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Posts Tagged ‘crocodile’

If you go into central Lausanne, Switzerland, you’re likely to pass the Palais du Remine, and if you do, I recommend you go inside. I was happy I did while visiting Lausanne for the AMAM2019 conference. A luxurious palace has been given over to house five (!) free (!) museums on science and culture. These include the canton’s (~state’s) museums of palaeontology and zoology, which I’ll showcase here (also a little of geology and archaeology museums). Tripadvisor’s reviews were good but not as glowing as I’d make mine, so I will remedy that. I’m a sucka for old-school museums, and that’s what these are. So if that sounds right for you, journey onward!

It’s nice.

As you may be expecting by now if you’ve been here before, it’s time for another museum photo blog!

Stomach-Churning Rating: 5/10 for bones, preserved organs, taxidermy aplenty, and animal developmental deformities.

Nice cathedral nearby, w/great view of the city.

Nice interior architecture. There’s lots of nice to behold.

Posters That Get You Excited 101. But you must wait. Like I did.

Quadrupedal human at Zoology museum entry.

Tomistoma, false gharial.

Not a bad collection of taxidermied Crocodylia!

Visually arresting cobra display.

I’ve never seen three Draco gliding lizards on display together!

Bipedal lizard taxidermy displays, freezing the dynamic in the static, are no easy feat.

Plenty of stuffed animals like these raptors/other large birds. Classical zoology museum style. Minimal signage. Just specimen labels, mainly.

Coelacanth!

Sperm whale jaw.

Open space with big specimens. A ~4m long great white shark included.

Second zoology hall: bones!

Gorilla standing tall next to human.

Ostrich skeleton up close, amongst the mammalz.

Cassowary skeleton.

Emu shoulder/arm bones in right side view.

Walrus skeleton in what seems like an odd pose to me, but then they are odd on land.

Alligator skeleton in repose.

Giant anteater, “knuckle-walking”.

Pangolin skeleton! And mounted digging into a nest– very well done!

Bernard Heuvelmans display, about the (in)famous cryptozoologist. This was quite a surprise to me. I’m sure I’d read his English-translated book “On the Track of Unknown Animals” as a kid, during my long stint as an avid reader of much zoology, crypto- and otherwise. He bequeathed a lot of his work to the museum.

Bernard’s handwritten CV!? With a “sea serpent” sketch.

A “sea serpent” vertebra… but if you know any anatomy, it’s not a snake’s vertebra at all but a fish’s, such as a basking shark‘s.

Are you ready for more weirdness? How about some “mutants”- congenital deformities of animals? Fascinating errors of developmental anatomy… somehow this two-headed calf survived awhile. Plenty more where that came from, as follows:

And then there’s all kinds of wonderful comparative anatomy. To be a student of this subject in Lausanne would be a lucky thing, with this museum’s collection at hand. These are valuable specimens, made with love and skill.

Jaws

Fish head anatomy. Some vertebrae on the left, too.

Developmental regions of the head: a lovely wax(?) model of an Echidna skull. A treasure.

Brains: alligator vs. pigeon.

Salamander muscles.

Pigeon muscles.

More spotted felids than you can shake a jar of catnip at.

Another pangolin!

Giant armadillo.

Petaurus: flying phalanger (a gliding marsupial).

Second zoology hall open area: left side.

Second zoology hall open area: right side.

A final hall with a more new-fangled display, on the topic of evolution and extinction. Attractive phylogeny graphic here. Birds at the “top”, of course. Poor lowly mammals!

Taxidermied giant auk- not a common sight! (Extinct)

The extinct southern pig-footed bandicoot. Also a rare sight of a whole specimen- in a Swiss museum, too.

NOW ON TO THE FOSSILS!

You’ve been very patient. Here, have a Toblerone.

Palaeo museum entry. Already there are cool things visible. Inside, we find it just like I prefer my zoo/palaeo museums (as above): stuffed with specimens and leaving plenty for you to wonder about and investigate. Not frilly; a well-stocked museum that mostly lets its specimens speak for themselves.

Sauriermuseum (Aathal) specimen of Plateosaurus: sculpt/cast. A very good, big skeleton of this common dinosaur, rearing up.

Rear view of same.

Real bones of same; vertebrae and pelvic (this is the “Frick specimen”).

Metaxytherium (current name), an ancient and large fossil dugong/seacow. Skull is in left side view. (that may help, as their skulls are odd!)

Anthracotherium upper jaw: ancient hippo-cousin.

Prolagus: the “Sardinian hare” (recently extinct; old lineage).

Potamotherium: to some an early otter-like mammal, more recently thought to be an ancient seal.

“Broke-ulum”: a walrus broke its penis bone (baculum) and was surely not pleased about it, but lived to heal— physically if not mentally. Yeesh!

Glyptodont tail club and armour.

Aepyornis elephant bird legs!

A partial/reconstructed skeleton of the dodo.

Velociraptor preparing to pounce from above. It’s too late for you!

Rhamphorhynchus fossil (2D slab) and sculpt/cast coming alive in 3D– good stuff.

Anhanguera pterosaur watches the chaos from above, fish snagged in its teeth.

Not-shabby metriorhynchid marine croc fossils, from Britain.

Lovely 3D plesiosaur bones (flippers, neck, etc.) from near RVC: Peterborough!

Mesosaur; early reptile.

The museum clearly is proud of its excellent “Mammoth of Brassus” skeleton, essentially complete.

Ice Age elk/moose, a 10,000 year old skeleton in fine shape.

Cave bear skull rawr

Purty ammonites!

Spiky ammonite!

Cretaceous sponge colony from France. I hadn’t seen something like this before, so here it is.

Trilobites, brittlestars and friends.

Well I did wander through the geology and archaeology museums too, and while I liked them I did not take so many photos. My non-human organismal bias is apparent. But check these final ones out:

Splendid cross-section of the stratigraphy of the Alps around Lausanne. I gazed at this for quite a few minutes, trying to figure out what was where in the landscape I’d seen and how old, how deformed, etc.

Slab of “dinosaur” tracks but it was not clear to me what dinosaurs/archosaurs/whatever made them. I wish my French was better. Closeup below shows two footprints superimposed.

At last, the coup de grace! What museum would be complete without a diorama!? (I love them) This one, with a goat sacrifice and early Stone Age people praying to heathen deities/spirits at an elaborate petroglyph array rocked my world. And so it makes a perfect final image. Enjoy, and conduct the proper rites.  \m/

 

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To me, there is no question that the Galerie de Paléontologie et d’Anatomie comparée of Paris’s Muséum national d’Histoire naturelle (MNHN) is the mecca of organismal anatomy, as their homepage describes. Georges Cuvier got the morphological ball rolling there and numerous luminaries were in various ways associated with it too; Buffon and Lamarck and St Hiliaire to name but a few early ones. It is easy to think of other contenders such as the NHMUK in London (i.e., Owen), Jena in Germany, the MCZ at Harvard (e.g. Romer) and so forth. But they don’t quite cut the dijon.

As today is John’s Freezer’s 7th blogoversary, and I was just at the MNHN in Paris snapping photos of their mecca, it’s time for an overdue homage to the magnificent mustard of that maison du morphologie. The exhibits have little signage and are an eclectic mix of specimens, but this adds to its appeal and eccentricity for me. I’ve chosen some of my favourite things I saw on exhibit on this visit, with a focus on things that get less attention (NO MESOZOIC DINOSAURS! sorry), are just odd, or otherwise caught my fancy. It’s a photo blog post, so I shall shut up now, much as I could gush about this place. I could live here.

Need plus-grand images? Clic!

Stomach-Churning Rating: 7/10 for some potentially disturbing anatomical images such as viscera, preserved bits, models of naughty bits etc.

Greetings. Note the stomach-churning rating above, please.

Right. We’ll get the amazing first view as one steps into the gallery done first. Mucho mecca. Anatomy fans simply must go here at least once in their life to experience it, and one cannot ever truly absorb all the history and profound, abundant details of morphology on exhibit.

Less-often-seen views from the balcony; one more below.

Indian Rhinoceros from Versailles’s royal menagerie; came to the MNHN in 1792.

Brown bear hindlimb bones.

Brown bear forelimb bones and pelvis.

Two baby polar bears; part of the extensive display of ontogeny (too often missing in other museums’ exhibits).

Asian elephant from Sri Lanka.

Lamb birth defect. Like ontogeny, pathology was a major research interest in the original MNHN days.

Wild boar birth defect.

Fabulous large Indian gharial skull + skeleton.

“Exploded” Nile crocodile skull to show major bones.

Let’s play name-all-the-fish-skull-bones, shall we?

Rare sight of a well-prepared Mola mola ocean sunfish skeleton.

Diversity of large bird eggs.

Asian musk deer (male), with tooth roots exposed.

Freaky gorilla is here to say that now the really odd specimens begin, including the squishy bits.

Freaky tamandua, to keep freaky gorilla company. Displaying salivary glands associated with the tongue/pharynx. These are examples of anatomical preparations using older analogues of plastination, such as papier-mâché modelling. I’m not completely sure how the preservation was done here.

Tamandua preserved head, showing palate/tongue/pharynx mechanism.

Chimp ears. Because.

Why not add another chimp ear?

Many-chambered ruminant stomach of a sheep.

Simpler stomach of a wolf. Not much room for Little Red Riding Hood, I’m afraid.

Expansive surface area of a hippo’s stomach; but not a multi-chambered ruminant gut.

Cervical air sacs of a Turquoise-fronted Amazon parrot.

Heart and rather complex pulmonary system of a varanid lizard.

It’s pharynx time: Keratinous spines of a sea turtle’s throat. All the better to grip squids or jellies!

Pharynx convergent evolution in a giraffe: keratinous spines to help grip food and protect the pharynx from spiny acacia thorns while it passes down the long throat.

Tongue/hyoid region of the pharynx of a varanid, showing the forked tongue mechanism.

Palaeontological awesomeness on the upper floor (the 2nd part of the gallery’s name). Here, the only Siberian woolly mammoth, I’m told, to have left Russia for permanent display like this. Frozen left side of face, here, and 2 more parts below.

Mammuthus primigenius freeze-dried lower ?left forelimb.

Skeleton that goes with the above 2 parts. It’s big.

But “big” is only relative- my large hand for scale here vs. a simply ginormous Mammuthus meridionalis; full skeleton below.

Four-tusked, moderate-sized Amebelodon elephantiform.

Naked woolly rhinoceros Coelodonta.

Extinct rhino Diaceratherium, with a pathological ankle (degenerative joint disease). I love spotting pathologies in specimens- it makes them stand out more as individuals that lived a unique life.

Glyptodont butt and thagomizer, to begin our tour of this business-end weaponry.

Eutatus leg bones, from a large fossil armadillo; Argentina. Really odd morphology; Xenarthrans are so cool.

Giant ground sloth (Megatherium) foot; ridiculously weird.

Giant ground sloth hand is full of WTF.

Metriorhynchus sea-crocodile from the Cretaceous: hind end.

Odobenocetops one-tusked whale that I still cannot get my head around, how it converged so closely on the morphology of a walrus.

Thalassocnus, the large marine sloth… few fossils are so strange to me as this one. But modern sloths swim well enough so why not, evolution says!

Rear end of the sea-sloth.

Megaladapis, the giant friggin’ lemur! Not cuddly.

A basilosaurid whale Cynthiacetus, one of the stars of the show, as the denouement of this post. Plan your visit now!

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I had a spare hour in Cambridge this weekend so I dared the crowds in the revamped UMZC’s upper floor. In my prior visit and post I’d experienced and described the lower floor, which is almost exclusively mammals. This “new” floor has everything else that is zoological (animal/Metazoa) and again is organized in an evolutionary context. And here is my photo tour as promised!

Inviting, soft lighting perfuses the exhibits from the entryway onwards.

All images can be clicked to mu-zoom in on them.

Stomach-Churning Rating: 5/10 for spirit animals, by which I mean dissected/ghostly pale whole specimens of animals in preservative fluids.

The exhibits are on a square balcony overlooking the lower floor, so you can get some nice views. It does make the balcony crowded when the museum is busy, so take that in mind if visiting. Strollers on this upper floor could be really difficult. But the ceiling is very tall so it is not cramped in a 3D sense. The lower floor is more spacious.

Like phylogenies? You got em! Tucked away at the beginning of each major group; not occupying huge valuable space or glaringly obvious like AMNH in NYC but still noticeable and useful. To me, it strikes a good balance; gives the necessary evolutionary context for the displayed specimens/taxa.

Introductory panels explain how names are given to specimens, how specimens are preserved and more.

The exhibits give due focus to research that the UMZC is doing or has been famous for. Hey I recognize that 3D tetrapod image in the lower left! 🙂

There is ample coverage of diversity throughout Metazoa but my camera tended to be drawn to the Vertebrata. Except in some instances like these.

Some larger chelicerates.

Some smaller, shadowy sea scorpion (eurypterid) fossils.

Watch here for more about ophiuroids (brittlestars) in not too long!

A BIG fish brain! Interesting!
Before I go through specimens in evolutionary “sequence”, I will feature another thing i really liked: lots of dissected spirit-specimens that show off cool anatomy/evolution/adaptation (and technical skills in anatomical preparation). Mostly heads; mostly fish.

Salps and other tunicates! Our closest non-vertebrate relatives- and some insight into how our head and gut came to be.

Salp-reflection.

Lamprey head: not hard to spot the commonalities with the salps; but now into Vertebrata.

Hagfish head: as a fellow cyclostome/agnathan, much like a lamprey but never forget the slime glands!

Shark head. Big fat jaws; all the better to bite prey with!

Lungfish (Protopterus) head showing the big crushing tooth plates (above).

Sturgeon vertebrae: tweak some agnathan/shark bits and here you are.

Worm (annelid) anatomy model, displaying some differences from/similarities to Vertebrata. (e.g. ventral vs. dorsal nerve cord; segmentation)

Dissected flipper from a small whale/other cetacean. Still five fingers, but other specializations make it work underwater.

Wonderful diversity of tooth and jaw forms in sharks, rays and relatives. I like this display a lot.

More of the above, but disparate fossil forms!

On with the evolutionary context! Woven throughout the displays of modern animals are numerous fossils, like these lovely placoderms (lineage interposed between agnathans, sharks and other jawed fish).

Goblin shark head.

I seem to always forget what ray-finned fish this is (I want to say wolffish? Quick Googling suggests maybe I am right), but see it often and like its impressive bitey-ness.

Bichir and snakefish; early ray-finned fish radiations.

Armoured and similar fish today.

Armoured fish of the past; some convergent evolution within ray-fins.

Convergence- and homology- of amphibious nature in fish is another evolutionary pattern exemplified here.

Gorgeous fossils of ray-finned fish lineages that arose after the Permian extinctions, then went extinct later in the Triassic.

Note the loooooong snout on this cornetfish but the actual jaws are just at the tip.

Flying fish– those ray-fins are versatile.

Diversity of unusual ray-finned fish, including deep-water and bottom-dwelling forms.

Can you find the low-slung jaws of a dory?

Recent and fossil perch lineage fish.

It’s hard to get far into talking about evolution without bringing up the adaptive radiation of east African cichlid fish, and UMZC researchers are keen on this topic too.

Lobe-fins! Everybody dance!

Rhizodonts & kin: reasons to get out of Devonian-Carboniferous waters.

A Cretaceous fossil coelacanth (skull); not extremely different from living ones’.

Let’s admire some fossil and modern lungfish skulls, shall we? Big platey things  (here, mainly looking at the palate) with lots of fusions of tiny bones on the skull roof.

Eusthenopteron fossils aren’t that uncommon but they are still great to see; and very important, because…

OK let’s stop messing around. The UMZC has one of the best displays of fossil stem-tetrapods in the world! And it should.

Another look at the pretty Acanthostega models.

Acanthostega vs. primate forelimb: so like us.

Ichthyostega parts keep Acanthostega company.

A closer look at the “Mr. Magic” Ichthyostega specimen, which takes some unpacking but is incredibly informative and was a mainstay of our 2012 model. Back of skull, left forelimb, and thorax (from left to right here).

Eucritta, another stem-tetrapod.

Closer look at Eucritta‘s skull.

Weird stem-tetrapod Crassigyrinus, which we’re still trying to figure out. It’s a fabulous specimen in terms of completeness, but messy “roadkill” with too many damn bones.

The large skull of Crassigyrinus, in right side view.

Early temnospondyl (true amphibian-line) skulls and neck.

Nectrideans or the boomerangs of the Palaeozoic.

Cool fossil frogs.

Giant Japanese salamander!

Fire salamanders: not as colourful as the real thing, but here revealing their reproductive cycle in beautiful detail.

Closeup of oviduct in above.

Sexual dimorphism in Leptodactylus frogs: the males have bulging upper arms to (I am assuming) help them hold onto females during amplexus (grasping in mating competitions).

Did I forget that Leptodactylus has big flanges on the humerus in males, to support those muscles? Seems so.

An early stem-amniote, Limnoscelis (close to mammals/reptiles divergence); cast.

Grand sea turtle skeleton.

One of my faves on display: a real pareiasaurian reptile skeleton, and you can get a good 3D look around it.

Details on above pareiasaurian.

Mammals are downstairs, but we’re reminded that they fit into tetrapod/amniote evolution nonetheless.

Let there be reptiles! And it was good.

Herps so good.  (slow worm, Gila monster, glass lizard)

A curator is Dr Jason Head so you bet Titanoboa is featured!

Crocodylia: impressive specimens chosen here.

It ain’t a museum without a statuesque ratite skeleton. (There are ~no non-avian dinosaurs here– for those, go to the Sedgwick Museum across the street, which has no shortage!)

Avian diversity takes off.

Glad to see a tinamou make an appearance. They get neglected too often in museums- uncommon and often seemingly unimpressive, but I’m a fan.

I still do not understand hoatzins; the “cuckoo” gone cuckoo.

Dodo parts (and Great Auk) near the entrance.

Wow. What an oilbird taxidermy display! :-O

There we have it. Phew! That’s a lot! And I left out a lot of inverts. This upper floor is stuffed with specimens; easier there because the specimens are smaller on average than on the lower floor. Little text-heavy signage is around. I give a thumbs-up to that– let people revel in the natural glory of what their eyes show them, and give them nuggets of info to leave them wanting more so they go find out.

Now it’s in your hands– go find out yourself how lovely this museum is! I’ve just given a taste.

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As 2017 approaches its end, there have been a few papers I’ve been involved in that I thought I’d point out here while I have time. Our DAWNDINOS project has been taking up much of that time and you’ll see much more of that project’s work in 2018, but we just published our first paper from it! And since the other two recent papers involve a similar theme of muscles, appendages and computer models of biomechanics, they’ll feature here too.

Stomach-Churning Rating: 0/10; computer models and other abstractions.

Mussaurus patagonicus was an early sauropodomorph dinosaur from Argentina, and is now widely accepted to be a very close relative of the true (giant, quadrupedal) sauropods. Here is John Conway’s great reconstruction of it:

We have been working with Alejandro Otero and Diego Pol on Mussaurus for many years now, starting with Royal Society International Exchange funds and now supported by my ERC grant “DAWNDINOS”. It features in our grant because it is a decent example of a large sauropodomorph that was probably still bipedal and lived near the Triassic-Jurassic transition (~215mya).

In our new study, we applied one of my team’s typical methods, 3D musculoskeletal modelling, to an adult Mussaurus’s forelimbs. This is a change of topic from the hindlimbs that I’ve myopically focused on before with Tyrannosaurus and Velociraptor [in an obscure paper that I should never have published in a book! pdf link], among other critters my team has tackled (mouse, elephant [still to be finished…], ostrich, horse, Ichthyostega… dozens more to come!). But we also modelled the forelimbs of Crocodylus johnstoni (Australian “freshie”) for a key comparison with a living animal whose anatomy we actually knew, rather than reconstructed.

Mussaurus above; Crocodylus below; forelimb models in various views; muscles are red lines.

The methods for this biomechanical modelling are now standard (I learned them from their creator Prof. Scott Delp during my 2001-2003 postdoc at Stanford): scan bones, connect them with joints, add muscle paths around them, and then use the models to estimate joint ranges of motion and muscle moment arms (leverage) around joints. I have some mixed feelings about developing this approach in our 2005 paper that is now widely used by the few teams that study appendicular function in extinct animals. As a recent review paper noted and I’ve always cautioned, it has a lot of assumptions and problems and one must exercise extreme caution in its design and interpretation. Our new Mussaurus paper continues those ruminations, but I think we made some progress, too.

On to the nuts and bolts of the science (it’s a 60 page paper so this summary will omit a lot!): first, we wanted to know how the forelimb joint ranges of motion in Mussaurus compared with those in Crocodylus and whether our model of Mussaurus might be able to be placed in a quadrupedal pose, with the palms at least somewhat flat (“pronated”) on the ground. Even considering missing joint cartilage, this didn’t seem very plausible in Mussaurus unless one allowed the whole forearm to rotate around its long axis from the elbow joint, which is very speculative—but not impossible in Crocodylus, either. Furthermore, the model didn’t seem to have forelimbs fully adapted yet for a more graviportal, columnar posture. Here’s what the model’s mobility was like:

So Mussaurus, like other early sauropodomorphs such as Plateosaurus, probably wasn’t quadrupedal, and thus quadrupedalism must have evolved very close to in the Sauropoda common ancestor.

Second, we compared the muscle moment arms (individual 3D “muscle actions” for short) in different poses for all of the main forelimb muscles that extend (in various ways and extents) from the pectoral girdle to the thumb, for both animals, to see how muscle actions might differ in Crocodylus (which would be closer to the ancestral state) and Mussaurus. Did muscles transform their actions in relation to bipedalism (or reversal to quadrupedalism) in the latter? Well, it’s complicated but there are a lot of similarities and differences in how the muscles might have functioned; probably reflecting evolutionary ancestry and specialization. What I found most surprising about our results was that the forelimbs didn’t have muscles well-positioned to pronate the forearm/hand, and thus musculoskeletal modelling of those muscles reinforced the conclusions from the joints that quadrupedal locomotion was unlikely. I think that result is fairly robust to the uncertainties, but we’ll see in future work.

You like moment arms? We got moment arms! 15 figures of them, like this! And tables and explanatory text and comparisons with human data and, well, lots!

If you’re really a myology geek, you might find our other conclusions about individual muscle actions to be interesting—e.g. the scapulohumeralis seems to have been a shoulder pronator in Crocodylus vs. supinator in Mussaurus, owing to differences in humeral shape (specialization present in Mussaurus; which maybe originated in early dinosaurs?). Contrastingly, the deltoid muscles acted in the same basic way in both species; presumed to reflect evolutionary conservation. And muuuuuuch more!

Do you want to know more? You can play with our models (it takes some work in OpenSim free software but it’s do-able) by downloading them (Crocodylus; Mussaurus; also available: Tyrannosaurus, Velociraptor!). And there will be MUCH more about Mussaurus coming soon. What is awesome about this dinosaur is that we have essentially complete skeletons from tiny hatchlings (the “mouse lizard” etymology) to ~1 year old juveniles to >1000kg adults. So we can do more than arm-wave about forelimbs!

But that’s not all. Last week we published our third paper on mouse hindlimb biomechanics, using musculoskeletal modelling as well. This one was a collaboration that arose from past PhD student James Charles’s thesis: his model has been in much demand from mouse researchers, and in this case we were invited by University of Virginia biomechanical engineers to join them in using this model to test how muscle fibres (the truly muscle-y, contractile parts of “muscle-tendon units”) change length in walking mice vs. humans. It was a pleasure to re-unite in coauthorship with Prof. Silvia Blemker, who was a coauthor on that 2005 T. rex hindlimb modelling paper which set me on my current dark path.

Mouse and human legs in right side view, going through walking cycles in simulations. Too small? Click to embiggen.

We found that, because mice move their hindlimb joints through smaller arcs than humans do during walking and because human muscles have large moment arms, the hindlimb muscles of humans change length more—mouse muscles change length only about 48% of the amount that typical leg muscles do in humans! This is cool not only from an evolutionary (mouse muscles are probably closer to the ancestral mammalian state) and scaling (smaller animals may use less muscle excursions, to a point, in comparable gaits?) perspective, but it also has clinical relevance.

Simulated stride for mouse and human; with muscles either almost inactive (Act=0.05) or fully active (Act=1). Red curve goes through much bigger excursions (along y-axis) than blue curve), so humans should use bigger % of their muscle fibre lengths in walking. Too small? Click to embiggen.

My coauthors study muscular dystrophy and similar diseases that can involve muscle stiffness and similar biomechanical or neural control problems. Mice are often used as “models” (both in the sense of analogues/study systems for animal trials in developing treatments, and in the sense of computational abstractions) for human diseases. But because mouse muscles don’t work the same as human muscles, especially in regards to length changes in walking, there are concerns that overreliance on mice as human models might cause erroneous conclusions about what treatments work best to reduce muscle stiffness (or response to muscle stretching that causes progressive damage), for example. Thus either mouse model studies need some rethinking sometimes, or other models such as canines might be more effective. Regardless, it was exciting to be involved in a study that seems to deliver the goods on translating basic science to clinical relevance.

Muscle-by-muscle data; most mouse muscles go through smaller excursions; a few go through greater; some are the same as humans’.

Finally, a third recent paper of ours was led by Julia Molnar and Stephanie Pierce (of prior RVC “Team Tetrapod” affiliation), with myself and Rui Diogo. This study tied together a bunch of disparate research strands of our different teams, including musculature and its homologies, the early tetrapod fossil record, muscle reconstruction in fossils, and biomechanics. And again the focus was on forelimbs, or front-appendages anyway; but turning back the clock to the very early history of fishes, especially lobe-finned forms, and trying to piece together how the few pectoral fin muscles of those fish evolved into the many forelimb muscles of true tetrapods from >400mya to much more recent times.

Humerus in ventral view, showing muscle attachments. Extent (green) is unknown in the fossil but the muscle position is clear (arrow).

We considered the homologies for those muscles in extant forms, hypothesized by Diogo, Molnar et al., in light of the fossil record that reveals where those muscles attach(ed), using that reciprocal illumination to reconstruct how forelimb musculature evolved. This parallels almost-as-ancient (well, year 2000) work that I’d done in my PhD on reconstructing hindlimb muscle evolution in early reptiles/archosaurs/dinosaurs/birds. Along the way, we could reconstruct estimates of pectoral muscles in various representative extinct tetrapod(omorph)s.

Disparity of skeletal pectoral appendages to work with from lobe-fins to tetrapods.

Again, it’s a lengthy, detailed study (31 pages) but designed as a review and meta-analysis that introduces readers to the data and ideas and then builds on them in new ways. I feel that this was a synthesis that was badly needed to tie together disparate observations and speculations on what the many, many obvious bumps, squiggles, crests and tuberosities on fossil tetrapods/cousins “mean” in terms of soft tissues. The figures here tell the basic story; Julia, as usual, rocked it with some lovely scientific illustration! Short message: the large number of pectoral limb muscles in living tetrapods probably didn’t evolve until limbs with digits evolved, but that number might go back to the common ancestor of all tetrapods, rather than more recently. BUT there are strong hints that earlier tetrapodomorph “fishapods” had some of those novel muscles already, so it was a more stepwise/gradual pattern of evolution than a simple punctuated event or two.

Colour maps of reconstructed right fin/limb muscles in tetrapodomorph sarcopterygian (~”fishapod”) and tetrapod most recent common ancestors. Some are less ambiguous than others.

That study opens the way to do proper biomechanical studies (like the Mussaurus study) of muscle actions, functions… even locomotor dynamics (like the mouse study)– and ooh, I’ve now tied all three studies together, tidily wrapped up with a scientific bow! There you have it. I’m looking forward to sharing more new science in 2018. We have some big, big plans!

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Nice GIF of the human biceps in action- By Niwadare - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=38718790

GIF of the human biceps (above) and its antagonist triceps (below) in action- By “Niwadare” – own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=38718790

Last year on Darwin Day I debuted “Better Know A Muscle” (BKAM), which was intended to be a series of posts focusing on one cool muscle at a time, and its anatomical, functional and evolutionary diversity and history. A year later, it’s another post on another muscle! Several dozen more muscles to go, so I’ve got my work cut out for me… But today: get ready to FLEX your myology knowledge! Our subject is Musculus biceps brachii; the “biceps” (“two-headed muscle of the arm”). Beloved of Arnie and anatomists alike, the biceps brachii is. Let’s get pumped up!

Stomach-Churning Rating: 7/10. Lots of meaty elbow flexion!

While the previous BKAM’s topic was a hindlimb muscle with a somewhat complex history (and some uncertainties), the biceps brachii is a forelimb muscle with a simpler, clearer history. Fish lack a biceps, just having simple fin ab/adductor muscles with little differentiation. Between fish and tetrapods (limb-bearing vertebrates), there was an explosion in the number of muscles; part of transforming fins into limbs; and the biceps is thenceforth evident in all known tetrapods in a readily identifiable anatomical form. In salamanders and their amphibian kin, there is a muscle usually called “humeroantebrachialis” that seems to be an undivided mass corresponding to the biceps brachii plus the brachialis (shorter humerus-to-elbow) muscle:

Most of the humerobrachialis muscle (purplish colour), in dorsal (top) view of the right forelimb of the fire salamander Salamandra salamandra (draft from unpublished work by my team).

Most of the humerobrachialis muscle (purplish colour), in dorsal (top) view of the right forelimb of the fire salamander Salamandra salamandra (draft from unpublished work by my team).

In all other tetrapods; the amniote group (reptiles, mammals, etc.); there is a separate biceps and brachialis, so these muscles split up from the ancestrally single “humeroantebrachialis” muscle sometime after the amphibian lineage diverged from the amniotes. And not much changed after then– the biceps is a relatively conservative muscle, in an evolutionary (not political!) sense. In amniote tetrapods that have a biceps, it develops as part of the ventral mass of the embryonic forelimb along with other muscles such as the shorter, humerus-originating brachialis, from which it diverges late in development (reinforcing that these two muscles are more recent evolutionary divergences, too).

Biceps brachialis or humerobrachialis, the “biceps group” tends to originate just in front of the shoulder (from the scapula/coracoid/pectoral girdle), running in front of (parallel to) the humerus. It usually forms of two closely linked heads (hence the “two heads” name), most obviously in mammals; one head is longer and comes from higher/deeper on the pectoral girdle, whereas the other is closer to the shoulder joint and thus is shorter. The two heads fuse as they cross the shoulder joint and we can then refer to them collectively as “the biceps”. It can be harder to see the longer vs. shorter heads of the biceps in non-mammals such as crocodiles, or they may be more or less fused/undifferentiated, but that’s just details of relatively minor evolutionary variation.

The biceps muscle then crosses in front of the elbow to insert mainly onto the radius (bone that connects your elbow to your wrist/thumb region) and somewhat to the ulna (“funny bone”) via various extra tendons, fascia and/or aponeuroses. The origin from the shoulder region tends to have a strong mark or bony process that identifies it, such as the coracoid process in most mammals (I know this well as I had my coracoid process surgically moved!). The insertion onto the radius tends to have a marked muscle scar (the radial tuberosity or a similar name), shared with the brachialis to some degree. A nice thing about the biceps is that, because it may leave clear tendinous marks on the skeleton, we sometimes can reconstruct how its attachments and path evolved (and any obvious specializations; even perhaps changes of functions if/when they happened).

Here are some biceps examples from the world of crocodiles:

Crocodile's right forelimb showing the huge pectoralis, and the biceps underlying it on the bottom right.

Crocodile’s right forelimb showing the huge pectoralis, and the biceps underlying it; on the bottom right (“BB”- click to embiceps it).

Crocodile left forelimb with biceps visible (

Crocodile left forelimb with biceps visible (“BB”) on the left.

Crocodile biceps muscle cut off, showing the proximal and distal tendons (and long parallel muscle fibres) for a typical amniote vertebrate.

Crocodile biceps muscle cut off, showing the proximal (to right) and distal (to left) tendons (and long parallel muscle fibres) for a typical amniote vertebrate.

What does the biceps muscle do? It flexes (draws forward) the shoulder joint/humerus, and does the same for the elbow/forearm while supinating it (i.e. rotating the radius around the ulna so that the palm faces upwards, in animals like us who can rotate those two bones around each other). In humans, which have had their biceps muscles studied by far the most extensively, we know for example that the biceps is most effective at flexing the elbow (e.g. lifting a dumbbell weight) when the elbow is moderately straight. These same general functions (shoulder and elbow flexion; with some supination) prevail across the biceps muscle of [almost; I am sure there are exceptions] all tetrapods, because the attachments and path of the biceps brachii are so conservative.

And this flexor function of the biceps brachii stands in contrast to our first BKAM muscle, the caudofemoralis (longus): that muscle acts mainly during weight support (stance phase) as an antigravity/extensor muscle, whereas the flexor action of biceps makes it more useful as a limb protractor or “swing phase” muscle used to collapse the limb and draw it forwards during weight support. However, mammals add some complexity to that non-supportive function of the biceps…

Hey mammals! Show us your biceps!

Jaguar forelimb with biceps peeking out from the other superficial muscles, and its cousin brachialis nicely visible.

Jaguar forelimb with biceps peeking out from the other superficial muscles, and its cousin brachialis nicely visible, running along the front of the forearm for a bit.

Elephant's left forelimb with the biceps labelled.

Elephant’s left forelimb with the biceps labelled.

Longitudinal slice thru the biceps of an elephant, showing the internal tendon.

Longitudinal slice thru the biceps of an elephant, showing the internal tendon that helps identify where the two bellies of the biceps fuse.

In certain mammals; the phylogenetic distribution of which is still not clear; the biceps brachii forms a key part of a passive “stay apparatus” that helps keep the forelimb upright against gravity while standing (even sleeping). The classic example is in horses but plenty of other quadrupedal mammals, especially ungulate herbivores, show evidence of similar traits:

Giraffe biceps cut away proximally to show the

Giraffe biceps cut away proximally to show the “stay apparatus” around the shoulder joint (upper right).

Zooming in on the

Zooming in on the “stay apparatus”; now in proximal view, with the biceps tendon on the left and the humeral head (showing some arthritic damage) on the right, with the groove for the biceps in between.

Hippo's humerus (upper left) and biceps muscle cut away proximally, displaying the same sort of

Hippo’s humerus (upper left) and biceps muscle cut away proximally, displaying the same sort of “stay apparatus” as in the giraffe. Again, note the stout proximal and distal tendons of the biceps. The proximal tendon fits into the groove of the humerus on the far left side of the image; becoming constrained into a narrow circular “tunnel” there. It’s neat to dissect that region because of its fascinating relationships between bone and soft tissues.

The biceps brachii, in those mammals with a stay apparatus, seems to me to have a larger tendon overall, especially around the shoulder, and that helps brace the shoulder joint from extending (retracting) too far backward, whilst also transmitting passive tension down the arm to the forearm, and bracing the elbow (as well as distal joints via other muscles and ligaments). It’s a neat adaptation whose evolution still needs to be further inspected.

Otherwise, I shouldn’t say this but the biceps is sort of boring, anatomically. Whether you’re a lizard, croc, bird or mammal, a biceps is a biceps is a biceps; more or less-ceps. But the biceps still has a clear evolutionary history and Darwin would gladly flex his biceps to raise a pint in toast to it.

So now we know a muscle better. That’s two muscles now. And that is good; be you predator or prey. Let’s shake on it!

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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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Seeking adaptations for running and swimming in the vertebral columns of ancient crocs

A guest post by Dr. Julia Molnar, Howard University, USA (this comes from Julia’s PhD research at RVC with John & colleagues)

Recently, John and I with colleagues Stephanie Pierce, Bhart-Anjan Bhullar, and Alan Turner described morphological and functional changes in the vertebral column with increasing aquatic adaptation in crocodylomorphs (Royal Society Open Science, doi 10.1098/rsos.150439). Our results shed light upon key aspects of the evolutionary history of these under-appreciated archosaurs.

Stomach-Churning Rating: 5/10; a juicy croc torso in one small photo but that’s all.

Phylogenetic relationships of the three crocodylomorph groups in the study and our functional hypotheses about their vertebrae. * Image credits: Hesperosuchus by Smokeybjb, Suchodus by Dmitry Bogdanov (vectorized by T. Michael Keesey) http://creativecommons.org/licenses/by-sa/3.0

Phylogenetic relationships of the three crocodylomorph groups in the study and our functional hypotheses about their vertebrae. * Image credits: Hesperosuchus by Smokeybjb, Suchodus by Dmitry Bogdanov (vectorized by T. Michael Keesey) http://creativecommons.org/licenses/by-sa/3.0

As fascinating as modern crocodiles might be, in many ways they are overshadowed by their extinct, Mesozoic cousins and ancestors. The Triassic, Jurassic, and early Cretaceous periods saw the small, fast, hyper-carnivorous “sphenosuchians,” the giant, flippered marine thalattosuchians, and various oddballs like the duck-billed Anatosuchus and the aptly named Armadillosuchus. As palaeontologists/biomechanists, we looked at this wide variety of ecological specializations in those species, the Crocodylomorpha, and wanted to know, how did they do it?

Of course, we weren’t the first scientists to wonder about the locomotion of crocodylomorphs, but we did have some new tools in our toolbox; specifically, a couple of micro-CT scanners and some sophisticated imaging software. We took CT and micro-CT scans of five fossil crocodylomorphs: two presumably terrestrial early crocodylomorphs (Terrestrisuchus and Protosuchus), three aquatic thalattosuchians (Pelagosaurus, Steneosaurus, and Metriorhynchus) and a semi-aquatic modern crocodile (Crocodylus niloticus). Since we’re still stuck on vertebrae (see, e.g., here; and also here), we digitally separated out the vertebrae to make 3D models of individual joints and took measurements from each vertebra. Finally, we manipulated the virtual joint models to find out how far they could move before the bones bumped into each other or the joints came apart (osteological range of motion, or RoM).

 

Our methods: get fossil, scan fossil, make virtual fossil and play with it.

Our methods: get fossil (NHMUK), scan fossil, make virtual fossil and play with it.

Above: Video of a single virtual inter-vertebral joint from the trunk of Pelagosaurus typus (NHMUK) showing maximum osteological range of motion in the lateral direction (video). Note the very un-modern-croc-like flat surfaces of the vertebral bodies! (modern crocs have a ball-and-socket spinal joint with the socket on the front end)

While this was a lot of fun, what we really wanted to find out was whether, as crocodylomorphs became specialized for different types of locomotion, the shapes of their vertebrae changed similarly to those of mammalian lineages. For example, many terrestrial mammals have a lumbar region that is very flexible dorsoventrally to allow up-and-down movements during bounding and galloping. Did fast-running crocodylomorphs have similar dorsoventral flexibility? And did fast-swimming aquatic crocodylomorphs evolve a stiffer vertebral column like that of whales and dolphins?

Above: Video of how we modelled and took measurements from the early crocodylomorph Terrestrisuchus gracilis (NHMUK).

Our first results were puzzling. The Nile croc had greater RoM in side-to-side motions, which makes sense because crocodiles mostly use more sprawling postures and are semi-aquatic, using quite a bit of side-to-side motions in life. The part that didn’t make sense was that we found pretty much the same thing in all of the fossil crocodylomorphs, including the presumably very terrestrial Terrestrisuchus and Protosuchus. With their long limbs and hinge-like joints, these two are unlikely to have been sprawlers or swimmers!

So we started looking for other parts of the croc that might affect RoM. The obvious candidate was osteoderms, the bony scales that cover the back. We went back to John’s Freezer and got out a nice frozen crocodile to measure the stiffness of its trunk and found that, sure enough, it was a lot stiffer and less mobile without the osteoderms. If the fairly flexible arrangement of osteoderms in crocodiles had this effect on stiffness, it seemed likely that (as previous authors have suggested; Eberhard Frey and Steve Salisbury being foremost amongst them) the rigid, interlocking osteoderms running from head to tail in early crocodylomorphs would really have put the brakes on their ability to move their trunk in certain ways.

Testing stiffness of crocodile trunks to learn the effects of osteoderms, skin, muscles, and ribs. We hung metric weights from the middle of the trunk and measured how much it flexed (Ɵ), then removed bits and repeated.

Testing the stiffness of (Nile) crocodile trunks to learn the effects of osteoderms, skin, muscles, and ribs. We hung metric weights from the middle of the trunk and measured how much it flexed (Ɵ), then removed bits and repeated. Click to em-croccen.

Another cool thing we found was new evidence of convergent evolution to aquatic lifestyles in the spines of thalattosuchians. The more basal thalattosuchians, thought to have been near-shore predators, had stiffness and RoM patterns similar to Crocodylus. But Metriorhynchus, which probably was very good at chasing down fast fish in the open ocean, seems to have had greater stiffness. (The stiffness estimates come from morphometrics and are based on modern crocodiles; see here again, or just read the paper already!) A stiff vertebral column can be useful for a swimmer because it increases the body’s natural frequency of oscillation, and faster oscillation means faster swimming (think tuna, not eel). The same thing seems to have happened in other secondarily aquatic vertebrate lineages such as whales, ichthyosaurs, and mosasaurs.

So, our results were a mixed bag of adaptations particular to crocs and ones that seem like general vertebrate swimming specializations. Crocodylomorphs are important because they are the only group of large vertebrates other than mammals that has secondarily aquatic members and has living members with a reasonably similar body plan, allowing us to test hypotheses in ways that would arguably be impossible for, say, non-avian dinosaurs and birds. The take-home message: crocodylomorphs A) are awesome, and B) can teach us a lot about how vertebrates adapt to different modes of life.

Another take on this story is on our lab website here.

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Even nine years later, I still keep thinking back to a day, early in my career as an academic faculty member based in England, that traumatized me. Today I’m going to share my story of that day. I feel ready to share it.

Stomach-Churning Rating: hmm that’s a tough call, but I’ll say 1/10 because it’s just photos of live crocs and such.

This day was part of a research trip that lasted a couple of weeks, and it was in Florida, not England, and little of that trip went well at first. It transpired almost exactly 9 years ago today; around 20 August 2005. I took two 2nd/3rd year undergraduate students and our lab technician with me to Florida, meeting up with Dr. Kent Vliet, an experienced crocodile specialist, to study the biomechanics of crocodile locomotion, a subject I’ve been slowwwwwwly working on since my PhD days (see recent related blog post here). We were funded by an internal grant from my university that was supposed to be seed money to get data to lay groundwork for a future large UK research grant.

Cuban crocodile adult relaxing in a nearby enclosure. Pound-for-pound, a scary croc, but these acted like puppies with their trainers.

Cuban crocodile adult relaxing in a nearby enclosure. Pound-for-pound, a scary croc, but these acted like puppies with their trainers.

I’m interested in why only some crocodylian species, of some sizes and age classes, will do certain kinds of gaits, especially mammal-like gaits such as bounding and galloping. This strongly hints at some kind of size-related biomechanical mechanism that dissuades or prevents larger crocs from getting all jiggy with it. And at large size, with few potential predators to worry about and a largely aquatic ambush predator’s ecology, why would they need to? Crocodiles should undergo major biomechanical changes in tune with their ecological shifts as they grow up. I want to know how the anatomy of crocodiles relates to these changes, and what mechanism underlies their reduction of athletic abilities like bounding. That’s the scientific motivation for working with animals that can detach limbs from your body. (The crocodiles we worked with initially on this trip were small (about 1 meter long) and not very dangerous, but they still would have done some damage if they’d chosen to bite us, and I’ve worked with a few really nasty crocs before.)

Me putting motion capture markers onto an uncooperative young Siamese crocodile.

Me putting motion capture markers onto an uncooperative young Siamese crocodile.

We worked at Gatorland (near Orlando) with some wonderfully trained crocodiles that would even sit in your lap or under your chair, and listened to vocal commands. The cuteness didn’t wear off, but our patience soon did. First, the force platform we’d borrowed (from mentor Rodger Kram’s lab; a ~$10,000 piece of useful gear) and its digital data acquisition system wouldn’t work to let us collect our data. That was very frustrating and even a very helpful local LabView software representative couldn’t solve all our problems. But at least we were able to start trying to collect data after four painstaking days of debugging while curious crocodiles and busy animal handlers waited around for us to get our act together. The stress level of our group was already mounting, and we had limited time plus plenty of real-life bugs (the bitey, itchy kind; including fire ants) and relentless heat to motivate us to get the research done.

Adorable baby Cuban crocodile.

Adorable baby Cuban crocodile.

Then the wonderfully trained crocodiles, as crocodiles will sometimes do, decided that they did not feel like doing more than a slow belly crawl over our force platform, at best. This was not a big surprise and so we patiently tried coaxing them for a couple of sweltering August days. We were working in their caged paddock, which contained a sloping grassy area, a small wooden roofed area, and then at the bottom of the slope was the crocodiles’ pond, where they sat and chilled out when they weren’t being called upon to strut their stuff for science. We didn’t get anything very useful from them, and then the weather forecast started looking ugly.

Hybrid Siamese crocodile in its pond in our enclosure, waiting to be studied.

Hybrid Siamese crocodile in its pond in our enclosure, waiting to be studied.

We’d been watching reports of a tropical storm developing off the southeastern coast of Florida, and crossing our fingers that it would miss us. But it didn’t.

When the storm hit, we were hoping to weather the edge of the storm while we packed up, because we decided we’d done our best but our time had run out and we should move to our next site, the Alligator Farm and Zoological Park in St Augustine, where I’d worked a lot before with other Crocodylia. But the storm caught us off guard, too soon, and too violently.

To give some context to the situation, for the previous several days the local croc handlers had told us stories of how lightning routinely struck this area during storms, and was particularly prone to hitting the fences on the park perimeter, which we were close to. There was a blasted old tree nearby that vultures hung out in, and they related how that blasting had been done by lightning. One trainer had been hit twice by (luckily glancing) blows from lightning hitting the fences and such.

Ominous onlooker.

Ominous onlooker.

The storm came with pounding rain and a lot of lightning, much of it clearly striking nearby- with almost no delay between flashes and thunder, and visible sky-to-ground bolts. We debated taking our forceplate out of the ground near the crocodile pond, because sensitive electrical equipment and rain don’t go well together, but this would take precious time. The forceplate was covered with a tarp to keep the rain off. I decided that, in the interest of safety, we needed to all seek shelter and let the forceplate be.

I’ll never forget the memory of leaving that crocodile enclosure and seeing a terrible sight. The crocodile pond had swiftly flooded and engulfed our forceplate. This flooding also released all the (small) crocodiles which were now happily wandering their enclosure where we’d been sitting and working before.

Another subject awaits science.

Another subject awaits science.

At that point I figured there was no going back. Lightning + deepening floodwater + electrical equipment + crocodiles = not good, so I wagered my team’s safety against our loaned equipment’s, favouring the former.

We sprinted for cars and keepers’ huts, and got split up in the rain and commotion. As the rain calmed down, I ventured out to find the rest of the team. It turned out that amidst the havoc, our intrepid lab technician had marshalled people to go fetch the forceplate out from the flooded paddock, storm notwithstanding. We quickly set to drying it out, and during some tense time over the next day we did several rounds of testing its electronics to see if it would still work. Nope, it was dead. And we still had over a week of time left to do research, but without our most useful device. (A forceplate tells you how hard animals are pushing against the ground, and with other data such as those from our motion analysis cameras, how their limbs and joints function to support them)

We went on to St Augustine and got some decent data using just our cameras, for a wide variety of crocodiles, so the trip wasn’t a total loss. I got trapped by remnants of the storm while in Washington, DC and had to sleep on chairs in Dulles Airport overnight, but I got home, totally wrecked and frazzled from the experience.

That poorly-timed storm was part of a series of powerful storms that would produce Hurricane Katrina several days later, after we’d all left Florida. So we had it relatively easy.

I’m still shaken by the experience- as a tall person who grew up in an area with a lot of dangerous storms, I was already uneasy about lightning, feeling like I had a target on my back. But running from the lightning in that storm, after all the warnings we’d had about its bad history in this area, and how shockingly close the lightning was, leaves me almost phobic about lightning strikes. I’m in awe of lightning and enjoy thunderstorms, which I’ve seen few of since I left Wisconsin in 1995, but I now hate getting caught out in them.

The ill-fated forceplate and experimental area.

The ill-fated forceplate and experimental area.

Moreover, the damage to the forceplate- which we managed to pay to repair and return to my colleague, and the failure of the Gatorland experiments, truly mortified me. I felt horrible and still feel ashamed. I don’t think I could have handled the situation much differently. It was just a shitty situation. That, and I wanted to show our undergrads a good time with research, yet what they ended up seeing was a debacle. I still have the emails I sent back to my research dean to describe what happened in the event, and they bring back the pain and stress now that I re-read them. But then… there’s a special stupid part to this story.

I tried to lighten the mood one night shortly after the storm by taking the team out to dinner, having a few drinks and then getting up to sing karaoke in front of the restaurant. I sang one of my favourite J Geil’s Band tunes– I have a nostalgic weakness for them- the song “Centerfold“. I not only didn’t sing it well (my heart was not in it and my body was shattered), and tried lamely to get the crowd involved (I think no one clapped or sang along), but also in retrospect it was a bad choice of song to be singing with two female undergrads there– I hadn’t thought about the song’s meanings when I chose to sing it, I just enjoyed it as a fun, goofy song that brought me back to innocent days of my youth in the early 1980’s. But it is not an innocent song.

So ironically, today what I feel the most embarrassed about, thinking about that whole trip and the failed experiment, is that karaoke performance. It was incredibly graceless and ill-timed and I don’t think anyone enjoyed it. I needed to unwind; the stress was crushing me; but oh… it was so damn awkward. I think I wanted to show to the team “I’m OK, I can still sing joyfully and have a good time even though we had a disastrous experiment and maybe nearly got electrified or bitten by submerged crocodiles or what-not, so you can relax too; we can move on and enjoy the rest of the trip” but in reality I proved to myself, at least, that I was not OK. And I’m still not OK about that experience. It still makes me cringe. Haunted, it took me many years to feel comfortable singing karaoke again.

It should have been a fun trip. I love working with crocodiles, but Florida is a treacherous place for field work (and many other things). I can’t say I grew stronger from this experience. There is no silver lining. It sucked, and I continually revisit it in my memory trying to find a lesson beyond “choose better times and better songs to sing karaoke with” or “stay away from floods, electricity and deadly beasts.”

So that wins, out of several good options, as the worst day(s) of my career that I can recall. I’ve had worse days in my life, but for uncomfortable science escapades this edges out some other contenders. Whenever I leave the lab to do research, I think of this experience and hope that I don’t see anything worse. It could have been much worse field work.

(Epilogue: the grants we’ve tried to fund for this crocodile gait project all got shot down, so it has lingered and we’ve done research on it gradually since, when we find time and students… And one of the students on this trip went on to do well in research and is finishing a PhD in the Structure & Motion Lab now, so we didn’t entirely scare them off science!)

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I visited the British Museum a while ago with my daughter and was struck by some of the animal imagery in the loot on display– particularly, as an archosaurophile, the crocodiles (Crocodylia, crocodylians, etc.; no alligatoroids to show in this post). So I decided to go back and photograph some of them for a blog post about the more obscure and rare animals that sometimes appear in human art and design.

It’s easy to think of horses, lions, dogs, eagles and other familiar, domestic or prized beasts in human decorations. Yet what roles do less common animals play? This post is the first of two on the unsung beasties of human artwork, as represented in the British Museum.

Stomach-Churning Rating: 1/10. Tame art and a dried crocodile skin.

Wherever humans and crocodiles coexist, the primeval appearance and dangerous potential of crocodiles are sure to impress themselves upon our psyche. Hence they will manifest themselves in art. This should especially apply in the early days of a civilization, before we extirpate local crocodiles or exclude them to the hinterlands, or in cases in which crocodylians become revered and protected.

Much of Western culture lacks such an emphasis, because it developed in more temperate climes where crocodiles were long since absent. It’s fun to think about what our culture would be like if it had developed with crocodiles as a prominent aspect, as in Egypt, which is the natural place to begin our tour, featuring mummies of course!

All images can be clicked to emcroccen them.

Small Nile crocodile mummy from >30 B.C, El Hiba, Egypt

Small Nile crocodile mummy from >30 B.C, El Hiba, Egypt

Second small Nile crocodile mummy from >30 B.C, El Hiba, Egypt

Second small Nile crocodile mummy from >30 B.C, El Hiba, Egypt

Those mummies remind me of a recent scientific study that used such mummies to reveal the history of the “cryptic” species Crocodylus suchus, a close relative of the Nile croc C. niloticus, and one that seems to be more threatened.

We proceed on our tour with a box showing an example of shabti, or doll-like funeral offerings of “enchanted” mummified figurines:

This shabti box was for a noble daughter, Neskshons, in Thebes, from around 650 B.C.

This shabti box was for a noble daughter, Neskshons, in Thebes, from around 650 B.C.

A crocodile deity receives the shabti from the departed soul, accompanied by  serpent god as well as a more human, ankh-bearing divinity.

A crocodile deity receives the shabti from the departed soul, accompanied by serpent god as well as a more human, ankh-bearing divinity.

Next, some amazingly preserved papyrus scrolls:

This papyrus is from around 900 B.C., with short blurbs about the woman Tentosorkon, part of a new style of funeral provisions in the 22nd Dynasty of Egypt.

This papyrus is from around 900 B.C., with short blurbs about the woman Tentosorkon, part of a new style of funeral provisions in the 22nd Dynasty of Egypt.

Crocodile featured in the story of Tentosorkon.

Crocodile featured in the story of Tentosorkon. What’s it doing? Why is a feathered snake-thing touching its butt? I wish I knew.

The "Litany of Ra", from around 1000 B.C., which is a style like that of the previous 22nd Dynasty papyrus and would have decorated a tomb's wall, dedicated to the lady Mutemwia. Ra, the sun god, is shown in his different manifestations, including a crocodile form, called Sobek-ra: http://www.princeton.edu/~achaney/tmve/wiki100k/docs/Sobek.html

The “Litany of Ra”, from around 1000 B.C., which is a style like that of the previous 22nd Dynasty papyrus and would have decorated a tomb’s wall, dedicated to the lady Mutemwia. Ra, the sun god, is shown in his different manifestations, including a crocodile form, called Sobek-ra (AKA Sebek); a protector and comforter of the dead:

egypt croc 1But crocodiles also feature prominently in other cultures around the world– I was hoping to find some in Thai, South American, or other cultures’ art (especially east/western Africa). However, the museum didn’t exhibit any I could find. I did find these, though, starting with this fantastic Roman armour with a great backstory (and hard to take photos of; argh!):

croc armour caption croc armour 1 croc armour 2 croc armour 3

Roman soldiers in a Sobek cult, running around Egypt while wearing badass armour and getting into all kinds of Bronze Age trouble: I DEMAND TO SEE A SWORD-AND-SANDALS MOVIE FEATURING THIS!

I searched for this next one but did not see it:

A crocodile mask from Mabuiag island near Australia- for some cool details, see this page where the image comes from (I didn’t get to see the original).

There were more tenuous links to crocodiles– surely some dragon images throughout the world relate at least partly to crocodiles, such as this one which seems very crocodylian to me:

A water spirit figure called a belum, from Sarawak, Malaysia, 18/1900s. Belief among  the Melanau people  was that these dragons would wrap their tails around someone's body to protect or drown them. Possibly inspired by saltwater or Phillipine crocs that they lived near.

A water spirit figure called a belum, from Sarawak, Malaysia, 18/1900s. Belief among the Melanau people was that these dragons would wrap their tails around someone’s body to protect or drown them. Possibly inspired by saltwater or Phillipine crocs that they lived near.

And that’s it- all I managed to find, but not a bad haul from this huge museum.  I looked for the Aztec croc-god Cipactli to no avail. If you have £850 to spare you might like to walk away with this one from the museum. I gladly accept donations of such things to my, err, research.

That’s just one museum’s view of crocodylians’ role in our culture. What crocodile imagery from human art around the world do you fancy?

 

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(John: here’s a guest post from my former PhD student, soon to be 100% legit PhD, Dr., and all that jazz, Julia Molnar!)

This is my first guest post, but I have been avidly following what’s in John’s freezer (and the blog too) for quite a while. I joined the lab in 2009 and left a month ago on the bittersweet occasion of surviving my PhD viva (oral exam/defense), so I’d like to take a moment here to thank John and the Structure & Motion Lab for a great 4 years!

Moving on to freezer-related matters; specifically, a bunch of frozen crocodile spines. It was late 2011, and the reason for the spines in John’s freezer was that John, Stephanie Pierce, and I were trying to find out more about crocodile locomotion. This was anticipated to become my first major, first-author research publication (but see my Palaeontologia Electronica paper on a related subject), and I was about to find out that these things seldom go as planned; for example, the article would not be published for more than three years (the research took a long time!). Before telling the story of how it lurched and stumbled toward eventual publication, I’ll give you some background on the project.

Stomach-Churning Rating: 3/10; x-ray of dead bits and nothing much worse.


A stumbly sort-of-bounding crocodile. They can do better.

First of all, why crocodiles? For one thing, they’re large, semi-terrestrial animals, but they use more sprawling postures than typical mammals. Along with alligators and gharials, they are the only living representatives of Crocodylomorpha, a 200+ million year-old lineage that includes wolf-like terrestrial carnivores, fish-like giants with flippers and a tail fin, even armored armadillo-like burrowers. Finally, crocodiles are interesting in their own right because they use a wide variety of gaits, including bounding and galloping, which are otherwise known only in mammals.

Nile croc

Nile crocodile skeletal anatomy

OK, so why spines? Understanding how the vertebral column works is crucial to understanding locomotion and body support on land, and inter-vertebral joint stiffness (how much the joints of the backbone resist forces that would move them in certain directions) in particular has been linked to trunk movements in other animals. For this reason, vertebral morphology is often used to infer functional information about extinct animals, including dinosaurs. However, vertebral form-function relationships have seldom been experimentally tested, and tests on non-mammals are particularly scarce. So we thought the crocodile spines might be able to tell us more about the relationship between vertebral morphology, mechanics, and locomotion in a broader sample of vertebrate animals. If crocodile spine morphology could be used to predict joint stiffness, then morphological measurements of extinct crocodile relatives would have some more empirical heft to them. Several skeletal features seem to play roles such as levers to mechanically stiffen crocodile spines (click to emcroc’en):

Croc vertebra-01

Anatomy of a crocodile vertebra

We decided to use a very simple technique that could be replicated in any lab to measure passive stiffness in crocodile cadavers. We dissected out individual joints were and loaded with known weights. From the movement of the vertebrae and the distance from the joint, we calculated how much force takes to move the joint a certain number of degrees (i.e. stiffness).

Julia w vertebra (480x640)

Me with crocodile vertebra and G-clamp

Xray

X-ray of two crocodile vertebrae loaded with a metric weight to calculate their joint’s stiffness

Afterwards, we boiled the joints to remove the soft tissues – the smell was indescribable! We took 14 measurements from each vertebra. All of these measurements had been associated with stiffness or range of motion in other studies, so we thought they might be correlated with stiffness in crocodiles also.

morphometrics

Some of the vertebral measurements that were related to stiffness

Despite my efforts to keep it simple, the process of data collection and analysis was anything but. I recall and exchange with Stephanie Pierce that went something like this:

Stephanie: “How’s it going?”

Me: “Well, the data are messy, I’m not seeing the trends I expected, and everything’s taking twice as long as it was supposed to.”

Stephanie: “Yes, that sounds like science.”

That was the biggest lesson for me: going into the project, I had been unprepared for the amount of bumbling around and re-thinking of methods when the results were coming up implausible or surprising. In this case there were a couple of cool surprises: for one thing, crocodiles turn out to have a very different pattern of inter-vertebral joint stiffness than typical mammals: while mammals have stiff thoracic joints and mobile lumbar joints, crocodiles have stiffer lumbar joints. Many mammals use large lumbar movements during bounding and galloping, so crocodiles must use different axial mechanics than mammals, even during similar gaits. While that’s not shocking (they did evolve their galloping and bounding gaits, and associated anatomy, totally independently), it is neat that this result came out so clearly. Another unexpected result was that, although several of our vertebral measurements were correlated with stiffness, some of the best predictors of stiffness in mammals from previous studies were not correlated with stiffness in crocodiles. The study tells a cautionary tale about making assumptions about extinct animals using data from only a subset of their living relatives or intuitive ideas about form and function.

Finally, the experience of doing the experiments and writing the paper got me interested in other aspects of crocodilian functional anatomy. For instance, how does joint stiffness interact with other factors, such as muscle activity and properties of the ribs, skin, and armor in living crocodiles? Previous studies by Frey and Salisbury had commented on this, but the influence of those factors is less tractable to experiment on or model than just naked backbones with passively stiff joints. In the future, I’d like to study vertebral movements during locomotion in crocodiles – especially during bounding and galloping – to find out how these patterns of stiffness relate to movement. In the meantime, our study shows that, to a degree, crocodile backbone dimensions do give some clues about joint stiffness and locomotor function.

To find out more, read the paper! It was just featured in Inside JEB.

Julia Molnar, Stephanie Pierce, John Hutchinson (2014). An experimental and morphometric test of the relationship between vertebral morphology and joint stiffness in Nile crocodiles (Crocodylus niloticus). The Journal of Experimental Biology 217, 757-768 link here and journal’s “Inside JEB” story

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