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Posts Tagged ‘boids’

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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I heard that the UMZC has some new exhibits open, so back I went! For the prior posts see here (mammals/basement) and here (everything else). Another photo tour! There’s a special (art) exhibit, too, so stick around to the end.

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

Stomach-Churning Rating: 3/10 mainly skeletons, some preserved critters in jars.

The first new section is an elaborated display on reptiles.

Clevosaurus, a Triassic relative of the living tuatara reptile, Sphenodon. Nice fossil hindlimbs!

Tuataras (Sphenodon), skeletal and preserved.

Tuatara embryos!

Nice chameleon mount w/tongue extended.

Thorny devil (Moloch), de-thorned and in the flesh.

Skull (cast) of Ninjemys, the giant turtle.

Pipe snakes! Snakes with vestigial hindlegs.

Istiodactylus pterosaur snout-tip (real fossil) from the Isle of Wight, UK. Nice 3D fossil.

The gharial (Gavialis), male with protuberance on snout (mating-related).

I dub thee Dinosaur Corner! For dinosaurs, the Sedgwick Museum across the street (also free; also classic and awesome) is the place to go but this corner does a good job fighting for the scientific conclusion that birds are dinosaurs.

And now a change of pace. On to the special exhibit!

A nice surprise to see naturalist superstar Jonathan Kingdon‘s scientific illustrations and nature-inspired artwork displayed here. I’ve added photos of ones I liked the most.

As the caption explains, Kingdon used art to explain the value of nature; via realistic images of life, dissections, and creative abstractions drawn from them.

Hammerhead bats: even freakier when skinned.

Begone if ye find not joy in aardvarks!

White-toothed shrew looking extra-ghoulish with flensed face.

Skinned sengis in action.

More sengis (elephant shrews); with a note explaining that they are not rodents/insectivores but afrotheres, cousins of aardvarks, elephants and kin.

Bronze Jackson’s chameleon bust.

Asian barbet faces: this was fascinating. Kingdon used the paintings to explain how barbet faces vary across species as recognition devices to aid in territorial defense, especially of their nest-holes in trees, in which they face outwards to display their coloured faces. The middle image shows one lone species that has no such territorial competitors and has evolved back into brown colour, perhaps due to relaxed selective pressure for colour. Neat!

Oh my, this took my breath away! Mixed media depicting the varied forms of facial ornaments in vultures; soft tissues used in communcation. And here mounted on a butcher’s rack. Do vulture bits mimic their grisly food?

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Today is the 210th anniversary of Charles R. Darwin’s birthday so I put together a quick post. I’d been meaning to blog about some of our latest scientific papers, so I chose those that had an explicit evolutionary theme, which I hope Chuck would like. Here they are, each with a purty picture and a short explainer blurb! Also please check out Anatomy To You’s post by Katrina van Grouw on Darwin’s fancy pigeons.

Stomach-Churning Rating: 1/10 science!

First, Brandon Kilbourne at the Naturkunde Museum in Berlin kindly invited me to assist in a paper from his German fellowship studying mustelid mammals (otters, weasels, wolverines, badgers, etc.; stinky smaller carnivorous mammals). Here we (very much driven by Brandon; I was along for the ride) didn’t just look at how forelimb bone shape changes with body size in this ecologically diverse group. We already knew bigger mustelids would have more robust bones, although it was cool to see how swimming-adapted and digging-adapted mustelids evolved similarly robust bones; whereas climbing ones had the skinniest bones.

The really exciting and novel (yes I am using that much-abused word!) aspect of the paper is that Brandon conjured some sorcery with the latest methods for analysing evolutionary trends, to test how forelimb bone shapes evolved. Was their pattern of evolution mostly a leisurely “random walk” or were there early bursts of shape innovation in the mustelid tree of life, or did shape evolve toward one or more optimal shapes (e.g. suited to ecology/habitat)? We found that the most likely pattern involved multiple rates of evolution and/or optima, rather than a single regime. And it was fascinating to see that the patterns of internal shape change deviated from external shape change such as bone lengths: so perhaps selection sometimes works independently at many levels of bone morphology?

Various evolutionary models applied to the phylogeny of mustelids.

Then there, coincidentally, was another paper originating in part from the same museum group in Berlin. This one I’d been involved in as a co-investigator (author) on a Volkswagen (yes! They like science) grant back about 8 years ago and since. There is an amazing ~290 million year old fossil near-amniote (more terrestrial tetrapod) called Orobates pabsti, preserved with good skeletal material but also sets of footprints that match bones very well, allowing a rare match of the two down to this species level. John Nyakatura’s team had 3D modelled this animal before, so we set out to use digital techniques to test how it did, or did not, move—similar to what I’d tried before with Tyrannosaurus, Ichthyostega and so forth. The main question was whether Orobates moved in a more “ancestral” salamander-like way, a more “derived” lizard-like way (i.e. amniote-ish), or something else.

The approach was like a science sledgehammer: we combined experimental studies of 4 living tetrapods (to approximate “rules” of various sprawling gaits), a digital marionette of Orobates (to assess how well its skeleton stayed articulated in various motions), and two robotics analysis (led by robotics guru Auke Ijspeert and his amazing team): a physical robot version “OroBOT” (as a real-world test of our methods), and a biomechanical simulation of OroBOT (to estimate hard-to-measure things in the other analyses, and matches of motions to footprints). And, best of all, we made it all transparent: you can go play with our interactive website, which I still find very fun to explore, and test what motion patterns do or do not work best for Orobates. We concluded that a more amniote-like set of motions was most plausible, which means such motions might have first evolved outside of amniotes.

OroBOT in tha house!

You may remember Crassigyrinus, the early tetrapod, from a prior post on Anatomy To You. My PhD student Eva Herbst finished her anatomical study of the best fossils we could fit into a microCT-scanner and found some neat new details about the “tadpole from hell”. Buried in the rocky matrix were previously unrecognized bones: vertebrae (pleurocentra; the smaller nubbins of what may be “rhachitomous” bipartite classic tetrapod/omorph structure), ribs (from broad thoracic ones to thin rear ones), pelvic (pubis; lower front), and numerous limb bones. One interesting trait we noticed was that the metatarsals (“sole bones” of the foot) were not symmetrical from left-to-right across each bone, as shown below. Such asymmetry was previously used to infer that some early tetrapods were terrestrial, yet Crassigyrinus was uncontroversially aquatic, so what’s up with that? Maybe this asymmetry is a “hangover” from more terrestrial ancestry, or maybe these bones get asymmetrical for non-terrestrial reasons.

The oddly asymmetrical metatarsals of Crassigyrinus.

Finally, Dr. Peter Bishop finished his PhD at Griffith University in Australia and came to join us as a DAWNDINOS postdoc. He blasted out three of his thesis chapters (starting here) with me and many others as coauthors, all three papers building on a major theme: how does the inner bone structure (spongy or cancellous bone) relate to hindlimb function in theropod dinosaurs (including birds) and how did that evolve? Might it tell us something about how leg posture or even gait evolved? There are big theories in “mechanobiology” variously named Wolff’s Law or the Trajectorial Theory that explain why, at certain levels, bony struts tend to align themselves to help resist certain stresses, and thus their alignment can be “read” to indicate stresses. Sometimes. It’s complicated!

Undaunted, Peter measured a bunch of theropod limb bones’ inner geometry and found consistent differences in how the “tracts” of bony struts, mainly around joints, were oriented. He then built a biomechanical model of a chicken to test if the loads that muscles placed on the joints incurred stresses that matched the tracts’ orientations. Hmm, they did! Then, with renewed confidence that we can use this in the fossil record to infer approximate limb postures, Peter scanned and modelled a less birdlike Daspletosaurus (smaller tyrannosaur) and more birdlike “Troodon” (now Stenonychosaurus; long story). Nicely fitting many other studies’ conclusions, Peter found that the tyrannosaur had a more straightened hindlimb whereas the troodontid had a more crouched hindlimb; intermediate between the tyrannosaur and chicken. Voila! More evidence for a gradual evolution of leg posture across Mesozoic-theropods-into-modern-birds. That’s nice.

Three theropods, three best-supported postures based on cancellous bone architecture.

If you are still thirsty for more papers even if they are less evolutionary, here’s the quick scoop on ones I’ve neglected until now:

(1) Former PhD student Chris Basu published his thesis work w/us on measuring giraffe walking dynamics with force plates, finding that they move mostly like other quadrupeds and their wobbly necks might cost them a little.

(2) Oh, and Chris’s second paper just came out as I was writing this! We measured faster giraffe gaits in the wilds of South Africa, as zoo giraffes couldn’t safely do them. And we found they don’t normally go airborne, just using a rotary gallop (not trot, pace or canter); unlike some other mammals. Stay tuned: next we get evolutionary with this project!

(2) How do you safely anaesthetize a Nile crocodile? There’s now a rigorous protocol (from our DAWNDINOS work).

(3) Kickstarting my broad interest in how animals do “extreme” non-locomotor motions, we simulated how greyhounds stand up, finding that even without stretchy tendons they should, barely, be able to do it, which is neat. Expect much more about this from us in due time.

(4) Let’s simulate some more biomechanics! Ashley Heers, an NSF research fellow w/me for a year, simulated how growing chukar birds use their wing muscles to flap their way up steeper inclines (“WAIR” for devotees), and the results were very encouraging for simulating this behaviour in more detail (e.g. tendons seem to matter a lot) and even in fossil species; and finally…

(5) Hey did you ever think about how bone shape differs between hopping marsupials (macropods) and galloping artiodactyl (even-toed) mammals? We did, in long-the-making work from an old BBSRC grant with Michael Doube et al., and one cool thing is that they mostly don’t change shape with body size that differently, even though one is more bipedal at faster speeds—so maybe it is lower-intensity, slower behaviours that (sometimes?) influence bone shape more?

So there you have the skinny on what we’ve been up to lately, messing around with evolution, biomechanics and morphology.

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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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An epiphysean Sispyhean task today: solve this mystery that has been bothering me for >15 years. It’s about bird knees. Read on.

Stomach-Churning Rating: 1/10- bones and brief words. Nothing to worry about.

Here is an ostrich. I was interviewing undergrads the other day and looked up to see it, then thought something like: “Oh yeah, that little bit of bone really bothers me. I cannot figure it out.” What little bit of bone?

Right leg, side view, ostrich…

This little bit of bone. Zooming in on that ostrich’s knee:

Who am I? (femur above; tibiotarsus below; “PTE” is the crest of bone with the white arrow on it)

The little bit of bone is not talked about much in the scientific literature on bird knees. But we know it’s there and it is part of the composite bone called the tibiotarsus (ancestral tibia, this bit of bone, and the proximal tarsal [ankle] bones on the other end; the astragalus and calcaneum of earlier dinosaurs).

What is it? We call it something like the proximal tibial epiphysis (PTE for short, here). An epiphysis is an end of a bone that fuses up with the shaft during growth, around the time of skeletal maturity; ultimately ending longitudinal (length-wise) growth of that bone. Mammals almost ubiquitously have them. So do lizards and tuataras. And some fossil relatives. Not much else– except birds, in this particular region (the two ends of the tibiotarsus; also in the foot region; the tarsometatarsus; which also has its share of mysteries such as the hypotarsus; I won’t go there today). You can see the PTE in mostly cartilaginous form if you take apart a chicken drumstick.

This PTE, like other well-behaving epiphyses, fuses with the tibiotarsus in mature birds, forming one bone. But the young ostrich’s knee above shows the PTE nicely; and other living birds show more or less the same thing.

It begs for explanations. I’ve talked about it in a few of my papers. But I’ve always punted on what it really means– does it have anything to do with the patella (they appear at similar times in evolution; we know that much, roughly)? Where does it come from, developmentally? (we sort of know that but more work is needed in different species and in high resolution) When did it evolve? What does it tell us? Why is it there in living birds and almost no other extinct birds/other dinosaurs? Does it have anything to do with why birds, during their evolution, seem to gradually increase the fusion of skeletal elements or ossify new ones (tendons, kneecaps, etc)? Why here and not in the femur or several other long bones of birds? How much do these PTEs vary between (or within) bird species?

This is the challenge in the post’s title. I present to you: solve this puzzle. Developmentally, biomechanically, evolutionarily, genetically, whatever– why does this PTE happen? There are hints– e.g. this paper proposes why growth rates of long bones favour the formation of “secondary centres of ossification” like this. But I’m unable to satisfy myself with any solutions I can find. Maybe you can complete The Bird Knee Challenge?

Have a go at it in the Comments below! There are plenty of papers or even a grant or something involved in sorting out this single mystery; one of the many basic mysteries about animal anatomy.

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Putting my morphologist hat back on today, I had an opportunity to dissect an Elegant-crested tinamou (Eudromia elegans) for the second time in my life. The last time was during my PhD work ~20 years ago. In today’s dissection I was struck by another reminder of how studying anatomy is a lifelong learning experience and sometimes it’s really fun and amazing even when it’s stinky.

Tinamou foot. I did know that tinamous don’t have a hallux; big “perching toe” (1st/”big toe” in us); true of ratites/palaeognaths more generally. Unlike a chicken or many other birds. Just the three main toes (2, 3 and 4) are here.

Stomach-Churning Rating: 7/10; you gotta have guts to learn about intestine-churning stuff.

Tinamous are neat little partridge-like ground birds but they are not close cousins of partridges or guineafowl at all. Their closest cousins are other ratites/palaeognaths such as ostriches and kiwis. And hence they are found in South America, especially Patagonia in Argentina. I’ve seen them there, much to my enjoyment.

Said tinamou.

What struck me today was that, as I delved into the digestive system of this bird, I saw features that were unfamiliar to me even after having dissected many species of birds from many lineages. The intestinal region was very lumpy, with little bud-like pockets full of dense droppings. Furthermore, on separating the tubes of the small and large intestines I realized that most of the intestinal volume itself was caecum (normally a modest side-pocket near the juncture of the small and large intestines). Indeed, that caecum was caeca (plural): it had two massive horns; it was a double-caecum, feeding back into the short rectum and cloaca. Birds have variable caeca and it is typical to see subdivision into two parts, but I’d never seen it to this degree.

Oh why not, here’s the gizzard/stomach showing its grinding pebbles and bits of food, plus the strong outer muscle layers (pink) for driving that grinding. Small intestine heads toward the bottom of the image. Yes, we do need a better dissection light…

I had to question my anatomical knowledge at this point, wondering if I was identifying things incorrectly—did I really screw up somehow and these were other organs, like giant ovaries? But no, they were clearly full of faecal matter; they were digestive organs. I finished the dissection, still puzzled, and hit the literature. Right away, Google-Scholaring for “tinamou caecum” I found the answer, here (free pdf link):

“at least one species (Elegant Crested Tinamou, [Eudromia elegans]), the ceca contain multiple sacculations, resulting in structures that look much like two bunches of fused grapes.”

The caeca in question.

OK buddy, those are the little lumpy buds I saw. Bunches of grapes—exactly.

And later:

“The paired ceca of the Elegant Crested Tinamou are extraordinary and probably unique within Aves (Fig. 3): long and wide (12.5-13.0 X 2.2- 2.5 cm; Wetmore 1926) and internally honeycombed by many small diverticula. These outpocketings gradually diminish in size and organization from the base to the tip of the organ, apically showing a more spiral form of internal ridges like ratite ceca. Externally, the basal diverticula protrude from the ceca as pointed lobes, gradually becoming flatter but still clearly apparent toward the organ’ s tip.”

Whoa! I never knew that! So I happened to be dissecting a bird, fairly common in its homeland, that has a really bizarre and singular form of caeca/ceca! That hit my morphologist sweet-spot so I was very pleased and decided to share with you. It is one of those many examples of times when you quickly go from confusion to illumination as a scientist, emerging with a neat fact about animal biology. And journal articles help you get there!

The bare “brood patch” on the back end of the tinamou’s belly; a nicely hotspot for keeping eggs warm. Perhaps for brooding bad puns, too.

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Uh oh, a “why?” question in biology! There are many potential, and not mutually exclusive, answers to such questions. Ultimately there is a historical, evolutionary answer that underpins it all (“ostriches evolved two kneecaps because…”). But we like ostrich knees and their funky double-kneecaps (patellae; singular = patella) so we wanted to know why they get so funky. One level of addressing that question is more like a “how?” they have them. So we started there, with what on the surface is a simple analysis. And we published that paper this week, with all of the supporting data (CT, MRI, FEA).

Stomach-Churning Rating: 6/10 because there is a gooey image of a real dissection later in the post, not just tidy 3D graphics.

First author Kyle Chadwick was my research technician for 2 years on our sesamoid evolution grant, and we reported earlier on the detailed 3D anatomy of ostrich knees (this was all part of his MRes degree with me, done in parallel with his technician post). Here, in the new paper with Sandra Shefelbine and Andy Pitsillides, we took that 3D anatomy and subjected it to some biomechanical analysis in two main steps.

Ostrich (right) knee bones. The patellae are the two knobbly bits in the knee.

First, we used our previous biomechanical simulation data from an adult ostrich (from our paper by Rankin et al.) to estimate the in vivo forces that the knee muscles exert onto the patellar region during moderately large loading in running (not maximal speed running, but “jogging”). That was “just” (Kyle may laugh at the “just”– it wasn’t trivial) taking some vectors out of an existing simulation and adding them into a detailed 3D model. We’ve done similar things before with a horse foot’s bones (and plenty more to come!), but here we had essentially all of the soft tissues, too.

Ostrich knee with muscles as 3D objects.

Second, the 3D model that the muscular forces were applied to was a finite element model: i.e., the original 3D anatomical model broken up into a mesh, whose voxels each had specific properties, such as resistance to shape change under loading in different directions. The response of that model to the loads (a finite element analysis; FEA) gave us details on the stresses (force/area) and strains (deformations from original shape) in each voxel and overall in anatomical regions.

Finite element model setup for our study. If you do FEA, you care about these things. If not, it’s a pretty, sciencey picture.

The great thing about a computer/theoretical model is that you can ask “what if?” and that can help you understand “how?” or even “why?” questions that experiments alone cannot address. Ostriches aren’t born with fully formed bony kneecaps; indeed those patellae seem to mature fairly late in development, perhaps well after hatching. We need to know more about how the patellae form but they clearly end up inside the patellar (knee extensor) tendon that crosses the knee. So we modelled our adult ostrich without bony patellae; just with a homogeneous patellar tendon (using the real anatomy of that tendon with the bony bits replaced by tendon); and subjected it to the loading environment for “jogging”.

The right knee of an ostrich hatchling. The patellae have yet to form; indeed there is little bone around the knee region at all, yet.

We then inspected our FEA’s results in light of modern theory about how tissues respond to loading regimes. That “mechanobiology” theory, specifically “tissue differentiation”, postulates that tendon will tend to turn into fibrocartilage if it is subjected to high compression (squishing) and shear (pushing). Then, the fibrocartilage might eventually be reworked into bone as it drops the compression and shear levels. So, according to that theory (and all else being equal; also ignoring the complex intermediate states that would happen in reality), the real ostrich’s kneecaps should be located in the same positions where the FEA, under the moderately large loads we applied, predicts the homogeneous tendon to have high compression and shear. But did the real anatomy match the mechanical environment and tissue differentiation theory’s predictions?

Tissue differentiation diagram displaying the theoretical pathways for transformation of tissues. If tendon (red) experiences high shear (going up the y-axis) and high compression (going toward the left), it should turn into fibrocartilage (purple). Transformation into bone (diagonally to the bottom right) would reduce the shear and compression.

Well, sort of. The image below takes some unpacking but you should be able to pick out the red areas on the bottom row where the patellae actually are, and the yellow shaded regions around some of those patellar regions are where the compression and shear regimes are indeed high and overlapping the actual patellar regions. The upper two rows show the levels of compression (or tension; pulling) and shear, but the bottom row gets the point across. It’s not a bad match overall for the first (“real”; common to all living birds) patella, located on top of the upper knee (femur). It’s not a good match overall for the second (unique to ostriches) patella, located below the first one (and attached to the tibia bone).

FEA results! (click to embiggen)

Kyle says, “Being a part of this project was exciting because of the application of engineering concepts to interesting biological (including evolutionary) questions. Also, it never gets old seeing people’s reactions when I tell them I study ostrich knees.

The study had a lot of nuances and assumptions. We only looked at one instant in slow running and only at one adult ostrich, not at the full development of ostrich anatomy and loading. That’s harder. We started simple. The tissue differentiation theory is used more for fracture healing than for sesamoid bone formation but there’s some reason to suspect that similar mechanisms are at play in both. And there’s much more; if you want the gory details see the paper.

So did we solve why, or how, ostriches have two kneecaps? We felt that the mechanical environment of our FEA was a good theoretical explanation of where the first patella forms. We originally expected the second patella, which evolved more recently and might be more mechanically sensitive as a result, to be a better match than the first one, but it was the opposite. C’est la science!

Enough models, let’s have some reality! I warned you this post would get messy, and here it is. Left leg (skinned) of an ostrich showing the muscles around the knee. The patellar region would be in the gloved hand of the lucky individual shown.

This study, for me, was a fun experience in moving toward more fusion of “evo-devo” and biomechanical analyses, a research goal of mine lately– but there’s still a ways to go with the “how?” and “why?” questions even about ostrich kneecaps.

We felt that the best conclusion supported by our analyses was that, rather than have homogeneous stresses and strains throughout their knee tissues (e.g. the patellar tendon), ostriches have a lot of regional diversity in how those tissues are loaded (in the condition we modelled, which is adequately representative of some athletic exertion). Look at the complex FEA coloured results above again, the top two rows: there are a lot of different shades of compression/tension and shear; not homogeneous strains. That diversity of regional loading sets those tissues up for potential transformation throughout growth and development. And thus ONE of the reasons why ostriches might have two kneecaps is that the heterogeneous loading of their knee tendon favours formation of heterogeneous tissue types.

Another, compatible, explanation is that these different tissues might have consequences for how the muscles, tendon and joint operate in movement behaviours. In due time there will be more about that. In the meantime, enjoy the paper if this post makes you want to know more about the amaaaaaazing knees of ostriches!

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