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Archive for May, 2012

Title is so meta?

OK Londoners, and Olympics visitors, and anatomy (or just science/biology) buffs, and those not lucky enough to see other versions of the animal Body Worlds show. You have a mission. And that mission is to go see “Animal Inside Out”, a special (£9 for adults is well worth it!) exhbit at the Natural History Museum, open until September 16. This blog will self destruct, very messily, by turning itself inside out in 5 seconds… Boom.

Hippopotamus attempting to outdo elephant guts.

Anatomy to me is beautiful even when it’s “ugly” (messy, wet, mucosal, intestinal, asymmetrical, unlike human, whatever), and that’s a major theme of this blog. Hence I am embarrassed that I hadn’t yet gone to see this Body Worlds spinoff exhibit until now, but can begin to shake off that shame by means of an almost exclusively effusive gushing of blood love for said exhibit. Wow, wow, wow! I went in with no particular expectations, having seen some pictures and knowing some of what to expect, and having other things on my mind. I came out very pleased; the NHM exhibits folks and von Hagens’s crew have created an inspirational spectacle that could do wonders for anatomical sciences and natural history. More about that at the end.

(Warning: possibility of spoilers, but the exhibit is so visual that I don’t think my descriptions can spoil it)

The entrance

No photos are allowed as usual, so all I have to show you is the entrance and some anatomy pics I’ve interspersed from my team’s research to lighten up the text. I suppose I could have asked for special permission to take photos for review usage but this was a very impromptu visit, and with ~4 months of showing left I may well be back again.

Weighing a hippo; spot on at 1600 kg!

There is a brief panel on homology and why it is the major concept underlying comparative anatomy (and a key part of evolution, co-opted from the not-so-evolutionary ideas of Sir Richard Owen, whom the NHM rightly mentions here). Another panel rightly brings up the issue of ethics, which has plagued Body Worlds before. It comforts the visitors that animals were not slaughtered just for this display and that the NHM applied its strict collections criteria to them. Convincing enough for me, and absolutely necessary to bring up early on.

The entry hall then presents you with about five cephalopods (labelled “squid” and “octopus”—a gripe is that species names/details are not given for most specimens on show) prominently occupying the view. The cephalopods, like basically everything else, are plastinated (by a now US-patented set of procedures, I learned from the exhibit book detailed later). They are stunningly frozen in lifelike poses or with gaping cuts to show their interior anatomy, although there was very little explanation here about cephalopod biology and anatomy (about 1 smallish panel). No mention of Cthulhu. Damn. He’d approve of the Grand Guignol scenery.

Toward the back of the first corridor of specimens and cases, there is a stunning scarlet haze outlining the body of a “shark” (species not given) with its huge liver lying below it. The haze, a technique used repeatedly throughout the exhibit, is some kind of corrosion cast of the circulatory system, I gather. A bunch of cross/longitudinal sections of cephalopods, crocodiles, fish, horse hooves and other animals decorate blank spaces on the walls, some with labels showing basic features and some just hung like paintings. Fair enough, but a missed opportunity for a bit more educational content here.

Gratuitious Melanosuchus (black caiman) shot.

A smallish whole shark confronts you as you turn the corner from the crimson chondrichthyan; again of unknown classification. One would think a museum exhibit would care about classification beyond “shark,” but oh well, I am banging the same drum here too much and missing the point, that the exhibit is really a visual, visceral expose rather than a deep prose-driven intellectual dissection. On one of the shark panels it is noted that sharks have red and white kinds of muscle used for slower and faster swimming, but not clarified that this is a very widespread vertebrate (chordate?) feature. This forms my second gripe, that a truly evolutionary approach, such as that taken by dozens of the museum’s research staff as their major paradigm of phylogenetic systematics, could have helped the public grasp the evolutionary, hierarchical nature of homology and depart with accurate information about what features characterize groups at which levels. I’m not asking for cladograms laid out on the floor as at the American Museum of Natural History, although maybe that could work, but the exhibit tended to fall back on an outmoded “this animal has this feature, and that animal has that feature, and these are cool adaptations” shopping list approach rather than a modern comparative approach. Granted, almost all museum exhibits fall into this trap, for various reasons and some of them justified. But with a spare word or phrase here or there, this could have been done better without drowning the visitors in that dreaded sea of bloodprose.

Passing the sharks, we come to one of several thematic sections about body systems, this first one on the skeleton (later, brain/nerves, circulation, muscles, etc.). A few small skeletal specimens of the type that are seen throughout the museum are presented, with a scallop reminding us that skeletons can come in many types among multicellular organisms. There is a horse skull and a stark white whole skeleton of a young-ish ostrich, which was very nicely mounted. However, I was caught off guard by the pelvis, which lacked the curved, ventral “boot” like connection of the pubic bones that ostriches have—presumably explained by its juvenile status although I wasn’t 100% sure it was even an ostrich pelvis. OK, I am having a serious pelvis-nerd moment here; forgive me as my PhD was on this stuff.

Ostrich in the midst of disassembling.

BUT, once again the small interpretive panel had a moment of Fail. The ostrich was explained to have two toes, in contrast to normal birds which have “five”.  HUH? Birds have three main toes and variably also a fourth, inner (first) toe called the hallux, used for perching and other activities including walking. None have a fifth toe; indeed their dinosaurian forebears lost that feature some 230ish million years ago. Just an embryonic vestige of the base of the fifth toe is visible in bird embryos today. Furthermore, the panel said that two toes in ostriches can grip the ground more strongly than more toes in other birds. I know of no evidence that shows this, and suspect that the contrary might be true. The standard explanation for toe reduction in ostriches is that it is a lightening feature characteristic of “cursorial” (long-legged, sometimes fleet/efficient) animals, to make swinging the long legs easier. These errors really should have been caught by involving experts in polishing the scientific content of the exhibit.

But I don’t want this post to grumble too much; wrong message. There was so much to celebrate in this exhibit, which was felt impressively spacious and full of cool specimens! Visitors pass some plastinated whole sheep and goats, with panels nicely explaining that goats and sheep look quite similar on the inside and are evolutionary relatives. Having “four stomachs” (technically, a four-chambered stomach; not four distinct organs that were duplicated) is attributed as a sheep trait, then being a ruminant is said to be a goat trait; this might get a little confusing for non—anatomists (both are ruminants and have similar stomachs).

I learned that goats have an extra tail muscle that allows them to swing up/down as well as side-to-side. Hey, I teach veterinary anatomy and I don’t know that!? I must tuck my tail between my legs in shame, but I am no goat so I do not think I can (do satyrs count?). But I wasn’t so sure that goats, as described, were the first animals to be domesticated—I thought that was dogs? Ahh, Wikipedia says dogs, then sheep, then pigs, then goats? I’m outside my expertise here, I admit, and resorting to Wikipedia out of ignorant desperation. Anyway, here, another instance of coulda-been-more-phylogenetically-specific presented itself: the forelimb of goats was said to be connected to the thorax by muscles and ligaments, not a joint, but this is a feature common to most Mammalia. Although audience attentions might be wandering at this point, waiting for the next big spectacle (goats and sheep are not a big crowd draw, even plastinated), some more care as to what was written would be good. Some reindeer and horses and other animals join in the fun later on. Good, but mostly ‘filler’ (wise to put these in the middle of the exhibit, after sharks/cephalopods and before climax) unless you’re a big fan of fairly familiar ungulates with fairly homogeneous postcrania. OK, my bias is showing…

Gratuitious image of emu curled up for CT scan.

Next along the path, a longitudinal section of a whole ostrich caught my attention. Wow again! I had no idea that one could make a section like this of such a large animal, all in one plastic sheet like a giant microscope slide! I stared at this for a while, wondering how both legs could be fit in a ~1cm thick panel, and gave up trying to understand the technology. Von Hagens, you got me there; I’m stumped. Were multiple sections glued together somehow to produce a pseudo-2D slice from many thin 3D sections? I could not tell, and felt humbled and deeply impressed by the technical skill shown in the exhibits so far…

And then the punches kept coming, one-two-three! The exhibit approaches its climax with a crescendo of great specimens in the final hall. First, another maroon marvel. A whole ostrich, standing with wings askew, showing off its entire circulatory system (plus a few wing plumes for aesthetics) from head to toes! Gorgeous, technically brilliant, and well worth at least a 5 minute walk around (you can stroll around many of the displays in 360 degrees- very good move!). A plastinated whole ostrich stands next to it, and for a muscular anatomy geek like me, it was nirvana. However, in a churlish moment I had to look away from a panel explaining that an ostrich is “too heavy to fly” (I admit some younger visitors may need reminding of this). But then I looked into the big open space of this main hall, and the climax was before me. I think I’d had my climax a few times since this, but wow this was enormous in so many ways. All the ways. Mind-blowingly, vastly, geektastically kewl.

Gratuitious rhinoceros leg.

Across from the two posed ostriches and flanked by numerous smaller specimens, the elephant and giraffe stand frozen in vigil. There is also a lovingly detailed dissection of a huge male gorilla by the back wall and exit, with a panel reminding us that gorillas are (among) “our closest relatives.” The giraffe is precariously poised on one front toe-tip, in mid-gallop. What a great pose! There is the requisite explanation of how they solve the blood pressure problem in their neck (e.g. arterial valves), but also the statement, news to me, that they are the only animals able to ruminate while running. Who figured that out and how? I really want to know! Must be hard to check. (or was walking intended? Are my notes wrong?) Across from the full-fleshed plastinated giraffe (which I could see with my eyes closed after all our dissections from a month ago), there was another visually arresting and technically monumental giraffe on exhibit: one represented completely by small, reddish cross-sectional slices, from head to toes in a standing pose. That took me a while to absorb, it was so lovely, almost like a hanging mobile of morphological splendour.

There is a panel about genes and variation and inheritance. It is brief. (and it belongs there) Thank you. Let’s celebrate anatomy for anatomy’s sake for once!

“But John,” you might say, “What about the elephant? No love for the elephant? The star of the show?”

Zoinks! I want one! Stoic and triumphant (except against death and plastination), the Asian elephant is the centrepiece of the collection. (The book explains it was “Samba” from Neunkirchen Zoo, Germany, dead of some circulatory problem in 2005 and the first one plastinated, plus the inspiration for the animal show). I was speechless and paralyzed for a moment. I didn’t even know how to start looking at the partly-exploded-to-show-its-insides elephant. I actually avoided it for a while, looking closely at the other specimens, and building up anticipation, before stepping up and taking a long, intense look at this tall drink of water.

Go see the elephant. If you know basic anatomy, look at its leg muscles. Check out the huge triceps, still attached to the elbow; I like to say it is the size of a graduate student. Same for the analogous superficial gluteal and somewhat-fused biceps femoris muscles on the rear end, around the thigh/knee joint. Huge! I’ve never been able to view a standing dissected elephant, so this really impressed me more than a table full of giant muscle slabs like I normally deal with. And best of all, for me, the “false sixth toes”; the prepollex and prehallux; are visible in all four feet (but not noted anywhere, even in the book; too bad, these things were widely known by anatomists before my work on them). So much to marvel at here. It is an anatomical treasure. I wish I had a 3D image of it to use for anatomical studies- it was so easy to identify every single muscle group (except for a few missing around the shoulder/neck), even in the distal limbs. Hmm, photogrammetry might be possible (nugget of idea begins to crawl around John’s brain like a Zimmerian parasite)…

Behold, the triceps muscle of an elephant!

Behind that gorgeous elephant, don’t miss the wall mountings of two cross-sectional slices: through the head/neck of a moderate-sized elephant (How!?!?) and distal leg (no predigits but good features). And definitely don’t miss the stool (non-fecal, furniture form). I almost did. A wooden stool is shaped like a newborn elephant and a cross-section of the body is adhered on top of it. I assume you cannot sit there, and I am very glad that it was not, as I first imagined, an actual plastinated baby elephant turned into a stool. That would be bad taste.

The exhibit is in very good taste, without exception, and although I am gore-desensitized to say the least, it is not gory in my view. The plastination process preserves the reality and even some of the colour faithfully, but renders it just unreal enough (past uncanny valley territory?) that it should not be very disturbing to most viewers.

You can’t leave with your own photographs, but you can be schnookered into buying the exhibit book (£12.99) and a couple of packages of nice colour postcards (£4 for six; excellent quality images and cardstock IMO). The book and postcards show many of the exhibit specimens but not all, and include some others that are not on exhibit. I was saddened that the bear was left out—very cool image of that in the book. I’ve only skimmed the book a bit. I was annoyed by a few mistruths about elephants (25mph running speed, “have no ankle joints, which is one of the reasons why elephants cannot jump”, the bones “do not contain any marrow”—wrong, 15mph and there are ankles, they just are not very flexible (but not immobile either); also the bones do contain marrow (how could a large vertebrate survive entirely without it???) but just not as much of it per unit volume, due to lots of spongy bone). But I am still very happy with the 139 pages chock fulla pretty images, which is all I really wanted. Indeed, the book is a great pictorial anatomical reference- some of the species such as elephants and giraffe lack a really good anatomical resource in the modern, or any, literature! The exhibit shop also sells some good anatomy texts, mostly on humans but I recommend “Animal Anatomy for Artists” very strongly; I use that regularly in my own work.

So, £29.99 of schnookering later (haha, poor victimized me!), I emerged and reflected more on what I’d seen. I’m still a bit giddy about it all. I like the minimalism in most aspects- black backgrounds, minimal signage (but just enough to make it educational—when they got the facts right), focus kept on the specimens. Well done there. The spectacle of the specimens I’ve raved plenty about- it is not at all disappointing. It is AWESOME in every sense. I feel I easily got £9 of value from the ticket, and would (probably will!) pay it again. It is a profound experience to see the rich anatomical detail exposed, and be able to circumnavigate the specimens to absorb multiple perspectives. If you know some anatomy, you’ll be doubly rewarded at least, and if you bring your own phylogenetic perspective that can be trebled.

Baby white rhinoceros. Sad infant mortality.

What makes me happiest after my visit is realizing that we are in an anatomical renaissance for science and public interest therein. Exhibits like this and documentaries like “Inside Nature’s Giants” have tapped a public interest and curiosity in the wonders of basic anatomy. Anatomy is at the core of so many biological sciences and is so immediately accessible to people, because we all have anatomy. Anatomy is at the crossroads of art and science; it is visual, variable and complex, yet concrete, objective and easy to relate to. “Animal Inside Out” is a spectacular blend of art and science. They nail the artistic aspect, and the science is done reasonably well (despite my few gripes)—the exhibit’s science speaks for itself, in a way, although many visitors will need a nudge to grasp that.

I’d like to make a call for a permanent exhibit of the likes of “Animal Inside Out” in the UK. We deserve this! Museum exhibits could use something new, other than lame, quickly broken digital pushbuttons and bland skeletons devoid of soft tissue context (although the latter can be sufficient, e.g. at the Paris NMNH). That’s what makes “Animal Inside Out” (and Body Worlds) such a hit- as Hagens is quoted on the book dustcover, animal anatomy that goes beyond digitized abstractions and dusty bones is able “to sharpen our sense of the extraordinary by looking at the self-evident.” I could not say it better myself. This exhibit is extraordinary; that is self-evident after even a peek. It is a loving tribute to how fantastic the totality of animal structure is. Go! Enjoy. Absorb. Gape. Stare. Thrill. Revel. Think. Question. IT’S BEAUTIFUL.

Impressive hippo mouth says “Farewell for now.”

Edit: @samjamespearson on Twitter has kindly posted some photos (for free NHM/AIO publicity) of the exhibits and here are the links, now that they’re out there– SPOILERS! And thanks, Sam! I don’t think these really spoil the intense visual experience of actually being there and walking around the specimens, not at all.

octopus, whelk, squid, needlefish, scarlet haze of shark, hare brain, cat nerves,  bactrian camel, another camel,  bull (I forgot to mention it; this one was pretty great!)

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Party time! Let the media onslaught begin! We’ve published a paper in Nature on the limb motions of Ichthyostega (and by implication, some other stem tetrapods). Since we did use some crocodile specimens from Freezersaurus (see below) in this study, I figured WIJF could cover it to help celebrate this auspicious event. Briefly. Particularly since we already did a quasi-blog on it, which is here:

http://www.rvc.ac.uk/SML/Research/Stories/TetrapodLimbMotion.cfm

and some juicy fossily images at:

http://www.rvc.ac.uk/SML/Research/Stories/TetrapodImages.cfm

However I want to feature our rockin’ cool animations we did for the paper, to squeeze every last possible drop of science communicationy goodness out of them. So here they are in all their digital glory. Huge credit to Dr. Stephanie Pierce, the brilliant, hardworking postdoc who spearheaded the work including these videos! Dr. Jenny Clack is our coauthor on this study and the sage of Ichthyostega and its relatives- her website is here. Also, a big hurrah for our goddess of artsy science, Julia Molnar, who helped with the videos and other images. Enjoy!

The computer model

The forelimb model

The hindlimb model

We used some of my Nile crocodile collection to do a validation analysis of our joint range of motion (ROM) methods, detailed in the Supplementary info of the paper, which I encourage anyone interested to read since it has loads more interesting stuff and cool pics. We found that a bone-based ROM will always give you a greater ROM than an intact fleshy limb-based ROM. In other words, muscles and ligaments (and articular cartilage, etc.). have a net effect of reducing how far a joint can move. This is not shocking but few studies have ever truly quantitatively checked this with empirical data from whole animals. It is an important consideration for all vert paleo types. Here is a pic of one of the crocodiles from the study, with (A) and without muscles (B; ligaments only):

I’ll close with Julia Molnar’s jaw-droppingly awesome flesh reconstruction from our model. Why Nature wouldn’t use this as a cover pic, I’ll never understand, but I LOVE it! When I first saw it enter my email inbox and then opened it to behold its glory, my squeal of geeky joy was deafening.

(edit: Aha! Fellow Berkeley alum Nick Pyenson’s group made the Nature cover, for their kickass study of rorqual whale anatomy, including a “new” organ! Well, we don’t feel so bad then. Great science– and a win for anatomy!!!)

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This post will walk through the basic steps we take to do some of the major, ongoing research in my team. It comes from our lengthy project aiming to determine how elephant legs work at the level of individual muscle/tendon/bone organs. We need fancy computer simulations because anatomy, mechanics, physiology, neural control etc. are all very complex and not only impossible to completely measure in a living, moving animal but also extremely unethical and unjustified in the case of a rare, fragile animal like an Asian elephant. We want to do such complex things to test hypotheses about how animals work. For example, we want to estimate how fast an elephant could run if it wanted to, or why they cannot (or will not) jump or gallop like smaller mammals do— even as baby elephants (~100 kg or 220 lbs), which is an ancillary question we’re tackling. That’s cool basic science, and that’s enough for me. But the applications once such models and simulations are established are manifold– human clinical research now routinely employs such approaches to help treat “crouch gait” in patients with cerebral palsy, plan corrective surgeries, aid in rehabilitation strategies, and even potentially optimize athletic performance. Non-human research is pretty far behind this kind of confident application, because there are too damn many interesting non-humans out there to study and not many people using these approaches to study them (but it’s catching on).

Breaking up the monotony of the text with a baby elephant we met during our research in Thailand (Chiang Mai, here) in 2001. It was just a few days old and VERY cuddly and playful (chewing on everything!) but it’s mother did not want us playing with it so we only gave a quick hello.

I use the term model to refer to a simple abstraction of reality (such as an anatomically realistic computer graphic of a limb), and a simulation as a more complex process that is more open-ended and generally uses a model to ask a question (such as what level of extreme athletic behaviour a modelled limb could support). We use models and simulations to test how all the structures of the limb work together to produce movement. This also reciprocally gives us insight into the question, as I like to say it, of why is there anatomy? What is anatomy for? Why does it vary so much within so many groups and not so much in others? This can more easily be addressed by focusing on the consequences of a given anatomy rather than the more tricky question of why it evolved.

These approaches also can answer the frightening question of “Does anatomy really matter?” Sometimes it does not. And those “sometimes” can be impossible to predict- although sometimes they can be easy to predict, too. I think we are not at a point in the maturity of biomechanics/functional morphology to usually know a priori when either is the case.  Many factors in addition to anatomy determine function, behaviour, or performance; that’s why; and biomechanics aims to unravel those relationships. A lot of anatomists, palaeontologists, etc. assume that form can be reliably used to predict function, but plenty of studies have shown already (and if you peer deeply into the details, it comes from first principles) that one cannot be sure without either measuring what anatomy is doing in a particular behaviour or estimating that function in a computer model or simulation.

Anyway, I’ve covered my perspective on this in a paper which you can read if you want to go into deep philosophical details of the science (and read me blabbering on more about this particular hobby horse of mine?). This post will proceed mostly with pretty images and simple explanations, although I welcome comments and queries at the end. As part of this post, I’ll try to give an idea of the timespans involved in doing the research. Some steps are quick and easy; others can take dauntingly long — especially to do well, without building a digital house of cards.

I’ll start, as my posts often do, with a deceased animal, and in this case it will again be an Asian elephant. Incidentally it is the same animal from the “Inside Nature’s Giants” series (see previous post).

Above: the hindlimb viewed from the rear, showing the medial (inside) region of the thigh skinned down to the superficial musculature. The hip is toward the left of the screen, and the knee is to the far right (whitish rounded area), with the shank (still bearing most of its grey hide) heading to the bottom right corner of the picture. Muscles pictured include ST (semitendinosus) and SM (semimembranosus); major hamstring muscles; as well as the thin, sheet-like gracilis, the straplike sartorius, and the massive adductors toward the top of the image.

When collecting data from dissections for functional analysis including computer models and simulations, we dissect the muscles one by one as we identify and photograph/sketch them, then remove them and do a suite of measurements to characterize how their form relates to some basic functional parameters. From the mass (weight) of the muscle and the length and angulation (pennation) of its fibres (bundled as fascicles) we can estimate what is called the physiological cross-sectional area (PCSA) of each muscle, which is known to strongly correlate with the force the muscle can produce. Different muscles have different PCSAs; for example check out these pictures of a long-fibred, lower-PCSA muscle and a short-fibred, highly pennate and high PCSA muscle:

Above: the long muscle fibres (bands running from left to right, somewhat diagonally from the bottom left corner toward the top right) of a hip adductor muscle in our specimen. The adductors are fairly simple muscles that run from the underside of the pelvis to the inside of the thigh (femur).

Above: the tensor fasciae latae (TFL; pretty sure of ID but going from memory) hip muscle of our specimen, cut open to show the short, angled fibres (each leading at around a 45 degree angle to attach onto a thick central internal tendon). The TFL is just out of view at the top of the screen in the whole leg anatomy picture above; it is on the front outer, upper margin of the hip/thigh and runs down to the outer side of the knee, invested with thick sheets of connective tissue (fascia).

The maximal isometric force (Fmax) of a muscle is computed as the PCSA times the muscle stress (force/unit area), which is fairly conservative in vertebrates. A square meter of PCSA can produce around 200-300 kilonewtons of force, or about 60,000 cheeseburger-weights (the standard unit of force on this blog). That’s a lot of quarter pounders! And an elephant has pretty close to that many cheeseburgers worth of leg muscle (around 150 kg mass, very close to a square meter of PCSA; total Fmax would be around 80,000 cheese-burger weights!). That much muscle is important because an Asian elephant like this one weighed 3550 kg or about 9000 cheeseburger-weights. So if all the muscles in one elephant hindlimb could push in one direction at once, in theory they could hold about 9 elephants aloft. However, as the picture above shows, they do not all act in the same direction. Furthermore, there are many other factors involved in determining how hard a leg can push, such as the leverage of the muscle forces versus the actions of gravity and inertia (mechanical advantage). All those factors, again, are why we need computer models to address the complexity. But the end result is that elephants cannot support 9 times their body weight on one hind leg.

Enough talk about cheeseburgers and enough possibly savory pictures of giant steak-like leg muscles. I don’t want to be blamed for hunger-induced health problems in my beloved blog-readership, dear Freezerinos! The above steps take about a week to complete for 2 legs of a big elephant, rushing against decomposition to try to get the best quality data we can. On to the digital stuff- let’s turn the geekitude dial up to 11 with some videos of computer modelling.

Our next step, often featured on this blog because I do this so often, is to take CT (and/or MRI) scans of the specimen that we wisely did before we cut it to bits, and use those to make a computer model. That’s the easy step; a scan nowaways takes me less than an hour to complete, including moving the specimen back and forth between the freezer and imaging centre. MRI scans can take quite a bit longer. Here is a CT scan of a similar hindlimb (right leg for the toes up to the knee, from a juvenile elephant; the above leg was too big for our scanner!). See what you can identify here:

And then here is a resulting computer model of the same animal (just knee down to toes), showing how we took each CT slice of even the muscles and turned them into fully or partially 3D digital organs, in our case using commercial software that makes this procedure (a step called segmentation) very easy:

The segmentation step for bones is usually incredibly simple; it can take anywhere from an hour to a day or so, depending on anatomical complexity and image quality. For muscles, this is harder because the images are often more hazy and muscles tend to interweave with each other, segue into tiny tendons, take sudden turns through bones or other narrow spaces, or even fuse with other muscles. So when we do this kind of musculoskeletal modelling, it gets pretty laborious, and can take weeks or months to finish.

Ahh, but once you’re done with the basic anatomy, the real fun begins! We take the 3D images of bones, muscles, etc. and import them into our biomechanics software. We use two packages: one commericial item called SIMM (Software for Integrative Musculoskeletal Modeling) for making models, and a nice freebie called OpenSim for doing simulations (although actually we’re finding SIMM is often better at doing both modelling and simulation for more unusual animals). Quite a bit more anatomical work is required to get the joints to move properly, then position the muscles in accurate or at least realistic 3D paths (depending on segmented image quality), then check the muscles to ensure they move properly throughout the joints’ ranges of motion, then import all the PCSA and Fmax and other data we need from dissections, then do a lot more debugging of the model… this takes months, at least.

But the greatest joy and pain comes in getting the biomechanics done with the models and simulations. You can get quite simple data out of the models alone; such as the leverages (moment arms) of individual muscles and how these change with limb joint position, across a gait cycle, etc… That’s pretty interesting to us, and can just take a few days to crank out from a finished model. Yet the ultimate goal is to do either a tracking simulation, in which we make the model try to follow forces and motions that we measured in experiments from the same or a similar animal (standard, harmless gait analyses), or a theoretical simulation, in which we set the model a task and some rules (‘optimization criteria’) and then set it to run (for hours, days or weeks) to solve that task while following the rules. In both cases, the simulations estimate the muscle activation timings (on/off and intensity) and forces, as well as the kinematics (motions) and kinetics (forces) of the limbs. Then we check the results, play around with the inputs (unknown parameters) as part of a sensitivity analysis, and re-run the analyses again, and again, and again… Here is a draft of a tracking simulation we’ve run for our elephant’s hindlimb:

Above: again, a right hindlimb of an Asian elephant. This test of our tracking simulation is replicating real experimental data (from motion capture and force platform analysis) of an elephant running at near its top speed; over 4 meters/second (>10 mph/16kph). The red lines are the individual muscles, and the green arrow is the ground reaction force, equal and opposite to the force that the limb applies to the ground. In a fast elephant that force can exceed the elephant’s body weight, so the muscles need to crank out kilo-cheeseburger-units of force!

And that’s about as far as I’ll get today. My team’s previous research (explore links for some fun videos) has shown that elephants can run about 7 meters/second (~15mph; 24kph) and that they have pretty poor mechanical advantage when they do run, so their muscles must have to work pretty hard (about 6 times more cheeseburger units in a fast run vs. a slower walk). So how do they do it? And what prevents them from going faster? What would happen if they jumped? What limits speed more; muscles, tendons or bones? Stay tuned. I’m still not sure how much longer this final step of the research will take… (presumably will precede the heat death of the universe by a long shot) But overall, the whole process when everything works nicely can take a year or so to do, proceeding from whole limbs to a simulated limbs.

As a final teaser, here is work we’ve done on using a different kind of model, called finite element analysis (FEA), to estimate how many cheeseburgers it would take to break an elephant’s femur (thigh bone), for example. How “overbuilt” are bones vs. muscles or tendons? This is still a poorly resolved question in biology. We’ve established some rigorous methodology for doing this, now we just need to see what answers it gives us…

(the colour shows the strain (deformation) in the bone in a simple bending experiment; “hot” colours are higher strain. The visualization of the strain is greatly exaggerated; in the real results they are barely visible, as bone only bends a tiny amount before fracturing)

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A superficial little post for you today, with a skinny specimen from the freezers. What is it, what/where from, etc; tell me what you know about it!

(upper object, not the ruler…)

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Like other birds, ostriches are fluffy. Too fluffy for some anatomists– so fluffy, it’s hard imagining or estimating what they look like beneath all the feathers. A few years ago, we received an ostrich from a UK farmer. The male bird had been killed by a kick to the neck from another rival, and at the time was supposedly “Britain’s largest ostrich.” As the feathers were valuable to him, the farmer delivered the animal to us whole but plucked. I wanted to dissect it mainly to refresh my memory on ostrich anatomy while developing a biomechanical model of their limbs (see below). Taphonomy expert Jason Moore then buried it for his studies of how bodies decompose.

[Side note: ostriches and other ratites (flightless birds, members of the palaeognath group, whose evolution remains fascinatingly complex) are often brought up as uniquely dinosaur-like. That's rather misleading; all birds are living dinosaurs, so all birds are descended from an ancestor that was equally 'dinosaur-like'. What we see of them today is a snapshot that is biased by their recent evolutionary history. During their apparently multiple losses of flight, ratite birds increased in body size and "re-evolved" (or simply enhanced) some traits that were more marked in extinct dinosaurs than in the most recent common ancestor of living birds. Some of those more 'primitive' traits may be due to flightlessness, some due to large size, some due to their extreme running specializations; science hasn't sorted all that out just yet. But the point is, ostriches and other ratites are far from the ancestral form that all birds sprung from, which was probably more like a small, flying tinamou-like animal. Their similarities are due to convergent evolution. And they're still quite different from something like an "ostrich-mimic" dinosaur- which is a sad misnomer because it's more that ostriches mimicked (in a naughty teleological sense) ostrich-mimic dinosaurs like Struthiomimus than the other way around; the ornithomimosaurs did it first (Huzzah!). Ratites have just gone back, in some ways but not others (e.g. no long tail or large arms) to a superficially more primitive body form. There have been some wacky ideas to the contrary before, such as the idea that ratites evolved entirely separately from other living birds from different dinosaur stock, but they're so discredited now by multiple lines of evidence that I won't glorify them by spending time discussing each. This tangent has gone on too long and must die.]

Anyway, back to the plucked ostrich in question. My first look at it really stunned me. It was a powerful example of just how ‘dinosaurian’ most of the anatomy of living birds is, for reasons noted above. I’d never seen a naked ostrich and now I’ll never look at them the same again. Maybe you won’t, either…

First, some images of the animal once it was brought into our dissection room (which you might recognize from the great Inside Nature’s Giants documentary).

The device near the top of the screen is a digital scale; we were weighing the bird before we cut in…

Close-up view of the hugely muscular legs (each leg is around 25% of the animal’s body weight, and mostly muscle; about 50% more bulky than our legs), and the arms (shown more below).

129 kg weight sans feathers; not bad! That’s about 284 pounds for those folks still mired in the medieval Imperial system of units. :)

The swollen, bloody region just below the head (on the left above) is where the mortal blow struck. Ouch!

I love the hands of ratite birds. Yes, those are little claws attached to the three vestigial fingers (thumb/first finger at top, long middle finger, and tiny third finger bound to it). Darren Naish covered some of this in a previous post, and let’s not forget SV-POW’s excellent series of “things to make and do” involving various critters including ostriches.

Ostriches and I go way back. Here I am from my less bald immature postdoctoral days at Stanford University in 2002, dissecting a smaller (female, 65kg) ostrich for some biomechanical modelling (still mostly unpublished; aaargh!).

And yes, I had a third hand back then; later lost during a tragic dissection incident involving a battleaxe and a bottle of tequila. I don’t want to talk about that.

Ostrich packed for transport. Just barely fit in the trunk of my little 1993 Toyota Tercel (R.I.P.)!

Once we complete dissections. we put everything together in some fancy biomechanical computer models (a subject of a future post), resulting in a nice, 3D,  poseable, anatomically-realistic model of the entire limb musculature, shown above. This is a right hindlimb in side view, with the individual muscle paths abstracted as red lines. More about this when it is finally published…

This is just a teaser showing off some of the cool external anatomy of ostriches-in-the-buff, and what we’ve done with the anatomical data we’ve gathered. I’ll do a post later showing what’s inside, which is also pretty amazing. Hope you enjoyed it!

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