Archive for February, 2013

We are coming up on the 1 year anniversary of this blog. I’ll discuss that anniversary and do a retrospective when the time comes; I have plans…

But first: Frosty feedback time! I want to involve current blog readers in guiding where this blog goes in the future. I renewed the URL for another year, so there will at least be that much more, and probably more than 1 year, since I have plenty of ideas and energy left and am enjoying this.

Let’s let the poll do the talking – and you, too! I hope for some discussion- please, your constructive criticism and suggestions! What do you honestly want more/less of, or totally new, within reason? Maybe I haven’t thought of everything I could do. In fact, I’m sure I haven’t.

3 choices at most per user (you don’t have to use all 3), please. And I think the poll will allow new entries (“Other”) to be added (EDIT: Hmm, doesn’t work the way I thought it did. If you do click “Other”, please add a comment below explaining it. Otherwise I don’t know what “other” means… EDIT EDIT– OK, if you’ve read this far, I will find out what you put in the “Other” box (it shows up in my WordPress admin stuff) but it isn’t made publically visible- see here if curious).

If there’s something you feel strongly about, such that 1 vote just doesn’t cut the mustard, speak out in the comments below. (Sorry, no, the bad jokes and terrible puns are here to stay ūüôā )

Go for it! I’ll let the poll run for a week or so. Blog lurkers, please de-lurk! I want to hear from you, too.


John of the Freezers


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‚Ķa daily picture of anatomy!¬†And today the pictures are a mysteryyyyyyy!¬†‚ôę

Welcome¬†back¬†again,¬†again, and¬†again¬†(gasp, pant)‚Äď and¬†again¬†(exhausted howl)… and… aaaaaagaiiiiin… to¬†Freezermas!¬†

This is the end. I’ve worked hard all week to bring you all-new content for Freezermas, and on the Seventh Day I get drunk rest— and make you do the work! Off into the hoary wilderness you go, seeking answers to eternal trivial mysteries.

Seven mystery photos of museum specimens today, each from a different museum (or other institution whose role it is to display critters, in 2/7 cases) and animal! I’ve visited all these facilities and taken these photos myself. Which specimens can you identify, and (ultra difficult)¬†can you identify the institution it’s from?

Stomach-Churning Rating: 2/10. Super tame.

You had some impromptu practice on day 2. Very well, then. This session counts for points. If you want a recap of points, see last Mystery Dissection.

But because the pictures are small and numerous (refer to them by number 1-7, please), the points/correct answer are simplified: 2 pts for correct answer, and maybe 1¬†bonus pt¬†for something clever but incorrect, 0 pts here just for shooting the breeze (“Superhuman effort isn’t worth a damn unless it achieves results.”–Ernest Shackleton), plus 1 pt extra credit if you correctly ID the museum/institution. Being first does not matter here. Just being correct. With 7 mysteries, you can freeze up a lot of points here! But…

Difficulty: Cropping. Lots of cropping. And therefore quite pixellated if you zoom in much; don’t even bother clicking to embigitate. However, there may or may not be themes between some pictures, or critical clues. They are identifiable.

Off you venture, brave Freezerinos! Wear multiple layers.

1) Freezermas7-1 2) Freezermas7-2

3) Freezermas7-3

4) Freezermas7-4 

5)Freezermas7-5 6)Freezermas7-6


But wait– there is a mystery eighth specimen, which even I am not completely sure what it is! No points for figuring it out, but mucho respect!



Happy Freezermas!¬†One last time– sing it: ‚ÄúOn the seventh day of Freezermas, this blo-og gave to me:¬†one tibiotarsus,¬†two silly Darwins,¬†three muscle layers,¬†four gory¬†hearts,¬†five doggie models, six mangled pangl’ins a-aaaaaaand seven specimens that are mysteries!‚Ä̬†‚ô™‚ôę

I hope you enjoyed Freezermas. Let’s hope we’re all thawed out in time for the next one.

CLUES/ANSWERS: Click these thumbnails to embigrinate them if you need help–

snapperpareiasaurs frogfish  Sclerocephalus  Suedinosauroidaardvarks

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‚Ķa daily picture of anatomy!¬†And today it is six picture-facts; doo-raa-dee!¬†‚ôę

Welcome¬†back¬†again,¬†again, and¬†again¬†(gasp, pant)— and again (exhausted howl)¬†to¬†Freezermas!¬†

And Happy World Pangolin Day!

Stomach-Churning Rating: 4/10; pretty tame images of anatomy today– but 9/10 if you consider how vile a practice it is to eat pangolins.

Much like rhinoceroses are, pangolins (“scaly anteaters”) are threatened with extinction across Africa and Asia largely¬†because tradition holds that they have magical skin. It comes down to that. It’s simply pathetic.

Pangolin in Borneo

Sunda pangolin,¬†Manis javanica; from Wikipedia. It’s not a pig in a convenient artichoke-like wrapper. It’s a precious, rare creature.

To make matters worse, pangolins are smaller than rhinos and covered in the tough armour that makes them so desirable, and hence they are more portable and easy to hide. They also are thought to taste delicious — or just have the social cachet that it is a sign of affluence to be able to afford to eat them — to some people, especially from some southeast Asian cultures.¬†Habitat loss/growing populations/deforestation/climate change aren’t helping, either.

Around 60,000 pangolins were illegally smuggled or otherwise slaughtered for human uses in 2012 worldwide; contrasting with 668 rhinos in South Africa that year (perhaps 2,000 worldwide?); so the scale of the problem is immense. Smaller-bodied pangolins will be more numerous in the wild than large, wide-roaming rhinos, but the drain on those numbers is obviously not sustainable. Sometimes pangolins are smuggled alive, a cruel practice that delivers them fresh but in a poor welfare state at the point of sale, compounding the urgency to turn the tide of exploitation.

Please take the time today to lend your hand to a good conservation group. Learn about the crisis facing pangolins (e.g. this recent article; and this video) and speak out about it. Of course, don’t eat pangolins, either.

Let’s not let humanity fail in its moral imperative of stewardship.

Pangolin body and skeleton

My photo of a pangolin body and skeleton, from the University of Cambridge Museum of Zoology’s exhibits.

In celebration of World Pangolin Day, for today’s Freezermas we have six impressive facts about pangolin anatomy. Much like rhinos, these are animals we don’t know as well as we should. I’ve never had one in my freezers, and would feel a bit weird if I did, since I find them so adorable, but they do have fascinating anatomy, natural history and evolutionary heritage. All the more reason to preserve them as they should be: alive and with the freedom they deserve.

Pangolin Fact 1: Pangolins have highly modified skulls with myrmecophagous adaptations-Рthese are specializations for eating arthropods (especially ants/termites): toothless, tubular snout, reduced mandibles, and moreРshown below.

Pangolin skull x-ray

X-ray of Malayan pangolin (Manis javanica) skull in side(1) and top(2) views, modified from Endo et al., 1998. The small arrow denotes the V-shaped, splint-like mandible, and the large arrow is directed at the jaw joint (zygomatic process on the temporal bone). The zygomatic arch, crossing from the jaw joint toward the front of the upper jaw (maxilla), is incomplete, so there is no bony bridge across the cheek as in many mammals. The large masseter and temporalis muscles run across this region, forming a more flexible, muscular cheek involved in feeding. Some nice labelled skull photos are here.

EDIT: Aaagh! Of course I should have checked Digimorph, which has a kickass CT scan/movie of the skull. Play with that; hours of anatomy-tainment!

Pangolin Fact 2: Pangolins have long tongues whose attachment extends way across the breastbone.

Pangolin tongue dissection

Tongue anatomy of a Malayan pangolin, from Prapong et al., 2009. This shows the chest region in ventral view (head is to the right side), with the main body of the sternum removed. A indicates muscles forming a sac around the tongue base; B is where the tongue finally inserts on the sternum/xiphoid processes; C is the ribcage; D is the xiphisternal joint (middle of the sternum parts).

Your tongue, even Gene Simmons‘s, just extends a little ways down your chin. It is, however, ¬†a common misconception that a pangolin’s tongue is longer than the animal. It can’t be longer than the distance between its sternal origin and the tip of the snout, so it might extend up to 40cm out of the mouth when fully extended in a large pangolin. Around 1988, there was the scientific misconception that the tongue extended way back to the pelvis (hips) or stomach. This is not true according to the latest literature I’ve read (e.g. in caption above), but is widespread in pangolin information on the internet. If someone has secondary confirmation of this either way, I’d love to see some concrete evidence.

EDIT: This image of a dissected pangolin fetus indicates a quite long tongue, maybe even long enough to attach near the pelvis, although that site agrees that there is no pelvic attachment. The latter site also depicts a fascinating cartilaginous sheath for the tongue. The misinformation about pangolin tongues does make me wonder: perhaps there is a lot of diversity in tongue attachments/lengths among the 8 pangolin species? Who knows.

Pangolin Fact 3: Pangolins have toughened, keratinized stomach linings.

Pangolin stomach histology

Click to embigitate. Histology of the stomach lining in Manis tricuspis (modified from Ofusori et al., 2008), showing layers of keratinized stratified squamous epithelium (thick stomach lining). These layers seems to act as a protective coating against the rasping, chitinous exoskeletons of the ants and termites that are consumed, helping to reduce the risk of ulcers while reportedly eating up to 200,000 ants/per night. There is also an increased preponderance of elastic and collagenous fibers in layers of the stomach, helping it to expand to enclose many ants from one feeding.

Pangolin Fact(ish) 4: Pangolins are not closely related to other ant-eating living mammals, but to carnivores.

Eurotamandua fossil

Eurotamandua; a possible fossil relative of pangolins from the early Eocene (Messel, Germany); image from Wikipedia.

Together, the eight living pangolin species are remnants of the group Pholidota, which has a respectable fossil record– particularly considering that they lack teeth, which are often such a diagnostic feature for mammalian fossils. Controversy persisted for many years about whether they were related to anteaters, sloths and armadillos (Xenarthra) within the group Edentata, along with possibly aardvarks (Tubulidentata) and other digging and/or myrmecophagous animals. There has also been controversy about some fossil mammals and their relationships, including Eurotamandua (above) and the Palaeonodonta— the latter seems to be approaching a consensus, though, as an extinct sister group to Pholidota.

Nonetheless, the main features that were once thought to unite ant-eating mammals as close relatives now seem to be a prime example of convergent evolution. Xenarthans are definitely closely related to each other, but aardvarks are afrotherians (closer related to hyraxes and elephants), and pangolins seem not to be closely related to either of those groups.

More conclusively, with the addition of genetic data, it has emerged that Pholidota is most closely related to Carnivora (mongooses, dogs, cats, bears, pinnipeds, etc.) among living mammals. A good example of this conclusion is the very recent paper by O’Leary et al. in Science. Furthermore,¬†this image shows a nice example of such a phylogenetic result. This relationship with Carnivora raises fascinating questions about the tempo and mode of the evolution of all their digging/ant-eating specializations- when, where and how did they become so much like other ant-eating mammals?

Pangolin Fact 5: Pangolins have many digging (fossorial) and climbing (scansorial) adaptations, especially in their forelimbs.

Pangolin hindfeet Feet of anteating mammals

Click to embignify. Above (modified from Gaudin et al., 2006; by Julia Morgan-Scott): drawings of hind feet of (left) the Eocene fossil pangolin Cryptomanis and (right) Manis; Below: line drawings of front feet (from Humphrey, 1869) showing the convergent evolution of digging/climbing hands in (left to right) pangolins, an anteater (2-toed; Myrmecophaga), Ai (3-toed sloth; Bradypus) and Unau (2-toed sloth; Choloepus).

A striking feature of pangolin claw bones (unguals); evident above; is their characteristic fissured anatomy (split ends), which even the fossils have. This probably is how they develop strong, keratinous digging claws that remain anchored to those bony claw cores. If you look really closely, you may be able to see the fused scaphoid and lunar (scapholunar) bones of the wrist in the manus of Manis. Cryptomanis (above left) had more climbing specializations than living pangolins; is this how pangolins first evolved, and then later added more ant-eating features? This makes sense in terms of their phylogeny (above), as they are related to primitively climbing carnivores.

Other possibly digging/climbing-related features characteristic of pangolins include the loss of a coracoid process on the pectoral girdle, and curious enrolled zygapophyses (joints) on the lumbar (lower back) vertebrae — the functional significance of the latter feature is almost unstudied, but is reminscent of the complex xenarthrous vertebrae that gave Xenarthra their name (see above and this past post). A nice photo of a pangolin ribcage/vertebrae is here. There is an exceptional page on pangolins and their once-thought-to-be-close relatives among Xenarthra here, with lots of anatomical detail.

A feature that first got me scientifically curious about pangolins in my research is the presence of “predigits“- prepollex and prehallux- in their hands and feet (“prh” in upper left two figures). Many mammals have these, and some have expanded them into larger structures like the “sixth toes of elephants” (hence my interest), but precious little is known about their evolution or function in many other groups.

Pangolin Fact 6: Pangolin skin armour, like rhinoceros horns, is just modified skin (hair/epidermis) keratin; shaped into imbricating scales.

Pangolin scales closeup Coat of pangolin scales

That apocryphally “magic skin”. Images from Wikipedia: closeup above, and below it a suit of armour made from those scales– ¬†coated in gold and given to King George III in 1820.

These scales, the double-edge sword of pangolins (both protecting them in nature and making them desirable in part of the human world for silly reasons), form as pangolins grow. In the fetus they are still soft, making fetuses more of a delicacy in some Asian cultures. Much like the stomach lining described above, the skin is formed from keratinized, stratified squamous epithelium– much more densely formed than in our skin, but more like in our fingernails. Asian pangolins, unlike African species, may have some more normal hairs beneath the scales, too.

There is no convincing evidence that the scales are any more healthy to eat, in any form, than your own fingernails, dead skin, or hair.¬†Given the ready availability of the latter to any humans, we’re all wearing, and growing, our own goldmine…

I’ve barely dug into the fascinating biology of pangolins. I haven’t talked about their bipedal locomotion, much as it fascinates me, because we know next to nothing about that. I’m not aware of good scientific studies on their prehensile tail, either. A great page on pangolin biology, with a focus on reproduction and anatomy, is here. A lovely illustration and discussion of the convergent evolution between anteaters and pangolins is here. Awesome photos and facts are here. More about pangolins’ plight here, and very thoroughly here.

If you have favourite links to more material, or want to provide more information or especially questions, don’t hold back and experience painful pang(olin)s of remorse– chime in in the comments below!

Happy World Pangolin Day! Visit these great pages, please! Here, here¬†and here!¬†And…

Happy Freezermas!¬†Sing it: ‚ÄúOn the sixth day of Freezermas, this blo-og gave to me: one tibiotarsus, two silly Darwins, three muscle layers, four gory¬†hearts,¬†five doggie models¬†a-and six facts of pangolin anatomy!‚Ä̬†‚ô™‚ôę

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‚Ķa daily picture of anatomy!¬†And today it is five pictures; zza-zza-zee!¬†‚ôę

Welcome back again, again, (gasp, pant) and again to Freezermas! 

I’m letting the dogs out today. Science gone barking mad! Hopefully my puns will not screw the pooch.

Stomach-Churning Rating:¬†4/10; a dog cadaver’s leg (not messy), then just tame digital images of anatomy.

I am working with Rich Ellis, a former MSc student at Univ. Colorado (see his cool new paper here!), for a fun new collaboration this year. He was awarded a prestigious Whitaker Foundation scholarship to do this research, which focuses on how different animals stand up from a squatting position, with the legs about as bent as they can be.

We want to know how animals do this standing up movement, because it is in some ways a very demanding activity. Very flexed/bent limb joints mean that the muscles (and some tendons) are stretched about as far as they ever will be. So this places them at disadvantageous lengths (and leverage, or mechanical advantage) for producing force. We know almost nothing about how any animal, even humans, does this-– how close to their limits of length are their muscles? Which muscles are closest? Does this change in animals with different numbers of legs, postures, anatomy, size, etc? Such fundamental questions are totally unaddressed. It’s an exciting area to blaze a new trail in, as Rich is doing. So far, we’ve worked with quail, humans, and now greyhounds; in the past I did some simple studies with horses and elephants, too. Jeff Rankin from my team and other collaborators have also worked on six species of birds, of varying sizes, to see how their squat-stand mechanics change. ¬†Thus we’ve covered a wide diversity of animals, and now we’re learning from that diversity. “Diversity enables discovery,” one of my former PhD mentors Prof. Bob Full always says. Too true.

Greyhounds are interesting because they are medium-sized, long-legged, quadrupedal, quite erect in posture, and very specialized for fast running. Fast runners tend to have big muscles with fairly short fibres. Short fibres are bad for moving the joints through very large ranges of motion. So how does a greyhound stand up? Obviously they can do it, but they might have some interesting strategies for doing so- the demands for large joint motion may require a compromise with the demands for fast running. Or maybe the two demands actually can both be optimized without conflict. We don’t know. But we’re going to find out, and then we’ll see how greyhounds compare with other animals.

To find out, we first have to measure some dogs standing up. We’ve done that for about 8 greyhounds. Here is an example of a cooperative pooch:

Those harmless experiments, if you follow me on Twitter, were live-tweeted under the hashtag #StandSpotStand… I dropped the ball there and didn’t continue the tweeting long after data collection, but we got the point across– it’s fun science addressing useful questions. Anyway, the experiments went well, thanks to cooperative pooches like the one above, and Rich has analyzed most of the data.

Now the next step involves the cadaver of a dog. We could anaesthetize our subjects and do this next procedure to obtain subject-specific anatomy. But it really wouldn’t be ethically justified (and if I were an owner I wouldn’t allow it either!) and so we don’t. A greyhound is a greyhound as far as we’re concerned; they’ll be more like each other than either is like a quail or a human. Individual variation is a whole other subject, and there are published data on this that we can compare with.

We get a dead dog’s leg — we don’t kill them; we get cadavers and re-use them:

Greyhound hindlimb for CT

We study the hindlimb because birds and humans don’t use their forelimbs much to stand up normally, so this makes comparisons simpler. We’re collecting forelimb data, though, as we work with quadrupeds, for a rainy day.

We then CT scan the leg, getting a stack of slices like this– see what you can identify here:

It’s not so clear in these images, but I was impressed to see that the muscles showed up very clearly with this leg. That was doggone cool! Perhaps some combination of formalin preservation, fresh condition, and freezing made the CT images clearer than I am used to. Anyway, this turned out to be a treat for our research, as follows.

We then use commercial software (we like Mimics; others use Amira or other packages) to “segment” (make digital representations in 3D) the CT scan data into 3D anatomy, partitioning the greyscale CT images into coloured individual objects– two views of one part of the thigh are shown below.

What can you identify as different colours here? There are lots of clues in the images (click to embiggen):

Hindlimb segmentation of greyhound

And here is what the whole thigh looks like when you switch to the 3D imaging view:

Quite fetching image, eh?!

The next steps after we finish the limb segmentation are to apply the experimental data we observed for greyhounds of comparable size by importing the model and those data into biomechanics software (SIMM/OpenSim). We’ve done about 40 models like this for various species.¬†I detailed this procedure for an elephant here.

Then, at long last, science will know how a greyhound stands up! Wahoo! Waise the woof! Stay tuned as we hound you with more progress on this research-as-it-happens. Rich just finished the above thigh model this week, and the rest of the leg will be done soon.

Many thanks to Rich Ellis for providing images used here. And thank you for persevering my puns; they will now be cur tailed.

Happy Freezermas!¬†Sing it: ‚ÄúOn the fifth day of Freezermas, this blo-og gave to me: one tibiotarsus, two silly Darwins, three muscle layers, four gory¬†hearts,¬†a-and five stages modelling a doggie!‚Ä̬†‚ô™‚ôę

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‚Ķa daily picture of anatomy!¬†And today it is four pictures; da-da-dee!¬†‚ôę

Welcome back again, again to Freezermas! 

Today I’m shimmying down your interwebz with a late delivery. I’ve promised before to show how we clean up our nasty gooey skeletons to preserve them for future research to use. This is the intended final destination of all critters that are tenants of my freezers– the freezer is just a lovely holiday home, but bony heaven is the end result. I’ve accumulated a little museum of the bones of exotic animals I’ve studied, using these cleaned specimens. Here is how I do that preservation– there are four basic steps, and I’ll show them in four photos.

Stomach-Churning Rating: 8/10; first just dry bones, but then some gooey bones and by the end we ratchet it up to bloody organs.

Step 1) We get the deceased animal from various zoos and other EU sources, CT/MRI scan it, and dissect it. That’s what most of this blog focuses on, so I won’t show that. But I will show the end result, and then how I get to that:


Those are some elephant and rhino bones, some of which you saw on the 2nd day of Freezermas. Elephant bones are super greasy; it’s almost impossible to get rid of that brown grease visible in this photo (upper LH side) without making the bones brittle and over-bleached. The bones of the whiter white rhino on the right show what I’m usually aiming for. How do I get this done? Well, here’s an example for an elephant shank:

Cookin' up elephant shank

I take the elephant shank and make soup. ¬†(above) An Asian elephant’s patella, tibia and fibula were dissected, frozen for many years (queued up for cleaning; much freezer burn occurred on this specimen— it was jerky-fied), and then thawed.¬†I put large specimens in this Rose cooker unit, which is a big ham cooker with a heater unit at the bottom. My baby, a Rapidaire MKV 5-ham unit is shown; oooh, ahhh!

The Rose cooker is filled up with tap water and been set it at around 60-90C. Then I let it cook away! A brothy soup develops, and sometimes it smells rather nice (my favourite aroma is giraffe leg). Sometimes… it’s not so nice.¬†We check it every few hours to top up the water and remove stray tissue, and then change the water every day or so.

An elephant shank like this will take 2-3 days of cooking, longer if only switched on during work hours. The key thing is not to let it cook dry, which happened once with a faulty Rose cooker that did not do its normal auto-shutoff when the water ran low… showing up to work to encounter some fire trucks and unhappy college Health & Safety rep is not a good way to start your day, trust me!

This step is only slightly different for smaller (<30cm) specimens. Rather than the Rose cooker, we use the lovingly named “Croc Crock”, which isn’t visually impressive but you can see it here. As the name indicates, we’ve mainly used it for small crocodiles, and it is a crock pot. (a helpful thing is to add some detergent to the water for these small specimens; then bleaching isn’t so necessary)

Step 2) Then I empty out the water through the bottom spout, do the very nasty job of cleaning out the fat and other tissue that has accumulated (think 20 gallons of goo), hose off the bone, and set it in a ~10% bleach solution for at least a day, or up to a week or so for an elephant bone. Once it’s cleared up, I leave it out to dry (for big elephant bones, copious amounts of grease may be emerging for a few weeks). And then…

Elephant shank bones

Step 3) I varnish the dry bones with a clear varnish, and let them dry. Here is how that elephant shank turned out. Pretty good! Finally, they get to join their friends:

The bone shelves

Step 4) The prepared bones are labelled, given a number/name that I file in a world class comprehensive electronic database (cough, get on that John, cough!), and they become part of my humble mini-museum, shown above. Voila! The chef’s job is finished. Let science be served!

Happy Freezermas!¬†Sing it: ‚ÄúOn the fourth day of Freezermas, this blo-og gave to me: one tibiotarsus, two Darwin pictures, three muscle layers, a-a-and four steps of bone cookery!‚Ä̬†‚ô™‚ôę

Oh it’s Valentine’s day, so, err, have a heart today. Have four, actually!

giraffe heart - 1 white-rhino-heart-Perez Windfall-ele 054


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…a daily picture of anatomy!¬†And today it is three pictures, scoob-a-dee!

Welcome back again to Freezermas! 

For the previous days of Freezermas we first had 1 picture, then 2, now guess how many we have today? Right, we’ve settled into a groove and have three (plus one silly one). Today is fresh beefy anatomy day! No focus on bones, but on soft tissues– however, once again, I’m representin’ bird legs! And this time, no mystery things to identify; sorry. But if you want to muscle in on some myology, today is the day for you. I will unwrap the thigh of an ostrich and consider the major muscles that power rapid running in this biped, and how they illuminate the evolution of bipedal motion along the line of descent to birds. For more ostrich escapades, see this old post. And we’re off!

Stomach-Churning Rating: 7/10; plenty of fresh, red, meaty meat from ostrich leg muscles.

Ostrich thigh muscles 1

Here you are looking at a right hindlimb of an ostrich, in side/lateral view. To help orient yourself, the hip lies deep in the middle of the image and the knee is the rounded bump near the bottom right corner, with the shank angling sharply back toward the bottom left.

I’ve labelled six muscles in yellow. As usual for sauropsid (bird/reptile) pelvic limb muscles, they have sensible names that reflect their attachments. They don’t have so many silly old mammalian names like pectineus or latissimus, which tell you rather little about the muscles themselves. We can thank 19th century anatomists like two of my anatomist heroes, Hans Gadow and Alfred Romer (who refined Gadow’s earlier work and made it more popular among English-speakers and palaeontologists), for that enlightened nomenclature.

The six muscles seen above are the IC (iliotibialis cranialis), IL (iliotibialis lateralis), “AMB2?” (one of the ambiens muscles– correctly identified; ignore the ?), ITC (iliotrochantericus caudalis), CFP (caudofemoralis pars pelvica) and FCLP (a mouthful to say: flexor cruris lateralis pars pelvica). The ambiens is the one oddly, non-anatomically named muscle, and has nothing to do with helping you sleep (pssst– wake up! Muscles are exciting!), but everything to do with the state of total awesomeness, which is what “ambiens” means. Maybe. Or I am making shit up.

Amazed ostrich

The IC, IL and AMB2 are parts of the triceps femoris group (discussed in my 1st Freeezermas post), or for mammal fans the quadriceps. The IC and AMB are in front of the hip so they flex it (move the thigh forward; protract it); the IL is right around the hip so it can flex or extend the hip (protract/retract the femur); all three of these can extend (straighten) the knee joint to varying degrees. The IC is fairly typical for a bird except for its size, and helps to quickly swing the leg through the air between steps. Some birds have multiple parts of the IL, but ostriches and many others have simplified it to one major mass; regardless, it is a major muscle used to support the weight of the body.

The AMB2 is a remarkable muscle unique to ostriches; it can also be called the dorsal ambiens muscle. Typical birds just have a single head of the AMB sitting on the preacetabular (pubic) tubercle, so in front of and below the hip. It has a crazy tendon that snakes past the knee (in some birds, perforating/grooving the patella) into the lower leg muscles and may be able to even pull on the toes. But ostriches, for some reason, added a second head of this muscle that was shifted way up onto the front of the pelvis (the ilium; dorsal bladelike bone). Crocodilians also have a 2nd ambiens muscle but in a different position, and almost certainly as an example of convergent evolution. The function of the ambiens is mysterious, but this muscle has featured prominently in avian systematics/taxonomy, evolution (invoked as a key muscle used in perching) and more.

These muscles of the triceps femoris group are easily identifiable in crocodiles and other reptiles because they are remarkably similar in their attachments. The main changes these muscles experienced during the evolution of bipedalism, dinosaurs and later birds are simply proportional– they got bigger, with stronger, larger attachments on the pelvis and the front of the knee (the CC/LC, if you remember from Freezermas day 1).

The ITC is a muscle that is very dear to me. I’ve written a lot about it, and I love saying the name “Iliotrochantericus caudalis”- it is musical to me. For mammal fans, think gluteal muscles (medial gluteal in particular). It is a huge, pennate muscle¬†(short and strongly angled muscle fibres in a “sandwich” with a tendinous sheet between the two layers of fibres). It has a short, broad tendon that wraps around the trochanteric crest (a structure on the upper front end of the femur with a history that goes wayyyy back into dinosaurs; long story!) to insert in a scarred depression. The ITC seems to mainly rotate the femur around its long axis to help support the body. I could go on and on about this muscle, which is part of the enigmatic “deep dorsal” thigh muscle group — the homologies of this group among land vertebrates are still controversial and confusing. But I will spare you the on-and-on. Incidentally, the ITC ¬†is the “oyster” in birds¬†that is the best cut of meat. And in ostriches it makes a massive steak.

The CFP also has a cool evolutionary history. It runs from the back of the pelvis to the middle of the femur, closely adjoined to the caudal head of the muscle (CFC), which is more vestigial. In birds the CFP is usually not a large muscle, but in other sauropsids/reptiles it can be fairly hefty, although almost never as hefty as its more famous counterpart the caudofemoralis longus¬†(= CFC in birds). Probably any dinosaur specialist is familiar with its origin and its insertion: respectively, the “brevis fossa” on the back of the ilium; a big shelf of bone; and the fourth trochanter of the femur; a crest of bone that is reduced to a scar/tubercle in birds. Much like its tail-based counterpart, the CFP became progressively reduced closer and closer to birds. This is related to a reduction in the amount of movement of the femur/thigh during locomotion, as birds shortened their tails and shifted their balance forward, as Steve Gatesy showed in a classic 1990 paper. Hopefully there will be more about this subject in a future paper from my team…

The FCLP is another muscle that didn’t change much, except by getting larger as we trace its evolution from early reptiles to birds. It is a “hamstring” muscle that is an important power source during locomotion in birds like the ostrich, because it retracts the lower limb (flexes the knee; hence flexor cruris in its name) as well as the femur/thigh (extends the hip). Your semitendinosus muscle is a good comparison to it. Indeed, these two differently named muscles are homologous– our very distant tetrapod ancestor had the same single muscle, and its descendants didn’t change it that much on our lineage or on the avian/reptile one.

Ostrich thigh muscles 3

I’ve reflected the IL muscle out of the way so we can see the second layer of muscles underneath it. Now we see two more muscles of the thigh, and large ones at that– the FMTL (femorotibialis lateralis) and ILFB (iliofibularis).

The FMTL simply is a part of the triceps femoris group that only comes from the femur and hence only, but due to its large size powerfully, straightens the knee. Unlike the other muscles in this group, it has no action about the hip joint. It is very similar to your vastus lateralis muscle: its fleshy origin dominates the surface of the femur (thigh bone). There are two other parts of that muscle, hidden in this figure, much like our vastus group has multiple parts. Again, this is a muscle that enlarged on the lineage leading to modern birds.

And that evolutionary enlargement applies, too, to the ILFB, whose prominent insertion I discussed on day 1 of Freezermas. This huge “biceps” muscle (it is single-headed unlike in humans, so the name “biceps” does not apply well) is the most powerful of the “hamstring”-type muscles that extend the hip and flex the knee. Therefore it is important for the “knee-driven” locomotion of birds. And hence the ILFB enlarged during avian evolution– which is very evident from changes of both its bony origin on the back of the pelvis/ilium and its insertion on the fibula.

Ostrich thigh muscles 2

Here, for the terminus of today’s trio of struthious tributes and tribulations, I’ve moved the ILFB ¬†out of the way so you can see the various inner/medial layer of thigh muscles. Some of the former muscles are more exposed now, and we can see three new ones: the FCM (flexor cruris medialis), PIFM+(PIF)L (the tongue-twisting puboischiofemoralis medialis et lateralis), and tiny ISF (ischiofemoralis).

The FCM (~mammalian semitendinosus) is merely another, smaller part of the FCLP’s “hamstring” group, and its thin tendon blends with that of the FCLP, so it very much works with that muscle in locomotion, and has a similar evolutionary history.

The PIFM+L are “adductors”, but in birds they don’t really do any adduction (drawing the legs inwards) because they are right behind, rather than below or inside, the hip. They act as hip extensors/retractors of the femur, and probably aid more in holding the femur steady (“postural muscles”) than playing a major role in producing power for locomotion like the ILFB/hamstring group does. In earlier reptiles, they were much more important, for preventing the legs from splaying too far away from the body.

The ISF is usually quite a large muscle in birds, but ostriches and some other ratites have reduced it to a thin slip of muscle– often mistaken for other muscles (indeed, like a few other muscles I’ve described here, modern anatomists still get confused by this muscle– an otherwise superb¬†recent description by Gangl et al., among others, mis-identifies this and some other muscles— an error an upcoming paper from my group will rectify). Normally the ISF sits atop a bone-free window on the outer surface of the pelvis, the ilio-ischiadic fenestra (literally a window in Latin) in birds; in ostriches it has moved more onto the ischium. In contrast, in other sauropsids it lies inside the pelvis, so during its evolution it became more lateral, but the insertion on the upper femur was maintained. It is a weak rotator and extensor of the hip, especially in ostriches in which its role is probably proportionately puny.

And there you have read a healthy chunk of my 2001 PhD thesis, condensed into less jargonious language. You might now know almost half of the key muscles of the avian hind limb. If you made it this far, you are one awesome anatomical enthusiast. If you eat meat, apply this lesson to the next chicken thigh you consume, to consumate this enthusiasm.

A broader point I’d like to make here is that anatomy is best conveyed not only along with the functional narrative (How does anatomy work?) but also the evolutionary tale (Where did anatomy come from and What were the consequences of its changes? Why did it change?). This takes it away from dry memorization of terms and locations, and carries it into the realm of explaining why nature is the way it is, and how every organism’s biology has a richly detailed and complex background. This style portrays nature as much more like that tangled bank that Darwin so enchantingly envisioned. I’ve tried to do that justice here, using this one ostrich whom we affectionately called Twinkletoes, or Twinkie, when we dissected it back in 2002.

Happy Freezermas!¬†Sing it: ‚ÄúOn the third day of Freezermas, this blo-og gave to me: one tibiotarsus, two silly pictures, a-and three muscle layers from Twinkie!‚ÄĚ

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…a daily picture of anatomy! And today it is two pictures, tra-la-lee!

Welcome back to Freezermas! And HAPPY DARWIN DAY! Last year our whole lab got involved in DD2012, but this blog was just a twinkling in my keyboard back then. This year it was a more mellow, somber occasion for DD2013. But Heinrich Mallison of the dinosaurpalaeo blog took part, and took photos (all credits go to him), and the result kicked ass and took names. Bring it on!

Darwin amidst the bones

Here is Darwin amidst a selection of greatest hits from my bone collection; post-freezer denizens. How many can you identify? Have a go in the comments below. A few should be quite¬†familiar to blog followers… More about these bones later this week. Incidentally, Darwin is standing on a Kistler forceplate. So biomechanics afficionados can geek out about this, too.

An offering to The Master

And here I am hamming it up again. Give it a rest, John! But ’tis merely a¬†humble offering to The Master. I’m sure he’d appreciate it. Any guesses what it is?

Happy Freezermas! Sing it: ‚ÄúOn the second day of Freezermas, this blo-og gave to me: one tibiotarsus, a-and two silly pictures with Chucky D!‚ÄĚ

(don’t know the song? Try this version)

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