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Posts Tagged ‘patella’

The Bird Knee Challenge

Posted in Anatomy Vignette, tagged , , , , , , , on December 10, 2017| 9 Comments »

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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You Thaw That, We Thaw These

Posted in Frozen Mammals, Mad Science, tagged , , , , , on November 23, 2017| Leave a Comment »

This week we conducted wallaby leg dissections for a study of the kneecaps of marsupials (pouched mammals). Placental (non-pouched) mammals like us almost all have bony kneecaps but many marsupials do not. Kneecaps do important things, acting like gears around the knee joints (e.g. this old post), and yet it is unclear why some marsupials have lost, kept or even re-evolved them as bones. So we’re investigating that and already noticed that one of our wallabies has bony kneecap(s) whereas the other doesn’t, so we’re checking out why and taking tissue samples to do histology (sectioning for microscopic imaging of tissue composition and structure) on so we can see what the knee tendon/kneecap tissues are made of. Some marsupials turn their kneecaps into fibrocartilage rather than bone or tendon and that can be impossible to identify without histology.

The wallabies are small, about 20lbs or so and just take a day or so. Like a turkey. And it’s Thanksgiving today, so here I am with a post about thawing specimens for science, rather than for food. Maybe the title will make sense now.

Stomach-Churning Rating: 7/10; thawed wallaby bits from the get-go.

Thawed lower leg and foot of wallaby. The stickers are for an old study that would take too long to explain…

This post was directly inspired by journalist Jason Bittel’s inquiry to me about my tweet on the wallaby thawing; he wondered if there might be a fun story linking thawing-for-science with thawing-for-Thanksgiving. Some highfalutin editors didn’t agree, so no printed/online story came of this, but I am not so highfalutin, hence this blog post.

Thawed wallaby forelimbs. I’m also looking into the “false thumbs” that some marsupials have (“sixth fingers”), much as elephants and other mammals may have.

Thawing is second nature for our lab’s team; we do it all the time. Avid readers will be unsurprised to learn that just about everything I’ve worked on has been frozen at some time, and thus has been thawed out at some time(s). Normally we don’t freeze if we need live tissue or undistorted tissue, e.g. to measure physiology or very fine microstructure– freezing disrupts all of that. We would instead use physiological saline solution or else a preservative like formalin. And you can only freeze and then thaw a specimen for two times or so before it becomes too useless even for anatomical study.

A small specimen like this salamander can be thawed out simply by running it under warm water for a little while or leaving it out for an hour.

We just leave specimens in a cart, or on a table or sometimes in a cold-room shelving area, for slower thawing. Space heaters tend to overdo things. We don’t do any rough calculation from some sort of thermodynamic first principles of time-to-thaw vs. specimen size (I wish we were that smart!); just seat-of-pants guessing and checking (yes, poking specimens to check their thawedness is a method of choice). Cutting things in half along the way, or skinning them, may be used to accelerate the thawing process. But it’s about as unscientific a method as we use.

The hardest specimens to thaw of course have been the largest specimens. Elephant legs can be >2 metres long and hundreds of kilograms (especially when frozen). A week at room temperature tends to work OK for getting them to a dissectable state. One has to balance the outer deterioration with the inner frigidness. We’re not so concerned about microbe growth in most cases, as one would be with a thawing turkey, and not at all about consumption. We just want to be able to dissect it and make observations, mostly via eyeballing the specimens as we dissect them,

Left hindfoot of an Asian elephant. Still frozen; this was bandthawed- I mean bandsawed- to see its internal anatomy nice and clearly. You may see this specimen again somewhere else– stay tuned! 🙂

Moisture and fluids can be a challenge: generally the rooms we thaw in are low humidity so moisture may not be an issue once the ice melts away, and we have drains nearby. We try to remove ice first or have towels to wipe/soak fluids up as thawing progresses. But if a specimen is sitting in a cart or storage bag with too much ice early on, that can thaw first and then turn the specimen into a nasty slurry of the stuff you’re interested in and the less desirable muck. So we try to avoid that.

De-thawing too early is bad. The smell gets progressively worse– and once the interior of the specimen is thawed enough, then bacteria get in there and the interior becomes a brewing ground for heat production (rather than remaining a cooler region), which accelerates decay, so we don’t want that. We have to check on thawing specimens regularly and move them to cooler storage areas, or begin dissection earlier, if the decay process is noticeably getting excessive.

Any insulation affects thawing time- so scales, feathers, thick skin, shells, fat (for a short while until it decays), and other layers will slow thawing—and may keep heat inside, if there begins to be thawing of the core. So sometimes you open up a specimen that seems dry and clean on the outside and the inside is unpleasant. But with experience that is not hard to avoid.

Thawed wallaby patella prepared for histology.

The foulest specimen I’ve thawed by far was a monitor lizard… it was shipped to me in California from Arizona when I was a PhD student. This was in August’s heat and the box of the big lizard sat thawing at the post office for 2 weeks before they contacted me and asked why a smelly box was bleeding. I came and got it and brought it back to our department but the smell was so bad it set off our building health & safety person’s alarm bells (sorry, David!) and they emailed around a “toxic alert” warning, until I bashfully made it clear that my lizard was the cause, not some toxic chemical. I got in some trouble and was very ashamed. But we put the specimen into a big tank of brine solution and the smell was reduced—the specimen may well still be preserved there 20 years later; I do wonder! Anyway, that experience was so horrendous – and I have a strong stomach—that I regularly recall it and seek to avoid a repeat. It was the most disgusting thing I’ve ever experienced. I do not recommend it.

What we tend to want to get from thawed specimens is: (1) descriptive anatomy (what connects where), and maybe (2) quantitative measurements (laborious metrics of “muscle architecture”– how much does each muscle weigh, how long is it, etc; over and over again for many muscles…). These data not only serve to tell us what makes animals different (and how this evolved) but also the data are used to test questions such as how animals work. In the case of things like wallabies, ultimately we’d love to know what their kneecaps do if they are bony or not; what difference does it make and why might there be differences? We’d spotted one wallaby already that seemed to have a bony kneecap on one leg, and a non-bony one on the other leg, so that asymmetry got us excited.

What’s surprising to learn about thawing animals for science? Well, my first thought is that it’s beautiful. I don’t tend to think of it as gross. I’ve rhapsodized about this before. Animals are wonderful inside and out, and I regularly pause during a dissection to marvel at how amazing the anatomical specializations of animals are. Simple details- shapes, colours, configurations- can be gorgeous. (Often the blood is minimal, drained out early, so that doesn’t detract from or hide the detailed imagery) The gentle yet complex path of a tendon around a joint can yield profound visual enchantment in its elegance. This is all the more true once one ponders how these complex structures evolved, and how much diversity of form and function is out there to study—and how little we know about it! We still don’t know well how to fix many problems humans have with their anatomy, and that’s orders of magnitude worst for most animals, because we don’t understand how anatomy works, or even what the anatomy is like in some cases. So that keeps me busy discovering things. Every specimen is different with surprising little variations, or big ones—sometimes there is one muscle, sometimes it is clearly divided into two muscles, in the same species or even the left vs. right legs. I love seeing those intricacies and wondering about them.

Thawed wallaby shank sliced open to show lovely digital flexors and gastrocnemius muscles. So many questions are raised by this!

If you’re thawing for Thanksgiving, or thawing for science, or thawing out family relations during a gathering, or thawing yourself out from the winter’s cold– my best wishes to you! May we all enjoy what we thaw.

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Why do ostriches have two kneecaps in each knee?

Posted in Exalting Archosauria, Shiverin' Sesamoids!, tagged , , , , , , , on June 8, 2017| 1 Comment »

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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“Everything” You Didn’t Know You Wanted to Know About Mammalian Kneecaps

Posted in Frozen Mammals, Shiverin' Sesamoids!, tagged , , , , , on March 21, 2017| 5 Comments »

The early, hippo-like mammal Coryphodon. I didn’t know it had a patella but it does. From Yale Peabody Museum.

I’m not shy about my fondness for the patella (kneecap) of tetrapod vertebrates, and neither are the other members of RVC’s “Team Patella”. We’ve had a fun 3+ years studying these neglected bones, and today we’ve published a new study of them. Our attention has turned from our prior studies of bird and lepidosaur kneecaps to mammalian ones. Again, we’ve laid the groundwork for a lot of future work by focusing on (1) basic anatomy and (2) evolutionary history of these sesamoid bones, with a lot of synthesis of existing knowledge from the literature; including development and genetics. This particular paper is a sizeable monograph of the state of play in the perusal of patellae in placental and other synapsids. Here’s what we did and found, focusing mostly on bony (ossified) patellae because that allowed us to bring the fossil record better to bear on the problem.

Reference: Samuels, M., Regnault, S., Hutchinson, J.R. 2016. Evolution of the patellar sesamoid bone in mammals. PeerJ 5:e3103 https://doi.org/10.7717/peerj.3103

Stomach-Churning Rating: 1/10; bones and more bones.

The short version of the story is that mammals evolved bony kneecaps about five times, with marsupials gaining and losing them (maybe multiple times) whereas monotremes (platypus and echidna) and placentals (us and other mammals) didn’t do much once they gained them, and a couple of other fossil groups evolved patellae in apparent isolation.

Evolution of the patella in mammals: broad overview from our paper. Click to zoom in.

The marsupial case is the most fascinating one because they may have started with a fibrocartilaginous “patelloid” and then ossified that, then reduced it to a “patelloid” again and again or maybe even regained it. There needs to be a lot more study of this group to see if the standard tale that “just bandicoots and a few other oddballs have a bony patella” is true for the Metatheria (marsupials + extinct kin). And more study of the development of patellae in this group could help establish whether they truly do “regress” into fibrocartilage when they are “lost” in evolution, or if other, more flexible patterns exist, or even if some of the cases of apparent “loss” of a bony patella are actually instances of delayed ossification that only becomes evident in older adults. Our paper largely punts on these issues because of an absence of sufficient data, but we hope that it is inspiration for others to help carry the flag forward for this mystery.

The higgledy-piggledy evolution of a patella in Metatheria, including marsupials. Click to zoom in.

Some bats, too, do funky things with their kneecaps, analogous to the marsupial “patelloid” pattern, and that chiropteran pattern also is not well understood. Why do some bats such as Pteropus fruit bats “lose” their kneecaps whereas others don’t, and why do some bats and other species (e.g. various primates) seem to have an extra thing near their kneecaps often called a “suprapatella”? Kneecap geeks need to know.

The short-nosed bandicoot (marsupial) Isoodon, showing a nice bony patella as typifies this group. From Yale Peabody Museum.

Otherwise, once mammals evolved kneecaps they tended to keep them unless they lost their hindlimbs entirely (or nearly so). Witness the chunky patellae of early whales such as Pakicetus and join us in wondering why those chunks persisted. The evolutionary persistence of blocky bits of bone in the knees of various aquatic animals, especially foot-propelled diving birds, may help answer why, as the hindlimbs surely still played roles in swimming early in cetacean evolution. Ditto for sea cows (Sirenia) and other groups.

Early whale Ambulocetus, showing hefty kneecaps.

But I’m still left wondering why so many groups of land vertebrates (and aquatic ones, too) never turned parts of their knee extensor tendons into bone. We know a bit about the benefits of doing that, to add leverage to those joints that enables the knee muscles to act with dynamic gearing (becoming more forceful “low gear” or more speedy “high gear” in function). Non-avian (and most early avian/avialan) dinosaurs, crocodiles, turtles, amphibians, early mammal relatives, and almost all other known extinct lineages except for those noted above got by just fine without kneecaps, it seems, even in cases where a naïve biomechanist would expect them to be very handy, such as in giant dinosaurs.

A quoll, Dasyurus, with what is probably a fibrocartilaginous “patelloid”. From Yale Peabody Museum.

However, tendons don’t turn to bone unless the right stresses and strains are placed upon them, so maybe kneecaps are a “spandrel” or “exaptation” of sorts, to abuse Gould’s ghost, whose adaptive importance is overemphasized. Maybe that adaptive myopia overshadows a deeper ontogenetic story, of how tissues respond to their history of mechanical loading environment. It has been speculated that maybe (non-marsupial) mammals have broadly “genetically assimilated” their kneecaps, fixing them into semi-permanence in their genetic-developmental programmes, whereas in contrast the few studies of birds indicate more responsiveness and thus less assimilation/fixation. That “evo-devo-mechanics” story is what now fascinates me most and we’ve poked at this question a bit now, with some updates to come- watch this space! Regardless, whether an animal has a bony vs. more squishy soft tissue patella must have consequences for how the knee joint and muscles are loaded, so this kind of question is important.

Giant marsupial Diprotodon (at NHM London); to my knowledge, not known to have had kneecaps- why?

In the meantime, enjoy our latest contribution if it interests you. This paper came about when first author Dr. Mark Samuels emailed me in 2012, saying he’d read some of my old papers on the avian musculoskeletal system and was curious about the evolution of patellae in various lineages. Unlike many doctors and vets I’ve run into, he was deeply fascinated by the evolutionary and fossil components of patellae and how those relate to development, genetics and disorders of patellae. We got talking, found that we were kindred kneecap-spirits, and a collaboration serendipitously spun off from that, soon adding in Sophie. It was a blast!

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Delight in the Museum

Posted in Museums are Cool, When Anatomy Goes Bad, tagged , , , , , on August 11, 2015| 13 Comments »

I have an impression that there is a large disparity between how the public views museums and how scientists who use museums view them. Presumably there are survey data on public attitudes, but surely the common impression is that museums mainly exist to exhibit cool stuff and educate/entertain the public. Yet, furthermore, I bet that many members of the public don’t really understand the nature of museum collections (how and why they are curated and studied) or what those collections even look like. As a researcher who tends to do heavily specimen-oriented and often museum-based research, I thought I’d take the opportunity to describe my experience at one museum collection recently. This visit was fairly representative of what it’s like, as a scientist, to visit a museum with the purpose of using its collection for research, rather than mingling with the public to oggle the exhibits — although I did a little of that at the end of the day…

Stomach-Churning Rating: 4/10; mostly bones except a jar of preserved critters, but also some funky bone pathologies! Darwin hurls once, totally blowing chunks, but only in text.

Early camel is sitting down on the job at the NHMLA.

Early camel is sitting down on the job at the NHMLA.

About two weeks ago, I had the pleasure to spend a fast-paced day in the Ornithology collection of the Natural History Museum of Los Angeles County (NHMLA or LACM). I arranged the visit (you have to be a credible researcher to get access; luckily I seemed to be that!) via email, took an Uber car to the museum, and was quickly cut loose in the collection. I was hosted by the Collections Manager Kimball Garrett, who is an avid birder (adept at citizen science, too!) and a longtime LA native.

Amongst museum curators and collections managers (there can be a distinction between the two but here I’ll refer to them all as “curators”), there is a wide array of attitudes toward and practices with museum collections, regarding how the curators balance their varied duties of not only making the museum collection accessible to researchers (via behind-scenes studies) and the public (via exhibits and behind-scenes tours etc.), but also curation (maintaining a record of what they have in their collection, adding to it, and keeping the specimen in good condition), research, admin, teaching and other duties.

Most curators I’ve known, like Kimball, are passionate about all of these things, and very generous with their time to help scientists make the most of the collection during their visit, offering hospitality and cutting through the bureaucracy as much as possible to ensure that the science gets done. There are those few curators that aren’t great hosts because they’ve had a bad day or a bad attitude (e.g. obsession with paperwork and finding obstacles to accessing specimens for research; or just not responding to communication), but they are few and far between in my experience.

Regardless, the curator is the critical human being that keeps the wheels of specimen-based museum research rolling, and I am appreciative of how deeply dedicated and efficient most curators are. Indeed, I enjoy meeting and chatting with them because they tend not only to be fun people but also incredibly knowledgeable about their collection, museum, and area of expertise. Sadly, this trip was so time-constrained that I didn’t get much time at all for socializing. I had about five hours to get work done so I plunged on in!

Images, as always, can be clicked to emu-biggen them. Thanks to the NHMLA for access!

My initial look down the halls of the osteology storage. Rolling cabinets (on the right) are a typical sight.

My initial look down the halls of the osteology storage. Rolling cabinets (on the right) are a typical sight.

Freezers ahoy!

Freezers ahoy! With Batman watching over them.

A jar of bats? Why not? Batman approves.

A jar of bats? Why not? Batman approves.

The curator cleared a space on a table for me to set bones on. Then the anatomizing and photographing began!

The curator cleared a space on a table for me to set bones on. Then the anatomizing and photographing began!

On entering a museum collection, one quickly gets a sense of its “personality” and the culture of the museum itself, which emerges from the curator, the collection’s history, and the museum’s priorities. There are fun human touches like the ones in the photos below, interspersed between the stinking carcasses awaiting skeletonization, the crumbling bone specimens on tables that need repair or new ID tags, or the rows upon rows of coffee cups ready to fuel the staff’s labours.

Yet another reason why Darwin kicks ass.

Yet another reason why Darwin kicks ass. And fine curator-humour!

Ironic bird pic posted on the wall.

Ironic bird pic posted on the wall.

Below a typical wall-hanging of a bovid skull, an atypical display of a clutch of marshmallow peeps. Contest to see whether the mammalian or pseudo-avian specimens last longest?

Below a typical wall-hanging of a bovid skull, an atypical display of a clutch of marshmallow peeps. Contest to see whether the mammalian or pseudo-avian specimens last longest?

The NHMLA’s collection is a world-class one, which I why I chose it as the example for this post. When I entered the collection, I got that staggering sense of awe that I love feeling, to look down the halls of cabinets full of skeletonized specimens of birds and be overwhelmed by the vast scientific resource it represents, and the effort it has taken to create and maintain it. Imagine entering a library in which every book had the librarian’s hand in writing and printing it, and that those books’ contents were largely mysteries to humanity, only some of which you could investigate during your visit. Museum collections exist to fuel generations of scientific inquiry in this way. Their possibilities are endless. And that is why I love visiting them, because every trip is an adventure into the unknown– you do not know what you will find. Like these random encounters I had in the collection’s shelves:

Sectioned moa thigh bones, showing thick walls and spars of trabecular bone criss-crossing the marrow cavities.

Sectioned moa thigh bones, showing thick walls and spars of trabecular bone criss-crossing the marrow cavities.

My gut reaction was that this is a moa wishbone (furcula)- not often seen! It is definitely not a shoulder girdle (scapulocoracoid), which would be larger and more robust, and have a proper shoulder joint. It could, though, be a small odd rib, I suppose.

My gut reaction was that this is a moa wishbone (furcula)- not often seen! It is definitely not a shoulder girdle (scapulocoracoid), which would be larger and more robust, and have a proper shoulder joint. It could, though, be a small odd rib, I suppose. EDIT: Think again, John! See 1st comment below, and follow-ups. I seem to be totally wrong and the ID of scapulocoracoid is right.

A cigar box makes an excellent improvised container for moa toe bones- why not?

A cigar box makes an excellent improvised container for moa toe bones- why not?

Moa feet: all the moa to love!

Moa feet: all the moa to love!

May the skull of the magpie goose (Anseranas semipalmata) haunt your nightmares.

May the skull of the magpie goose (Anseranas semipalmata) haunt your nightmares.

Double-owie: headed shank (tibiotarsus) bone of a magpie goose (Anseranas semipalmata). No mystery why this guy died: vet staff at the zoo tried to fix a major bone fracture, and it had time to heal (frothy bone formation) but presumably succumbed to these injuries/infection.

Healed shank (tibiotarsus) bone of the same magpie goose as above. It had its own nightmares! No mystery why this guy died: vet staff at the zoo tried to fix a major bone fracture (bracing it with tubes and metal spars), and it had time to heal (see the frothy bone formation) but presumably succumbed to these injuries/infection.

Kiwi (Apteryx australis mantelli) hand, showing feather attachments and remnant of finger(s).

Kiwi (Apteryx australis mantelli) hand, showing feather attachments and remnant of finger(s).

Now that I’m in the collection shelves area, it brings me to this trip and my purpose for it! I wanted to look at some “basal birds” for our ongoing patella (kneecap) evolution project, to check which species (or individuals, such as juveniles/adults) have patellae. Every museum visit as a scientist is fundamentally about testing whether what you think you know about nature is correct or not. We’d published on how the patella evolved in birds, but mysteries remain about which species definitely had a patella or how it develops. Museum collections often have the depth and breath of individual variation and taxonomic coverage to be able to address such mysteries, and every museum collection has different strengths that can test those ideas in different, often surprising, ways. So I ventured off to see what the NHMLA would teach me.

Shelves full of boxes, begging to be opened- but unlike Pandora's box, they release joyous science!

Shelves full of boxes, begging to be opened- but unlike Pandora’s box, they release joyous science!

Boxes of kiwis, oh frabjous day! A nice sample size like this for a "rare" (to Northern hemispherites) bird is a pleasure to see.

Boxes of kiwis, oh frabjous day! A nice sample size like this for a “rare” (to Northern hemispherites) bird is a pleasure to see.

Well, in my blitz through this museum collection I didn’t see a single damn patella!

As that kneecap bone is infamously seldom preserved in nice clean museum specimens, this did not surprise me. So I took serendipity by the horns to check some of my ideas about how the limb joints in birds in general develop and evolve. One thing I’ve been educating myself about with my freezer specimens and with museum visits (plus the scientific literature) is how the ends (epiphyses) of the limb bones form in different species of land vertebrates (tetrapods). There are complex patterns linked with evolution, biomechanics and development that still need to be understood.

Left side view of the pelvis of a very mature, HUGE Casuarius casuarius (cassowary). The space between the ilium (upper flat bone) and ischium (elongate bone on middle right side) has begun to be closed by a mineralization of the membrane that spanned those bones in life. A side effect of maturity, most likely. But cool- I've never seen this in a ratite bird before, that I can recall.

Left side view of the pelvis of a very mature, HUGE Casuarius casuarius (cassowary). The space between the ilium (upper flat bone) and ischium (elongate bone on middle right side) has begun to be closed by a mineralization of the membrane that spanned those bones in life. A side effect of maturity, most likely. But cool- I’ve never seen this in a ratite bird before, that I can recall.

Hatchling ostrich thigh bones (femora), showing the un-ossified ends that in life would be occupied by thick cartilage.

Hatchling ostrich thigh bones (femora), showing the pitted, un-ossified ends that in life would be occupied by thick cartilage.

A more adult ostrich's femora, with more ossified ends and thinner cartilages.

A more adult ostrich’s femora, with more ossified ends and thinner cartilages.

Rhea pennata (Darwin's rhea) femora (thigh bones), left (top) one with major pathology on the knee end; overgrown bone. Owie!

Rhea pennata (Darwin’s rhea) femora; right (top) one with a major pathology on the knee end; overgrown bone (osteoarthritis?). Owie!

Also very-unfused knee joints of a Darwin's rhea. Cool Y-shape!

Also very-unfused knee joints of a Darwin’s rhea hatchling. Cool Y-shape!

In birds, most of the bones don’t have anything that truly could be called an epiphysis– the bone ends are capped with thick cartilage that only gradually becomes bone as the birds get older, and even old-ish birds can still have a lot of cartilage (see photos above)– no “secondary centre” (true epiphysis) of bone mineralization ever forms inside that cartilage. However, there are two curious apparent exceptions to this absence of true epiphyses in avian limbs:

(1) in the knee joint, something like an epiphysis forms on the upper end of the tibia (shank bone) and fuses during growth (shown below). Sometimes that unfused epiphysis is confused with a patella, as our recent paper discussed; in any case, where that “epiphysis” came from in avian evolution is unclear. But also:

(2) in the ankle joint, several bones on both sides (shank and foot) of the joint fuse to the long-bones of the limbs, acting like epiphyses. It is well documented by the fossil record of non-avian and avian dinosaurs that these were the tarsals: at least five different bones (astragalus, calcaneum and distal tarsals) were individual bones for millions of years in various dinosaurs, then these all fused to form the “epiphyses” of the shank and foot, eventually completing this gradual fusion within the bird lineage. Modern birds obliterate the boundaries between these five or more bones as they grow.

These are worthwhile questions to pursue because they show us (1) how odd, little-explored features of the avian skeleton came to be; and (2) potentially more generally why limb bones develop the many ways they do in vertebrates, and how they might develop incorrectly — or heal if damaged.

Images below from the NHMLA collections show how this is the case. Fortunately(?) for me, they supported how I thought the “epiphyses” of avian limbs develop/evolved; there were no big surprises. But I still learned neat details about how this happens in individual species or lineages, especially for the knee joint.

Juvenile kiwi's shank (tibiotarsus) bones viewed from the top (proximal) ends, showing the bubbly nubbins of bone (very bottom of each bone image) that are the "cranial tibial epiphyses" often mistaken for patellae.

Juvenile kiwi’s shank (tibiotarsus) bones viewed from the top (proximal) ends, showing the bubbly nubbins of bone (very bottom of each bone image; lighter region) that are the “cranial tibial epiphyses” often mistaken for patellae.

Subadult kiwi's tibiotarsi in same view as above, showing the epiphyses fusing onto the tibiae.

Subadult kiwi’s tibiotarsi in same view as above, showing the smooth triangular epiphyses fusing onto the tibiae.

Adult kiwi's tibiotarsi (sorry, blurry photo) in which all fusion is complete.

Adult kiwi’s tibiotarsi (sorry, blurry photo) in which all fusion is complete.

Looking down at the top/ankle end of the tarsometatarsal (sole) bones in a hatchling ostrich: the three bones are separate and hollow, where "cartilage cones" would have filled them in.

Looking down at the top/ankle end of the tarsometatarsal (sole) bones in a hatchling ostrich: the three bones are separate and hollow, where “cartilage cones” would have filled them in. The left and right bones have different amounts of ossification; not unusual in such a young bird.

Ossified tendons (little spurs of long, thin bone) on the soles of the feet (tarsometatarsal bones) of a brush-turkey (Alectura lathami)- seldom described in this unusual galliform bird or its close relatives, and thus nice to see. These would be parts of the toe-flexor tendons.

Ossified tendons (little spurs of long, thin bone) on the soles of the feet (tarsometatarsal bones) of a brush-turkey (Alectura lathami)- seldom described in this unusual galliform bird or its close relatives, and thus nice to see. These would be parts of the toe-flexor tendons. Another nice thing about these two tarsometatarsus specimens is that their fusion is basically complete- each is one single bone unit, as in normal adult birds, rather than five or more.

My visit to the NHMLA bird bone collection was a lot of fun, because I got to do what I love: opening box after box of bone specimens, with bated breath wondering what would be inside. In this case, familiarity was inside, but my knowledge of avian bone development and evolution still improved. I got to look at a lot of ostriches, rheas, cassowaries and kiwis, more than I’d seen in one museum before, and that broadened my sample of young, juvenile and adult animals that I’d seen for these species. Their knees and ankles all grew in grossly similar ways, supporting this assumption in my prior work and building my confidence in published ideas. It’s always good to check such things. Each box opened takes some careful observation and cross-checking against all the facts and ideas swirling around in your head. You take notes, scale photos, measurements, do comparisons between specimens, and just explore; letting your curiosity run unleashed as you assemble knowledge, Tetris-like, in your mind.

And I had a lot of fun because a museum collection visit is like swimming in anatomy. You’re surrounded by more specimens than you could ever fully comprehend. Sometimes you run across an odd specimen whose anatomy tells you something about its life, like pathologies such as the terrible fractured magpie goose leg shown above. Or you see some curatorial touch that makes you chuckle at an apparent inside joke or mutter respect for their careful organization in tending their charges. That feeling of pulling open a museum drawer or box lid and peering inside is like few others in science — there might be disappointment inside (e.g. “Crap, that specimen sucks!”), boredom (“Oh. Another one of these!?”) or the joy of discovery (“Holy *@$£, I’ve never seen that before!”). My first scientific publication (in 1998) came from rummaging through the UCMP museum collections as a grad student and spotting an obscure pelvic bone that turned out to be highly diagnostic for the equally obscure clade of bird-like dinosaurs called alvarezsaurids. I happened to open that drawer with the alvarezsaurid specimen at the right time, shortly after the first ever specimen of that dinosaur had been described in the literature (~1994). Before then, no one could have identified what that bone was!

There is time for hours of quiet introspection during museum collection studies, immersed in this wealth of anatomical resources and isolated in a silent, climate-controlled tomb-like hall. It is relaxing and overwhelming at the same time. Especially in my case with just five hours to survey numerous species, you have to budget your time and think efficiently. It’s a unique challenge to explore a museum collection as a researcher. If you don’t learn something — especially in a good museum collection — you’re doing it wrong. In this time of tight finances and trends to close museums or stow away precious collections, it is important to vocally celebrate what a vast treasure museum collections are, and how the people that maintain them are vital stewards of those treasures.

I set the cat amongst the pigeons by also visiting the Page Museum at the La Brea Tar Pits in LA, to study fossil cats-- like this American lion (Panthera atrox) code-named "Fluffy", that we CT scanned during my LA visit-- more about that later!

I set the cat amongst the pigeons by also visiting the Page Museum at the La Brea Tar Pits in LA, to study fossil cats– like this American lion (Panthera atrox), code-named “Fluffy”, that we CT scanned during my LA visit– more about that later!

EDIT: I hurried this post off during my free time today, and still feel I didn’t fully capture the deep, complex feelings I have regarding museum collections and the delight I get from studying them. Other freezerinos, please add your thoughts in the Comments below!

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Deck the ‘Nets With PeerJ Papers

Posted in Exalting Archosauria, tagged , , , , , , , , , on December 23, 2014| 7 Comments »

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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A Chance Encounter with Darwin’s Chickens. And Cake.

Posted in Exalting Archosauria, Geeking Out, Museums are Cool, tagged , , , , , , , on May 14, 2013| 8 Comments »

Bovids to the right of me, pinnipeds above, what's a guy to do but squee?

Bovids to the right of me, pinnipeds above, what’s a guy to do but squee?

I’ve been doing some osteological studies of the patella (bone in the major tendon in front of the knee; termed a sesamoid) that have included frequent visits to the Natural History Museum’s avian skeleton collection at Tring. It’s a cute little town, northeast of London, in the green county of Hertfordshire where I live and work. The museum at NHM-Tring is a great old school multi-storey display packed with skeletons and stuffed animals in dark wood cabinets, with many critters hanging from wrought iron railings or other suspensions above (see above). I blogged about the Unfeathered Bird exhibit (and book) that just finished up its tour there yesterday. And I’ll be blogging later, as I keep promising, about the cool things I’ve learned during the past year of my studies of the form, function, development and evolution of the patella.

As an aside, I heartily recommend doing research at the NHM-Tring. It’s away from the bustle (and arduous Tube trip) of the South Kensington NHM, and the curatorial staff are immensely helpful… and there is something else that makes the trip even more enjoyable, but you must read more below to find out about it.

Stomach-Churning Rating: 2/10; 150-year-old dry bones. But an advance warning to (1) diabetics and (2) pun-haters, for reasons that will become evident.

Dr Heather Paxton and Dr Jeffrey Rankin, postdoc researchers working on our collaborative BBSRC chicken biomechanics grant (see thechickenofthefuture.com), explain their science to an attentive Darwin.

Dr Heather Paxton and Dr Jeffery Rankin, postdoc researchers working on our collaborative BBSRC chicken biomechanics grant (see thechickenofthefuture.com), use the Structure & Motion Lab whiteboard to explain their science to an attentive Darwin.

Today I have a short pictorial exhibit of something wonderful I ran into while patellavating in the NHM collections. As often happens while doing museum research, I had a serendipitous encounter with a bit of history that blew my mind a little, and had me geeking out. These things happen because museum collections are stuffed with specimens that, to the right eyes or the right mindset, pack a profound historical whallop. As a scientist who is pretty keen on chickens (Gallus gallus), there are probably no museum specimens of chickens that would get me more excited about than the chickens Darwin studied in his investigations of artificial selection. In fact, most museum specimens of domestic chickens would not be that interesting to me, especially after seeing these ones.

Darwin wielded the analogy between artificial selection and his conceptual mechanism of natural selection in the first ~4 chapters of On the Origin of Species to clobber the reader with facts and try to leave them with no doubt that, over millennia, nature could craft organisms in vastly more complex and profound ways than human breeders could mould them over centuries. While people most often speak of Darwin’s pigeons when referring to Darwin and avians or artificial selection and variation, his chickens appear in The Origin and other writings quite often, too (most prominently, The Variation of Animals and Plants Under Domestication in 1868– more about that here). For example, from my 1st edition facsimile of The Origin from Harvard University Press, pp. 215-216:

“Natural instincts are lost under domestication… It is not that chickens have lost all fear, but fear only of dogs and cats, for if the hen gives the danger-chuckle, they will run… and conceal themselves in the surrounding grass or thickets; and this is evidently done for the instinctive purpose of allowing, as we see in wild ground-birds, their mother to fly away. But this instinct retained by our chickens has become almost useless under domestication, for the mother-hen has almost lost by disuse the power of flight.”

Well told, Mr D!

I am also reminded of how chickens and Darwin have had darker relationships, such as this sad story. Or how evolution via Darwinian mechanisms crosses paths with pop culture in fowl ways, such as how tastes-like-chicken evolved, or how some say that chickens, over great periods of time, have been naturally selected in such a way that they are now heritably predisposed to cross roads, or that the amniote egg preceded the evolution of the genus Gallus by some 325+ million years. I see I am drifting and drifting further away from the topic at hand, so let me segue back to Darwin’s chickens. We’ll take this corridor there:

Inside the avian osteology collection at Tring. Sterlie at it might seem, places like this are fertile breeding grounds for scientific discovery.

Inside the avian osteology collection at Tring. Sterile at it might outwardly seem, places like this are fertile breeding grounds for scientific discovery. And a sterile-looking collection means well cared-for specimens that will persevere for future discoveries.

So anyway, when museum curator Jo Cooper said to me something like “I have some of Darwin’s chickens out over on the other counter, do you want to have a look or shall I put them away?” my answer was quick and emphatic. YES! But only after lunch. I was hungry, and nothing stops me from sating that hunger especially when the sun is out and there are some fine pubs within walking distance! I settled on the King’s Arms freehouse, and had a delicious cheeseburger followed by a spectacularly good apple-treacle-cake with ice cream, expediently ingested while out on their sunny patio. Yum! I cannot wait to have that cake again. What a cake! Darwin’s bushy eyebrows would have been mightily elevated by the highly evolved flavour, which would have soothed his savage stomach ailments. He would have been like:

“Damn, Emma! Holy s___ this is great apple-cake; here, try some! There is grandeur in this tasty cake, with its several flavours, having been originally cooked into a few baking trays or into one; and that, whilst this pub has gone on serving fine food according to the fixed hygiene laws of Tring, from so simple a beginning endless foods most beautiful and most wonderful have been, and are being, devoured.” And Emma, cake then firmly in hand, would have said something like, “My dear Charles, I shall try this enticing dessert, and I am glad to see you so enthused about something other than barnacles. Write a letter to Huxley or Lyell about that cake later. You need to focus on concocting an ending to that big species book of yours, not cakes. It’s been 20 bloody years, dude; cake can wait. End the book on a high note.” And so it must have happened.

Working at a museum collection is like having an extra home/office for a day or more. You get familiar with the environment while working there, and start to settle in and enjoy the local environs while taking work breaks. Or I do, anyway. So this post is also partly about how cake and other provisions are an important part, or even a perk, of life as a visiting museum researcher. Put in some good solid work, then it’s cake time, but where are the cakes? You explore, and you discover them– opening the door of an unfamiliar shop or pub near a museum can be like opening a museum cabinet to discover the goodness inside. Just don’t get them mixed up. Museum specimens: for research; subjects for science. Cakes: for eating; fuel for scientists. Got it?

But I digest digress. This post is not about my lunch. Not so much, anyway, although I did enjoy the cake quite a bit. Back to the chickens. Here, try some!

Darwins-chickens (1)Darwins-chickens (6)

Darwins-chickens (5) Darwins-chickens (4)

Above: Views of Darwin’s chickens laid out at the NHM-Tring.  (all photos in this post can be clucked to emchicken them)

The chickens, much like the pub lunch, did not disappoint in the least. Here I had before me Darwin’s own personal specimens, which I envisioned him dissecting and defleshing himself, studying them in deep introspection, then handing them over to the museum for curation once his lengthy researches were complete (all the ones I studied dated back to around 1863-1868, so they were curated shortly after The Origin was published (1859)). Perhaps the museum gave him some fine sponge-cake in return. There was at least one male and female adult of each of numerous breeds, many of them still bearing the dried flesh of centuries past. This was great for me, as the patella often gets removed and clucked chucked in the bin with its tendon when museum specimens of birds are prepared (much as elephant “sixth toe” sesamoids are). All of the specimens had their honking huge patellae on display, so that’s what a lot of my photos feature. I do so lament that I did not take a photo of the cake. Did I tell you about that cake? Oh… Check out these examples of Darwin’s chickens:

XXXX breed in right side view, with the patella indicated by a red arrow. It is still attached to the tibiotarsus by the patellar tendon (often misnamed the patellar "ligament", but it is just a continuation of the proximal tendon).

African rooster (wild variety? Darwin’s label was not clear) in right side view, with the patella indicated by a red arrow. That patella is still attached to the tibiotarsus by the patellar tendon (often misnamed the patellar “ligament”, but it is just a continuation of the proximal tendon).

Darwin's handwritten label and the well-endowed patella of the Spanish Cock. What? Oh, you. Stop it.

Darwin’s handwritten label and the well-endowed patella of the Spanish Cock. What? Oh, you. Stop it. That has nothing to do with cake, and only cake-related humour is allowed in this post.

Some other fascinating features exhibited by Darwin’s chickens, which he doubtless mulled over while nibbling on fine cakes, included the following:

The hindlimb of a Polish Silver Laced breed, nicely showing the ossified tendons (red arrow) along the tarsometatarsus. Why these tendons turn into bone is one of the great unsolved mysteries of bone biology/mechanics and avian evolution. Check out the famed feather crest here.

The hindlimb of a Polish Silver Laced breed, nicely showing the ossified tendons (red arrow) along the tarsometatarsus. Why these tendons turn into bone is one of the great unsolved mysteries of bone biology/mechanics and avian evolution.

Check out the famed feather crest of the Silver (Laced) Polish here; it gets so extreme in males that they have a hard time seeing, and can get beaten up by other cockerels when kept in mixed breed flocks.

Here on this blog, and of course on the companion blog “Towards the Chicken of the Future,” domestic chickens and wild junglefowl have often come up, most recently with the Dorking Chicken (another of Darwin’s own specimens that I studied) in the “Mystery Museum Specimen” poetry round of late. Dorkings are HUGE chickens; easily twice the weight of even a broiler chicken, up to 4-5kg. The Dorking-characteristic polydactyly featured in that post is also observed at a relatively high incidence in Silkie and Sultan breeds, I’ve learned. Like this one! (I was so patella-focused, or cake-somnolescent, that I missed it while studying at the museum and only noticed it now while browsing through my photos, bereft of cake)

Nice leg of a Sultan hen. There is an extra toe here as in the Dorking chicken; a duplicate hallux (first toe). This is not, as it might at first seem, a pathological condition as in modern "twisted toe"-suffering domestic chickens.

Nice leg of a Sultan hen. There is an extra toe here as in the Dorking chicken; a duplicate hallux (first toe). This is not, as it might at first seem, a pathological condition as in modern “twisted toe”-suffering domestic chickens.

Malays are another giant breed like the Dorking, but with longer and more muscular legs and longer necks, looking much more like a classic, badass wild junglefowl than a fancy, pampered chicken. But here, undressed to the bare bones, it just looks like a skinny chicken leg, albeit perhaps a bit svelte compared to the Dorking or Sultan.

Hindlimb of a Malay breed of chicken, which Wikipedia nicely tells the story of its misnomer (it may originate from Pakistan, not Malaysia!). Can you find the nice patella? Check out Darwin's lovely label, too.

Hindlimb of a Malay breed of chicken, which Wikipedia nicely tells the story of its misnomer (it may originate from Pakistan, not Malaysia!). Can you find the nice patella? Check out Darwin’s lovely label, too.

You may have come across wild-eyed news stories 5 years ago about “OMG Darwin was sooooooo wrong about chickens!”, referring to his writings on the origin of domestic chickens from Red junglefowl. As Greg Laden adeptly wrote, Darwin (say it with me) didn’t really get it very wrong after all. He did quite well, in fact. Some media outlets did get it more wrong, probably inspired by this press release. Oh well; the science they were reporting about definitely was interesting- modern chickens seem to have some of their yellow skin pigmentation-related genes from Grey junglefowl, although they are still largely descendants of Red junglefowl.

Here, have a JUMBLE-fowl, or rather a junglefowl cockerel, with another Darwin label:

Darwin's example of a wild-type chicken; a Red Junglefowl. As he suspected, these Asian birds were the ancestors of domestic chickens, but today evidence suggests that domestication occurred multiple times in Asia and with different wild varieties of junglefowl bred/mixed in different regions.

Darwin’s example of a wild-type chicken; a Red junglefowl. As he suspected, these Asian birds were the ancestors of domestic chickens, but today evidence indicates that domestication may have occurred multiple times in Asia and with different wild varieties of junglefowl bred/mixed in different regions.

Some breeds aren’t so funky inside, of course, but just have cool feather patterns on the outside, like the “pencilling” (dark streaks on white feathers) evident in pencil breeds; also called triple-laced. Like this fine chap below once would have had, before Darwin tore off his feathers and reduced him to a research-friendly naked skeleton:

A Golden Pencil Hamburgh breed of chicken (cockerel), whose skeleton features the leg and a fine articulated patella.

A Golden Pencil(led) Hamburg breed of chicken (cockerel), whose skeleton features the leg and a fine articulated patella.

Also known as the Holland Fowl, several European countries including the UK claim the Hamsburg as an original breed from their respective realm, and no surprise they do- it’s a lovely spangled chicken. Then, later in the 1800’s the Americans got involved in breeding them, too, and it’s all a big mess. They should get together, have some delectable cakes, and just sort it out.

Scaly, still-greasy foot and hindlimb of what Darwin labelled as the male of a "Game" breed.

Scaly, still-greasy foot and hindlimb of what Darwin labelled as the male of a “Game” breed.

We thus close with another leg of another chicken. Darwin was a bit naughty here, or else terminology of breeds has changed a lot since the 1850’s (very possible), as he just labelled this as a “Game” cockerel. Now, Gamefowl is a big category of breeds. I’m guessing this one was either (1) a Cornish/Indian Game variety or (2) an Old or Modern English Game Fowl. Maybe a person who knows their chicken breeding far better than me (that’s not hard!) will opine differently. The latter varieties were popular in Darwin’s time — the (Muffed) Old English version was mated with other breeds (Malay?) to produce the Modern English form as cockfighting “sports” became banned in 1849 and breeder attentions shifted to the polar opposite of producing showy, fancy birds instead. And thus the bufante, feathered-hair-adorned 1980s pop-rock group was created, to sing about mating or moulting or melting with people or something terribly disgusting and probably having nothing at all to do with chickens,  cake, or cockfighting, or other more seemly pursuits.

So, we have come to the end of my photos of Darwin’s chicken leg bones and such. If you’ve learned something here about chicken breeds, patellae, cake, or Darwin, that’s simply frabjous. Enough of those poncey pigeons, already! I’m crying fo… no, I won’t use that pun. Nevermind. Not even remotely cake-related. Let’s give Darwin’s chickens their just desserts, is the point– and a much better pun, too. Darwin’s chickens are an important part of Darwiniana, and an interesting evolutionary study in and of themselves. I’ve certainly become impressed during my researching for this blog post by the diverse, fascinating biology of chicken breeds. My copy of the “Complete Encyclopedia of Chickens” will be getting some more thorough reading shortly.

Today, however, I am off to return to the NHM-Tring and peruse their other, non-chickeny Galliformes and Anseriformes, with a detour to the mythical hoatzin. But… but… there may be a cake detour involved, too. I shall report back in due course. Off I go!

No, hopefully not that cake.

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Come do a heavily freezer-based PhD studentship with me!

Posted in Shiverin' Sesamoids!, tagged , , , , , , on October 30, 2012| 9 Comments »

A short(ish) post, but to me an important one. As I’ve mentioned here before, and still mean to write a detailed post on, I’m on a 1-year Royal Society Leverhulme Trust senior research fellowship (pause to breathe… long phrase there!) to study the mechanics and evolution of the kneecap (patella) in birds. Knees are very cool, and the patella is one of the coolest parts of the knee. My fellowship is aimed at returning to my roots, i.e. my PhD research on theropod dinosaur hindlimb evolution (anatomical and functional), to focus in great detail on just the patella (this, not this).

The patella is a mysterious structure: a sesamoid bone like I’ve argued elephant predigits are, and probably the best known sesamoid, but still quite enigmatic– especially in non-humans and most particularly in non-mammals. Why did it evolve three different times, at least? What mechanical/developmental environment encourages it to form? Why don’t some species have them? Does the presence of a patella tell us anything about posture, gait, or anything else? Why did no giant dinosaurs evolve patellae?

Anyway, I now have a related PhD studentship that I need a great EU/UK-based student to apply for, and I’m casting a wide net. It’s a very, very freezer-based PhD: imagine cutting up the knees of the frozen zoo of critters that I’ve shown on this blog already, to your heart’s content! And studying fossils, and doing histology (cool imaging techniques with RVC faculty Michael Doube and Andy Pitsillides, along with bone uber-guru Alan Boyde), and conducting experiments with real animals, and computer modelling both experimental and fossil data… this PhD has it all.

Here are the details. If you know anyone in the EU/UK looking for a good PhD that seems to fit the bill very well, send them my way please!

We now return you to your regularly scheduled frozen organisms… and there is a fun post coming tomorrow!

The knee of an emu from my freezer, showing the many muscles and other tissues that connect to or surround the patella. It’s complicated, and that makes for fun science!

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RVC Anatomy Museum, Part 6- Skeleton Crew

Posted in Museums are Cool, tagged , , , , , , on August 18, 2012| Leave a Comment »

Well, I happened to take some more photos of a few of my favourite skeletons/bones from our Anatomy Museum during my last jaunt over to our Camden campus, and figured I might as well share them. So here you go! (Right now it’s so hot I wish I was a skeleton! Gigantothermy is not always so great) First, two views of our seated polar bear, which I learned this week is a celebrity— a model for the kickass armoured polar bears in the film The Golden Compass:

 

Then, also out in our cafe area you’ll find some nice smaller specimens in addition to our elephant. Such as:

A decent mount of a three-toed sloth is above; and below I’ll share several skulls including a second hippo (male? quite different morphology from the other one I showed):

And another charismatic megafauna, a ?black? rhinoceros (shown previously as a mounted skeleton in our old hall):

And a small gharial (Gavialis) skull:

Which can be nicely juxtaposed with a more robust Caiman (or our earlier Alligator):

And then a small wallaby:

Let’s go back inside. I have a few more friends for you to meet. Such as our chimp next to a Lucy skeleton (both casts), briefly glimpsed in my first post:

And a really, really gnarly-faced bulldog! Shudder.

During my brief perusal of the exhibits the other day, I realized I had never shared our nice knee joint dissection in my post on those specimens, nor had I included it in my knotations about knee joints. This is particularly egregious as I am now doing a year-long fellowship/sabbatical to study knee joints, in particular the patella (kneecap) of birds. Here, a dog, with helpful labels of the anatomy around the stifle:

And that’s all folks! I’m preparing a particularly wacky post for later, which will include lots of whimsical anatomy, so stay tuned and keep coooooooool!

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