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Deck the ‘Nets With PeerJ Papers— please sing along!

♬Deck the ‘nets with PeerJ papers,
Fa la la la la, la la la la.
‘Tis the day to show our labours,
Fa la la la la, la la la la.

Downloads free; CC-BY license,
Fa la la, la la la, la la la.
Read the extant ratite science,
Fa la la la la, la la la la.

See the emu legs before you
Fa la la la la, la la la la.
Muscles allometric’ly grew.
Fa la la la la, la la la la.

Follow the evolvin’ kneecaps
Fa la la la la, la la la la.
While we dish out ratite recaps 
Fa la la la la, la la la la.

Soon ostrich patellar printing
Fa la la la la, la la la la.
Hail anat’my, don’t be squinting
Fa la la la la, la la la la.

Dissections done all together
Fa la la la la, la la la la.
Heedless of the flying feathers,
Fa la la la la, la la la la♪

(alternate rockin’ instrumental version)

Stomach-Churning Rating: 5/10: cheesy songs vs. fatty chunks of tissue; there are no better Crimbo treats!

Today is a special day for palaeognath publications, principally pertaining to the plethora of published PeerJ papers (well, three of them anyway) released today, featuring my team’s research! An early Crimbo comes this year in the form of three related studies of hind limb anatomy, development, evolution and biomechanics in those flightless feathered freaks of evolutionary whimsy, the ratites! And since the papers are all published online in PeerJ (gold open access), they are free for anyone with internet access to download and use with due credit. These papers include some stunning images of morphology and histology, evolutionary diagrams, and a special treat to be revealed below. Here I’ll summarize the papers we have written together (with thanks to Leverhulme Trust funding!):

1) Lamas, L., Main, R.P., Hutchinson, J.R. 2014. Ontogenetic scaling patterns and functional anatomy of the pelvic limb musculature in emus (Dromaius novaehollandiae). PeerJ 2:e716 http://dx.doi.org/10.7717/peerj.716 

My final year PhD student and “emu whisperer” Luis Lamas has published his first paper with co-supervisor Russ Main and I. Our paper beautifully illustrates the gross anatomy of the leg muscles of emus, and then uses exhaustive measurements (about 6524 of them, all done manually!) of muscle architecture (masses, lengths, etc.) to show how each of the 34 muscles and their tendons grew across a more than tenfold range of body mass (from 6 weeks to 18 months of age). We learned that these muscles get relatively, not just absolutely, larger as emus grow, and their force-generating ability increases almost as strongly, whereas their tendons tend to grow less quickly. As a result, baby emus have only about 22% of their body mass as leg muscles, vs. about 30% in adults. However, baby emus still are extremely athletic, more so than adults and perhaps even “overbuilt” in some ways.

This pattern of rapidly growing, enlarged leg muscles seems to be a general, ancestral pattern for living bird species, reflecting the precocial (more independent, less nest-bound), cursorial (long-legged, running-adapted) natural history and anatomy, considering other studies of ostriches, rheas, chickens and other species close to the root of the avian family tree. But because emus, like other ratites, invest more of their body mass into leg muscles, they can carry out this precocial growth strategy to a greater extreme than flying birds, trading flight prowess away for enhanced running ability. This paper adds another important dataset to the oft-neglected area of “ontogenetic scaling” of the musculoskeletal system, or how the locomotor apparatus adapts to size-/age-related functional/developmental demands as it grows. Luis did a huge amount of work for this paper, leading arduous dissections and analysis of a complex dataset.

Superficial layer of leg muscles in an emu, in right side view.

Superficial layer of leg muscles in an emu, in right side view. Click any image here to emu-biggen. The ILPO and IC are like human rectus femoris (“quads”); ILFB like our biceps femoris (“hams”); FL, GM and GL much like our fibularis longus and gastrocnemius (calf) muscles, but much much bigger! Or, perhaps FL stands for fa la la la la?

Data for an extra set of emus studied by coauthor Russ Main in the USA, which grew their muscles similarly to our UK group. The exponents (y-axis) show how much more strongly the muscles grown than isometry (maintaining the same relative size), which is the dotted line at 1.0.

Data for an extra set of emus studied by coauthor Russ Main in the USA, which grew their muscles similarly to our UK group. The exponents (y-axis) show how much more strongly the muscles grew than isometry (maintaining the same relative size), which is the dotted line at 1. The numbers above each data point are the # of individuals measured. Muscle names are partly above; the rest are in the paper. If you want to know them, we might have been separated at birth!

2) Regnault, S., Pitsillides, A.A., Hutchinson, J.R. 2014. Structure, ontogeny and evolution of the patellar tendon in emus (Dromaius novaehollandiae) and other palaeognath birds. PeerJ 2:e711 http://dx.doi.org/10.7717/peerj.711

My second year PhD student Sophie Regnault (guest-blogger here before with her rhino feet post) has released her first PhD paper, on the evolution of kneecaps (patellae) in birds, with a focus on the strangeness of the region that should contain the patella in emus. This is a great new collaboration combining her expertise in all aspects of the research with coauthor Prof. Andy Pitsillides‘s on tissue histology and mine on evolution and morphology. This work stems from my own research fellowship on the evolution of the patella in birds, but Sophie has taken it in a bold new direction. First, we realized that emus don’t have a patella– they just keep that region of the knee extensor (~human quadriceps muscle) tendon as a fatty, fibrous tissue throughout growth, showing no signs of forming a bony patella like other birds do. This still blows my mind! Why they do this, we can only speculate meekly about so far. Then, we surveyed other ratites and related birds to see just how unusual the condition in emus was. We discovered, by mapping the form of the patella across an avian family tree, that this fatty tendon seems to be a thing that some ratites (emus, cassowaries and probably the extinct giant moas) do, whereas ostriches go the opposite direction and develop a giant double-boned kneecap in each knee (see below), whereas some other relatives like tinamous and kiwis develop a more “normal”, simple flake-like bit of bone, which is likely the state that the most recent common ancestor of all living birds had.

There’s a lot in this paper for anatomists, biomechanists, palaeontologists, ornithologists, evo-devo folks and more… plenty of food for thought. The paper hearkens back to my 2002 study of the evolution of leg tendons in tetrapods on the lineage that led to birds. In that study I sort of punted on the question of how a patella evolved in birds, because I didn’t quite understand that wonderful little sesamoid bone. And now, 12 years later, we do understand it, at least within the deepest branches of living birds. What happened further up the tree, in later branches, remains a big open subject. It’s clear there were some remarkable changes, such as enormous patellae in diving birds (which the Cretaceous Hesperornis did to an extreme) or losses in other birds (e.g., by some accounts, puffins… I am skeptical)– but curiously, patellae that are not lost in some other birds that you might expect (e.g., the very non-leggy hummingbirds).

Fatty knee extensor tendon of emus, lacking a patella. The fatty tissue is split into superficial (Sup) and deep regions, with a pad corresponding to the fat pad in other birds continuous with it and the knee joint meniscus (cushioning pad). The triceps femoris (knee extensor) muscle group inserts right into the fatty tendon, continuing over it. A is a schematic; B is a dissection.

Fatty knee extensor tendon of an emu, showing the absence of a patella. The fatty tissue is split into superficial (Sup) and deep regions, with a pad corresponding to the fat pad in other birds continuous with it and the knee joint meniscus (cushioning pad). The triceps femoris (knee extensor) muscle group inserts right into the fatty tendon, continuing on over it. A is a schematic; B is a dissection.

Sectioning of a Southern Cassowary's knee extensor tendon, showing: A Similar section  as in the emu image above. revealing similar regions and fibrous tissue (arrow), with no patella, just fat; and B, with collagen fibre bundles (col), fat cells (a), and cartilage-like tissue (open arrows) labelled.

Sectioning of a Southern Cassowary’s knee extensor tendon, showing: A, Similar section as in the emu image above. revealing similar regions and fibrous tissue (arrow), with no patella, just fat; and B, With collagen fibre bundles (col), fat cells (a), and cartilage-like tissue (open arrows) labelled.

Evolution of patellar form in birds. White branches indicate no patella, blue is a small flake of bone for a patella, green is something bigger, yellow is a double-patella in ostriches, and grey is uncertain. Note the uncertainty and convergent evolution of the patella in ratite birds, which is remarkable but fits well with their likely convergent evolution of flightlessness and running adaptations.

Evolution of patellar form in birds. White branches indicate no patella, blue is a small flake of bone for a patella, green is something bigger, yellow is a double-patella in ostriches, black is a gigantic spar of bone in extinct Hesperornis and relatives, and grey is uncertain. Note the uncertainty and convergent evolution of the patella in ratite birds (Struthio down to Apteryx), which is remarkable but fits well with their likely convergent evolution of flightlessness and running adaptations.

3) Chadwick, K.P., Regnault, S., Allen, V., Hutchinson, J.R. 2014. Three-dimensional anatomy of the ostrich (Struthio camelus) knee joint. PeerJ 2:e706 http://dx.doi.org/10.7717/peerj.706

Finally, Kyle Chadwick came from the USA to do a technician post and also part-time Masters degree with me on our sesamoid grant, and proved himself so apt at research that he published a paper just ~3 months into that work! Vivian Allen (now a postdoc on our sesamoid bone grant) joined us in this work, along with Sophie Regnault. We conceived of this paper as fulfilling a need to explain how the major tissues of the knee joint in ostriches, which surround the double-patella noted above, all relate to each other and especially to the patellae. We CT and MRI scanned several ostrich knees and Kyle made a 3D model of a representative subject’s anatomy, which agrees well with the scattered reports of ostrich knee/patellar morphology in the literature but clarifies the complex relationships of all the key organs for the first time.

This ostrich knee model also takes Kyle on an important first step in his Masters research, which is analyzing how this morphology would interact with the potential loads on the patellae. Sesamoid bones like the patella are famously responsive to mechanical loads, so by studying this interaction in ostrich knees, along with other studies of various species with and without patellae, we hope to use to understand why some species evolved patellae (some birds, mammals and lizards; multiple times) and why some never did (most other species, including amphibians, turtles, crocodiles and dinosaurs). And, excitingly for those of you paying attention, this paper includes links to STL format 3D graphics so you can print your own ostrich knees, and a 3D pdf so you can interactively inspect the anatomy yourself!

(A) X-ray of an ostrich knee in side view, and (B) labelled schematic of the same.

Ostrich knee in side view: A, X-ray, and (B) labelled schematic.

3D model of an ostrich knee, showing: A, view looking down onto the top of the tibia (shank), with the major collateral ligaments (CL), and B, view looking straight at the front of the knee joint, with major organs of interest near the patella, sans muscles.

3D model of an ostrich knee, showing: A, View looking down onto the top of the tibia (shank), with the major collateral ligaments (CL), and B, View looking straight at the front of the knee joint, with major organs of interest near the patella, sans muscles.

You can view all the peer review history of the papers if you want, and that prompts me to comment that, as usual at PeerJ (full disclosure: I’m an associate editor but that brings me £0 conflict of interest), the peer review quality was as rigorous at a typical specialist journal, and faster reviewing+editing+production than any other journal I’ve experienced. Publishing there truly is fun!

Merry Christmas and Happy Holidays — and good Ratite-tidings to all!

And stay tuned- the New Year will bring at least three more papers from us on this subject of ratite locomotion and musculoskeletal anatomy!

♬Should auld palaeognathans be forgot, 
And never brought for scans? 
Should publications be soon sought, 
For auld ratite fans!♪

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Construction of the Phyletisches Museum in Jena, Germany began on Goethe’s birthday on August 28, 1907. The Art Nouveau-styled museum was devised by the great evolutionary biologist, embryologist and artist/howthefuckdoyousummarizehowcoolhewas Ernst Haeckel, who by that time had earned fame in many areas of research (and art), including coining the terms ontogeny (the pattern of development of an organism during its lifetime) and phylogeny (the pattern of evolution of lineages of organisms through time) which feature prominently in the building’s design and exhibits (notice them intertwined in the tree motif below, on the front of the museum). Ontogeny and phylogeny, and the flamboyant artistic sensibility that Haeckel’s work exuded, persist as themes in the museum exhibits themselves. Haeckel also came up with other popular words such as Darwinism and ecology, stem cell, and so on… yeah the dude kept busy.

Cavorting frogs from Haeckel's masterpiece Kunstformen der Natur (1904).

Cavorting frogs from Haeckel’s masterpiece Kunstformen der Natur (1904).

I first visited the Phyletisches Museum about 10 years ago, then again this August. Here are the sights from my latest visit: a whirlwind ~20 minute tour of the museum before we had to drive off to far-flung Wetzlar. All images are click-tastic for embiggenness.

Stomach-Churning Rating: 3/10 for some preserved specimens. And art nouveau.

Willkommen!

Willkommen!

Frog ontogeny, illustrated with gorgeous handmade ?resin? models.

Frog ontogeny, illustrated with gorgeous handmade ?resin? models.

Fish phylogeny, illustrated with lovely artistry.

Phylogeny of Deuterostomia (various wormy things, echinoderms, fish and us), illustrated with lovely artistry.

Phylogeny of fish and tetrapods.

Phylogeny of fish and tetrapods.

Slice of fossil fish diversity.

Slice of fossil fish diversity.

Plenty of chondryichthyan jaws and bodies.

Plenty of chondrichthyan jaws/chondrocrania, teeth and bodies.

Awesome model of a Gulper eel (Saccopharyngiformes).

Awesome model of a Gulper Eel — or, evocatively, “Sackmaul” auf Deutsch (Saccopharyngiformes).

Lobe-finned fishes (Sarcopterygii)- great assortment.

Lobe-finned fishes (Sarcopterygii)- great assortment including a fossil coelacanth.

Lungfish body/model and skeleton.

Lungfish body and skeleton.

Coelacanth!

Coelacanth!

Coelacanth staredown!

Coelacanth staredown!

Fire salamander! We love em, and the museum had several on display- given that we were studying them with x-rays, seeing the skeleton and body together here in this nice display was a pleasant surprise.

On into tetrapods– a Fire Salamander (Salamandra salamandra)! We love ’em, and the museum had several on display- given that we were studying them with x-rays, seeing the skeleton and body together here in this nice display was a pleasant surprise.

A tortoise shell and skeleton, with a goofball inspecting it.

A tortoise shell and skeleton, with a goofball inspecting it.

In a subtle nod to recurrent themes in evolution, the streamlined bodies of an ichthyosaur and cetacean shown in the main stairwell of the museum, illustrating convergent evolution to swimming locomotor adaptations.

In a subtle nod to recurrent themes in evolution, the streamlined bodies of an ichthyosaur and cetacean shown in the main stairwell of the museum, illustrating convergent evolution to swimming adaptations.

Phylogeny of reptiles, including archosaurs (crocs+birds).

Phylogeny of reptiles, including archosaurs (crocs+birds).

Gnarly model of an Archaeopteryx looks over a cast of the Berlin specimen, and a fellow archosaur (crocodile).

Gnarly model of an Archaeopteryx looks over a cast of the Berlin specimen, and a fellow archosaur (crocodile). The only extinct dinosaur on exhibit!

Kiwi considers the differences in modern bird palates: palaeognathous like it and fellow ratites/tinamous (left), and neognathous like most living birds.

Kiwi considers the differences in modern bird palates: palaeognathous like it and fellow ratites/tinamous (left), and neognathous like most living birds.

Echidna skeleton. I can't get enough of these!

Echidna skeleton. I can’t get enough of these!

Skulls of dugong (above) and manatee (below).

Skulls of dugong (above) and manatee (below), Sirenia (seacows) closely related to elephants.

Fetal manatee. Awww.

Fetal manatee. Awww.

Adult Caribbean manatee, showing thoracic dissection.

Adult Caribbean manatee, showing thoracic dissection.

Hyraxes, which Prof. Martin Fischer, longtime curator of the Phyletisches Museum, has studied for many years.  Rodent-like elephant relatives.

Hyraxes, which Prof. Martin Fischer, longtime curator of the Phyletisches Museum, has studied for many years. Rodent-like elephant cousins.

Old exhibit at the Phyletisches Museum, now gone: Forelimbs of an elephant posed in the same postures actually measured in African elephants, for the instant of foot touchdown (left pic) and liftoff (right pic). Involving data that we published in 2008!

Old exhibit at the Phyletisches Museum, now gone: Forelimbs of an elephant posed in the same postures actually measured in African elephants, for the instant of foot touchdown (left pic) and liftoff (right pic). Involving data that we published in 2008!

Gorilla see, gorilla do. Notice "bent hip, bent knee" vs. "upright modern human" hindlimb postures in the two non-skeletal hominids.

Eek, primates! Gorilla see, gorilla do. Notice the primitive “bent hip, bent knee” vs. the advanced “upright modern human” hindlimb postures in the two non-skeletal hominids.

Phylogeny of select mammals, including the hippo-whale clade.

Phylogeny of artiodactyl (even-toed) mammals, including the hippo-whale clade.

Hand (manus) of the early stem-whale Ambulocetus.

Hand (manus) of the early stem-whale Ambulocetus.

Carved shoulderblade (scapula) of a bowhead whale (Balaena mysticetus), which apparently Goethe owned. Quite a relic!

Carved shoulderblade (scapula) of a bowhead whale (Balaena mysticetus), which apparently Goethe owned (click to emwhalen and read the fine print). Quite a relic!

One of Haeckel's residences. There is also a well-preserved house of his that one can visit, but I didn't make it there.

One of Haeckel’s residences, across the street from the museum. There is also a well-preserved house of his that one can visit, but I didn’t make it there. I heard it’s pretty cool.

Jena is tucked away in a valley in former East Germany, with no local airport for easy access- but get to Leipzig and take a 1.25 hour train ride and you’re there. Worth a trip! This is where not just ontogeny and phylogeny were “born”, but also morphology as a modern, rigorous discipline. Huge respect is due to Jena, and to Haeckel, whose quotable quotes and influential research still resonate today, in science as well as in art.

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I Can’t Remember Freezermas…
Can’t Tell Dissection from a CT.
Deep down Inside I Feel to Freeze.
These Wonderful Scenes of Anatomy!
Now That the Week Is Through with Me,
I’m Waking up; Ratites I see
And There’s Not Much Left of These:
Nothing remains but bones now

(digested from Metallica’s “One“, in …And Justice For All, the pummeling, slickly produced, huge-sounding, Jason Newsted-bass-playing leviathan of a thematic album (1988). It was all downhill for Metallica after this one, but it was a good year for rock! The song is about a soldier who had traumatic injuries and was left paralyzed, “locked-in” to his own mind. Themes/footage from “Johnny Got His Gun” (1939 book/1971 movie) are interspersed. Did you see this track coming? If so, you’re just as demented as I am; congrats!)

And so another year ends; we’re at the final post of Freezermas 2014: The Concept Album. We had 7 tracks involving leitmotifs of ostriches and cats and 2 vs. 4 legs, and CTs and x-rays, and epic dissections, and disturbing pathologies, and some twisted lyrics that mangled classic albums. There are so many more concept albums I could have touched on- great ones by Rush, Yes, Savatage, Helstar, Mastodon… many more. But I’ll give you a chance to sit in the DJ’s seat in this post!

Stomach-Churning Rating: 6/10. Some internal organs.

Today’s one mystery dissection photo is of two things, and the Mystery Anatomy challenge is to identify both (the 2-part brown thing and the 1-part whitish thing). They are from our friend the ostrich.

Your task is to weave your answer into the lyrics of a song from any concept album (2 lines or more)– you must identify the song, artist and album with your answer so we can figure out the tune. Any genre is OK as long as it is clearly a concept album (music, that is). You have freedom. Use it wisely! As always, bonus points for extra cleverness.

Whazzat?

We’ll let Maytagtallica sing us out:

♫Hold my breath as I wait for points
Oh Please John, blog more?♫

no

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And I post my blog and stare
Into x-rays of an ostrich
I’ve always known that radiographs never lie
People always say “that’s cool”
To see x-rays of an ostrich
So keen to know what
Lies behind the skin

(evolved from “Eyes of A Stranger” by Queensrÿche, from the epic masterpiece of Operation: Mindcrime (1988). One of my favourite albums of all time, and a fantastic concept album too. The band was operating at their peak. Tight! Drug addict Nikki gets brainwashed by the evil Dr. X and made to assassinate a nun, Sister Mary, who was a prostitute, and then there’s like a revolution or something, and things get all screwed up and no one ends up happy – or alive. All the while, Geoff Tate is singing his guts out. Anyway, I got to see them play the whole album live in 1990 in Madison, WI, for the filming of Operation: Livecrime, which was like a Mecca moment for me back then. Look for me (pre-bald years) in about the 6th row. )

What does that album have to do with the number 2 (two days left in Freezermas)? Hmm… Track 2 is the instrumental Anarchy-X, and today’s post is about X-rays as well as that funky ostrich (2 legs good! 2 toes good, too!) again, so I’m satisfied, and by this point you’re probably just oggling the mind-blowing images below anyway, so fuck it!

Stomach-Churning Rating: 2/10; just X-rays.

Tech/MRes Kyle Chadwick, Renate Weller and the equine imaging team at the RVC took these x-rays of our birdie for us and for an artist who is doing a big x-ray animal art show (more news on this soon!)– thanks to all of them for some truly awesome images! I could stare at the intricate details in these images for hours– go ahead, do it. Click to emostrichinate them (this post needs to be viewed on nice big screen), and oggle away…

Head and neck.

Head and neck.

Another view of the same.

Another view of the same. The highly flexible esophagus and trachea can be seen going diagonally across the neck; twisting from ventral to dorsal. It’s floppy, so it can do that.

Neck near the head; tapering.

Neck near the head; tapering.

Middle of neck. Check out the rings of the trachea!

Middle of neck. Check out the rings of the trachea!

Base of neck and shoulder

Base of neck and shoulder.

Shoulder and chest. Hard to image; thick and dense (still was frozen).

Shoulder and chest. Hard to image; thick and dense (still was frozen), hence the whiteout toward the left side of the image.

Check out that wing!!

Check out that wing!!

Ankle- note the big calloused pad that ostriches rest on (right side of image).

Ankle- note the big calloused pad that ostriches rest on (right side of image).

That two-toed foot... but did you know that normally the missing 2nd toe is still there as a fibrous remnant on the 3rd toe?

That two-toed foot… but did you know that normally the missing 2nd toe is still there as a fibrous remnant on the 3rd toe?

Tomorrow: the final day of Freezermas. What will it be?

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Freezermas continues! Today we have a treat for you. Lots of detailed anatomy! This post comes from my team’s dissections of an ostrich last week (~3-7 February 2014), which I’ve been tweeting about as part of a larger project called the Open Ostrich.

However, before I go further, it’s as important as ever to note this:

Stomach-Churning Rating: 9/10: bloody pictures of a dissection of a large ostrich follow. Head to toes, it gets messy. Just be glad it wasn’t rotten; I was glad. Not Safe For Lunch!

If the introductory picture below gets the butterflies a-fluttering in your tummy, turn back now! It gets messier. There are tamer pics in my earlier Naked Ostriches post (still, a rating of 6/10 or so for stomach-churning-ness there).

All photo credits  (used with permission) on this post go to palaeoartist Bob Nicholls (please check out his website!), who got to attend and get hands-on experience in extant dinosaur anatomy with my team and Writtle College lecturer Nieky VanVeggel (more from Nieky soon)!

Research Fellow Jeff Rankin, myself and technician/MRes student Kyle Chadwick get to work.

Research Fellow Jeff Rankin, myself and technician/MRes student Kyle Chadwick get to work, removing a wing.

This is a male ostrich, 71.3 kg in body mass, that had gone lame in one foot last summer and, for welfare reasons, we had to put down for a local farmer, then we got the body to study. We took advantage of a bad situation; the animal was better off being humanely put down.

The number for today is 6; six posts left in Freezermas. But I had no idea I’d have a hard time finding a song involving 6, from a concept album. Yet 6 three times over is Slayer’s numerus operandi, and so… The concept album for today is Slayer’s  1986 thematic opus “Reign in Blood” (a pivotal album for speed/death metal). The most appropriate track here is the plodding, pounding, brooding, then savagely furious “Postmortem“, which leads (literally and figuratively, in thunderous fashion) to the madness of the title track, after Tom Araya barks the final verse:

“The waves of blood are rushing near, pounding at the walls of lies

Turning off my sanity, reaching back into my mind

Non-rising body from the grave showing new reality

What I am, what I want, I’m only after death”

I’m not going to try to reword those morbid lyrics into something humorous and fitting the ostrich theme of this post. I’ll stick with a serious tone for now. I like to take these opportunities to provoke thought about the duality of a situation like this. It’s grim stuff; dark and bloody and saturated with our own inner fears of mortality and our disgust at what normally is politely concealed behind the integumentary system’s viscoelastic walls of keratin and collagen.

But it’s also profoundly beautiful stuff– anatomy, even in a gory state like this, has a mesmerizing impact: how intricately the varied parts fit together with each other and with their roles in their environment, or even the richness of hues and multifarous patterns that pervade the dissected form, or the surprising variations within an individual that tell you stories about its life, health or growth. Every dissection is a new journey for an anatomist.

OK I’ve given you enough time to gird yourself; into the Open Ostrich we go! The remainder is a photo-blog exploration of ostrich gross anatomy, from our detailed postmortem.

(more…)

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A photo blog post for ya here! I went to Dublin on a ~28 hour tour, for a PhD viva (now-Dr Xia Wang; bird feather/flight evolution thesis) earlier this month. And I made a beeline for the local natural history museum (National Museum of Ireland, Natural History building) when I had free time. So here are the results!

Stomach-Churning Rating: Tame; about a 1/10 for most, but I am going to break my rule about showing human bodies near the end. Just a warning. The bog bodies were too awesome not to share. So that might be 4/10-8/10 depending on your proclivities. They are dry and not juicy or bloody, and don’t look as human as you’d expect.

Simple Natural History museum entrance area.

Simple Natural History museum entrance area.

Adorable frolicking topiaries outside the NHM.

Adorable frolicking topiaries outside the NHM.

Inside, it was a classical Victorian-style, dark wood-panelled museum stuffed with stuffed specimens. It could use major refurbishment, but I do love old-fashioned exhibits. Get on with it and show us the animals; minimize interpretive signage and NO FUCKING INTERACTIVE COMPUTER PANELS! So by those criteria, I liked it. Some shots of the halls: hall2 hall1 hall3 hall4 hall5 hall6 And on to the specimens!

Giant European deer ("Irish elk"). I looked at these and thought, "why don't we see female deer without antlers ever? then noticed one standing next to these; photo was crappy though. :(

Giant European deer (“Irish elk”). I looked at these and thought, “why don’t we see female deer without antlers ever? then noticed one standing next to these (you can barely see it in back); too bad my photo is crappy.

Superb mounted skeleton of giraffe (stuffed skin was standing near it).

Superb mounted skeleton of giraffe (stuffed skin was standing near it).

A sheep or a goat-y thingy; I dunno but it shows off a nice example of the nuchal ligament (supports the head/neck).

A sheep-y or a goat-y beastie; I dunno but it shows off a nice example of the nuchal ligament (supports the head/neck).

Yarr, narwhals be internet gold!

Yarr, narwhals be internet gold!

Giant blown glass models of lice!

Giant blown glass models of lice!

Who doesn't like a good giant foramanifera image/models? Not me.

Who doesn’t like a good giant foramanifera image/model?

"That's one bigass skate," I murmured to myself.

“That’s one bigass skate,” I murmured to myself.

"That's one bigass halibut," I quipped.

“That’s one bigass halibut,” I quipped.

Tatty basking shark in entry hall.

Tatty basking shark in entry hall.

Irish wolfhound, with a glass sculpture of its spine hanging near it, for some reason.

Irish wolfhound, with a glass sculpture of its spine hanging near it, for some reason.

Stand back folks! The beaver has a club!

Stand back everyone! That beaver has a club!

Skull of a pilot whale/dolphin.

Skull of a pilot whale/dolphin.

Nice anteater skeleton and skin.

Nice anteater skeleton and skin.

Nice anteater skeleton and skin.

Nice wombat skeleton and skin.

Sad display of a stuffed rhino with the horn removed, and signage explaining the problem of thefts of those horns from museum specimens of rhinos worldwide.

Sad display of a stuffed rhino with the horn removed, and signage explaining the problem of thefts of those horns from museum specimens of rhinos worldwide.

But then the stuffed animals started to get to me. Or maybe it was the hangover. Anyway, I saw this…
creepy proboscis (1) creepy proboscis (2)

A proboscis monkey mother who seemed to be saying “Hey kid, you want this yummy fruit? Tough shit. I’m going to hold it over here, out of reach.” with a disturbing grimace. That got me thinking about facial expressions in stuffed museum specimens of mammals more, and I couldn’t help but anthropomorphize as I toured the rest of the collection, journeying deeper into surreality as I progressed. What follows could thus be employed as a study of the Tim-Burton-eseque grimaces of stuffed sloths. Click to emslothen.

sloths (1) sloths (5)sloths (4) sloths (3) sloths (2)

Tree anteater has a go at the awkward expression game.

Tree anteater has a go at the awkward expression game.


This completed my tour of the museum; there were 2 more floors of specimens but they were closed for, sigh, say it with me… health and safety reasons. Balconies from which toddlers or pensioners or drunken undergrads could accidentally catapult themselves to their messy demise upon the throngs of zoological specimens below. But the National Museum’s Archaeology collection was just around the block, so off I went, following whispered tales of bog bodies. There will be a nice, calm, pretty photo, then the bodies, so if peaty ~300 BCE cadavers are not your cup of boggy tea, you can depart this tour now and lose no respect.

Impressive entrance to the National Museum's Archaeology building.

Impressive entrance to the National Museum’s Archaeology building.

The bog bodies exhibit is called “Kingship and Sacrifice“. It is packed with cylindrical chambers that conceal, and present in a tomb-like enclosed setting, the partial bodies of people that were killed and then tossed in peat bogs as honoraria for the ascension of a new king. The peaty chemistry has preserved them for ~2300 years, but in a dessicated, contorted state. The preservation has imparted a mottled colouration and wrinkled texture not far off from a Twix chocolate bar’s. Researchers have studied the bejesus out of these bodies (including 3D medical imaging techniques) and found remarkable details including not just wounds and likely causes of death (axes, strangling, slit throats etc) but also clothing, diet, health and more.

Here they are; click to (wait for it)… emboggen:

BogBodies (1) BogBodies (2) BogBodies (3) BogBodies (4) BogBodies (5) BogBodies (6)

Did you find the Celtic armband on one of them?

Finally (actually this happened first; my post is going back in time), I visited UCD’s zoology building for the PhD viva and saw a few cool specimens there, as follows:

Giant deer in UCD zoology building foyer.

Giant deer in UCD zoology building foyer, with a lovely Pleistocene landscape painted on the wall behind it.

Sika deer in awkward posture in Univ Coll Dublin zoology building's foyer.

Sika deer in an awkward posture (what is it supposed to be doing?) in Univ Coll Dublin zoology building’s foyer.

The pose of this ?baboon? struck me as very peculiar, and menacing- reminiscent of a vampire bat's pose, to me.

The pose of this ?baboon?mandrill struck me as very peculiar and menacing- reminiscent of a vampire bat’s pose.

A whole lotta chicken skeletons in a UCD teaching lab.

A whole lotta chicken skeletons in a UCD teaching lab.

After the viva we went out for some nice Chinese food and passed some Dublin landmarks like this:

Trinity College entrance, I think.

Trinity College entrance, I think.Former Irish Parliament; now the Bank of Ireland.

And we wandered into a very posh Irish pub called the Bank (on College Green), which displayed this interesting specimen, as well as some other features shown below:

Replica of illuminated old Gaelic manuscript.

Replica of illuminated 9th Century gospel manuscript “The Book of Kells”, with gorgeous Celtic art.

Vaults near toilets in the Bank pub.

Vaults near toilets in the Bank pub. Almost as cool as having giant freezers down there.

Nice glass ceiling of the Bank pub.

Nice glass ceiling of the Bank pub.

And Irish pub means one big, delicious thing to me, which I will finish with here– much as I finished that night off:

Ahhh...

Ahhh… ice cold.

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Less words, more pictures in this post, and I’ll get the one lame cake joke out of the way early. I’ve nearly finished my research blitz through the postcranial material of the NHM-Tring’s osteological collection and have made some pit-stops for cake skulls now and then when I see one that pleases me. Now I shall present a survey of some of the species I’ve examined. I’ll proceed up from the base of the crown clade of living birds (Neornithes/Aves; the most recent common ancestor of living birds and all its descendants) and first take a tour of Palaeognathae; the ratites and kin; then move another step up into the Neognathae, first featuring the lineage featuring the ground fowl (Galliformes) and then the waterfowl (Anseriformes). If all this taxonomy and phylogeny is a bit much, check out this page for a brush-up on the bushy branches of bird biodiversity.

First, lots of bones of our cast of currasows, chachalacas, cassowaries and other kooky characters. And then, perhaps, a stop to the excessive alliteration. Finally, I will finish with some examples of species oddity (hat tip to Chris Hadfield).

Stomach-Churning Rating: 2/10- some bony pathologies but still just dry bones. Minimal cake jokes, and no filthy swearing this time.


BRING ON THE BONES:

My photographs are shown with kind permission from the Natural History Museum, London.

Exploded skull of an ostrich/ This takes skill.

Exploded skull of an ostrich, Struthio camelus. This kind of careful preparation takes crazy skill, and creates a thing of rare beauty.

Neat skull of a cassowary, Casuarius casuarius.

Imposing skull of a cassowary, Casuarius casuarius, with a rather worn head casque.

Mummified Owen's Little Spotted kiwi, Apteryx owenii.

Mummified Owen’s Little Spotted Kiwi, Apteryx owenii. The feathers were still soft and fluffy, but I would not call this specimen cuddly.

Dorsal view of the back/hips of the Great Spotted kiwi, Apteryx haasti.

Dorsal view of the back/hips of the Great Spotted Kiwi, Apteryx haasti. I like this photo and am not sure why. The symmetry and shading pleases me, I guess.

Front view of the back/hips of the Great Spotted kiwi, Apteryx haasti.

Front view of the back/hips of the Great Spotted Kiwi, Apteryx haasti, watching over my laptop and watching me while I write this blog on my laptop… so meta(ornithine)!

Wing of a kiwi, showing the fragile bones and feather attachments.

Wing of a kiwi, showing the fragile bones and feather attachments. “Apteryx” = “no wings”… well not quite. Click to emkiwi(?) so you can identify the individual bones, from the humerus right down to the fingers! I love this specimen.

The left leg (in front view) of the elephant-bird, Aepyornis maximus, from Madagascar, with a small moa nearby in left side view.

The titanic left leg (in front view) of the Elephant Bird, Aepyornis maximus, from Madagascar, with a small moa nearby in left side view. There’s so much awesomeness about elephant birds I don’t know where to start, but this is one good place to do so.

Mummified Unulated tinamou, Crypturellus undulatus.

The smaller end of the palaeognath scale: a mummified Undulated Tinamou, Crypturellus undulatus. Somehow the head got stuck into the abdominal cavity underneath the sternum, so this tinamou almost had its head up its arse. A tinamou with head in its proper position looks and sounds like this (video).

And now we take a left turn into the Galloanseres, most basal branch of the neognath birds, to see some of the neglected, strange early branches off from the “main line” that led to the modern diversity of ducks, geeses and swans (Anatinae, Anserinae).

Screamers (Anhimidae) are to Anseriformes as megapodes (see below; brush turkeys) are to Galliformes. By that I mean that both screamers and megapodes are very early branches off the main line of their respective lineages’ evolution, and both are quite strange when seen in that context… an unfair one, frankly; over-focused on the most familiar, “modern” or most speciose group. More about this issue further below.

This was my first hands-on experience with screamer anatomy; I was familiar from reading Tetrapod Zoology and other material about them. Check out the sound that gives them their name here! I’m now a big fan- they have so many strange features: oddly chunky but often very light bones, big feet with long toes, and then these switchblade-wrists, which would make Batman jealous:

Crested screamer, Chauna torquata, showing the wicked spur on the carpometacarpus.

Crested Screamer, Chauna torquata, showing the wicked spur (and smaller one) on the carpometacarpus.

Horned screamer, Anhima cornuta; similar carpometacarpal spur as in Chauna.

Horned Screamer, Anhima cornuta; similar carpometacarpal spurs as in Chauna.

Torso of a screamer seen in top view. Nice narrow body.

Torso of a screamer seen in top view. Nice narrow body, and no uncinate processes (spur-like bony struts that cross the ribs and act as levers for the muscles that move the ribcage during breathing)

The long, gracile, clawed toes of a screamer.

The long, gracile, clawed toes of a screamer. Those toes, especially as they belong to an animal called a screamer, are spooky for me. Note also: very little toe-webbing for a “waterfowl.”

Not to be outdone, on the Galliformes side of Galloanserae, we have some funky headgear in the Maleo (a megapode bird/Megapodiidae; a very basal branch of “brush turkeys” and kin) and curassows (part of the Cracidae; odd South American birds whose males make booming sounds, presumably using their head-casques as resonating chambers?):

Skull of a male maleo, Macrocephalon maleo.

Skull of a male Maleo, Macrocephalon maleo. AR Wallace famously pursued it, and here is its funky call.

Australian brush-turkeys, Alectura lathami i, at the Alma Park Zoo near Brisbane, Australia; they run wild there. Here they are doing what they are best known for: making a mound-like nest.

Australian brush-turkeys, Alectura lathami, at the Alma Park Zoo near Brisbane, Australia; they run wild there. Here they are doing what they are best known for: making a mound-like nest. We were doing kangaroo biomechanics experiments and they were everywhere. I was in awe to see such exotic (to me) birds; locals seemed not so enthused (the birds are loud and make a lot of mess).

Skull of Helmeted curassow, Crax/Pauxi pauxi.

Skull of Helmeted Curassow, Crax/Pauxi pauxi,  showing that resonating chamber. Along with this boom-boom-room, the male uses a piece of food that he holds to draw in the female; if she takes it, then it’s sexy time.

Foot of a Russian Black Grouse, Tetrao tetrix (nothing to do with a certain videogame), with and without flesh.

Foot of a Siberian Black Grouse, Tetrao tetrix (nothing to do with a certain videogame), with and without flesh. Regard the broad, feathered feet, well insulated and with plenty of surface area for prancing around in the snow or moorlands. Tetrao engage in a cool display pattern called lekking, in which the males group together and show off to watching females.

A theme in the section above that is not to be missed is that there is some amazing disparity of anatomical forms in these basal lineages of poultry-relatives. Don’t dismiss the Galloanserae as just boring food-birds! Heaps of not-so-well-studied species exist here, surely with a treasure trove of cool neontological and evolutionary questions waiting for the right person to ask! Darwin’s chickens may get their share of neglect, but that pales in comparison to how little we understand about many basal Galloanserae.

What a lot of people think of as a “ground fowl” or galliform way of life is more of a way of life somewhat typical of the Phasanidae- chickens, pheasants and their familiar kin. Megapodes, curassows, guans, grouse and other Galliformes do not necessarily do things in the “typical” ground fowl way, much as the earlier branches of the Anseriformes don’t always look/act like “proper water fowl” (i.e. Anatidae). The phenomenon at play here is one of the great bugaboos in biology: essentialism— the often implicit misconception that variation away from some abstract ideal is negligible, uninteresting or just not conceivable due to mental blinders. When we say something like “the chicken is a fascinating species” we are sliding down the essentialistic slope. There is no “the chicken.” Not really. Oh dear, speaking of slippery slopes, I’d best stop here before I start talking about species concepts. And no one wants that to happen! Anyway, essentialism still pervades a lot of modern scientific thinking, and has its place as a conceptual crutch sometimes. But in biology, essentialism can be very insidious and misleading. It burrows in deep into the scientific mind and can be hard to root out. Unfortunately, it is entrenched in a lot of science education, as it makes things easier to teach if you sweep aside the exceptions to the essentialist “rules” in biology. I catch myself thinking in static, essentialist ways sometimes. The punishment is no cake for a week; so awful. 🙂

And speaking of “normal” or “typical,” morphology is of course often not that way even within a species, age class or gender. Pathology is a great example; by definition it is abnormal. It is a shattering of the “essence” of animals, brought on by some malady.

Next I’ve highlighted some of the amazing pathologies I’ve seen in the Tring skeletons. There have been so many I’ve been unable to keep track of them– some of these birds had the stuffing beaten out of them, and I’m not talking about Thanksgiving turkeys. Some were captive animals, in which the pathology might be blamed on living an inappropriate environment, but some were wild-caught — given the extreme pathologies, it’s a wonder those even survived to be found, but perhaps less a surprise that they were caught.


BONES GONE BONKERS:

View of left knee of a specimen of the Highland guan, Penelopina nigra, showing some nasty osteoarthritis around the whole joint.

View of left knee of a specimen of the Highland Guan, Penelopina nigra, showing some nasty osteoarthritis around the whole joint. Eew.  A happier Guan sounds like this.

Femora and tibiae of the Blue-throated Piping Guan, Aburria cumanensis. Amazing pathology involving the left femur (broken, rehealed) and tibiotarsus (secondary infection?).

Femora and tibiotarsi of the Blue-throated Piping Guan, Aburria cumanensis. Amazing pathology involving the left femur (broken, rehealed) and tibiotarsus (secondary infection?). Interestingly, the non-fractured limb also showed some pathology, perhaps indicating general infection and/or arthritis in reaction to the severe damage to the other leg, or just increased load-bearing on that leg.

Little Chachalaca, Ortalis motmot, showing a broken and rehealed right femur and the tibiotarsus.

Little Chachalaca, Ortalis motmot, showing a broken and rehealed right femur and the tibiotarsus. As in the guan above, this animal was not walking for many weeks; its femur had snapped in two, but somehow melted back together. The tibiotarsus didn’t look too great, either; lumpy and bendy. In better times, the Chachalaca does the cha-cha like this.

These two specimens blew my mind. On the right is a normal Tetrao tetrix (Black grouse); on the left is one hybridized with another (unknown) species.

These two specimens blew my mind. On the left is a normal Tetrao tetrix (Black Grouse); on the right is one hybridized with another (unknown) species.

In the picture above, what amazed me first was the very unusual flattened pelvis/synsacrum of Tetrao, which characteristically is light and wide. But in the hybrid this morphology was completely gone; the pelvis had a more standard “galliform” (read: Phasianid)-like shape, deeper and narrower and more solid in build. I am guessing that the hybrid was a cross with a pheasant like Phasianus itself, whose anatomy would be more like this. Somewhere in here there is a fantastic evo-devo/morphometrics project waiting to happen.

That’s my quick specimen-based tour of “basal birds”. Beyond these two clades of Palaeognathae and Galloanseres, there lies the forebidding territory of Neoaves: much of living avian diversity, and extremely contentious in its phylogenetic relationships. I’m tackling them next for my research on the evolution of the patella/kneecap. But first, I’ll be at the NHM-Tring today for a whirlwind tour through the respectably speciose “normal” Galloanseres clades of Phasianidae and Anserinae+Anatidae, so off I go! (It’s my wife’s birthday celebration, so cake may have to wait for later this time)

So what do you think? What’s your favourite neglected “primitive” bird group (more apropos: early branching avian lineage that may still be very specialized, rare and poorly understood), or cool factoid about palaeognaths and basal neognaths?

No quaggas were harmed during the writing of this post.

No quaggas were harmed during the writing of this post. Polly wanna quagga?

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