-o-meter up to 11. Steel yourself, gentle reader, before checking out the result here.

Speaking of bones, here’s a turkey cervical from Mike’s magisterial work in this area, which first appeared as a tack-on to a post about the holotype dorsal vertebra of the now-defunct genus Ultrasauros. The huge version of the composite photo has its own page on Mike’s website, where it is available in three different background colors. The lateral view also turned up in one of my rhea neck posts.

From the serving platter to publication: when I was young and dumb, I used a photo of a broken turkey vert to illustrate the small air spaces, or camellae, that are commonly found in the pneumatic bones of birds and some sauropods (Wedel and Cifelli 2005:fig. 11F).

I made a much better version by sanding the end off a cleaned-up vertebra, and used that in Wedel (2007), in this popular article on pneumaticity (which has instructions for making your own), and way back in Tutorial 3–only the 12th ever post on SV-POW!

Finally, it would be remiss of me not to point out that turkeys are not only readily accessible, tasty sources of anatomical information, they are also pretty interesting while they’re still alive. Don’t stare at the disgusting freak in the photo above or you might lose your will to eat. Instead, head over to Tetrapod Zoology v2 for Darren’s musings on caruncles, snoods, and other turkey parts that don’t even sound like words.

That does it for now. If you actually follow all of the links in this post, you might just have enough reading to keep you occupied during that post-holiday-meal interval when getting up and moving around is neither desirable nor physically possible. If you’re in the US, have a happy Thanksgiving; if you’re not, have a happy Thursday; and no matter where you are, take a moment to give thanks for turkeys.

References

This is the second post on the Wedel lab’s recently acquired skull of Ursus americanus, the American black bear. The first installment covered ended with the disinterred-but-still-filthy skull bits sitting on my dining room table. This post covers putting the teeth back in, and just enough anatomy to justify putting up more cool pictures.

About five minutes after I took the last picture from the last post, I put the cranium and mandible to soak in warm, soapy water and spent the rest of the day doing other things. Last night I got a couple of old toothbrushes and scrubbed off most of the dirt from the external surfaces of the skull. I alternated toothbrush work with running water from the bathtub faucet over and through the skull bits. I also used one of the rubber nasal aspirator bulbs (or “snot suckers”, as new parents in the real world invariably call them)–which make tremendous water guns–to sluice out some of the grimier cavities. It was fun to force water into the mandibular foramen and see it come shooting out the mental foramen, along the canal traveled by the inferior alveolar nerve and vessels.

All of the teeth were loose in their sockets, and the incisors and upper canines were either falling out or could be pulled out without too much trouble. I yanked all of the teeth that I could, figuring that it was better to yank-and-glue rather than leaving them loose. I set the loose teeth on separate plates, one upper, one lower, arranged in the same order they were in the alveoli, and let everything air dry overnight.

Shown above is my setup for replacing the teeth:

  • a trash bag for protecting the table
  • a dish towel to provide a soft surface
  • the bear skull pieces
  • loose teeth on their respective plates
  • five minute epoxy
  • toothpicks for mixing and spreading the epoxy

I had been going to use something less hardcore for the gluing, but fortunately Vicki got home and I was able to draw on her experience from reconstructing loads of human skulls from archaeological and forensic sites. She said just go with epoxy, and so I went.

Here we are about halfway through the process. A few tips, some obvious, some maybe less so:

  • Even if you’ve done a perfect job of keeping the teeth in order, test-fit them anyway. If nothing else, this will give you a visceral sense of what the tooth feels like sliding into the socket, and it will help you figure out how much glue to apply. Also, test fit adjacent teeth together so you’ll know if they have to go back in in a particular order; sometimes one tooth is at a subtle angle and blocks the next tooth from coming out or going back in.
  • Better to put the glue in the socket than on the tooth. The roots are not much smaller in diameter than the alveoli and the crowns stand out a bit from the bone (although the ‘exposed’ roots would have been covered with gums in life). If you put the glue on the tooth you’re liable to either have it bulldozed off by the alveolar rim as you slide the tooth into the socket, or you’ll put too much on and have a bunch of worthless glue on the exposed portion of the root.
  • If the teeth are worn, like the incisors are here, it’s nice to do a bunch at once so you can get all of the wear surfaces lined up as they were in life. Better than having one tooth set up completely and then realizing it was all the way forward/back/in/out and the other teeth can’t match its orientation.

Everything back in. There are a couple of incisors still AWOL, and a few premolars, but the dentition is still reasonably complete (remember that I am used to working on Early Cretaceous North American sauropods, so a little completeness goes a long way). I ran a thin bead of epoxy around the bases of all of the teeth that had not come out of the alveoli, to hopefully rein in any future wanderlust on their parts.

Sweet action. I wish I had something more intellectual to say here, but I really don’t.

Nasal turbinates. Holy crap, were these a pain to get clean. I didn’t get them completely clean, there’s probably enough dirt up in there to germinate something. But I asymptotically approached the point where removing more dirt would have meant damaging the turbinates, which are at least manilla-envelope-thin if not laser-printer-paper-thin.

A closeup of the infraorbital foramen on the right, which transmitted the infraorbital artery and vessels in life. The neurovascular tracks on the external surface of the bone are pretty sweet; you can see them on the left side, in context, two photos up.

In addition to closing our jaws in a hinge-like motion, we can slide them fore and aft and also from side to side. Those kinds of motions are fine when you’ve got comparatively weak jaws like ours, and we still occasionally get into trouble–jawbreakers are so named for a reason. But those non-hinge-like motions would be disastrous for something that can close its jaws with several hundred pounds of force. So most big carnivores have wide, almost cylindrical jaw joints that constrain the motion to being almost purely hinge-like. In mustelids (weasels and kin), which have the strongest bites for their sizes of any mammals, the condyle is so cylindrical and the fossa so deeply enclosing (imagine a Q sitting inside a very slightly larger C–that’s the jaw joint seen from the side) that sometimes you simply can’t get the jaws to disarticulate after death. This ain’t quite that extreme, but it’s closer to the mustelid condition than the human. Not surprising, since weasels are united with bears and seals in the clade Arctoidea.

And here’s why bears need those cylindrical jaw joints: check out the muscle attachment scars on the back of the mandible. These are for the temporalis and masseter muscles, the same muscles you can feel bulging out on the side of your head and the corners of your jaw when you bite down forcefully or grit your teeth. IIRC, the maximum bite force a human can exert is around 180 pounds, and lions can do something like 900 pounds. Not sure where Ursus americanus falls, but definitely on the please-don’t-bite-me end of the scale.

And here’s why those muscle attachment scars are so big. The zygomatic arches are only partly complete here, but you can see how wide is the space between the left arch and the braincase. All of that space–two full inches, mediolaterally–was filled with temporalis muscle that provided most of the power for jaw-closing. This is why pit bulls have such wide, flat-looking heads: they have normal-sized dog brains and huge, thick jaw muscles. See also: my hyena dissection photos.

Looking very dog-like here in anterior view. There are some butchery marks on the skull, most noticeably across the external nares here, and along the mandibles. Not sure what that’s all about, since I can’t reconcile the stated backstory–cop shoots dangerous bear, buries head in backyard–with a need to make repeated cuts across the snout and jaws. And no, they’re not shovel marks. I knew that already, and Vicki confirmed that the marks are peri-mortem (around the time of death, but impossible to confirm as pre- or post-mortem). Anyway, I’m not complaining. Despite the damage, the skull is still an awesome thing, and the cut marks add a touch of mystery. I’ll post more pictures when I get the left temporal region glued back on.

After three months as a paleontology grad student, this morning Vanessa I. Graff got to sink a shovel in the service of science. Now, it was a bear skull, deliberately buried in someone’s back yard, so technically today’s exploits fall under the heading of contemporary zooarcheology rather than paleontology, but we’ll take what we can get.

This story has a backstory. The guy on the right here is Hossein Aziz, one of my advisees among the DO students at Western. His landlady’s ex-husband is in law enforcement, and about a year and a half ago he had to shoot a bear that had become a threat to humans. He buried the head in the backyard and separated from his then wife. She found out from Hossein that one of his professors was a paleontologist and offered to donate the skull to science, if only we’d come dig it up. So we did. Involved in the excavation (right to left in the above photo) were Hossein, his girlfriend Lia, my son London, Vanessa, and yours truly.

Additional note: Hossein’s landlady is a British expatriate, and she served us proper English tea. It was the most civilized dig I have been on, which, admittedly, is sort of like being the least worthless Kardashian. Anyway, the tea was great, and we all had a good time.

My wife, Dr. Vicki Wedel, was out of  town, but she lent us her archaeological toolkit, so we had nice trowels and kneepads and such. Here Hossein is pretending to advise Vanessa and London on what they should be doing, which is funny because that’s usually my job (pretending, that is).

After about half an hour of digging, we found intact vertebrate remains! And there was much rejoicing.

First out of the ground was the mandible, which is in essentially perfect shape.

Ursus americanus mandible and lower dentition, Homo goofballensis for comparison and scale.

Lia and London clearing dirt from around the cranium, which looks disturbingly hominoid from this angle.

There really aren’t any words for what’s going on here. Just bask a moment in the glory and move on.

We were going for American Gothic here, but Vanessa blew it by smiling. Standard.

Lia and Hossein marveling at what is, after all, a pretty badass critter. Even a small bear has seriously impressive teeth, which you hope to never find embedded in your flesh.

Still, it can be fun to pretend otherwise.

Here’s what we have. The occipital region is just gone. The left temporal region is more intact and has a long crack leading away across the frontals. On the right, everything from the zygomatic process of the maxilla to the occiput is just gone. So I reckon the rifle bullet went in on the left and blew out an exit wound the size of an orange on the right side of the bear’s head.

After a good rinse in the tub, all the bits are now soaking in soapy water. I’ll post more pictures when I get it all cleaned up and  presentable. In the meantime, many thanks to Hossein’s landlady for the skull, the tea, and her amused tolerance at having a bunch of dirty people digging in her yard, and to Hossein, Lia, Vanessa, and London for their work. It was a pretty darned good way to start the weekend.

Update: cleaning and re-arming the bear skull.

The gloves are off!

October 12, 2011

A package!  A package has arrived!

What can it be?

All right!  Let’s get down to business?

Now, where did I leave that monitor-lizard neck skeleton?  Ah yes …

That’s what I’m talkin’ about.

Stay tuned for exciting news about turkey zygapophyses.

 

With our baby’s appearance in National Geographic this week, she’s now been in four mainstream magazines:

That’s National Geographic at top left, Macleans  next to it; The Scientist at bottom left, and National Geographic Kids next to that.  (The articles in the first three of these are available online here, here and here, but I can’t find anything on the NG Kids web-site.)

There is a point to this post, beyond gloating celebrating Brontomerus: it’s that diligent preparation improves a study’s chance of getting good coverage.  A few people have asked us to write a bit about what we did, so at the risk of sounding self-congratulatory, here it is.

Most of Brontomerus‘s visibility is due to the hard work of the UCL Publicity team, and especially the excellent and widely-reproduced video that they made in the Grant Museum.  But we made it easy for UCL to take an interest by preparing a bunch of materials ahead of time, before they even knew that there was a paper coming out.  We called it the Brontomerus press pack, and made sure it contained everything anyone could need for writing and illustrating stories about our animal:

In short, we tried to give journalists, and radio and TV researchers, everything they needed to put together a story aimed at their own audience.  More than that — we tried to make it easy for them.  They have plenty going on, after all: Brontomerus came out on the day that the Libyan protests really took off, so it’s not as though news editors were short of material to fill their slots.  I suspect that if we’d not got all the ducks in such a neat row, Brontomerus would have disappeared from the news schedule in double-quick time.

Another important thing you can do to make news editors’ jobs easier: make sure that the images you provide are in high resolution, so they don’t pixellate when they’re blown up to fill a screen; and be explicit about image/video credit, copyright and permissions.  Let them know what they can use and under what conditions.  If you make them hunt for that information, or even chase you for it, they’ll probably lose interest and do a different piece instead.  And we really wanted the artist who’d done the Brontomerus work to be credited: Paco Gasco did a fantastic job, and deserved to be known for it.

Equally important, by getting as much material as possible ready before even contacting the university publicity people, we made their job easier.  Once they were on board, we were able to extend the page with extras like an official press release and the video, but the framework was all in place ahead of time.

In short, there is a whole load that you can do to prepare a study for media coverage.  Not much of it is rocket-science.  It’s basically just about getting the work done.  And it is work, plenty of it.

Still.  It’s worth it.

And another thing …

You should all get across to Heinrich Mallison’s new blog and check it out.  Lots of excellent palaeo-photography, even if today’s post is about a stinkin’ mammal.

Addendum (from Matt)

First, some credit where it’s due. We didn’t figure all of this out on our own. For Brontomerus in particular, we took a lot of cues from  the fact sheet that Irmis et al. put together for their 2007 “rise of dinosaurs” paper that made the cover of Science.

Second, we did figure some of it out on our own, but not all at once. If you look at Mike’s unofficial online press packs for Xenoposeidon (2007), our neck posture paper (2009), and Brontomerus (2011), you’ll see that each one is better than the one before.

Finally, you may be saying to yourself, “Okay, I understand that I’m supposed to make things easy for journalists and have a bunch of stuff queued up for them. But where do I put it?”

Well, online, obviously. If you don’t already have a blog, WordPress and Blogger and probably a zillion other services give them out for free, and you can make an ad hoc, one-shot blog for every press-release-worthy paper, as Mark Witton and Darren did for their azhdarchid paleobiology paper in PLoS ONE.

But let me wax preachy for a minute. If you’re a young researcher and you’re trying to make an impact, why aren’t you blogging? It’s not an intolerable commitment. Sure, regular posting brings more readers, but irregular posting brings more readers than not having a blog at all.

We started SV-POW! as a joke, and continued it during the actually-posting-weekly-about-sauropod-vertebrae phase (which lasted for 2.5 years) because it was fun and challenging, and maintain it now because it’s fun, we enjoy the wacky discussions that get going from time to time in the comments, and, frankly, we’re addicted to having a soapbox where we can say pretty much whatever we want. We didn’t explicitly plan it as a way to funnel readers to our scientific work, but that has been one of its great exaptive benefits. I’d be shocked if the same isn’t true for other researchers who blog.

So, moral of the story: if you’re a researcher and you’re not blogging, you’re missing out. Your work is reaching fewer people than it might. Come out and play. Join the conversation. Interact. Your future self will thank you.

Okay, special dissection post, coming to you live from the Symposium  of Vertebrate Palaeontology and Comparative Anatomy in Lyme Regis, on the Jurassic coast of England, well past my bedtime. First, check out this comment from Neil and see the linked image of some neck muscles in the anhinga. Here’s a small version I’m swiping. There are a couple of short, single-segment muscles shown, but the big long ones in this image are longus colli ventralis (on the ‘front’ or ‘bottom’ of the neck) and longus colli dorsalis (on the ‘back’ or ‘top’).

Now, grok these photos of the same dorsal muscle. Or muscle group, if you prefer. Note that in all cases shown here and in the link–anhinga, rhea, and turkey–the muscle inserts on the anterior cervical vertebrae, and not on the skull.

In Rhea:

In Meleagris (turkey):

The rhea was dissected by Vanessa back at Western a couple of weeks ago, the turkey by me on Mike’s dining room table on Monday. Full story to follow…at some point.

In the meantime, go buy your own turkey and cut up its neck. It’s cheap and you’ll learn a ton.

Wedel’s Theorem:

freezer full of interesting dead animals + great anatomy student who actually wants to get up on Saturday morning and dissect = happiness

The rhea has been the gift that keeps on giving. Saturday was my fourth session with some part of this bird, going back to 2006 (previous posts are here, here, and here). The first two sessions were just about reducing the bird to its component parts, and the last session was all about midline structures.

The goal for the neck is to dissect down to the vertebrae and document everything along the way–muscles, tendons, fascia, blood vessels, and especially diverticula. In the past I have been pessimistic about the chances of seeing diverticula without having them injected with latex or resin or something. But this bird is changing my mind, as we saw in a previous post and as you can see below.

The goal for Vanessa is to grok all of this anatomy, and hopefully make some publishable observations along the way. She has a chance to do something that I think is rather rare for a sauropod paleobiologist, which is to get a firm, dissection-based grounding in bird and croc anatomy before she first sets foot in a museum collection to play with sauropod bones.

That sounds awesome, and probably will be awesome, but before there can be any awesomeness, the fascia has to be picked off the neck. And by ‘picked’ I mean ‘actually cut away, millimeter by arduous millimeter’. It wasn’t that bad everywhere–the fascia over the long dorsal muscles came off very easily. But the lateral neck muscles were actually originating, in part, from the inner surface of the fascia. That’s not unheard of, it happens in the human forearm and leg all the time, but I’ve never seen it as consistently as in this rhea. So picking fascia took a loooong time–that’s what Vanessa is doing in the photo at top.

Once the fascia was off, Vanessa started parting out the long tendons of the hypaxial muscles in the left half of the neck. Meanwhile, I started stripping fascia from the right half. I had forgotten that the right half of the neck still had the trachea and esophagus adhered to the side. That probably sounds weird, given that our trachea and esophagus–and those of most mammals–run right down the middle of our necks and aren’t free to move around much. In birds, they’re more free-floating and can drift around between the skin and the vertebral muscles, sometimes even ending up dorsal to the  vertebral column–there’s a great x-ray of a duck in a  2001 paper that shows this, which I’ll have to blog sometime.

Anyway, when I cut the fascia to pull back the trachea and esophagus, I found that they were separated from the underlying tissues by a dense network of pneumatic diverticula winding through the fascia.

I had heard, anecdotally, of networks of diverticula described as looking like bubble wrap. I can now confirm that is true, for at least some networks. What was especially cool about these is that they were occupying space that would be filled with adipose or other loose connective tissue in a mammal, which illustrates the point that pneumatic epithelium seems to replace many kinds of connective tissue, not just bone–something Pat O’Connor has talked about, and which I also briefly discussed in this post.

I should mention that there was no connection between these diverticula and the trachea, as there is between the subcutaneous throat sac and the trachea in the emu (story and pictures here).

While I was geeking out on diverticula, Vanessa was methodically separating the long hypaxial muscles, which looked pretty cool all fanned out.

And that’s all we had time for on Saturday. But we’re cutting again soon, so more pictures should be along shortly.

Matt recently told us how to get ideas for papers, but if you’ve not previously published, you may be wondering how you get from idea to actual manuscript.  I’ve written about twenty palaeontology papers now, not counting trivial ones like encyclopaedia entries and corrections (plus a few in computer science).  So while there are plenty of people out there with much bigger CVs than mine, I’ve accumulated enough different experiences over the last six or seven years that hopefully I can shed a bit of light on the process.  DISCLAIMER: this means I am going to be citing myself like crazy, and will look like a complete egomaniac.  That really is not the point of this exercise.

Before I plough in, a digression: you may legitimately wonder why, if I’ve written 20 papers, my publications page lists only fourteen.  A couple are in press but not yet out: my work on those is done, I just have to wait for the wheels to grind exceeding fine.  A few more are in review.  Others, though once completed, are now in the process of being revised, either in response to reviewers’ comments or because they were rejected outright and need retooling for submission to another journal.  Maybe the most interesting category, though, is that I have two or three papers that I think are dead: they’ve been submitted and rejected, and I think I will probably never resubmit them.  In two cases — dinosaur diversity surveys — the manuscripts have aged badly, because the rapid rate of new dinosaurs being named is rendering them more and more obsolete.  To bring these up to publishable standard again would involve rebuilding the database and redoing the stats, and I just can’t summon up enthusiasm for that work when I have other projects going on that are so much more fun.

Anyway, we’re not here to talk about how to abandon finished manuscripts — we’re here to talk about how to get them finished in the first place.

In my projects, I have used three broad approaches.  Let’s look at them in turn.

Approach 1. Gather notes first

If you take this approach, you’ll begin by gathering all your thoughts on the subject of the manuscript-to-be into one place — these days, most likely a single file or folder on your computer, but in the old days it might well have been a physical notebook.  Don’t think about the structure of the manuscript, or about narrative flow, at this stage.  Don’t worry about what to include and what to exclude: just gather everything you can, pour it into a pot, and stir it.  You can think about the other stuff later.

The idea here is to separate “left-brain” and “right-brain” activity, so you can concentrate on one of them at a time.  During the gathering phase, you’re being creative, an artist playing with ideas.  When you’re done, you switch into engineer mode, and your task becomes to synthesise some or all those ideas into a coherent argument.  It’s easier to think about one of these things at a time than both at once, so the theory goes.

Handy household hint: you don’t have to put all your ideas into a single paper.  Find a set of thoughts that fit together into a narrative, and build the paper around that.  The other ideas will find homes in subsequent papers, they’re not lost.

The right-brain-then-left-brain approach sounds good; but in practice, I’ve found this doesn’t work well for me.  In fact, looking back over my submissions, it looks like I’ve only done it twice, and both times it’s resulted in a huge amount of work.  Those two papers are the Taylor et al. (2009) paper on habitual sauropod neck posture and Taylor et al. (2011) on sexual selection of sauropod necks.  These were three- and four-way collaborations between myself, Matt, Darren, and for the latter David Hone.  And for such short papers (eight and twelve pages respectively) they took an amazingly long time to put together.  They went through long sequence of revisions and rewrites before reaching their final forms, and lead authorship swapped hands many times along the way — we all held it at one time or another on both papers.

So what was the problem?  Only this: that “synthesise all those ideas into a coherent argument” sounds like a straightforward mechanical process, but it’s not.  It’s an art in itself — it requires taste, judgement, and most of all a lot of hard work.  (And of course, this is especially true when working with a team, when everyone has different ideas.)  When you start the composition process using a big ol’ bucket full of observations, it’s hard to tie them all together in a sequence that makes sense; and sure enough, we didn’t.  Early “complete” drafts of the neck-posture paper contained all the same information as the published version, but they were incoherent and repetitive.  One moment you’d be reading about some assertion that Stevens and Parrish had made about ONP being habitual, then next you’d be reading something about semi-circular canal orientation, then it would be be some observation on extant animal behaviour, then it would be back to DinoMorph, and so on.  Reading it felt like being batted around inside a pinball machine.

We probably could have submitted it in that form, and found a venue for it.  But we didn’t, because we wanted our paper not just to contain a bunch of relevant facts, but to lay out an argument, a connected sequence of observations and deductions, that would tell a story, make a compelling case.  We wanted our paper to convince.  And doing that is an art — hence the many, many, revisions and rewrites.  We got there in the end, and all three of us are happy with how the paper came out, but it was a real hack to get there, and it left me wondering whether we’d gone about it the wrong way.

On the other hand, what other way is there to write a genuinely three- or four-cornered collaborative paper?  Most of the other collaborative papers I’ve been involved with have had a very clear lead author who contributed the bulk of the prose, with the remaining authors contributing specific passages of text – and of course other input, just as important, such as the discussions that gave rise to the project in the first place.  The genesis of the neck-posture project was that we each contributed a stack of notes — some about what has previously been written on the subject, some about the flaws in those assertions, some about the behaviour of extant animals — and I just don’t see a significantly better way of melding all those into a coherent narrative than the multiple-pass approach that we adopted.

So anyway, what I’ve mostly done instead is:

Approach 2. Just write a manuscript

There is something enormously empowering about firing up OpenOffice (or MS-Word, if you must), choosing File → New, looking at that brand new white page, and typing a title.  Once you’ve done that, you’re up and running.  You’re really doing it.  It gets much harder to procrastinate.  Even if you end up changing that title half a dozen times, and rejigging the order of the manuscript, and rewriting the conclusions, and retaking the photos and doing the figures again, and reworking the statistical analysis because new data has come in, none of that changes the fact that once you’ve started a manuscript, you’ve started.  It doesn’t matter if it gets three new heads and five new shafts along the way, it’s still the axe the George Washington used to chop down the cherry tree.

So with this approach, the idea is that after accumulating information and internalising it, you just sit down and start writing — telling the story in an order that makes sense and draws the reader in.  The liberating thing is not trying to use any of the actual wording of your notes, not feeling obliged to work them all into the manuscript, just writing.

A technique that people often recommend at this stage — and one that in theory at least I endorse — is not to bother with your citations and references at this stage, or even with boring typographical details like italicising your genus and species names.  You don’t want to let yourself get sucked into any of that detailed clerical work — it will break the flow of your thoughts, and prevent you from getting them all down in a sequence that makes sense.  You want to be writing in the same spirit that you would explain the ideas to an intelligent friend in a pub, after maybe the second pint, waving your hands wildly to get you through the difficult bits, but not worrying about that because the point is to get your idea across — or rather, your sequence of ideas, that gets the listener from A to B.  You can go back in fill in the references later.

Like I said, in theory I endorse this technique.  In practice, I don’t seem to be able to do it: when I start to write, the citations just thrust themselves into my mind and I’m not able to write a perfectly simple sentence like “the humeri of brachiosaurids are the longest known in any sauropods, exceeding 2 m in length” without shoving in a “(Janensch 1961)”, and nine times out of ten going and re-checking that paper so I can specifically cite the table on page 187.  Whether this is a good or a bad thing, I couldn’t say — maybe if I could discipline myself not to do this, I’d save myself the pain later in the writing process of having to shuffle the text to get it into an order that tells the right story.

A digression on story-telling

I’ve used the metaphor of story-telling a couple of times, and I think it’s absolutely central here. You want to draw your reader through the paper.

Of course, what we mean by “story” is very different from one paper to another.  For example, in my short paper surveying dinosaur diversity (Taylor 2006), the story could hardly have been different from how it turns out: here’s where the data was from, here’s what I did with it, here are the results, and then end with some discussion.  By contrast, there were lots of different ways I could have structured my plea to the ICZN to recognise electronic publication (Taylor 2009b), but I went for an approach where the section headings outlined the core argument even if you didn’t read the actual text: 1. Background: the availability of the name Darwinius masillae; 2. The Code is in danger of becoming an irrelevance; 3. Paper journals are going away; 4. The time to act is now; 5. Electronic documents are different from electronic media; 6. We must come to terms with the ubiquity of PDF; 7. The current rules are too hard to get right (and finally a Conclusion).

For a fairly hardcore descriptive paper like the Xenoposeidon description (Taylor and Naish 2007, natch), you’re more limited in how much of a story you can tell, and pretty much constrained by the usual Introduction, Systematic Palaeontology, Description, Systematics, Discussion structure.  But even there, we laid out what I think is a fairly compelling story by splitting the “description” section into two parts: one that was purely descriptive, and a subsequent one containing all the comparisons.  Only after those two sections did we progress to the phylogenetic analysis that weakly corroborated our inferences.

For my Brachiosaurus/Giraffatitan paper (Taylor 2009a), though, I subverted the usual structure by postponing the Systematic Palaeontology until after I’d done all the necessary descriptive work to support the generic separation, rather than presenting the systematic conclusion up front and then going back and justifying it.  I also gave that paper a very, very short introduction (116 words incuding citations and taxonomic authorities), pushing the rest of what would normally be considered introductory material back into a separate Historical Background section.  Why?  Because that way I could put the end-of-introduction subsections on Anatomical Nomenclature, Anatomical Abbreviations and Institutional Abbreviations up front on the first page where they belong, rather than buried on the sixth page as they would otherwise have been.

Well, it seems that I have have drifted a bit from what I intended to talk about, and got onto the subject of how to structure a paper; but since that’s sort of relevant, I won’t let it spoil my day.

Anyway, the two approaches I’ve discussed so far really bracket the range of ways to put a manuscript together, and most projects will fall somewhere on the continuum between them.  But every now and then an opportunity comes up to use a third way:

Approach 3. Convert from another medium

I already mentioned my paper on electronic publication (Taylor 2009b), but long-time SV-POW! readers will remember that much of the material in this paper was cannibalised from a sequence of SV-POW! posts (notably Non-Open Academic Publishing Is Dead) as well as a few comments that I’d left on relevant posts on other people’s blogs.  On paper, you’d say this is a lot like approach 1, in that while I had much of material to hand, it needed sorting, integrating and rewriting.  In fact, it went much more smoothly than the neck-posture paper’s editing process, perhaps because all the source material was my own rather than having come from several different authors; and perhaps because the posts and comments were already in a chronological order which reflected the way my thoughts had arrived at the position where they eventually landed.

But a more interesting example of this route is the survey of the history of sauropod studies (Taylor 2010).  This started life as a slideshow, the accompaniment for my talk at the conference Dinosaurs: A Historical Perspective.  (Yes, the very same talk which Fiona fell asleep in, when I rehearsed it on her.)  To put together a talk, you already have to have your story together — the sequence in which things happen, the sections that you chop it all up into, the references forward to things you’re going to say, and back to things you’ve said.  So transcribing that all down into a manuscript is surprisingly straightforward — at least, it was for me, for this project.  It really was, almost literally, as case of taking each slide in turn, writing a little essay about what it depicted, and moving on.

So I kind of recommend that.  In fact, I’d go further: do not ever give a conference talk without immediately transcribing your slides into a manuscript.  If you do, you’re throwing away a super-easy publication: you’ve already done all the hard work.

(I didn’t know I was going to say that, just as I didn’t know I was going to digress onto story-telling earlier.  Turns out that this is an essay in the literal French sense of “an attempt”, something that you only figure out as you’re writing it.  Now that I’ve said you should always turn your slideshows into papers, I find myself wondering whether I’ve taken my own advice …  Hmm, quick check of the old publications list and I see that, hmm, I have roughly three sets of unconverted slides.  So that gives me something to do in the evenings, then.)

Actual writing

I only have two things to say about this, and they have both been said better by other people (computer scientists, as it happens):

Say what you mean, simply and directly.

— Brian W. Kernighan and P. J. Plauger

and:

Present to inform, not to impress; if you inform, you will impress.
— Frederick P. Brooks

In short, do not write “the taxon under consideration exhibits a tendency towards velocitous aerial locomotion” when you could write “it flies fast”.

A final thought

All I’ve done here is list and discuss what’s worked for me (and some of the things that haven’t).  If these things don’t work for you, don’t do them.  If you find a way that works better, then by all means use that.

But if you’re struggling to find a way to get started, then follow Approach 2 above.  Just start writing, and keep going until you’re finished.

Hope that’s helpful.

References

[Once more, I’m sorry that the reference list is so me-centric, but I had to use my own papers as examples because I don’t know the genesis of anyone else’s.]