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Our special guest post this week comes from Dr. Liz Clark of Yale University in New Haven, Connecticut, USA. She continues to bring biomechanics-fu to echinoderms– the weird marine critters like seastars and sea urchins. Including fossils, as you’ll see today! You may remember her from blog posts such as “Guest Post: Brittle Star Arms Are Weird“.

Stomach-Churning Rating: 1/10; echinoderms are inoffensive.

Imagine that you’re stuck in a cardboard box on the beach, holding a small stick. Could you use the stick to move yourself forward? What would you do? You could try digging into the sediment ahead of you to pull yourself along. You could try rowing side to side, as if you were in a rowboat. Or maybe it’s not possible and you’d give up, decide to stay put, and wave your stick in the air for help.

Believe it or not, this is a strange-but-important dilemma that some paleobiologists- like me!- have been wrestling with for generations. My research specialty is in the biomechanics of locomotion– how organisms use their bodies to get from one place to the next (through walking or swimming, for instance). We can learn a lot about an animal by studying their locomotion, such as why their body is shaped the way that it is, or what role they occupy in their ecosystem. Animal motion is a major inspiration for robotic design, and I work with engineers to apply the novel insights on animal locomotion from my research to create new kinds of devices.

Studying the biomechanics of motion in living organisms is (relatively) straightforward. We can use high-speed cameras, motion capture software, and 3D imaging tools to visualize and understand how organisms move in real-time, informing our inferences about how they perform certain tasks. Inferring locomotion in fossil organisms, on the other hand, is tricky since we can’t observe the organism’s behavior like we could if the organism were alive. Instead of being able to watch the organism move, we’re left with a snapshot of the animal frozen in place in a rock. We’re also missing a lot of physical information: locomotion in most animals requires soft tissue and hard skeletal structures, but typically with fossils, only the hard structures get preserved.

However, we can often garner some insights from living organisms to determine the locomotion strategies that fossil organisms use. Most organisms in the fossil record look at least somewhat similar to organisms alive today. If our fossil has four legs, for instance, we can study locomotion in living tetrapods (four-legged animals) to help us create a framework for deriving inferences about locomotion in our extinct tetrapod fossil animal. But for some really strange-looking animals- ones without obvious modern analogues- we’re not so lucky. For me, this is where the fun begins.

Figure 1: Stylophorans! Here are four fossilized stylophorans from the Helderberg Group of the Early Devonian (YPM 036413)

So getting back to the cardboard box and the stick. These are metaphorical examples of the different locomotion strategies that have been proposed for a group of fossil animals known as stylophorans (Figure 1). Stylophorans are extinct organisms related to sea stars and sea urchins, but with a body structure unlike any organism on the planet today. They have a large, relatively flat body called a theca (i.e., the cardboard box), and a long, thin segmented tail known as the aulacophore (i.e. the stick) (Figure 2). They’re known in the paleontological community as some of “the strangest-looking animals of all time.”

Figure 2: Stylophoran anatomy. The “theca” is the body cavity, and the “aulacophore” comprises of the proximal aulacophore, the stylocone, and the distal aulacophore.

By reconstructing stylophoran locomotion, we can unlock the mechanics of a unique system for motion and its potential applications to engineering. We can also understand more about how this organism lived and functioned in its ancient ecosystem. And, by developing a new approach to understand locomotion in stylophorans, we can apply this strategy to analyze locomotion and movement in other unusual fossil animals as well!

For years, scientists have been documenting the incredible array of stylophoran diversity in the fossil record and making their best predictions about how they would have been able to move (or not!). These predictions are based on their morphology– the structure of an organism’s body. For stylophorans, that means the shape and structure of the theca and aulacophore. There are a variety of stylophoran thecal shapes, ranging from ovoid in Enopleura to trapezoidal in Ceratocystis to almost crescent-shaped in Cortnurnocystis. There’s a similarly wide array of aulacophore morphologies as well.

Figure 3: Left: One half of the concretion within which the stylophoran fossil we analyzed is preserved. Right: The 3D digital image of the stylophoran fossil, created by micro-CT scanning the fossil specimen.

We developed a new approach using 3D imaging (Figure 3) to create a digital model of a stylophoran specimen. We used the model to test if several different locomotion strategies that had been proposed before were physically possible or impossible for a stylophoran to actually perform.

First, we used a micro-CT scanner to image a fossil stylophoran. This outputs a digital 3D picture of the stylophoran fossil that we can look at and analyze on a computer. Next, we developed a program to calculate the joint centers- the point at which one skeletal structure rotates relative to another-within the digitized stylophoran’s aulacophore (Figure 4). This created a digital marionette– a rig of our stylophoran fossil that flexes at the junctures between aulacophore segments as it would have in life. We then rotated each segment at the joint center to calculate the aulacophore’s total range of motion– a reconstruction of how far the aulacophore could flex in each direction (Figure 5).

Figure 4: A look into some of the nuts and bolts of the 3D model we created. Tri-colored axes demarcate where the joint centers are in the proximal aulacophore. 

We used this 3D range of motion model to evaluate several locomotion strategies that had been previously hypothesized for this group of stylophorans. One hypothesis suggested that these stylophorans dug their aulacophores into the substrate– sediment on the ocean floor- to pull themselves forward. Another suggested that they moved the aulacophore side to side in order to push themselves along. We found that the first hypothesis would have been impossible to conduct based on the range of motion we calculated, but the second strategy was theoretically possible! We’ll need to do more work to see how likely it was that stylophorans would have actually used this technique. Nevertheless, through this investigation, our team produced the first objective, data-driven methodology for analyzing locomotion in fossil invertebrates, which is a big step in the right direction for the study of fossil invertebrate biomechanics! Our technique can be applied to study other organisms with rigid skeletons as well, like crabs, insects, or sea stars, for instance, and we’re looking forward to seeing our technique used to uncover more interesting locomotion strategies!

Figure 5: A snapshot of the 3D model where we can observe how dorsal and ventral range of motion compare to the originally preserved orientation of the aulacophore (highlighted in green).

Do you want to know more? You can! We published a paper on this topic here!

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Ho ho ho! The vagaries of the scientific publication system today brings forth TWO open access papers on crocodylian functional anatomy, evolution and biomechanics, from my team with others’; including our DAWNDINOS project in part. Get ready to bite down on the science! I’ve loved crocodylians throughout my life– “dacadile” was among my first words, for a beloved stuffed croc toy, and “Alligators All Around” was an early favourite song (it’s still GREAT).

One of the many large adult alligators in St. Augustine, Florida.

Stomach-Churning Rating: 1/10; bones and movies of awesome behaviours.

First, I am so relieved and pleased to finally publish an experimental study I began over 17 years ago. This is my most-delayed paper ever, due to my own perfectionism, overcommitment and failures at funding it more broadly. But published is published and I’m glad to see it out. We collected a large experimental dataset from 15 species of Crocodylia at the St Augustine Alligator Farm Zoological Park (a conservation/education centre) in Florida. (No matter how you species-ify them, that’s a good chunk of diversity; roughly half or more.) This was a non-invasive study of 42 individuals ranging from 0.5 to 43 kg in body mass (hatchlings to adults). Larger adults were too dangerous or too slow to work with. It took 3 years (2002, 2004, 2005) of data collection to assemble this, with some twists and turns (including a close brush with Hurricane Katrina), and then a lot of analysis and reanalysis; and I’d do it all very differently if I did it today but that’s a moot point. So what’s the paper about?

Adorable Siamese crocodile family “cuddling”. Crocs are great parents! IIRC, that is the father shown.

Some Crocodylia (the inclusive modern name for all crocs, caimans, gharials, gators) are known to use what we call asymmetrical gaits: “mammal-like” footfall patterns in which the left and right limbs do not move as mirror images of each other. In particular, these gaits include galloping (rotary or transverse; either way a “4-beat” pattern with left-right hind- followed by right/left forefoot contacts) and bounding or half-bounding (the former being the most extreme, with left-right hind- and then forefoot contacts as synchronous pairs). Often people just say that crocs can “gallop” but this confuses/conflates the issue and omits that they can use these faster bounding gaits. Regardless, we’ve known about these gaits at least since HB Cott’s 1961 photographic documentation of them in Nile crocodiles; and more detailed studies of Australian freshwater and saltwater crocodiles in the 1970s-2000s. But very often, scientists and popular natural history accounts ascribe the asymmetrical gaits to only a few species or young individuals.

“Freshie” croc bounding in the wilds of Australia; credit Kent Vliet.

Osteolaemus dwarf African crocodile getting marked up for study.

That’s where we came in. We had access to a huge collection of captive Crocodylia and a very supportive institution (with coauthors from there as a result). I wanted to know which Crocodylia do use asymmetrical gaits, having a very strong suspicion from the literature that Alligatoroidea, the alligator and caiman lineage, don’t use them, whereas their cousins the “true crocodiles” in Crocodyloidea do. And I wanted to test how body size interacted with this ability, as prior accounts hinted that asymmetrical gaits got lost with increasing size or in adults. Finally, I was interested in what the benefits of asymmetrical gaits were– did they give those that used them marked boosts in performance, especially maximal speed? Answering that would help understand why these gaits are used.

Cuban crocodile Crocodylus rhombifer in preparation. A gorgeous but aggressive species that we handled carefully.

So we walked and ran our subjects across some platforms past video cameras and collected about 184 useful trials or strides of gait across level ground at a wide range of speeds; and a LOT of not-so-useful data (mostly subjects just sitting and pouting). We found that, yes, most Crocodyloidea we studied could bound or gallop; and no Alligatoroidea did. In the latter case, we didn’t use as large a sample of subjects as we could have, partly because it already seemed evident that alligators did not use asymmetrical gaits, and partly because those alligatoroids we did try to coax to move quickly either only used symmetrical gaits (e.g. trotting) or would only sit and fight or hiss. And we found that bigger animals moved at least relatively more slowly and less athletically, and perhaps even more slowly in absolute terms (metres/second).

Most intriguingly to me, it didn’t matter what gait alligatoroids or crocodyloids used. They all could move at roughly similar top speeds if they wanted to; less than 5 m/s or 11 mph. It’s just that crocodyloids tended to use asymmetrical gaits, especially bounding, at top speeds– but not always: some even chose to trot at their top speeds. We don’t know why, and we still don’t know why asymmetrical gaits are chosen but they likely have other benefits such as acceleration and manoeuvrability.

It’s a thrill to finally be able to share the huge dataset, including a gigantic file of videos (with some highlights shown here), with the paper, closing this study at last. It should be very useful to anyone studying Crocodylia or wanting to educate people about locomotion. I’m a bit tired of hearing that galloping is a mammalian behaviour when we know so well that many species of animals do it, or something like it. And it was absolutely thrilling to see five species of Crocodylia bound or gallop when they hadn’t been properly documented to do it before– enough anecdotes, here’s cold hard facts from video on what happens. What remains is a mystery: did Crocodylia have this ability to use asymmetrical gaits as an ancestral trait, as almost everyone assumes (and thus alligators and caimans have lost or essentially never express the ability), or did crocodiles uniquely evolve this ability more recently? I would join most scientists in wagering on the former; and there are good reasons to suspect the ability goes deeper into extinct Crocodylomorpha.

(my favourite video is below!)

Want more cool videos? Try my Youtube channel— or if you want ALL of the videos, go here!


Next, Torsten Scheyer was kind enough to invite me to join his team in studying a fossil I’ve long been fascinated by: the “giant caiman” Purussaurus mirandai, from the Miocene (~6 million years ago?) of Venezuela, in the Urumaco Formation‘s very weird biota. Purussaurus has been known of for >125 years but Torsten’s team noticed that Purussaurus (mirandai) specimens tended to add one of their trunk vertebrae to their hip girdles (sacrum; normally only two vertebrae in Crocodylia but here three), and that the shoulder and hip girdles had unusual bone morphology (straighter, more vertical relative to the body). So they asked me to help interpret these features. And here’s the paper!

Infographic by Torsten Scheyer’s team– click to emcroccen!

Three-vertebra sacrum and other traits of Purussaurus; with living caiman bones for comparison. E (bottom): inwards-facing femur head. (see paper for more info)

It became evident that, together, those odd traits conveyed a signal that the skeleton was transformed to aid in supporting the huge body against gravity. For example, I found it quite interesting how the head of the femur (thigh bone) was oriented more directly into the hip socket in multiple specimens, more like a dinosaur’s hip, and specialised for support and fore-aft motions. I used Haley O’Brien et al’s data to estimate just how big P. mirandai might have been and it came out as perhaps 3000 kg and 8 metres total length; as we’d thought, among the largest Crocodylia (and there are larger Purussaurus known, too).

Reconstruction of Purussaurus and morphology of the girdles. (see paper for more info)

The team also put a cool “evo-devo-biomechanics” spin on the study. It is well known that the regional identities of vertebrae (e.g. neck, trunk, sacrum, tail) are largely determined by Hox (homeobox) regulatory genes, early in development. So changes of vertebral identity intimate changes of genetic controls. Crocodylia don’t normally add a trunk vertebra to their sacrum, and only a few fossil crocodyliforms (extinct cousins) ever did either, but we noticed that some specimens of Crocodylia would at least partially make this transformation in pathological states (below). Hence the controls to make these changes exist and sometimes manifest in living crocs, but it’s probably not an “easy” transformation to achieve. One could speculate that under intense selection, such as that imposed by giant body size and some degree of activity on land, that transformation could more easily get permanently “fixed” in a species.

Palaeosuchus palpebrosus (Cuvier’s dwarf caiman) with pathological partial-three-vertebra-sacrum; and lots more morphology. (see paper for more info)

As a nice tie-in to the asymmetrical gait study above, we can safely infer that the giant Purussaurus wasn’t a fast animal on land, by any means. But its skeleton is consistent with it having found novel ways to maintain the ability to stand and move on land, even if slowly.

Happy holidays! Santa Jaws is watching you– be good!

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Our special guest post this week comes from Dr. Liz Clark of Yale University (you may have heard of it?) in New Haven, Connecticut, USA. She is bringing some biomechanics-fu to echinoderms– the weird marine critters like seastars and sea urchins. Did you see her 9-awesome-things-about-echinoderms blog post on Anatomy to You? You should. And you should check this out– and check out our new paper on this topic, which just came out! Remember: all images below can be clicked to zoom in. That’s so fun!

Eversible Stomach-Churning Rating: 2/10; no Uni sushi here.

I remember the first time I saw one. I was at the Duke Marine Lab staring at a chunk of dredged-up oyster shells in a glass dish, when all of a sudden a mass of big, black spines obscured my view. I looked up from the microscope to see a creature with a round body the size of a nickel and a flurry of long, skinny, spiny arms skulking hurriedly across the dish. It wasn’t quite a spider- the five-fold symmetry gave its echinoderm affinity away- but it wasn’t quite a starfish, either. Starfish appear graceful as their tiny tube-feet make hurried and unseen movements underneath them to transport them slowly across the sand- appearing nearly motionless to the naked eye. This animal, on the other hand, was making rapid, whip-like strikes with its arms so that it clambered forward, rapidly and fearlessly scaling the uneven terrain of the shells in a bold attempt to escape the dish. I was hooked. I had to know who this monster was, and learn as much about it as I could.

Brittle star arm set up to study its ossicle-joint mobility with CT scanning (below).

That was the day I was introduced to the brittle star. The name “brittle star” is a bit of a misnomer, since they are really anything but. Brittleness implies rigidity and stiffness, suggesting they have a delicate nature with the impossibility of repair or to adapt, which couldn’t be farther from the truth. Their long arms are incredibly flexible, each made of around 100 tiny segments that allow them to bend in any direction or loop them around in circles. I bet that their name comes from the ease at which they can cast off their arms, which they do intentionally to escape predators or pesky researchers trying to grab them, which deceitfully suggests fragility when in fact their arms are incredibly sturdy and packed with powerful muscles. They can flawlessly regenerate their arms, and, in the meantime, even after they lose several of them, they adjust their strategy for locomotion so that they keep prowling across the seafloor unphased. Their physical flexibility and ability to repair and adapt in the face of damage makes them anything but brittle. The Japanese name for brittle star roughly translates to “spider-human-hand,” which I think much more accurately captures the ethos of this group.

Brittle stars have internal skeletons, and each segment of their arms are made of a cluster of small skeletal elements (ossicles). Researchers in the past have made the assumption that differences in the shape of these ossicles between species change how they move, but I wasn’t so sure. So, John and I decided to work together to figure it out.

We didn’t dive into the freezer for this one- sorry to disappoint all of the diehard fans of John’s freezer out there (but in my defense can you imagine how tough it would have been to even find them in the sea of rhinos, giraffes, and crocs?!). [JOHN: awwwwwww!! It’s more of a wall keeping in the wildlings, than a sea right now though!] Instead we ordered some brittle stars off the internet! The first thing we did was make some measurements of how flexible the arms of brittle stars are when they’re alive. Then we digitized their skeletons by micro-CT scanning them so we could see the articulations between the ossicles and the segments in 3D. We scanned them in a few different positions so we could see the articulations between the ossicles as their arms bend. Then we incorporated all of that data into a 3D model that allowed us to visualize what’s going on in the inside of brittle star arms as they move them around.

We made several different models using this strategy to see if different ossicle shapes change how their arms move. We looked at the differences between arm ossicles in two different speciesOphioderma brevispina and Ophiothrix angulata, which represent two of the three different major morphologies of brittle star arms.  We also looked at the difference in the movement mechanics at the tip and base of the arms in O. brevispina, since the ossicles at the tip are thin and elongated compared to wide and flat at the base.

We found that the tip of the arm of Ophioderma brevispina was more flexible than the base due, at least in part, to the shape of the ossicles. We also found several major differences between the two species, including the location of their joint center and the degree to which they could laterally flex. However, none of these differences were easily attributable to any specific morphological feature that set Ophiothrix angulata and O. brevispina apart, which cautions against making assumptions of brittle star functional capabilities by only looking at the shape of the ossicles. We also found that some of the smaller ossicles within each segment shift their position to accommodate arm flexion, when they were originally thought to limit the motion of the arm! We only looked at a few individuals of two species, but the methods for model-building we developed provide a framework to incorporate a broad sample of brittle star species in the future. We’re curious if the results we found stand when more brittle stars are brought into the mix!

It was incredible to take the journey from initially being surprised and captivated by the movement of these animals to eventually building 3D digital models to discover how they are able to do so. It made me realize that opportunities to be inspired by the natural world are around every corner, and that there are so many interesting questions out there that are still unanswered. Thanks to John and our other team members Derek Briggs, Simon Darroch, Nicolás Mongiardino Koch, Travis Brady, and Sloane Smith for making this project happen!

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A Confuciusornis fossil; not the one from our study but prettier (more complete).

Today almost three years of collaboration come together in a publication that is a fun departure from my normal research, but also makes sense in light of it. Professor Baoyu Jiang from Nanjing University in China has been being working on the taphonomy of the Early Cretaceous Jehol biota from northeastern China (Manchuria) for a while, and he found a lovely Confuciusornis (early bird) fossil; one of thousands of them; from the volcanic pyroclastic flow-based lake deposits there.

Although at first glance the skeletal remains of that fossil are not fabulous compared with some other Confuciusornis, what makes this one lovely is that, on peering at it with multiple microscopic and other imaging techniques, he (and me, and a China-UK collaboration that grew over the years) found striking evidence of very well-preserved fossil soft tissues. Our paper reporting on these findings has gone live in Nature Communications so I can blog about it now.

Reference: Jiang, B., Zhao, T., Regnault, S., Edwards, N.P., Kohn, S.C., Li, Z., Wogelius, R.A., Benton, M., Hutchinson, J.R. 2017. Cellular preservation of musculoskeletal specializations in the Cretaceous bird Confuciusornis. Nature Communications 8:14779. doi: 10.1038/NCOMMS14779

Stomach-Churning Rating: 3/10; gooey, but fossil gooey, except for some colourful, gastrically-tolerable histology of bird tissue.

Front view of the ankle/foot of our specimen.

Back view of the ankle/foot of our specimen.

What has been fun about this collaboration is that, for one, it fits in perfectly with my prior work. Ever since my PhD thesis I’d been wondering about odd bones in the legs of birds, including a very puzzling and very, very neglected bit of bone called the tarsal sesamoid, on the outside of the upper end of the ankle joint. Furthermore, a tunnel of tissue called the tibial cartilage sits next to that sesamoid bone, and then across the ankle joint there is a bony prominence with grooves and tunnels that vary highly among bird species; that is called the hypotarsus. These structures are all known in living birds and, to a degree, in extinct fossil cousins. Our specimen seems to reveal an earlier stage in how these little features of bird ankles originated, which we concluded to be a step along the transition to the more crouched legs that modern birds have.

This study has also challenged me to broaden my horizons as a scientist. Although this was a big collaboration and thus we had several specialists to apply supercharged technological techniques to our fossil, I had to learn something about what all that meant. My kind colleagues helped me learn more about tissue histology, scanning electron microscopy, synchrotron mapping, FTIR and mass spectrometry and more. I won’t go through all of these techniques but there are some pretty pictures sprinkled here and in the paper, and a lot more detail in the paper for those who want the gory techno-detail. Basically we threw the kitchen sink of science at the fossil to crack open some of its secrets, and what we found inside was nifty.

Scanning electron micrograph image of probable tendon or ligament fibres (arrow) in cross-section, from near the ankle joint.

We found preserved cells and other parts of connective tissues including tendons and/or ligaments, fibrocartilage (the tougher kind) and articular cartilage (the softer joint-padding kind). That’s great, although not unique, but the kitchen sink also flushed out even more reductionist data: those tissues included some organic residues, including what appear to be bits of proteins (amino acids); particularly the collagen that makes up tendons.

Fibrocartilage (“fc”) from the ankle joint region.

Hopefully we’re right, and we included as much of the data as we could manage so that others can look at our findings. The specimen is crushed into nearly two dimensions, like all Jehol biota organisms, so its anatomy was hard to interpret but we think we got it right. All of the other kitchen-sinky tools have their own nuances and pitfalls but we did our best with a superb team of experts. We’ve had to wait 125 million years to uncover this specimen and a few more years to find out if we’ve looked at the right way is no greater test of patience.

I thank my coauthors, especially Baoyu Jiang for the kind invitation to participate and the very fun experience of collaborating. I think I’ll remember this study for a long time because, for me, it takes a step beyond just describing Another Case of Jaw-Dropping Fossilization (can you hear the hipsters recounting the excitement and cynicism of the 1990s when this all was dawning? I was there and maybe now I’m one of them). By combining all of those methods we learned new things about the palaeobiology of birds and the evolution of traits within birds. Confuciusornis, not shockingly, had ankles that should have functioned in ways intermediate between those of bog-standard non-avian theropods and modern birds.

Same anatomical regions in an extant bird as in the main fossil specimen. Left distal tibiotarsus (TT; below) and proximal tarsometatarsus (TMT; above) from an adult helmeted guineafowl (Numida meleagris) after formalin fixation. (from our paper’s Supp Info)

I’m hopeful that more synthesis of molecular/cellular, imaging, biomechanical and other tools (not to mention good old palaeontology and anatomy!) can wash away some more of this mystery. And it was fun to be a part of a study that adds to overwhelming evidence that was heretical ~25 years ago: some hardy biomolecules such as collagen and keratin can survive hundreds of millions of years, not just thousands. Pioneers such as Prof. Mary Schweitzer led the original charge that made reporting on discoveries like ours much easier today.

I know how the birds fly, how the fishes swim, how animals run. But there is the Dragon. I cannot tell how it mounts on the winds through the clouds and flies through heaven. Today I have seen the Dragon.“– Confucius, ca. 500 BCE.

Let’s finish with some images of a living bird’s ankle region, by co-author and PhD student Sophie Regnault. We considered these for inclusion in the paper but they didn’t fit quite right. I love them anyway so here they are:

Patchwork of histology slide images, from a guineafowl’s ankle (as per photo above). The numbered squares correspond to zoomed-in images below. The tibiotarsus is on the proximal end (bottom left); the tarsometatarsus is on the distal end (right side); and the enigmatic tarsal sesamoid is at the top. Magnification: 20x overall.

Region 1. nice (fibro)cartilage-bone inferface at ligament insertion.

Region 2: longitudinal slice through ligaments connecting the tibiotarsus to the tarsometatarsus across the ankle joint.

Region 3: front (bottom) of the tibiotarsus/upper ankle.

Region 4: tendon fibres in longitudinal section; on the back of the tibiotarsus. Some show mineralization into ossified tendons (“metaplasia”); another curious feature of modern birds.

Region 5: muscle attachment to the back of the upper tarsometatarsus bone. Small sesamoid fragment visible.

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Sorry about the title. It’s the best I could do. In case you missed it on our Anatomy to You blog, we unleashed a hefty database of CT (and some MRI) scans of our frozen crocodile cadavers last week, for free public usage. In total, it’s about 34 individuals from 5 species, in 53 databases constituting around 26,000 individual DICOM file format slices of data. This page has a table of what the data/specimens are. I am writing this post to share some more images and ensure that word gets out. We’re thrilled to be able to finally release this first dataset. We have plans to let loose a LOT more such data in the future, for various organisms that we study.

Stomach-Churning Rating: 2/10- be glad that these data don’t come with an olfactory component, especially the five rotten, maggot-ridden Morelet’s croc specimens, which are among the stinkiest things I’ve dealt with.

Crocodiles are no strangers to this blog, of course, as these past links testify. Indeed, most of the crocodile images I’ve blogged with come from specimens that are in this scan dataset. We even released a “celebrity crocodile, “WCROC” or FNC7 in our dataset, which is the 3.7m long Nile croc from “Inside Nature’s Giants”. It broke our CT scanner back in ~2009 but we got the data, except for the torso, and we also got some MRI scans from it, so we’re chuffed.

Above: The only spectacled caiman (Caiman crocodilus); and indeed the only alligatorid; in our dataset. To watch for: stomach contents/gastroliths, and all the damn osteoderms that I did/didn’t segment in this quickly processed file. This specimen had its limbs dissected for one of our studies, so only the right limbs are visible.

There are some more specimens to come- e.g. five baby Nile crocs‘ datasets (“GNC1-5”) are hiding somewhere in our drives and we just need to dig them up. You might also know that we published some scan data for crocodile vertebral columns (including fossils) in our recent paper with Julia Molnar et al. (and related biomechanical data discussed here), and we published all of our anatomical measurements for a huge set of crocodylian species in our papers by Vivian Allen et al. And then I had an enjoyable collaboration with Colleen Farmer and Emma Schachner on the lung anatomy of various crocodylian species, using these same specimens and related scan datasets.

 

Above: rotating Crocodylus moreletii (specimen FMC5 from our database) in a happy colour.

Sharing these kind of huge datasets isn’t so easy. Not only do few websites host them cheaply, and with reasonable file size limits, and limited headaches for what info you have to provide, and with some confidence that the websites/databases will still exist in 5-20 years, but also we were hesitant to release the dataset until we felt that it was nicely curated. Researchers can now visit my lab and study the skeletons (or in some cases, the still-frozen specimens) matched up with the scan data, and known body masses or other metadata. We’re not a museum with dedicated curatorial staff, so that was not trivial to reliably organize, and I still worry that somewhere in the dataset we mis-identified a specimen or something. But we’ve done our best, and I’m happy with that for now.

Above: rotating Osteolaemus tetraspis (specimen FDC2 from our database), which was obviously dissected a bit postmortem before we could scan it, but still shows some cool features like the extensive bony armour and the cute little doglike (to me, anyway) skull. I worked with these animals (live) a bit >10 years ago and came to love them. Compared to some other crocodiles we worked with, they had a pleasant demeanour. Like this guy:

Osteolaemus (resting) set up with motion capture markers for a yet-to-be-published study that we did in 2005 (ugh!). It wasn't harmed by this.

Osteolaemus (resting) set up with motion capture markers for a yet-to-be-published gait study that we did in 2005 (ugh!). It wasn’t harmed by this.

Anyway, as a person who likes to maintain quality in the science we do, I also was hesitant to “just” release the DICOM file data rather than beautiful segmented 3D skeletal (or other tissue) geometry that is ready for 3D printing or animation or other uses, or interactive online tools like Sketchfab. Other labs (e.g. Witmerlab) do these kind of things better than we do and they inspire us to raise our game in the future, but I am sure that we will be forgiven for releasing big datasets without gorgeous visuals and more practical, processed files — this time. 🙂  We agree with many other scientists that sharing data is part of modern, responsible science– and it can be fun, too! Oddly enough, in this case we hadn’t used the CT/MRI data much for our own studies; most of the scans were never fully digitized. We just scan everything we get and figured it was time to share these scans.

Enjoy. If you do something cool with the data that we’ve made accessible, please let us know so we can spread the joy!

And if you’re a researcher headed to ICVM next week, I hope to see you there!

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I hinted at another post in last round, and here I deliver. (The “amazeballs” in the title is a running joke with our Xmas guests here in England, but it applies to the subject of these images, too… which will be the subject of a future blog post involving a dissection of the subject!)

This will end the 2014 round of Mystery Anatomy. What 2015 will bring, I am not sure, but here we have 15 images for my 15th mystery CT post and 2015 around the corner.

I do have a new, fun regular anatomy post idea planned for 2015 but I’ll explain that later.

Stomach-Churning Rating: 2/10; digital images; the cadaver is gutted but I am chuffed.

Mystery Anatomy 2014same rules as before.

Identify (1) the animal shown in the 15 slices, to species level (max. 5 pts), and then the major features (anatomical regions) evident in as many of the 15 slices as you can; details help (max. 5 pts for thoroughness and accuracy). 

Difficulty: No scale, sort of. Otherwise, pretty easy.

Answers will come on New Year’s Day, to ease your hangovers (or encourage vomiting).

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MysteryCT15(15)

15

Onward!

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It has been a long time since we had some Mystery Anatomy fun here, so I am cutting loose with a double-barrelled blast of images– dive for cover!

I’m also giving out a Crimbo present as a bigger post, on a special day coming soon, count on that. This is just an advent snack.

Stomach-Churning Rating: 2/10 and 7/10: digital body and glistening, snotty.

Mystery Anatomy 2014same rules as before; remember that the scoreboard has been reset.

Identify (1) the animal shown in the four-panel top images (CT scan/reconstruction), and (2) the DIFFERENT animal (and/or the main central, pink structure) shown in the big, gooey bottom image (Dissection). No special rules. Potential for double points!

And someone will get these, I am sure. This might be the final round of 2014’s Mystery Anatomy game.

Difficulty: Plenty.

Mystery CT 14

Mystery CT 14

Mystery Anatomy 15

Mystery Anatomy 15

Go forth!

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I awoke on the floor in the aisle of my United Airlines flight to Los Angeles, with three unfamiliar men crouched around me, bearing serious expressions as they looked down on my prone body.

I was next to my seat. My daughter was crying inconsolably in her seat next to mine, and my wife was calling to me with an urgent tone from the next seat over.

Gradually, as my confusion faded and the men let go of me (I’d been cursing them out, in mangled words because I had bitten my tongue), I became aware that I was in intense pain, I could not move much, and my wife’s words became clearer:

I’d had a seizure. And so our relaxing family holiday, which had only just begun, ended. And so my waking nightmare began.

Stomach-Churning Rating: 5/10; lots of Anatomy Fail CT/x-ray images and gruesome descriptions, and a photo of some bruising.

I was helped back into my seat as I regained my senses, I noticed blood on me from my tongue, and I learned that we were 2 hours away from L.A. As I was acting more normal, and we were 5/6 of our journey along, there was no need to prematurely land the flight. I had fallen asleep while watching “22 Jump Street”, about 1.5 hrs in, and that’s when my seizure struck– much like the previous two seizures I’d had. Jonah Hill could be ruled out as a culprit, but going to sleep was an enabling factor. I got some over-the-counter painkillers and sat in a daze as time ticked by, we landed, and paramedics boarded the plane to whisk me off to the hospital with my family.

Two gruelling days and nights in a California hospital later, with my first night spent in a haze of clinical tests, begging for painkillers, yelling in pain every time I moved, and otherwise keeping my hospital roommate awake, the story became clearer: my seizure was so intense that I’d dislocated my right shoulder (unfortunately I’d not had much pain relief when the emergency room staff popped it back into my glenoid), probably dislocated my left shoulder too but then relocated it myself admist my thrashing, and done this (cue Anatomy Fail images):

Left shoulder, with the offending greater tubercle/tuberosity of the humerus showing fracture(s).

Left shoulder, with the offending greater tubercle/tuberosity of the humerus showing fracture(s).

Right shoulder x-ray, showing dislocation of the head of the humerus from the glenoid. Compare with above image- humerus has been shifted down. BUT no fractures, yay!

Right shoulder x-ray, showing dislocation of the head of the humerus from the glenoid. Compare with above image- humerus has been shifted down, the shoulder joint is facing you. BUT no fractures, yay!

CT scan axial slice showing my neck (on left), then scapula with fractured coracoid process ("bad") and displaced, fractured greater tubercle of humerus on right side.

CT scan axial slice showing my spine (on left), then scapula with fractured coracoid process (“Bad”) and displaced, fractured greater tubercle of humerus on right side (“V bad”).

So, that explains most of the pain I was in.

What’s amazing is that the fractures most likely occurred purely via my own uncontrolled muscle contractions. All the karate and weight-training I’d been doing certainly had made me stronger in my rotator cuff muscles, which attach to the greater tubercle of the humerus. And with inhibition of my motoneurons turned off during my seizure, and both agonist and antagonist muscles near-maximally turned on, rapid motions of my shoulders by my spasming muscles would have dislocated my shoulders and then wrenched apart some of the bony attachments of those same muscles. I’m glad I don’t remember this happening.

I had also complained of pain in my neck, so they did a CT scan and x-ray there too:

X-ray: No broken neck. This is good.

X-ray: No broken neck. This is good. Just muscle strain, which soon faded.

The left shoulder injuries created a hematoma, or mass of blood beneath my skin, and soon that surfaced and began draining down my arm (via the lymphatic system under gravity’s pull), creating fascinating patterns:

Bruises migrating; no pain associated with these, just superficial drainage of old blood.

Bruises migrating; no pain associated with these, just superficial drainage of old blood. This is tame, tame, tame compared to what my left ribcage looked like. I’ve spared you that.

But then more fundamentally there was the question of, why a seizure? With no clear warning? As I’ve explained before, I’d had a stroke ~12 yrs ago that caused a similar seizure but with no injuries to my postcranial body. So a series of MRI and CT scans ensued (the radiation I’ve had from the latter is good fodder for a superhero/villain origin tale? Marvel, I’ll await your call), and there was no clear damage or bleeding, and hence no stroke evident. Good news.

There are, however, at least two sizeable calcifications in my brain that are likely to be hardened scar tissue from my stroke. These may or may not have an identifiable affect on me or linkage with the seizure. Brain calcifications can happen for a variety of reasons, sometimes without clear ill effects.

Calcification in ?ventricle? of my cerebrum.

Calcification in parietal lobe of my cerebrum, from axial CT scan slice. But no bleeding (zone of altered density/contrast).

That is the state of the evidence. I’ve since had what semblance of a L.A. family holiday I could manage, benefitting from a touching surge of support from my family, friends and colleagues that has kept me from sinking entirely into despair and has brought quite a few smiles.

The plane flight home was tense. We were in the same seats again and one of the flight attendants recognized us and came to chat, eager to learn what had happened after we left the plane a week ago. He was very nice and the doctors had given me an “OK to fly” letter. But it was an evening flight. I needed to sleep, yet it was clear to me that sleep was no longer the fortress of regenerative sanctity that I was used to it being. Sleep had taken on a certain menace, because it was a state in which I’d now had three seizures. Warily, I drifted off to sleep after having some hearty chuckles at the ending to “22 Jump Street”. And while it was not very restful slumber, it was the friendly kind of slumber that held no convulsive violence within its embrace. We returned home safely.

In a rush, I cancelled my attendance at the Society of Vertebrate Paleontology conference this week, turning over the symposium I’d convened to honour one of my scientific heroes, biomechanist R. McNeill Alexander (who also could not attend due to ill health), to my co-convenors Eric Snively and Andreas Christian (by accounts I heard, all went well). I missed out on a lot of fun and the joy of watching 2 of my PhD students present posters on preliminary results of their research. Thanks to social media and email, however, I’ve been able to catch a lot of the highlights and excitement from that conference in Berlin.That has helped distract me somewhat from other goings-on.

Meanwhile, I’ve been resting, doing a minimal amount of catching up with work, having a lot of meetings with doctors to arrange treatment, and pondering my situation– a lot.

I know this much: I’ve had two violent seizures in a month (the previous one was milder but still bad, and not a story I need to tell here), and so I’m now an epileptic, technically. When and if I’ll have another seizure is totally uncertain, but to boost the odds in my favour I’m on anti-convulsant drugs for a long time now.

In about half of seizure cases, it’s never clear what caused the seizures. What caused my 2002 stroke is somewhat clear, but the mechanism behind that remains a mystery, and my other health problems likewise have a lot of question marks regarding their genesis and mutually causative relationships, if any. The outcome of this new development in my medical history is likely to be: “maybe your brain calcifications and scar tissue helped stimulate your new seizures, but we can’t be sure. The treatment is the same regardless: stay on anti-convulsants for a while, try going off them later, and see if seizures manifest themselves again or not.” Brains are freaking complicated; when they go haywire it can be perplexing why.

As a scientist, I thrill at finding uncertainty in my research topics because that always means there is work left to be done. But in my own life outside of science, stubborn, independent, strong-willed control freak that I can certainly be at times, I am not such a fan of uncertainty. In both cases the goal is to minimize that uncertainty by gathering more information, but in our lives we often encounter unscalable walls of uncertainty that persist because of lack of knowledge regarding a problem that vexes us, especially a medical problem. We then can feel in a helpless state, adrift on the horizon of science, waiting for explorers to push that horizon further and with it advance our treatment or at least our insight into ourselves.

When the subject of that uncertainty is not some detached, objective, unthreatening, exciting research topic but rather ourselves and our own future constitution and mortality, it thus becomes deeply personal and disconcerting. I’m grateful that I don’t have brain cancer or some other clear and present threat to my immediate vitality. Things could be a lot worse; I am here writing this blog after all. I’ll never forget now being in the ambulance and thinking “this may be the end of it all; I might not last much longer”, and choking out a farewell to my wife just in case things took a bad turn. I’m grateful for the amazing things that modern medicine and imaging techniques can do– these have saved my life so many times over, I cannot fathom how to quantify it. And I’m grateful for the people that have helped me through this so far. Fiercely independent as I may be, I can’t face everything alone.

I am reminded of words I read recently by Baruch Spinoza, “The highest activity a human being can attain is learning for understanding, because to understand is to be free.” To further paraphrase him, we love truth because it is knowledge that enables us to stay alive- without it, we are flying blind and soon will crash. With the freedom it brings, we know the landscape of our own life and where the frontiers of uncertainty lie (“here be dragons”).

here_be_dragons

The past two weeks have been horrendous for me. I’d been feeling healthy and stronger than ever in many ways, and my life as of my birthday a month ago felt pretty damn good. But now everything has come crashing down in disaster, and I have been suffering from the realization, once again, of how vulnerable I am and how little I can control, and the darkness that ushers in as the odds begin to stack up against our future lives. I am acutely aware now of where the “dragons” are.

I am taking one important step forward, though, in wresting life back onto the rails again- this week I undergo surgery to put my left shoulder back together. While that’s scary, to be sliced open and have my rotator cuff and bones carpentered back where they should be, I know I’m in good hands with a top UK shoulder surgeon and methods that are tried-and-true. The risks are small, although the recovery time will be long. There won’t be any hefting of big frozen elephant feet in my research soon, not for me, and so my enjoyable anatomy studies are going to have to change their track for coming months while I regain my strength and rely on others’ help.

(do you know the movie reference?)

(do you know the movie reference? I have a new empathy for Ash.)

Then we’re on to the frightening task of tackling the spasmodic-gorilla-in-the-room with neurologists. We’ll see where that journey leads.

One thing is certain: I’m still me and there’s still a lot of fight left in me, because I have a lot left to fight for, and people and knowledge to aid me in that fight. I can shoulder the burden of uncertainty in my life because I have all that. Off I go…

20 November UPDATE:

I’ve had surgery to put my greater tuberosity back where it belongs. Thanks to a skilled surgeon’s team, some sutures and nickel-titanium staples, I am back closer to my normal morphology and can begin recovering my (currently negligible) shoulder joint’s range of motion via some physiotherapy. Surgery went very well; I was just in hospital for ~30 hours; but the 9 days of recovery since have been brutally hard due to problems switching medications around. Today I got my stitches out and a beautiful x-ray showing plentiful healing; yay!

This is a slightly oblique anterior (front) view of my left shoulder/chest. Fracture callus means healing is working well!  Four surgical staples (bright white thingies on upper RH side of image): forever now a part of my anatomy.

This is a slightly oblique anterior (front) view of my left shoulder/chest. Fracture callus means healing is working well!
Four surgical staples (bright white thingies on upper RH side of image): forever now a part of my anatomy.

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MysteryCT12
Here’s an image that struck me as cool and possibly perplexing. And so we have another Mystery Anatomy post! Brought to you by some free time on my current trip to Gondwanaland.

Stomach-Churning Rating: 1/10; simple CT scan slice… of something.

Mystery Anatomy 2014same rules as before; remember that the scoreboard has been reset.

Identify the animal in the CT slice shown above, as specifically as you can. No special rules.

Difficulty: Plenty.

Begin!

 

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Short and sweet post here; it’s sunny outside and I want to be there BBQing!

I had a buried folder of CT files labelled as a species of fish, but on digging them out and segmenting them I realize it is not what I expected (inner fish or not!), as you will see.

Stomach-Churning Rating: 2/10; simple CT scan of a body.

Mystery Anatomy 2014same rules as before; remember that the scoreboard has been reset.

Identify the animal in the CT scout/pilot image below, as specifically as you can. But… (READ THE SENTENCE BELOW FIRST BEFORE ANSWERING!)

Today’s special rule: Summertime is coming and that means superhero films! Your answer must be in the form of a dialogue between a superhero(ine) and a supervillain(ess)! 

Difficulty: Even I am not 100% sure what this is but I have a decent idea. Not super hard, but not a super good segmentation.

Pow! Bam! Biff! Go forth and conquer! Then invite the Human Torch to your BBQ.

 

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