Tutorial 42: how to get a paper written

May 1, 2022

Yes, we’ve touched on a similar subject in a previous tutorial, but today I want to make a really important point about writing anything of substance, whether it’s a scientific paper, a novel or the manual for a piece of software. It’s this: you have to actually do the work. And the way you do that is by first doing a bit of the work, then doing a bit more, and iterating until it’s all done. This is the only way to complete a project.

Yes, this is very basic advice. Yes, it’s almost tautological. But I think it needs saying because it’s a lesson that we seem to be hardwired to avoid learning. This, I assume, is why so many wise sayings have been coined on the subject. Everyone has heard that “A journey of a thousand miles begins with a single step”, attributed to Lao Tzu in maybe the 5th Century BC. More pithily, I recently discovered that Williams Wordsworth is supposed to have said:

To begin, begin.

I love that. In just three words, it makes the point that there is no secret to be learned here, no special thing that you can do to make beginning easier. You just have to do it. Fire up your favourite word processor. Create a new document. Start typing.

And to Wordsworth’s injunction, I would add this:

To continue, continue

Because, again, there is no secret. You just have to do it.

Mounted skeleton of Diplodocus carnegii holotype CM 84 in the rare dorsal view.

At the moment I am working on four separate but related papers. Honestly, sometimes it’s hard even keeping them straight in my head. Sometimes I forget which one I am editing. It would be easy to get overwhelmed and … just not finish. I don’t mean it would be easy to give up: that would be a decision, and I don’t think I would do that. But if I listened to my inner sluggard, I would just keep on not making progress until the matter become moot.

So here is what I do instead:

  • I pick one of the papers, which is the one I’m going to work on that evening, and I try not to think too much about the others.
  • I figure out what needs to be in that paper, in what order.
  • I write the headings into a document, and I put an empty paragraph below each, which just says “XXX”. That’s the marker I use to mean “work needed here”.
  • I use my word-processor’s document-structuring facilities to set the style of each of the headings accordingly — 1st, 2nd or occasionally 3rd level.
  • I auto-generate a table of contents so I can see if it all makes sense. If it doesn’t, I move my headings around and regenerate the table of contents, and I keep doing that until it does make sense.
  • I now have a manuscript that is 100% complete except in the tiny detail that it has no content. This is a big step! Now all I have to do is write the content, and I’ll be finished.
  • I write the content, one section at a time. I search for “XXX” to find an unwritten section, and I write it.
  • When all the “XXX” markers have been replaced by text, the paper is done — or, at least, ready to be submitted.

Caveats:

First, that list makes it sound like I am really good at this. I’m not. I suck. I get distracted. For example, I am writing this blog-post as a distraction from writing a section of the paper I’m currently working on. I check what’s new on Tweetdeck. I read an article or two. I go and make myself a cup of tea. I play a bit of guitar. But then I go back and write a bit more. I could be a lot more efficient. But the thing is, if you keep writing a bit more over and over again, in the end you finish.

Second, the path is rarely linear. Often I’m not able to complete the section I want to work on because I am waiting on someone else to get back to me about some technical point, or I need to find relevant literature, or I realise I’m going to need to make a big digression. That’s fine. I just leave an “XXX” at each point that I know I’m going to have to revisit. Then when the email comes in, or I find the paper, or I figure out how to handle the digression, I return to the “XXX” and fix it up.

Third, sometimes writing a section blows up into something bigger. That’s OK. Just make a decision. That’s how I ended up working on these four papers at the moment. I started with one, but a section of it kept growing and I realised it really wanted to be its own paper — so I cut it out of the first one and made it its own project. But then a section of that one grew into a third paper, and then a section of that one grew into a fourth. Not a problem. Sometimes, that’s the best way to generate new ideas for what to work on: just see what come spiralling out of what you’re already working on.

None of these caveats change the basic observation here, which is simply this: in order to get a piece of work completed, you first have to start, and then have to carry on until it’s done.

 

Posted by Mike Taylor
Filed in Diplodocus, mounts, Tutorial, writing
5 Comments »

Tutorial 41: distinguishing nerves and arteries in dissection

October 27, 2021

I whipped up these doodles with a handwritten list of characteristics during office hours recently, and then realized that this should be a tutorial post.
 
Most of the stuff listed in the image is pretty self-explanatory, but I want to expand a bit on the textures. Nerves are bundles of axons, bound together in sheets of connective tissue. As you follow nerves outward, from the central nervous system toward the axon targets or receptive nerve endings, they will branch and branch, again and again, down to the level of individual axons. So although the axons themselves are too small to see in a gross dissection, the collected bundles of axons inside each nerve often give nerves a striated texture. 
 
In contrast, arteries are hollow muscular tubes that carry blood, and they look like hollow muscular tubes. A weird and IMHO under-appreciated fact is that arteries can’t be nourished directly by the blood that they carry; their walls are too thick. So they have tiny vessels in and on their walls, called vasa vasorum, or “vessels of the vessels”. The vasa vasorum are hair-fine when they are visible at all, and they squiggle just like macro-scale arteries, so texturally arteries often look vaguely hairy, with fine reddish threads winding across their surfaces.
 
In practice, though, the directness of the course — or lack thereof — and branching pattern is usually enough to make the call. Basically, nerves do not have time for your crap. They are hell-bent on getting where they are going with a minimum of farting around. In contrast, arteries never travel in straight lines if they can avoid it. They’re always throwing in a saucy swoop or curve, for no other reason than because it looked fun.
 
Why haven’t I talked about veins? By rights I should, since arteries usually travel with veins, and complete neurovascular bundles — each consisting of a nerve, an artery, and a vein — are common in vertebrate bodies. But in my experience students are almost never confused about the difference between arteries and veins. But for the sake of completeness, veins tend to be dark-colored in embalmed bodies, because they don’t completely empty of blood, and they are visibly thin-walled and floppy. Because veins are thin-walled, if they do empty out they can also flatten out, and look wider than the neighboring arteries. On the other hand, it’s not unusual to see a bifurcated vein, with one branch running on either side of the corresponding artery.
 
A couple of caveats about all of the above:
  • I made the infographic specifically for med students working with embalmed tissue. The colors in particular may be different in fresh tissue, and in my experience less vibrant and therefore harder to tell apart. The other factors are much less affected by the embalming process.
  • Most of these differences break down to some extent in very small vessels and nerves. If you can track them back to larger, more proximal parent vessels or nerves, it’s easier to tell, but sometimes you run across a tiny little thread and can’t tell if it’s a tube or a wire — in which case, good luck.
Posted by Matt Wedel
Filed in human anatomy, Tutorial
3 Comments »

Tutorial 39: how not to conclude a talk or paper

March 19, 2021

“And in conclusion, this new fossil/analysis shows that Lineageomorpha was more [here fill in the blank]:

  • diverse
  • morphologically varied
  • widely distributed geographically
  • widely distributed stratigraphically

…than previously appreciated.” 

Yes, congratulations, you’ve correctly identified that time moves forward linearly and that information accumulates. New fossils that make a group less diverse, varied, or widely distributed–now that’s a real trick.

Okay, that was snarky to the point of being mean, and here I must clarify that (1) I haven’t been to a conference in more than a year, so hopefully no-one thinks I’m picking on them, which is good, because (2) I myself have ended talks this way, so I’m really sniping at Old Matt.

And, yeah, new fossils are nice. But for new fossils or new analyses to expand what we know is expected. It’s almost the null hypothesis for science communication–if something doesn’t expand what we know, why are we talking about it? So that find X or analysis Y takes our knowledge beyond what was “previously appreciated” is good, but it’s not a particularly interesting thing to say out loud, and it’s a really weak conclusion.

(Some cases where just being new is enough: being surprisingly new, big expansions [like hypothetically finding a tyrannosaur in Argentina], and new world records.)

Don’t be Old Matt. Find at least one thing to say about your topic that is more interesting or consequential than the utterly pedestrian observation that it added information that was not “previously appreciated”. The audience already suspected that before you began, or they wouldn’t be here.

I showed this post to Mike before I published it, and he said, “What first made you want to work on this project? That’s your punchline: the thing that was cool enough that you decided to invest months of effort into it.” Yes! Don’t just tell the audience that new information exists, tell them why it is awesome.

Posted by Matt Wedel
Filed in rants, Science communication, Tutorial
2 Comments »

Tutorial 38: little projects as footsteps toward understanding

January 11, 2021

This is a very belated follow-up to “Tutorial 12: How to find problems to work on“, and it’s about how to turn Step 2, “Learn lots of stuff”, into concrete progress. I’m putting it here, now, because I frequently get asked by students about how to get started in research, and I’ve been sending them the same advice for a while. As with Tutorial 25, from now on I can direct the curious to this post, and spend more time talking with them about what they’re interested in, and less time yakking about nuts and bolts. But I hope the rest of you find this useful, too.

Assuming, per Tutorial 12, that you’ve picked something to investigate–or maybe you’re trying to pick among things to investigate–what next? You need a tractable way to get started, to organize the things you’re learning, and to create a little structure for yourself. My recommendation: do a little project, with the emphasis on little. Anyone can do this, in any area of human activity. Maybe your project will be creating a sculpture, shooting and editing a video, learning–or creating–a piece of music, or fixing a lawn mower engine. My central interest is how much we still have to discover about the natural world, so from here on I’m going to be writing as a researcher addressing other researchers, or aspiring researchers.

Arteries of the anterior leg, from Gray’s Anatomy (1918: fig. 553). Freely available courtesy of Bartleby.com.

I’ll start with a couple of examples, both from my own not-too-distant history. A few years ago I got to help some of my colleagues from the College of Podiatric Medicine with a research project on the perforating branch of the peroneal artery (Penera et al. 2014). I knew that vessel from textbooks and atlases and from having dissected a few out, but I had never read any of the primary (journal) literature on it. As the designated anatomist on the project, I needed to write up the anatomical background. So I hit the journals, tracked down what looked like the most useful papers, and wrote a little 2-page summary. We didn’t use all of it in the paper, and we didn’t use it all in one piece. Some sentences went into the Introduction, others into the Discussion, and still others got dropped entirely or cut way down. But it was still a tremendously useful exercise, and in cases like this, it’s really nice to have more written down than you actually need. Here’s that little writeup, in case you want to see what it looks like:

Wedel 2013 anatomy of the perforating branch of the peroneal artery

Pigeon spinal cord cross-section, from Necker (2006: fig. 4).

More recently, when I started working with Jessie Atterholt on weird neural canal stuff in dinosaurs, I realized that I needed to know more about glycogen bodies in birds, and about bird spinal cords generally. I expected that to be quick and easy: read a couple of papers, jot down the important bits, boom, done. Then I learned about lumbosacral canals, lobes of Lachi, the ‘ventral eminences’ of the spinal cord in ostriches, and more, a whole gnarly mess of complex anatomy that was completely new to me. I spent about a week just grokking all the weird crap that birds have going on in their neural canals, and realized that I needed to crystallize my understanding while I had the whole structure in my head. Otherwise I’d come back in a few months and have to learn it all over again. Because it was inherently visual material, this time I made a slide deck rather than a block of text, something I could use to get my coauthors up to speed on all this weirdness, as well as a reminder for my future self. Here’s that original slide deck:

Wedel 2018 Avian lumbosacral spinal cord specializations

If you’re already active in research, you may be thinking, “Yeah, duh, of course you write stuff down as you get a handle on it. That’s just learning.” And I agree. But although this may seem basic, it isn’t necessarily obvious to people who are just starting out. And even to the established, it may not be obvious that doing little projects like this is a good model for making progress generally. Each one is a piton driven into the mountainside that I’m trying to climb: useful for me, and assuming I get them out into the world, useful for anyone I’d like to come with me (which, for an educator and a scientist, means everyone).

A view down the top of the vertebral column in the mounted skeleton of Apatosaurus louisae, CM 3018, showing the trough between the bifurcated neural spines.

If you’re not active in research, the idea of writing little term papers may sound like purgatory. But writing about something that you love, that fascinates you, is a very different proposition from writing about dead royalty or symbolism because you have to for a class.* I do these little projects for myself, to satisfy my curiosity, and it doesn’t feel like work. More like advanced play. When I’m really in the thick of learning a new thing–and not, say, hesitating on the edge before I plunge in–I am so happy that I tend to literally bounce around like a little kid, and the only thing that keeps me sitting still is the lure of learning the next thing. That I earn career beans for doing this still seems somewhat miraculous, like getting paid to eat ice cream.

* YMMV, history buffs and humanities folks. If dead royalty and symbolism rock your world but arteries and vertebrae leave you cold, follow your star, and may a thousand gardens grow.

Doing little projects is such a convenient and powerful way to make concrete progress that it has become my dominant mode. As with the piece that I wrote about the perforating branch of the peroneal artery, the products rarely get used wholesale in whatever conference presentation or research paper I end up putting together, but they’re never completely useless. First, there is the benefit to my understanding that I get from assembling them. Second, they’re useful for introducing other people to the sometimes-obscure stuff I work on, and nothing makes you really grapple with a problem like having to explain it to others. And third, these little writeups and slideshows become the Lego bricks from which I assemble future talks and papers. The bird neural canal slide deck became a decent chunk of our presentation on the Snowmass Haplocanthosaurus at the 1st Palaeontological Virtual Congress (Wedel et al. 2018)–and it’s about to become something even better. (Four months later: it did!)

The operative word at the start of the last paragraph is ‘concrete’. I don’t think this was always the case, but now that I’m in my mid-40s ‘what I know’ is basically equivalent to ‘what I remember’, which is basically equivalent to ‘what I’ve written down’. (And sometimes not even then–Mike and I both run across old posts here on SV-POW! that we’ve forgotten all about, which is a bit scary, given how often we put novel observations and ideas into blog posts.) Anyway, this is why I like the expression ‘crystallize my understanding’: the towers of comprehension that I build in my head are sand castles, and if I don’t find a way to freeze them in place, they will be washed away by time and my increasingly unreliable cerebral machinery.

Really nice Stegosaurus plate on display at Dinosaur National Monument.

Also, if I divide my life into the things I could do and the things I have done, only the things in the latter category are useful. So if you are wondering if it’s worthwhile to write a page to your future self about valves in the cerebral arteries of rats, or all of the dinosaurs from islands smaller than Great Britain, or whatever strange thing has captured your attention, I say yes, go for it. Don’t worry about finding something novel to say; at the early stages you’re just trying to educate yourself (also, talks and papers need intro and background material, so you can still get credit for your efforts). I’ll bet that if you set yourself the goal of creating a few of these–say, one per year, or one per semester–you’ll find ways to leverage them once you’ve created them. If all else fails, start a blog. That might sound flip, but I don’t mean for it to. I got my gig writing for Sky & Telescope because I’d been posting little observing projects for the readers of my stargazing blog.

A final benefit of doing these little projects: they’re fast and cheap, like NASA’s Discovery missions. So they’re a good way to dip your toes into a new area before you commit to something more involved. The more things you try, the more chances you have to discover whatever it is that’s going to make you feel buoyantly happy.

You may have noticed that all of my examples in this post involved library research. That’s because I’m particularly interested in using little projects to get started in new lines of inquiry, and whenever you are starting out in a new area, you have to learn where the cutting edge is before you can move it forward (Tutorial 12 again). Also, as a practical consideration, most of us are stuck with library research right now because of the pandemic. Obviously this library research is no substitute for time in the lab or the field, but even cutters and diggers need to do their homework, and these little projects are the best way that I’ve found of doing that.

P.S. If you are a student, read this and do likewise. And, heck, everyone else who writes should do that, too. It is by far the advice I give most often as a journal editor and student advisor.

P.P.S. As long as you’re reading Paul Graham, read this piece, too–this whole post was inspired by the bit near the end about doing projects.

References

Posted by Matt Wedel
Filed in Apatosaurus, neural spine, stinkin' mammals, stinkin' ornithischians, stinkin' theropods, Tutorial
4 Comments »

Tutorial 37: how to record your talk (audio and slides) on a Mac

March 16, 2020

When I gave the talk about vertebral orientation for the 1st Palaeo Virtual Congress at the end of 2018, I had to prepare it as a video — so I saved it on YouTube so it would outlive the conference:

Having figured out the practicalities of doing this, it made sense to similarly make a permanent record of my SVPCA 2019 talk, The Past, Present and Future of Jensen’s “Big Three” sauropods:

I promised back then that I would put together a tutorial post on how to make these videos; then I forgot all about it. Thanks to David Roberts for reminding me: here it is!

I’m using a MacBook, so the details of what I write here will be appropriate for that platform. If you’re on Linux or (heaven help you) Windows, then there will be similar software that you can use. Perhaps commenters could tell us what that software is?

Anyway …

1. Preparation

Set yourself up with a microphone. You can get a simple headset for £20 or so on Amazon, and it’s well worth doing for the improved audio clarity over what you’ll get with the inbuilt mic. Test that it’s working with the Sound panel in System Preferences. When you talk, you’ll see the input level meter moving.

Cue up your presentation slides, ready to go.

(Oh, and obviously: be sure to have practiced your talk so you know what you’re going to say on each slide.)

2. Recording

Open the QuickTime Player application. You’ll find it in the usual Applications area, having installed as part of the operating system.

Its user interface is a bit odd — it basically doesn’t have one, apart from the menus. If you inadvertently click onto another window, and so switch application (for example because you’re writing a blog post) you won’t be able to click on the QuickTime Player window to bring it back to the front, because there isn’t one. If this happens, Cmd-Tab until you reach it.

From the File menu, choosen New Screen Recording. A small recording window pops up. (It, too, has an audio meter, so you can see the microphone signal.)

Make sure that the volume at the bottom is down to zero: all it does is play back what you’re saying into the mic, which is distracting and could potentially cause feedback.

There’s a small drop-down menu to the right of the red button:

Be sure you’re using the right microphone: not the internal one if you have a headset!

You want to turn off Show Mouse Clicks in Recording, as they will just be distracting visual noise. (You’re probably using arrow keys to move through your slides anyway, but some people use mouse clicks.)

Click on the red button. A message pops up in the middle of the screen:

Click once anywhere on the screen. The message will disappear and a tiny Stop button will appear up in the top right of your menu area. It’s the square-in-a-circle to the far left of this screenshot:

You are recording.

Start your slideshow, making sure you are in full-screen mode. Give you talk, paging through slides and speaking just as though you had a live audience.

When you have finished, exit the slideshow. As you come out of full-screen mode, the tiny stop button will reappear, along with the rest of the menu bar.

Click the stop button.

3. Cleaning and exporting

What happens now can be disorienting. The recording is complete, and QuickTime Player will now display it in a window. That window fills almost the entire screen, and contains a copy of the screen, so you can easily lose your bearings and assume you’re looking at your desktop. You’re not. I find it helpful to drag that playback window down to a smaller size, to reduce that confusion:

You can click the Play button to watch your talk back. Take a moment to feel pleased with your fine presentation.

Now from the Edit menu, choose Trim…. You will see a video playback window similar to what was there before, but now with a yellow trimming timeline at the bottom:

Drag the left handle of the yellow bar forward, past the early part of the video where you were starting up the slideshow, and drop it where the presentation has gone full-screen, just before when you began the speaking. Similaly, drag the right handle backwards, before the end part where you came out of full screen and hit the tiny Stop button. When you’re happy with both ends, hit the Trim button. (You can do this as many times as you need to, so if in doubt, leave more of the video in place rather than less, then trim a bit more off.)

If you wish, you can save the project in QuickTime Player’s own format (File → Save…), but there’s not much point unless you’re going to come back and edit it further.

What you need to do is export the video in a format that can be uploaded for viewing. Choose File → Export As and pick a resolution: the software offers 4K, 1080p, 720p and 480p. As always, there’s a trade-off between file-size (and therefore upload time) and image quality. For something that’s intended for viewing on YouTube, my feeling is that 720p (i.e. resolution that is 720 pixels deep) is plenty.

Choose a filename, and hit the Save button. The result should be a .mov file which you can watch in QuickTime Player (natch), VLC or any standard media player.

4. Uploading

You might want to reposit your video file somewhere official, such as an institutional repository. That makes sense. You should probably do that, for posterity.

But the reality is people are going to actually watch your talk on YouTube. Go to youtube.com and log in. Hidden away in the top right is a tiny tiny video-camera icon, rendered in pale grey on a dark white background.

This, believe it or not, is a way you upload a video. Click it, and choose Upload video from the menu that pops up. From here, it should be a matter of following the instructions.

Don’t forget to give your uploaded video an informative title such as Mike Taylor on “Should science always be open?” at ESOF2014, and a description containing everything the viewer might want to know, such as

Mike Taylor’s talk from the session “Should science always be open?” at 1:30pm on Wednesday 23 June 2014, in the Glyptotek Hall, Carlsberg Museum, Carlsberg District of Copenhagen, Denmark.

The three speakers were each given ten minutes to expound their own area of openness (open access, open innovation, open data), and that was followed by round-table discussion and a panel. Mine was the first talk of the three.

See also: https://www.youtube.com/watch?v=ITH4FFbhqmk

The slides are hard to make out in this video. You can download in:
Powerpoint format: http://www.miketaylor.org.uk/dino/pubs/misc/Taylor-ESOF2014-yes-science-should-always-be-open.ppt
PDF format: http://www.miketaylor.org.uk/dino/pubs/misc/Taylor-ESOF2014-yes-science-should-always-be-open.pdf

Then click MORE OPTIONS near the bottom of the page to get the License and distribution section. You can use this to change the terms from the Standard YouTube Licence (basically all rights reserved) to Creative Commons Attribution (CC By). A few more clicks and you’re done.

Go to it! Never let one of your talks go unrecorded. Think about how much time and effort and expertise you’ve put into your talk, and about how many people could benefit from it. The Past, Present and Future of Jensen’s “Big Three” sauropods has been watched more than 300 times — which is means I’ve quadrupled its audience since I spoke to less than a hundred people at SVPCA.

Publish!

Posted by Mike Taylor
Filed in Tutorial, video
6 Comments »

Tutorial 36b: the sauropod axis in detail, illustrated by Camarasaurus

December 8, 2019

When I visited Dinosaur National Monument in October with Brian Engh and Yara Haridy, we spent a decent amount of time checking out DNM 28, a skull and associated bits of Camarasaurus. In particular, I got some shots of the axis (the second cervical vertebra behind the head), and it got me thinking about pneumaticity in this unusual element. Why I failed to get a full set of orthogonal shots is quite beyond my capacity, but we can roll with what I have. Before we go on, you might want to revisit Tutorial 36 to brush up on the general parts of the atlas-axis complex.


Here’s the axis in left lateral view (so, anterior to the left).

And a labeled version of the same. A few things to note:

  • One oddity of sauropod axes (and of axes of most critters) is that not only are the articular facets of the prezygapophyses not set forward of the neural arch, they’re set backward, well behind the forward point of the arch.
  • The dens epistrophei or odontoid process is sticking out immediately below the neural canal. This is the tongue of bone that articulated with the atlas (first cervical vertebra) in life.
  • Check out the prominent epipophysis above the postzygapophysis, which anchored the long dorsal neck muscles. (For more on epipophyses, see these posts, and especially this one.)
  • The diapophysis and parapophysis articulated with a cervical rib, which is not shown here. In fact, I don’t remember seeing it in the drawer that this vert came from. The atlantal and axial cervical ribs are small, apparently fused late in life if they fused at all, and are easily lost through taphonomic processes.
  • At least three pneumatic features are visible in this lateral view: the lateral fossa on the centrum, which is referred to as the “pleurocoel” in a lot of older literature; a ventral fossa that lies between the parapophysis and the midline ventral keel; and a fossa on the neural arch, behind the postzygodiapophyseal lamina. In the nomenclature of Wilson et al. (2011), this is the postzygocentrodiapophyseal fossa.

“Postzygocentrodiapophyseal fossa” is a mouthful, but I think it’s the only way to go. To be unambiguous, anatomical terminology needs to references specific landmarks, and the schemes proposed by Wilson (1999) for vertebral laminae and Wilson et al. (2011) for vertebral fossae are the bee’s knees in my book.

Nomenclatural issues aside, how do we know that these fossae were all pneumatic? Well, they’re invasive, there’s no other soft-tissue system that makes invasive fossae like that in archosaur vertebrae (although crocs sometimes have shallow fossae that are filled with cartilage or fat), and the same fossae sometimes have unambiguous pneumatic foramina in other vertebrae or in other sauropods.

Most of the features labeled above are also visible on the right side of the vertebra, although the ventral fossa is a little less well-defined in this view, and I can’t make out the prezyg facet. Admittedly, some of the uncertainty here is because of my dumb shadow falling across the vertebra. Specimen photography fail!

The paired ventral fossae are more prominent in this ventral view, on either side of the midline ventral keel (anterior is to the top).

And here’s a labeled version of the same ventral view.

Finally, here’s the posterior view. It’s apparent now that the neural spine is a proportionally huge slab of bone, like a broad, tilted shield between the postzygapophyses (which are also quite large for the size of this vertebra). The back side of the neural spine is deeply excavated by a complex fossa with several subfossae (kudos again to Jeff Wilson [1999] for that eminently useful term).

Here’s the same shot with some features of interest labeled. If I’ve read Wilson et al. (2011) correctly, the whole space on the back side of the neural spine and above the postzygs could be considered the spinopostzygapophyseal fossa, but here I’ve left the interspinous ligament scar (ILS) unshaded, on the expectation that the pneumatic diverticula that created that fossa were separated on the midline by the interspinous ligament. I might have drawn the ILS too conservatively, conceivably the whole space between the large deeply-shadowed subfossae was occupied by the interspinous ligament.

I’m particularly interested in those three paired subfossae, which for convenience I’m simply calling A, B, and C. Subfossa A may just be the leftover space between the spinopostzgyapophyseal laminae laterally and the interspinous ligament medially. I think subfossa B is invading the ramus of bone that goes to the epipophysis and postzygapophysis, but I didn’t think to check and see how far it goes (that might require CT anyway).

Subfossa C is the most intriguing. Together, those paired fossae form a couple of shallow pits, just on either side of the midline, and aimed straight forward. They can’t be centropostzygapophyseal fossae, which used to be called peduncular fossae, because they’re not in the peduncles on either side of the neural canal, they’re up above the lamina that connects the two postzygapophyses. Could they be ligament attachments? Maybe, but I’m skeptical for at least four reasons:

  1. Although interspinous ligament attachments often manifest as pits in the cervical vertebrae of birds, in sauropods they usually form rugosities or even spikes of bone that stick out, not inward. Furthermore, these pits are smooth, not rough like the interspinous ligament scars of birds.
  2. The interspinous ligament in tetrapods is typically a single, midline structure, and these pits are paired.
  3. Similar pits in front of the neural spine are present in some sauropod caudals, and they appear to be pneumatic (see Wedel 2009: p. 11 and figure 9).
  4. Pits at the base of the neural spine seem to be fairly uncommon in sauropod vertebrae. If they were attachment scars from the universally-present interspinous ligaments, we should expect them to be more prominent and more widespread.

But if these paired pits are not ligament scars, what are they? Why are they present, and why are they so distinct? Sometimes (often?) subfossae and accessory laminae look like the outcome of pneumatic diverticulum and bone reacting to each other (I almost wrote ‘playing together’), in what looks like a haphazard process of adaptation to local loading. But the symmetry of these pits argues against them being incidental or random. They don’t seem to be going anywhere, so maaaybe they are the first hoofbeats of the embossed laminae and “unfossae” that we see in the vertebrae of more derived sauropods (for which see this post), but again, their symmetry in size and placement isn’t really consistent with the “developmental program gone wild” appearance of “unfossae”. I really don’t know what to make of them, but if you have ideas, arguments, or observations to bring to bear, the comment field is open.

In summary, sauropod axes are more interesting than I thought, even in a derpasaurus like Cam. I’ll have to pay more attention to them going forward.

References

 

Posted by Matt Wedel
Filed in atlas-axis complex, camarasaurs, cervical, hands used as scale bars, stinkin' appendicular elements, stinkin' mammals, Tutorial
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Tutorial 35: Finding work experience relevant to palaeontology

October 25, 2019

I don’t know if this exists in the US, but here in Britain it’s common for kids in Year 11 at school (age 15 or 16) to have a week allocated where they find a position (usually unpaid) and do some work outside the school. It’s called “work experience”.

A friend of a friend has a son that age, and he wants to be a palaeontologist. I was asked if I had any advice. Here’s what I wrote, lightly edited: I hope it’s useful to other enthusiastic kids.

Palaeontology, being the study of ancient life through the medium of fossils, is really the intersection of two fields: geology (the study of rocks) and biology (the study of life). Your first decision is whether you see yourself primarily as a geologist whose favourite rocks happen to be fossils; or as a biologist whose favorite organisms happen to be long dead. Myself, I fall 100% in the latter category — I know almost nothing about geology — which means I call myself a palaeobiologist. But because historically palaeontology grew out of geology in England, most palaeontology happens in geology departments. (That’s why my acacdemic address is “Department of Earth Sciences” despite my near-total ignorance of earth sciences.)

If you want to come into palaeo via the geology end of things, I’m not really sure what to suggest. Perhaps talk to oil companies or someone like that? Maybe surveying companies — perhaps someone who is working on the HS2 route and might know about work being done to understand the nature of the ground that the new railway is to be built on?

But if you want to come in via the biology route, you have a lot of options to do with extant (i.e. non-extinct) animals and plants. In your position, I would be writing to every zoo in travelling distance — or where I could stay with a friend or relative — trying to get a placement at one of them. Alternatively, you might be able to get a placement at a veterinary surgery (as our youngest did), which would be great for learning some animal anatomy. Or even a farm might be useful. Or if you’re interested in ancient plants, then perhaps an arboretum or nursery could give relevant experience with extant plants.

Finally, the other obvious thing to try would be a museum. Even if you land up in one that has no palaeontology collection, it will be useful for you to get to understand how museums work, how access to collections happens, how specimens are stored, indexed, etc.

Our eldest son knew from about fourteen or fifteen that he was interested in economics and government, and he ended up doing three “work experience”-like placements: first the official school-sanctioned one in the Treasury in London (thanks to a family friend who worked there); then on his own school-holiday time in local government in Birmingham (thanks to another family friend!); and finally during the summer working in the constituency office of our MP Mark Harper (due to sheer persistence and chutzpah). I think having done all three of these gave him a really good, broad perspective on the kinds of things he was interested in. If I were you, I would be looking for three placements, too — one school-sanctioned and two in forthcoming holidays. And I’d ideally want a zoo, a veterinary surgery and a museum.

Hope that’s helpful!

Posted by Mike Taylor
Filed in Tutorial
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Tutorial 19g: Open Access definitions and clarifications, part 7: why your open-access journal should use the CC By licence

October 15, 2019

Matt and I are about to submit a paper. One of the journals we considered — and would have really liked in many respects — turned out to use the CC By-NC-SA license. This is a a very well-intentioned licence that allows free use except for commercial purposes, and which imposes the same licence on all derivative works. While that sounds good, there are solid reasons to prefer the simpler CC By licence. I wrote to the journal in question advocating a switch to CC By, and then I thought the reasoning might be of broader interest. So here’s what I wrote, lightly edited.

First, CC By neatly expresses the one requirement all academics have of their work: that they get credit for it. When we publish papers, we are happy for them to be freely distributed, but also want people to build on them, re-using parts in whatever way helps, provided we’re credited — and that is exactly what CC By enables.

Second, because of this, many funders that require the work their grantees do to be published open access specifically require the CC By licence, in the expectation that it will provide the greatest societal benefit in exchange for their investment. Most famously, this is the case for the Gates Foundation (the largest private foundation in the world), but for a partial list of the many other funders with this policy, see https://www.springernature.com/gp/open-research/funding/funders-requiring-cc-by-for-articles — funders whose grantees, as things stand, are not allowed to publish their work in your journal.

Third, CC By is almost universal among well established and respected open-access journals, including all the PLOS journals, PeerJ, the BioMed Central journals, the Hindawi journals, eLIFE, Nature’s Scientific Reports, and palaeo journals such as Acta Palaeontologica Polonica and Palarch’s Journal of Vertebrate Paleontology. This is important because CC By-licenced journals can’t freely use material published under more restrictive licences such as your journal’s CC By-NC-SA. Instead, authors of such articles must labouriously seek exemptions from the copyright holders of the material they wish to reuse or adapt.

Fourth and last, other online resources also use CC By (or optionally CC By-SA in the case of Wikipedia), which means that, while material from PLOS ONE, Scientific Reports et al. can be freely used in Wikipedia articles, text and illustrations from articles in your journal cannot, limiting its use in outreach. Similarly, even on our own palaeontology blog, we would have concerns about using By-NC-SA materials as we use Patreon to solicit donations and our blog is arguably therefore commercial. (Part of the problem with the NC clause is that there is no rigorous definition of “commercial”.)

For all these reasons, we believe that your journal would better serve its authors, its readers, the academic community and broader society if its articles were published under the CC By licence. We hope that, if you agree, you are able to some point to help the journal make this transition. And if there’s anything Matt or I can do to assist that process, we’ll be happy to.

Posted by Mike Taylor
Filed in CC BY, CC BY-NC, Creative Commons, Gold open access, open access, recycled, Science communication, Shiny digital future, Tutorial
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Tutorial 34: How to document a specimen

March 4, 2019

As noted in the last post, Matt and I are off to spend a week at the Carnegie Museum from 11th-15th March. We expect to see many, many fascinating specimens there: far more than we’ll be able to do proper work on in the five days we have. So our main goal is to exhaustively document the most important specimens that we see, so we can work on them later after we’ve got home. I think of this as the “harvesting” phase of research, with the grinding and baking to follow.

I was going to write a checklist for myself, to ensure that I cover all the bases and we don’t find ourselves in six months’ time looking at our records and saying “I can’t believe we forgot to do X for this specimen” — because, believe me, we have spent far too much of our lives doing this already. But then I realised I should share it with the world, in case it’s helpful to others, too.

So here’s what to do when dealing with, for example, an apatosaurine cervical like this one. Let me know in the comments if I forgot anything!

BYU 20178, cervical vertebra from an apatosaurine sauropod. ventral view, anterior to the left. Note that the scalebar is held at approximately half the height of the vertebra; and that the catalogue card is in view and legible, giving a record who collected the specimen, when, and where.

Sketch the specimen, even if (like me) you are a terrible artist. The process of sketching forces you to really look at it — at each part of it in turn — and often results in you noticing something you would otherwise have missed. It would be worth doing this even if you immediately threw the sketch away: but don’t do that, because you’re going to want to …

Measure the specimen, using a tape measure, digital calipers or both as appropriate. You want to get at least all the measurements that you’ll include in a formal description — total length, total height, width across zygapophyses, etc. — but it’s often useful to also get other, more obscure measurements, just to make sure you’ve got your head around the shape. For example, in the vertebra above, you might measure the diagonal distances from the anteriormost projection of each cervical rib to to opposite side’s posterolateralmost part of the centrum. You record measurements in a table in your notebook, but some measurements are hard to describe: so just write them straight onto your sketch. To keep things straight, it can be useful to do the sketch in one colour and the measurements in another; or the sketch in pencil and the measurements in pen.

Now we come to photography. You want a lot of different kinds of photo, so lets consider them separately.

Take photographs of the specimen with its specimen label, ideally from several different aspects. This will make it easy to remember later which specimen is which. In a typical museum visit — especially a reconnaisance visit like our upcoming Carnegie trip — you’re going to see a lot of different specimens, and when you revisit your photos in six months it’ll be hard to keep them all straight. Make it easy on yourself. Also: the specimen label often contains other  useful information such as the quarry where the specimen was found. Capture that. Get a good close-up photo of the label alone, to ensure all the text is captured cleanly.

Take photographs from the cardinal directions. To illustrate a specimen nicely in a descriptive paper, you will at minimum want photos from anterior, posterior, dorsal, ventral and left and right lateral aspects (or as many of these are possible to obtain: you can’t always turn big specimens). Since these are the photos you’re likely to use in a publication, take extra care with these. Set up a plain-coloured background when possible so it’s easier to crop out later. Set up the best lighting you can. Take each photo several times so you can keep the best one. Use a tripod if you have one. (For much more on this, see Tutorial 8 on how to photograph big bones.)

Take photographs with a scalebar. This will give you a way to sanity-check your measurements later. Think carefully about scalebar placement. If you put it on top of the specimen so it obscures part of the fossil, be sure that’s not your only photo from that aspect: you won’t want to be left without good images of the whole bone. A scalebar placed on top of the specimen will appear larger than the same scalebar placed on the floor or the bench next to the specimen, thanks to perspective, which means your measurements are more trustworthy than photos of the scalebar. If you can easily arrange for it to be raised to half the total height of the specimen, you’ll get a more honest reading.

Photograph individual features of the bone with some kind of note. The reason I say “with some kind of note” is that I have hundreds of close-up photos of bits of sauropod vertebra which I evidently took in the hope of highlighting some specific bit of morphology, but I have no idea what morphology. Get a scrap of paper and scribble something like “big nutrient foramen”, draw an arrow on it, and place the scrap on the bone so that the arrow points at the feature. Take a photo; then remove the paper and take another photo. The first one is your note to yourself; the second is the raw material for an illustration that you might prepare later, highlighting the relevant feature in a more elegant way.

Do a video walkaround with narration. For some reason, we didn’t start doing this until very recently, but it’s a great way to get a rough-and-ready reminder of important aspects of the specimen. You can just do this with a phone, moving it around the specimen, pointing to interesting bits and saying things about them. Here’s an example of Matt pointing out some features of the preserved cervical vertebrae of Suuwassea, and here he is again pointing out how pelican vertebrae are made of nothing.

Take a shedload of undifferentiated photos from every possible angle. Your goal here is that you’ll be able to use photogrammetry later to make a 3D model of the fossil. I admit to my shame that I’ve still never successfully done this — but thanks to the kindness of my good friend Heinrich Mallison, who is an expect in this area, I do have some fine models, including the Xenoposeidon model that was published as a supplementary file to my 2018 paper. Even if you don’t have access to someone as helpful as Heinrich, it’s worth getting these comprehensive photo-sets because photogrammetry software is likely to get progressively easier to use. Hopefully in a couple more years there will be nothing to it but loading a bunch of photos and pressing a button.

Up till here, we’ve been concentrating on gathering information about the specimen in a form that we’ll be able to return to later and use in comparisons and illustrations. But we can do more than that now we’re here with the physical specimen:

Look at the bone texture. Figure out how much of it is real, and how much is reconstructed — a particular problem with older specimens. Keep an eye out for rugosities for muscle and ligament attachments, smooth areas and pockets for pneumatic diverticula (or fat pads in boring mammal verts), and any odd growths that might be ossified soft tissues or pathological reactive bone growth. These kinds of things are often much easier to see in the actual specimens than in even the very best photographs.

Check for areas where the specimen is under-prepared. It’s very common for a neural canal to remain filled with matrix — and easy to spot, so in a sense not a problem. But how often is a pneumatic feature obscured because it’s still full of matrix? This is probably part of the reason that caudal pneumaticity so often goes unobserved, and it will very often obscure foramina within the neural canal. Similarly, I don’t know whether the huge club on the end of the right cervical rib of NHMUK PV R173b (formerly BMNH R173b) is pathological bone or a mineral concretion, because all I have to go from is my lame photos. I should have figured that out while I was with the actual specimen.

Discuss the specimen with a friend. I just can’t overstate how important this is. When Matt and I visit a collection together, we discover much, much more than twice as much as either of us would alone. Isaac Asimov is said to have observed “The most exciting phrase to hear in science, the one that heralds new discoveries, is not “Eureka!” (I found it!) but “That’s funny …””. Whether or not he ever actually said it (it’s not in any of his written works) it’s certainly true that the key moment in investigating a specimen is frequently when one person says “Hey, take a look at this”. Two minds can spark off each other in a way that a single mind can’t.

Last of all, it’s worth giving a little bit of thought to the possibility that you’ll one day be doing publicity for this specimen. So:

Get someone to take photos of you with the specimen. You’ll need them for press releases and media packs. I’ve only once in my life been in physical proximity with the Brontomerus specimen: during the three-day 2007 visit when I did much of the descriptive work for the paper. Idiotically, although I was there with three colleagues (Matt, Randy Irmis and Sarah Werning), I didn’t get anyone to take a photo of me with the material. So when we needed a photo for the publicity:

The Brontomerus mcintoshi holotype specimen OMNH 27761-27800, 61248 and 66429-66432 with the authors of the paper that described it. Back row (L to R): Mike Taylor, Matt Wedel, Rich Cifelli.

There was no good way to get it. I certainly wasn’t going to fly back out to the USA just to get a photo. So we got our Emmy award-winning special-effects-wizard friend Jarrod Davis to photoshop me into a photo that the museum had been able to take of Matt and Rich. (You can see the evidence here and here if you want to see how it was done. And, yes, before he could even start composing me in, Jarrod had to rescue a ludicrously under-exposed base image.)

Much better to avoid such nonsense. Get good photos of you with the specimens, like the one at the top of the Sauropocalypse post, and then if you ever need ’em you’ve got ’em.

 

Posted by Mike Taylor
Filed in Apatosaurus, Brontomerus, cervical, Supersaurus, Tutorial
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Photogrammetry: index to Heinrich Mallison’s tutorials

November 25, 2017

Having benefitted so hugely from 3D models that Heinrich Mallison made for me — most notably, the Xenoposeidon model that is the supplementary data file for the recent preprint — I realised the time has come for me to learn to do this for myself. To that end, I am going to read all the tutorials he’s written on the subject. This page is a link-farm to those tutorials, which I made for my own benefit, but which I hope others will also benefit from.

There is also Heinrich’s paper, with Oliver Wings, Photogrammetry in paleontology – a practical guide (Mallison and Wings 2014), which he announced in its own blog-post.

Reference

 

Posted by Mike Taylor
Filed in photogrammetry, Tutorial
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