Posts Tagged ‘biomechanics’

A very short post here to plug BBC Radio 4’s excellent second series of “Just So Science”. These are 15 minute stories involving a reading of parts of Rudyard Kipling’s great British/natural history stories, and then examining how the science of today informs us about the real lives of animals, without resorting to just-so stories a la Kipling (co-opted as a term in evolutionary biology, too!). I was featured last year on rhinos.

I’m featured this year on kangaroos (now available online) and elephants (also available online now). I just listened to the kangaroo episode and it was good fun. I’ve studied the biomechanics of kangaroos a bit, in as-yet unpublished work featured here in a BBC News story (video from that work is below), and we’ve done other work on their bone morphology and how it relates to body size that is sure to come out in not too long.

Don’t blink! Or, for your enjoyment, a looping GIF:

kangaroo hop

My freezers feature heavily in one bit, in which you can hear me vent my frustrations about an unlabelled bag and stacks of specimens– where is the wallaby? And what’s that crinkling noise?

Best beloved, it is the sound of science. Just so. Enjoy!

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(John: here’s a guest post from my former PhD student, soon to be 100% legit PhD, Dr., and all that jazz, Julia Molnar!)

This is my first guest post, but I have been avidly following what’s in John’s freezer (and the blog too) for quite a while. I joined the lab in 2009 and left a month ago on the bittersweet occasion of surviving my PhD viva (oral exam/defense), so I’d like to take a moment here to thank John and the Structure & Motion Lab for a great 4 years!

Moving on to freezer-related matters; specifically, a bunch of frozen crocodile spines. It was late 2011, and the reason for the spines in John’s freezer was that John, Stephanie Pierce, and I were trying to find out more about crocodile locomotion. This was anticipated to become my first major, first-author research publication (but see my Palaeontologia Electronica paper on a related subject), and I was about to find out that these things seldom go as planned; for example, the article would not be published for more than three years (the research took a long time!). Before telling the story of how it lurched and stumbled toward eventual publication, I’ll give you some background on the project.

Stomach-Churning Rating: 3/10; x-ray of dead bits and nothing much worse.

A stumbly sort-of-bounding crocodile. They can do better.

First of all, why crocodiles? For one thing, they’re large, semi-terrestrial animals, but they use more sprawling postures than typical mammals. Along with alligators and gharials, they are the only living representatives of Crocodylomorpha, a 200+ million year-old lineage that includes wolf-like terrestrial carnivores, fish-like giants with flippers and a tail fin, even armored armadillo-like burrowers. Finally, crocodiles are interesting in their own right because they use a wide variety of gaits, including bounding and galloping, which are otherwise known only in mammals.

Nile croc

Nile crocodile skeletal anatomy

OK, so why spines? Understanding how the vertebral column works is crucial to understanding locomotion and body support on land, and inter-vertebral joint stiffness (how much the joints of the backbone resist forces that would move them in certain directions) in particular has been linked to trunk movements in other animals. For this reason, vertebral morphology is often used to infer functional information about extinct animals, including dinosaurs. However, vertebral form-function relationships have seldom been experimentally tested, and tests on non-mammals are particularly scarce. So we thought the crocodile spines might be able to tell us more about the relationship between vertebral morphology, mechanics, and locomotion in a broader sample of vertebrate animals. If crocodile spine morphology could be used to predict joint stiffness, then morphological measurements of extinct crocodile relatives would have some more empirical heft to them. Several skeletal features seem to play roles such as levers to mechanically stiffen crocodile spines (click to emcroc’en):

Croc vertebra-01

Anatomy of a crocodile vertebra

We decided to use a very simple technique that could be replicated in any lab to measure passive stiffness in crocodile cadavers. We dissected out individual joints were and loaded with known weights. From the movement of the vertebrae and the distance from the joint, we calculated how much force takes to move the joint a certain number of degrees (i.e. stiffness).

Julia w vertebra (480x640)

Me with crocodile vertebra and G-clamp


X-ray of two crocodile vertebrae loaded with a metric weight to calculate their joint’s stiffness

Afterwards, we boiled the joints to remove the soft tissues – the smell was indescribable! We took 14 measurements from each vertebra. All of these measurements had been associated with stiffness or range of motion in other studies, so we thought they might be correlated with stiffness in crocodiles also.


Some of the vertebral measurements that were related to stiffness

Despite my efforts to keep it simple, the process of data collection and analysis was anything but. I recall and exchange with Stephanie Pierce that went something like this:

Stephanie: “How’s it going?”

Me: “Well, the data are messy, I’m not seeing the trends I expected, and everything’s taking twice as long as it was supposed to.”

Stephanie: “Yes, that sounds like science.”

That was the biggest lesson for me: going into the project, I had been unprepared for the amount of bumbling around and re-thinking of methods when the results were coming up implausible or surprising. In this case there were a couple of cool surprises: for one thing, crocodiles turn out to have a very different pattern of inter-vertebral joint stiffness than typical mammals: while mammals have stiff thoracic joints and mobile lumbar joints, crocodiles have stiffer lumbar joints. Many mammals use large lumbar movements during bounding and galloping, so crocodiles must use different axial mechanics than mammals, even during similar gaits. While that’s not shocking (they did evolve their galloping and bounding gaits, and associated anatomy, totally independently), it is neat that this result came out so clearly. Another unexpected result was that, although several of our vertebral measurements were correlated with stiffness, some of the best predictors of stiffness in mammals from previous studies were not correlated with stiffness in crocodiles. The study tells a cautionary tale about making assumptions about extinct animals using data from only a subset of their living relatives or intuitive ideas about form and function.

Finally, the experience of doing the experiments and writing the paper got me interested in other aspects of crocodilian functional anatomy. For instance, how does joint stiffness interact with other factors, such as muscle activity and properties of the ribs, skin, and armor in living crocodiles? Previous studies by Frey and Salisbury had commented on this, but the influence of those factors is less tractable to experiment on or model than just naked backbones with passively stiff joints. In the future, I’d like to study vertebral movements during locomotion in crocodiles – especially during bounding and galloping – to find out how these patterns of stiffness relate to movement. In the meantime, our study shows that, to a degree, crocodile backbone dimensions do give some clues about joint stiffness and locomotor function.

To find out more, read the paper! It was just featured in Inside JEB.

Julia Molnar, Stephanie Pierce, John Hutchinson (2014). An experimental and morphometric test of the relationship between vertebral morphology and joint stiffness in Nile crocodiles (Crocodylus niloticus). The Journal of Experimental Biology 217, 757-768 link here and journal’s “Inside JEB” story

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What a week!

My team had a new technician arrive, Kyle Chadwick from Uni. Virginia, and NSF Postdoctoral Research Fellow, Dr. Ashley Heers (see here for an example  of new stuff she’s starting here at the RVC!), started working with me at the RVC, and then these guys showed up…


Woo hoo!

First a tiger salamander (Ambystoma) paid a visit, for filming an episode of the Windfall Films/PBS documentary “Your Inner Fish” (a la the famous book):

So cute! Tiger salamander, soon to be a TV celebrity.

So cute! Tiger salamander, soon to be a TV celebrity.

Dr. Stephanie Pierce (who was also a coauthor on a great open access croc paper in Proc Roy Soc B this week) was filmed with Prof. Jenny Clack to recap some of our past work on tetrapod locomotion. Watch out for the 3-part series!

And that gorgeous salamander was a star performer in strutting his stuff for the camera to demonstrate the locomotion of modern tetrapods, including some lovely slo-mo footage from our lab cameras:

(if that’s too slow for you, try the normal-speed footage. I’ll admit, salamanders don’t really need slo-mo video for normal walking, but I like it)

So cool!

But then we got a special package… with three frozen fire salamanders (Salamandra salamandra) from colleagues in Germany!

Three new occupants of the freezers, for planning our studies of salamander locomotion

Three new occupants of the freezers, for planning our studies of salamander locomotion

This marks the start of an exciting new period in my team’s work in the lab. I’ve always liked salamanders and newts, and we’ve scanned and modelled plenty (e.g. this old post), but now we’re going to work with live fire salamanders (a first for me)! We are using the dead ones to plan the new studies with the live ones– these new studies will involve lots of high speed videos and force platform analysis (as shown above), in conjunction with XROMM (biplanar fluoroscopy/3D skeletal motion analysis) and other techniques including computer simulations. We got initial approval this week to work with these salamanders, and found a reputable source this week too, so it was definitely Salamander Week in my group!

This research all will feed into our upcoming studies of extinct tetrapods: we’re using salamanders to figure out how salamanders move and what limits their speed and gait, and then we’re using the same sorts of computer tools to try to estimate how extinct tetrapods may have moved and how locomotion evolved, in much more specific detail than our prior work had done, which was mainly about using 3D reconstructions of anatomy to show what those animals could not do. More about the project here.

Watch this space for more scampering salamanders!

UPDATE: And here’s one! Not quite scampering, but…

Setting up our two fluoroscopes for a test run of our gait studies-- but with one of the deceased salamanders. Gotta get a good image  before any live animal work!

Setting up our two fluoroscopes for a test run of our gait studies– but with one of the deceased salamanders. Gotta get good images before any live animal work begins!

An example of the kind of footage we’re aiming for (single 2D fluoroscope view from Nadja Schilling’s team’s research; see XROMM website for more details on the methodology)


I did a CT scan with a normal medical grade CT scanner at the highest resolution we can manage (0.625 mm slices). Check out the results below, which amuse me:

Looks like a toy; too crude resolution. But we can see major structures, and we can very nicely see the “microchip” (which looks HUGE) that was placed in this animal’s back when in captivity, and then another structure is visible near the pelvis which might be another chip or else remains of some food, pathology, or a really odd pelvis– I am not totally sure!

So this is why we tend to use microCT, which can go down to as low as ~5 micron resolution, to get 3D anatomy of animals this small. It’s no surprise to me, but it is fun to see how far we could push our normal CT machine. The results aren’t horrid but wouldn’t have much scientific value for us. They did confirm for us that this specimen is heavily ossified, so the faint images of bone that we are getting in our x-ray fluoroscopes (above) are due to something going wrong with our camera system, not the animal’s immature skeleton. Stay tuned for more updates as the science happens!


20 wonderful adult Fire Salamanders have joined our team and are relaxing over the coming week before we start taking them for walks. Here is one exploring its new home:

Fire salamanderUPDATE 4:

August 11-15, 2014 we are in Jena, Germany using their fancy biplanar radiography system (“x-ray video”) to study our salamanders, at last! Follow the tweets starting here, for more information as it happened! https://twitter.com/JohnRHutchinson/status/500187568416518144

and this video of “Jabba” the corpulent salamander walking-

with a top view, too-

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So in my last post I promised to put up the videos of my cat biomechanics footage online (cut scene from “The Secret Life of the Cat” documentary). Here I deliver on that promise.

Note that all this footage was filmed at 250 frames/second, so it is 10 times faster than conventional UK/EU (PAL format) video and thus it plays 10x slower if replayed at PAL format speeds. Hence it is often called “slo-mo”/slow motion video. However, most experts would call it high speed video due to the high frame rate that gives us higher temporal resolution, ideal for studying fast movements.

It was cold that day; indeed the Colchester Zoo area where we filmed the tiger videos below had been snowed in earlier; so the posting of these videos on my freezer-based blog is DEFINITELY apropos.

First, the cat (named Ricochet, not Rocket, I now recall; I’m sure you’re all ineffably outraged at this mistake in my prior post) that we filmed to show how a standard; if rather shy; cat walks:

Second, here I am goofing off. High speed video is so fun! OK actually I was testing the video camera to ensure it worked; we only got one chance with each of 2 tigers. As you can imagine it’s not easy to get a tiger back in its indoor enclosure when it’s nice and sunny outside! So my gear needed to work, and it did, despite the cameraman’s bum being in the shot here:

Third, a tiger whom we filmed at Colchester Zoo. It nonchalantly strolled out of its indoor enclosure upon release. No drama. It was a bit unnerved by our presence but took its time.

Finally, this is the video that we were really hoping for with the tiger; a dramatic turn and gallop out of the “tiger chute” into its main enclosure:

Pretty nice! And thanks to the magic of blogging, you get to see it, rather than having it banished forever to the purgatorial cutting room floor!

Here are some parting shots of the male tiger happily checking out his snowy paddock upon release, and then…

Tiger outdoors

I turned around and he was checking me out; I was just on the other side of the fence. That was a fun surprise! Some close-up time with a curious tiger.2013-03-12 12.38.13

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…a daily picture of anatomy! And today it is five pictures; zza-zza-zee! ♫

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

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

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

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

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

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

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

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

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

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

Greyhound hindlimb for CT

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

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

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

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

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

Hindlimb segmentation of greyhound

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

Quite fetching image, eh?!

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

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

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

Happy Freezermas! Sing it: “On the fifth day of Freezermas, this blo-og gave to me: one tibiotarsus, two silly Darwins, three muscle layers, four gory hearts, a-and five stages modelling a doggie!” ♪

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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:


and some juicy fossily images at:


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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