Archive for the ‘Exalting Archosauria’ Category

Hi, sorry for the social media spam but this is important to me: I got EU money to study dinosaur movement and we made a website for the project. There will be some fun stuff posted there and nowhere else, such as new palaeo-art that we commissioned specifically for this project. Oh, and science, too! Five years of science!

So please have a look at it now that it is live!


I love our logo (by Andrew Bourne) so I will spray paint it everywhere I can.

Work from the DAWNDINOS project won’t be featured here much, so either watch that new website or me on other social media to find out what’s up!

And coming up on John’s Freezer: another episode of “Better Know A Muscle”! Yeah, baby!

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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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A Confuciusornis fossil; not the one from our study but prettier (more complete).

Today almost three years of collaboration come together in a publication that is a fun departure from my normal research, but also makes sense in light of it. Professor Baoyu Jiang from Nanjing University in China has been being working on the taphonomy of the Early Cretaceous Jehol biota from northeastern China (Manchuria) for a while, and he found a lovely Confuciusornis (early bird) fossil; one of thousands of them; from the volcanic pyroclastic flow-based lake deposits there.

Although at first glance the skeletal remains of that fossil are not fabulous compared with some other Confuciusornis, what makes this one lovely is that, on peering at it with multiple microscopic and other imaging techniques, he (and me, and a China-UK collaboration that grew over the years) found striking evidence of very well-preserved fossil soft tissues. Our paper reporting on these findings has gone live in Nature Communications so I can blog about it now.

Reference: Jiang, B., Zhao, T., Regnault, S., Edwards, N.P., Kohn, S.C., Li, Z., Wogelius, R.A., Benton, M., Hutchinson, J.R. 2017. Cellular preservation of musculoskeletal specializations in the Cretaceous bird Confuciusornis. Nature Communications 8:14779. doi: 10.1038/NCOMMS14779

Stomach-Churning Rating: 3/10; gooey, but fossil gooey, except for some colourful, gastrically-tolerable histology of bird tissue.

Front view of the ankle/foot of our specimen.

Back view of the ankle/foot of our specimen.

What has been fun about this collaboration is that, for one, it fits in perfectly with my prior work. Ever since my PhD thesis I’d been wondering about odd bones in the legs of birds, including a very puzzling and very, very neglected bit of bone called the tarsal sesamoid, on the outside of the upper end of the ankle joint. Furthermore, a tunnel of tissue called the tibial cartilage sits next to that sesamoid bone, and then across the ankle joint there is a bony prominence with grooves and tunnels that vary highly among bird species; that is called the hypotarsus. These structures are all known in living birds and, to a degree, in extinct fossil cousins. Our specimen seems to reveal an earlier stage in how these little features of bird ankles originated, which we concluded to be a step along the transition to the more crouched legs that modern birds have.

This study has also challenged me to broaden my horizons as a scientist. Although this was a big collaboration and thus we had several specialists to apply supercharged technological techniques to our fossil, I had to learn something about what all that meant. My kind colleagues helped me learn more about tissue histology, scanning electron microscopy, synchrotron mapping, FTIR and mass spectrometry and more. I won’t go through all of these techniques but there are some pretty pictures sprinkled here and in the paper, and a lot more detail in the paper for those who want the gory techno-detail. Basically we threw the kitchen sink of science at the fossil to crack open some of its secrets, and what we found inside was nifty.

Scanning electron micrograph image of probable tendon or ligament fibres (arrow) in cross-section, from near the ankle joint.

We found preserved cells and other parts of connective tissues including tendons and/or ligaments, fibrocartilage (the tougher kind) and articular cartilage (the softer joint-padding kind). That’s great, although not unique, but the kitchen sink also flushed out even more reductionist data: those tissues included some organic residues, including what appear to be bits of proteins (amino acids); particularly the collagen that makes up tendons.

Fibrocartilage (“fc”) from the ankle joint region.

Hopefully we’re right, and we included as much of the data as we could manage so that others can look at our findings. The specimen is crushed into nearly two dimensions, like all Jehol biota organisms, so its anatomy was hard to interpret but we think we got it right. All of the other kitchen-sinky tools have their own nuances and pitfalls but we did our best with a superb team of experts. We’ve had to wait 125 million years to uncover this specimen and a few more years to find out if we’ve looked at the right way is no greater test of patience.

I thank my coauthors, especially Baoyu Jiang for the kind invitation to participate and the very fun experience of collaborating. I think I’ll remember this study for a long time because, for me, it takes a step beyond just describing Another Case of Jaw-Dropping Fossilization (can you hear the hipsters recounting the excitement and cynicism of the 1990s when this all was dawning? I was there and maybe now I’m one of them). By combining all of those methods we learned new things about the palaeobiology of birds and the evolution of traits within birds. Confuciusornis, not shockingly, had ankles that should have functioned in ways intermediate between those of bog-standard non-avian theropods and modern birds.

Same anatomical regions in an extant bird as in the main fossil specimen. Left distal tibiotarsus (TT; below) and proximal tarsometatarsus (TMT; above) from an adult helmeted guineafowl (Numida meleagris) after formalin fixation. (from our paper’s Supp Info)

I’m hopeful that more synthesis of molecular/cellular, imaging, biomechanical and other tools (not to mention good old palaeontology and anatomy!) can wash away some more of this mystery. And it was fun to be a part of a study that adds to overwhelming evidence that was heretical ~25 years ago: some hardy biomolecules such as collagen and keratin can survive hundreds of millions of years, not just thousands. Pioneers such as Prof. Mary Schweitzer led the original charge that made reporting on discoveries like ours much easier today.

I know how the birds fly, how the fishes swim, how animals run. But there is the Dragon. I cannot tell how it mounts on the winds through the clouds and flies through heaven. Today I have seen the Dragon.“– Confucius, ca. 500 BCE.

Let’s finish with some images of a living bird’s ankle region, by co-author and PhD student Sophie Regnault. We considered these for inclusion in the paper but they didn’t fit quite right. I love them anyway so here they are:

Patchwork of histology slide images, from a guineafowl’s ankle (as per photo above). The numbered squares correspond to zoomed-in images below. The tibiotarsus is on the proximal end (bottom left); the tarsometatarsus is on the distal end (right side); and the enigmatic tarsal sesamoid is at the top. Magnification: 20x overall.

Region 1. nice (fibro)cartilage-bone inferface at ligament insertion.

Region 2: longitudinal slice through ligaments connecting the tibiotarsus to the tarsometatarsus across the ankle joint.

Region 3: front (bottom) of the tibiotarsus/upper ankle.

Region 4: tendon fibres in longitudinal section; on the back of the tibiotarsus. Some show mineralization into ossified tendons (“metaplasia”); another curious feature of modern birds.

Region 5: muscle attachment to the back of the upper tarsometatarsus bone. Small sesamoid fragment visible.

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Short post here– I have 4 jobs now opened on my team, 1 short-term one (~4 months or less) and 3 long-term ones (5 years; negotiable down to 2-3 minimum) as follows:

Stomach-Churning Rating: -10/10 Let’s do some SCIENCE!

  1. Research Technician in Vertebrate Anatomical Imaging; until ~1 December 2016 (some flexibility), on our Leverhulme Trust sesamoid bone grant. Lots of flexibility here and on a super fun, established project! Deadline to apply: 11 August (interviews will be 22 August)
  2. Part-time (50%) Research Administrator, on our ERC dinosaur evolution/locomotion grant until 2021. I’m hunting for someone that’s super organized and enthusiastic and not afraid of paperwork (it is EU funding, after all), but there is sure to be some involvement in science communication, too. Deadline to apply: 11 August  (interviews will be 31 August)
  3. Research Technician in Biomechanics; until 2021 as above. This post will not “just” be technical support but hands-on doing science. Some vital experience in biomechanics will be needed as the research will begin very quickly after starting. If the right person applies, we could agree for them to do a part-time PhD or MRes related to the grant research (but that’s not guaranteed in advance). Deadline to apply: 26 August (interviews will be 7/8 September)
  4. Postdoctoral Researcher in Biomechanics; until 2021 as above. This second postdoc on the project will join Dr. Vivian Allen and the rest of my team to push this project forward! I am keenest on finding someone who is good at biomechanical computer simulation, i.e., has already published on work in that general area. But the right person with XROMM (digital biplanar fluoroscopy), other digital imaging and biomechanics experience might fit. Deadline to apply: 23 August (interviews will be 7/8 September)

Update: all jobs have closed for applications.

Update 2: BUT not all the jobs are 5-year contracts. Some may open up again for new people in the future (but not very soon). Stay tuned…

Note that on the bottom of each page linked above, there are Person Specification and Job Description documents that explain more what the jobs are about and what skills we’re looking for in applicants. I strongly encourage any applicants to read these before applying. If those documents don’t describe you reasonably well, it is probably best not to apply, but you can always contact me if you’re not sure.

The project for jobs 2-4 is about testing the “locomotor superiority hypothesis”, an old idea that dinosaurs gained dominance in the Triassic-Jurassic transition because something about their locomotion was better in some way than other archosaurs’. That idea has been dismissed, embraced, ignored and otherwise considered by various studies over the past 40+ years but never really well tested. So in we go, with a lot of biomechanical and anatomical tools and ideas to try to (indirectly) test it! As usual for projects that I do, there is a healthy mix of empirical (e.g. experiments) and theoretical (e.g. models/simulations) research to be done.

Please spread the word if you know of someone right for any of these roles. I am casting a broad net. The next year (and beyond) is going to be a very exciting time on my team, with this big ~£1.9M ERC Horizon 2020 grant starting and lots of modelling, simulation, experiments, imaging and more. Non-EU/EEA/UK people are very welcome to apply– “Brexit” is not expected to affect this project. If you’re not familiar with my team, check out my “mission statement” for what we stand for professionally and as a team. Join us!

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Sorry about the title. It’s the best I could do. In case you missed it on our Anatomy to You blog, we unleashed a hefty database of CT (and some MRI) scans of our frozen crocodile cadavers last week, for free public usage. In total, it’s about 34 individuals from 5 species, in 53 databases constituting around 26,000 individual DICOM file format slices of data. This page has a table of what the data/specimens are. I am writing this post to share some more images and ensure that word gets out. We’re thrilled to be able to finally release this first dataset. We have plans to let loose a LOT more such data in the future, for various organisms that we study.

Stomach-Churning Rating: 2/10- be glad that these data don’t come with an olfactory component, especially the five rotten, maggot-ridden Morelet’s croc specimens, which are among the stinkiest things I’ve dealt with.

Crocodiles are no strangers to this blog, of course, as these past links testify. Indeed, most of the crocodile images I’ve blogged with come from specimens that are in this scan dataset. We even released a “celebrity crocodile, “WCROC” or FNC7 in our dataset, which is the 3.7m long Nile croc from “Inside Nature’s Giants”. It broke our CT scanner back in ~2009 but we got the data, except for the torso, and we also got some MRI scans from it, so we’re chuffed.

Above: The only spectacled caiman (Caiman crocodilus); and indeed the only alligatorid; in our dataset. To watch for: stomach contents/gastroliths, and all the damn osteoderms that I did/didn’t segment in this quickly processed file. This specimen had its limbs dissected for one of our studies, so only the right limbs are visible.

There are some more specimens to come- e.g. five baby Nile crocs‘ datasets (“GNC1-5”) are hiding somewhere in our drives and we just need to dig them up. You might also know that we published some scan data for crocodile vertebral columns (including fossils) in our recent paper with Julia Molnar et al. (and related biomechanical data discussed here), and we published all of our anatomical measurements for a huge set of crocodylian species in our papers by Vivian Allen et al. And then I had an enjoyable collaboration with Colleen Farmer and Emma Schachner on the lung anatomy of various crocodylian species, using these same specimens and related scan datasets.


Above: rotating Crocodylus moreletii (specimen FMC5 from our database) in a happy colour.

Sharing these kind of huge datasets isn’t so easy. Not only do few websites host them cheaply, and with reasonable file size limits, and limited headaches for what info you have to provide, and with some confidence that the websites/databases will still exist in 5-20 years, but also we were hesitant to release the dataset until we felt that it was nicely curated. Researchers can now visit my lab and study the skeletons (or in some cases, the still-frozen specimens) matched up with the scan data, and known body masses or other metadata. We’re not a museum with dedicated curatorial staff, so that was not trivial to reliably organize, and I still worry that somewhere in the dataset we mis-identified a specimen or something. But we’ve done our best, and I’m happy with that for now.

Above: rotating Osteolaemus tetraspis (specimen FDC2 from our database), which was obviously dissected a bit postmortem before we could scan it, but still shows some cool features like the extensive bony armour and the cute little doglike (to me, anyway) skull. I worked with these animals (live) a bit >10 years ago and came to love them. Compared to some other crocodiles we worked with, they had a pleasant demeanour. Like this guy:

Osteolaemus (resting) set up with motion capture markers for a yet-to-be-published study that we did in 2005 (ugh!). It wasn't harmed by this.

Osteolaemus (resting) set up with motion capture markers for a yet-to-be-published gait study that we did in 2005 (ugh!). It wasn’t harmed by this.

Anyway, as a person who likes to maintain quality in the science we do, I also was hesitant to “just” release the DICOM file data rather than beautiful segmented 3D skeletal (or other tissue) geometry that is ready for 3D printing or animation or other uses, or interactive online tools like Sketchfab. Other labs (e.g. Witmerlab) do these kind of things better than we do and they inspire us to raise our game in the future, but I am sure that we will be forgiven for releasing big datasets without gorgeous visuals and more practical, processed files — this time. 🙂  We agree with many other scientists that sharing data is part of modern, responsible science– and it can be fun, too! Oddly enough, in this case we hadn’t used the CT/MRI data much for our own studies; most of the scans were never fully digitized. We just scan everything we get and figured it was time to share these scans.

Enjoy. If you do something cool with the data that we’ve made accessible, please let us know so we can spread the joy!

And if you’re a researcher headed to ICVM next week, I hope to see you there!

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Last year we finally, after about 14 years of slow work, released our biomechanical model of an ostrich’s hindleg. We showed how it informed us about the potential leverages (moment arms; contributions to mechanical advantage of the joints) of all of the muscles. It was a satisfying moment, to understate it, to finally publish this work from my postdoc at Stanford. Today, we begin to deliver on that model’s promise. And it only took 4 years or so, roughly? The journal Royal Society Interface has published our study of how we used this musculoskeletal model to simulate walking and running dynamics. Those simulations join an intimidatingly broad and complex literature using similar models to study human (and some other primate) locomotion or other functions at the level of individual muscles (for whole limbs/bodies) in vast detail and growing rigor. I have Dr. Jeffery Rankin, a research fellow finishing up his post with me after ~6 years of hard work on many projects, to thank for driving this work forward, and Dr. Jonas Rubenson (now at PennState) for his patient collaboration that has continued since the early 2000’s.

Stomach-Churning Rating: 2/10; computer models of muscle actions. The underlying anatomical data are goopy, as prior ostrich-dissection-focused posts show!

Our model; in right side view (on the left) and frontal view (on the right), with muscles in red and the leg's force as the blue arrow; frozen at the middle of a step.

Our model; in right side view (on the left) and frontal view (on the right), with muscles in red and the leg’s force as the blue arrow; frozen at the middle of a running step.

Simulations like these predict things that we can’t easily measure in living animals, such as how much force muscles and tendons generate, how quickly those tissues change length, how much mechanical energy they thus contribute to the joints, limbs and whole body, how much metabolic energy their actions cost, and much more. There are more ways to use these tools than I have space or time to explain, but simply put we forced our ostrich simulation to match experimental measurements of the motions and forces of a representative walking and running ostrich stride, from contact of one foot until the next time that foot hit the ground. It then used optimization methods (minimizing target criteria like muscle stress) to estimate how the muscles and tendons were used to generate those motions and forces. This is a ways ahead of some prior ostrich simulations such as this one that I recall from classes during my PhD studies.

Any modeller worth their salt knows that their models and simulations are wrong at some level. This is much as most science is “wrong”; i.e. a simplification of reality with some errors/noise introduced by assumptions, variation, methods and such. But generally these kinds of musculoskeletal dynamic simulations hold up pretty well against experimental data. A standard “validation” is to test how closely the simulations’ predictions of muscle activity match the “real” (measured in life, also with some uncertain error) activity of muscles. Science still lacks those data for ostriches, but fortunately measurements from other birds (by Steve Gatesy and colleagues) indicate that muscles tend to follow fairly conservative patterns. Grossly speaking, avian leg muscles tend to either be active mainly when the foot is on the ground (stance phase) or off the ground (swing phase). Some studies acknowledge that this is an oversimplification and other muscles do act across those two phases of a stride, either in multiple pulses or as “transitional” (stance-to-swing or swing-to-stance) switch-hitters in their activations. Our ostrich predictions matched the qualitative patterns for avian muscle activations measured to date, so that’s good. The results also reinforced the notion of transitional or multi-phasic muscle activation as still having some importance, which bears more study.

Yet what did the simulations with our ostrich model tell us that other ostrich experiments or other bird species didn’t? Three main things. First, we could calculate what the primary functions of muscles were; they can act as motors (generating energy), brakes (absorbing energy), springs (bouncing energy back and forth) or struts (just transmitting force). We could then sum up what whole muscle groups were doing overall. The image below shows how these broad functions of groups vary across the stance phase (swing phase is harder to condense here so I’ve left it out).

Positive work can speed things up; negative work can slow things down.

Positive work can speed things up; negative work can slow things down. Solid bars are running; striped bars are walking. (from our Fig. 13) You may need to click to em-broaden this image for the gory biomechanical details.

There’s a lot going on there but a few highlights from that plot are that the hip extensor (antigravity) muscles (biarticular hip/knee “hamstrings”) are acting like motors, the knee extensors (like our quadriceps) are mainly braking as in other animals and the ankle is fairly springy as its tendons (e.g. digital flexors; gastrocnemius) suggest. We often characterize birds as “knee-driven” but it’s more accurate biomechanically to say that their hips drive (power; i.e. act as motors) their motion, whereas their knees still act as brakes — in both cases as in many other land vertebrates. Thus in some ways bird legs don’t work so unusually. Birds like ostriches are, though, a little odd in how much they rely on their hamstring muscles to power locomotion (at the hip) rather than their caudofemoral muscles, which are reduced. Zooming in on some particular muscles such as parts of the hip or knee extensors, the functions sometimes weren’t as predictable as their similar anatomy might suggest. Some muscles had parts that turned on during swing phase and other parts used during stance phase. Neural control and mechanics can produce some unexpected patterns.

Second, we looked at one important methodological issue. Simulations of musculoskeletal dynamics can vary from simple static (assuming each instant of a motion is independent from the others; e.g. ignoring acceleration, inertia, tendon effects, etc.) to more complex grades of fully dynamic flavours (e.g. assuming rigid or flexible tendons). We looked across this spectrum of assumptions, for both walking and running gaits, with the expectation that more static assumptions would work less well (vs. more dynamic ones; by various criteria) for running vs. walking. This also showed us how much tendons influence our simulations’ estimates of muscle mechanics—a fully rigid tendon will make the muscle do all of the work (force times length change) whereas a flexible tendon can literally take up some (or even all) of that slack, allowing muscles to remain closer to their isometric (high force-generating, negligible length change) quasi-optimum.

Nicely, our predicted muscle functions weren’t influenced much by these methodological variations. However, static assumptions  clearly were in some ways less appropriate for running than for walking, as were flexible tendons. Somewhat surprisingly, making the simulations more dynamic didn’t lower the levels of activation (and thus presumably the metabolic costs) of muscles, but actually raised those levels. There are good reasons why this might be realistic but it needs further study. It does muddy the waters for the issue of whether assuming that rapid locomotion can be modelled as static is a “bad” thing such as for estimating maximal speeds—yes, tendons can do more (elastic energy storage, etc.) if more dynamic models are used, but co-contraction of antagonistic muscles against each other also brings in some added costs and might lead to slower speed estimates. We’ll see in future work…

Finally, one often overlooked (sometimes even undiscussed!) aspect of these simulations is that they may silently add in extra forces to help muscles that are struggling to support and move their joints. The justification is typically that these extra “reserve actuators” are passive tissues, bony articular forces and other non-muscular interactions. We found that the hip joint muscles of ostriches were very weak at resisting abduction (drawing the thigh away from the body) and this needed resisting during the stance phase, so our simulations had very high reserve actuators switched on there. That fits the anatomy pretty well and needs more investigation.

Want to know more? Happily, not only is the paper free for anyone to view but so are all of the data including the models (modified slightly from our last paper’s). So, although the software (Opensim) isn’t ideal for 4-year-olds to play with (it is fancy engineering stuff), if you have the interest and dilligence it is there to play with and re-use and all that. But also watch this space for future developments, as there is more to happen with our steadily improving models of ostriches and other beasties. Anyway, while this paper is very technical and challenging to explain I am not too bashful to say it’s one of the finer papers from my career; a big stride forward from what we’ve done before. I have been looking forward for a long time to us getting this paper out.

P.S. Our peer reviewers were splendid- tough but constructive and fair. The paper got a lot better thanks to them.

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Happy Darwin Day from the frozen tundra sunny but muddy, frosty lands of England! I bring you limb muscles as peace offerings on this auspicious day. Lots of limb muscles. And a new theme for future blog posts to follow up on: starting off my “Better Know A Muscle” (nod to Stephen Colbert; alternative link) series. My BKAM series intends to walk through the evolutionary history of the coolest (skeletal/striated) muscles. Chuck Darwin would not enjoy the inevitable blood in this photo-tour, but hopefully he’d like the evolution. Off we go, in search of better knowledge via an evolutionary perspective!

There is, inarguably, no cooler muscle than M. caudofemoralis longus, or CFL for short. It includes the largest limb muscles of any land animal, and it’s a strange muscle that confused anatomists for many years– was it a muscle of the body (an axial or “extrinsic” limb muscle, directly related to the segmented vertebral column) or of the limbs (an “abaxial” muscle, developing with the other limb muscles from specific regions of the paraxial mesoderm/myotome, not branching off from the axial muscles)? Developmental biologists and anatomists answered that conclusively over the past century: the CFL is a limb muscle, not some muscle that lost its way from the vertebral column and ended up stranded on the hindlimb.

The CFL is also a muscle that we know a fair amount about in terms of its fossil record and function, as you may know if you’re a dinosaur fan, and as I will quickly review later. We know enough about it that we can even dare to speculate if organisms on other planets would have it. Well, sort of…

Stomach-Churning Rating: 8/10. Lots of meaty, bloody, gooey goodness, on and on, for numerous species. This is an anatomy post for those with an appetite for raw morphology.

Let’s start from a strong (and non-gooey) vantage point, to which we shall return. The CFL in crocodiles and most other groups is (and long was) a large muscle extending from much of the front half or so of the tail to the back of the femur (thigh bone), as shown here:

Julia Molnar's fabulous illustration of Alligator's limb muscles, from our 2014 paper in Journal of Anatomy.

Julia Molnar’s fabulous illustration of Alligator‘s limb muscles, from our 2014 paper in Journal of Anatomy. Note the CFL in blue at the bottom right.

As the drawing shows, the CFL has a friend: the CFB. The CFB is a shorter, stumpier version of the CFL restricted to the tail’s base, near the hip. The “B” in its name means “brevis”, or runty. It gets much less respect than its friend the CFL. Pity the poor CFB.

But look closer at the CFL in the drawing above and you’ll see a thin blue tendon extending past the knee to the outer side of the lower leg. This is the famed(?) “tendon of Sutton“, or secondary tendon of the CFL. So the CFL has two insertions, one on the femur and one (indirectly) onto the shank. More about that later.

Together, we can talk about these two muscles (CFL and CFB) as the caudofemoralis (CF) group, and the name is nice because it describes how they run from the tail (“caudo”) to the femur (“femoralis”). Mammal anatomists were late to this party and gave mammal muscles stupidly unhelpful names like “gluteus” or “vastus” or “babalooey”. Thanks.

But enough abstract drawings, even if they rock, and enough nomenclature. Here is the whopping big CFL muscle of a real crocodile:

Huge Nile crocodile, but a relatively small CFL.

Huge Nile crocodile, but a relatively small CFL.

Bigger crocs have smaller legs and muscles.

Bigger crocs have smaller legs and thus smaller leg muscles, relatively speaking. CFL at the top, curving to the left.

The giant Nile croc's CFL muscle removed for measurements.

The giant Nile croc’s CFL muscle removed for measurements. 2.35 kg of muscle! Not shabby for a 278 kg animal.

However, maybe crocodile and other archosaur CFL muscles are not “average” for leggy vertebrates? We can’t tell unless we take an evolutionary tack to the question.

Where did the CFL come from, you may ask? Ahh, that is shrouded in the fin-limb transition‘s mysteries. Living amphibians such as salamanders have at least one CF muscle, so a clear predecessor to the CFL (and maybe CFB) was present before reptiles scampered onto the scene.

But going further back through the CF muscles’ history, into lobe-finned fish, becomes very hard because those fish (today) have so few fin muscles that, in our distant fishy ancestors, would have given rise eventually to the CF and other muscle groups. With many land animals having 30+ hindlimb muscles, and fish having 2-8 or so, there obviously was an increase in the number of muscles as limbs evolved from fins. And because a limb has to do lots of difficult three-dimensional things on land while coping with gravity, more muscles to enable that complex control surely were needed.

OK, so there were CF muscles early in tetrapod history, presumably, anchored on that big, round fleshy tail that they evolved from their thin, finned fishy one — but what happened next? Lizards give us some clues, and their CFL muscles aren’t all that different from crocodiles, so the CFL’s massive size and secondary “tendon of Sutton” seems to be a reptile thing, at least.

Courtesy of Emma Schachner, a large varanid lizard's very freshly preserved CFL and other hindlimb muscles.

Courtesy of Emma Schachner, a large varanid lizard’s very freshly preserved CFL and other hindlimb muscles.

Courtesy of Emma Schachner, zoomed in on the tendons and insertions of the CFL muscle and others.

Courtesy of Emma Schachner, zoomed in on the tendons and insertions of the CFL muscle and others. Beautiful anatomy there!

Looking up at the belly of a basilisk lizard and its dissected right leg, with the end of the CFL labelled.

Looking up at the belly of a basilisk lizard and its dissected right leg, with the end of the CFL labelled. It’s not ideally dissected here, but it is present.

An unspecified iguanid(?) lizard, probably a juvenile Iguana iguana, dissected and showing its CFL muscle at its end. The muscle would extemd about halfway down the tail, though.

An unspecified iguanid(?) lizard, probably a juvenile Iguana iguana, dissected to reveal its CFL muscle near its attachment to the femur. The muscle would extend further, about halfway down the tail, though.

Let’s return to crocodiles, for one because they are so flippin’ cool, and for another because they give a segue into archosaurs, especially dinosaurs, and thence birds:

A moderate-sized (45kg) Nile crocodile with its CFL muscle proudly displayed.

A moderate-sized (45kg) Nile crocodile with its CFL muscle proudly displayed. Note the healthy sheath of fat (cut here) around the CFL.

American alligator's CFL dominates the photo. Photo by Vivian Allen.

American alligator’s CFL dominates the photo [by Vivian Allen].

Black caiman, Melanosuchus, showing off its CFL muscle (pink "steak" in the middle of the tail near the leg).

Black caiman, Melanosuchus, showing off its CFL muscle (pink “steak” in the middle of the tail near the leg), underneath all that dark armour and fatty superficial musculature.

A closer look at the black caiman's thigh and CFL muscle.

A closer look at the black caiman’s thigh and CFL muscle.

Like I hinted above, crocodiles (and the anatomy of the CFL they share with lizards and some other tetrapods) open a window into the evolution of unusual tail-to-thigh muscles and locomotor behaviours in tetrapod vertebrates.

Thanks in large part to Steve Gatesy’s groundbreaking work in the 1990s on the CFL muscle, we understand now how it works in living reptiles like crocodiles. It mainly serves to retract the femur (extend the hip joint), drawing the leg backwards. This also helps support the weight of the animal while the foot is on the ground, and power the animal forwards. So we call the CFL a “stance phase muscle”, referring to how it mainly plays a role during ground contact and resisting gravity, rather than swinging the leg forwards (protracting the limb; i.e. as a “swing phase muscle”).

The “tendon of Sutton” probably helps to begin retracting the shank once the thigh has moved forward enough, facilitating the switch from stance to swing phase, but someone really needs to study that question more someday.

And thanks again to that same body of work by Gatesy (and some others too), we also understand how the CFL’s anatomy relates to the underlying anatomy of the skeleton. There is a large space for the CFL to originate from on the bottom of the tail vertebrae, and a honking big crest (the fourth trochanter) on the femur in most reptiles that serves as the major attachment point, from which the thin “tendon of Sutton” extends down past the knee.

Femur bones (left side) from an adult ostrich (Left) and Nile crocodile (Right).

Femur bones (left side; rear view) from an adult ostrich (left) and Nile crocodile (right). Appropriate scale bar is appropriate. The fourth trochanter for the CFL is visible in the crocodile almost midway down the femur. Little is left of it in the ostrich but there is a bumpy little muscle scar in almost the same region as the fourth trochanter, and this is where the same muscle (often called the CFC; but it is basically just a small CFL) attaches.

That relationship of the CFL’s muscular anatomy and the underlying skeleton’s anatomy helps us a lot! Now we can begin to look at extinct relatives of crocodiles; members of the archosaur group that includes dinosaurs (which today we consider to include birds, too), and things get even more interesting! The “tendon of Sutton”, hinted at by a “pendant” part of the fourth trochanter that points down toward the knee, seems to go away multiple times within dinosaurs. Bye bye! Then plenty more happens:

A large duckbill dinosaur's left leg, with a red line drawn in showing roughly where the CFL would be running, to end up at the fourth trochanter. Many Mesozoic dinosaurs have skeletal anatomy that indicates a similar CFL muscle.

A large duckbill dinosaur’s left leg, with a red line drawn in showing roughly where the CFL would be running, to end up at the fourth trochanter. Many Mesozoic dinosaurs have skeletal anatomy that indicates a similar CFL muscle.

We can even go so far as to reconstruct the 3D anatomy of the CFL in a dinosaur such as T. rex ("Sue" specimen here; from Julia Molnar's awesome illustration in our 2011 paper), with a fair degree of confidence.

We can even go so far as to reconstruct the 3D anatomy of the CFL in a dinosaur such as T. rex (“Sue” specimen here; from Julia Molnar’s awesome illustration as part of our 2011 paper), with a fair degree of confidence. >180kg steak, anyone?

As we approach birds along the dinosaur lineage, the tail gets smaller and so does the fourth trochanter and thus so must the CFL muscle, until we’re left with just a little flap of muscle, at best. In concert, the hindlimbs get more crouched, the forelimbs get larger, flight evolves and voila! An explosion of modern bird species!

Ozburt (72)

Left femur of an ostrich in side view (hip is toward the right side) showing many muscles that attach around the knee (on the left), then the thin strap of CF muscle (barely visible; 2nd from the right) clinging near the midshaft of the femur.

Another adult ostrich's CF muscle complex, removed for study.

Another adult ostrich’s CF muscle complex, removed for study. Not enough ostrich myology for you yet? Plenty more in this old post! Or this one! Or this one… hey maybe I need to write less about ostriches? The CF muscle complex looks beefy but it’s no bigger than any other of the main hindlimb muscles, unlike the CFL in a crocodile or lizard, which puts everything else to shame!

STILL not enough ostrich for you yet? Take a tour of the major hindlimb muscles in this video:

And check out the limited mobility of the hip joint/femur here. No need for much femur motion when you’re not using your hip muscles as much to drive you forwards:

But I must move on… to the remainder of avian diversity! In just a few photos… Although the CF muscles are lost in numerous bird species, they tend to hang around and just remain a long, thin, unprepossessing muscle:

Chicken's right leg in side view. CFC (equivalent of CFL) muscle outlined and labelled.

Chicken’s right leg in side view. CFC muscle (equivalent of CFL; the ancestral CFB is confusingly called the CFP in birds, as it entirely resides on the pelvis) outlined and labelled.

A jay (species?) dissected to show some of the major leg muscles, including the CF. Photo by Vivian Allen.

A jay (species? I forget) dissected to show some of the major leg muscles, including the CFL-equivalent muscle; again, smallish. [Photo by Vivian Allen]

Finally, what’s up with mammals‘ tail-to-thigh CF-y muscles? Not much. Again, as in birds: smaller tail and/or femur, smaller CF muscles. Mammals instead depend more on their hamstring and gluteal muscles to support and propel themselves forward.

But many mammals do still have something that is either called the M. caudofemoralis or is likely the same thing, albeit almost always fairly modest in size. This evolutionary reduction of the CF muscle along the mammal (synapsid) lineage hasn’t gotten nearly as much attention as that given to the dinosaur/bird lineage’s CFL. Somebody should give it a thoroughly modern phylogenetic what-for! Science the shit outta that caudofemoralis…

Yet, oddly, to give one apparent counter-example, cats (felids) have, probably secondarily, beefed up their CF muscle a bit:

Cats have a pretty large CF muscle in general, and this jaguar is no exception! But mammals still tend to have fairly wimpy tails and thus CF muscles, or they even lose them (e.g. us?).

Cats have a pretty large CF muscle in general, and this jaguar is no exception! But mammals still tend to have fairly wimpy tails and thus CF muscles, or they even lose them (e.g. us?). [photo by Andrew Cuff, I think]

In summary, here’s what happened (click to embeefen):

Better Know A Muscle: The Evolution of M. caudofemoralis (longus)

Better Know A Muscle: the evolution of M. caudofemoralis (longus).

I hope you enjoyed the first BKAM episode!
I am willing to hear requests for future ones… M. pectoralis (major/profundus) is a serious contender.

P.S. It was Freezermas this week! I forgot to mention that. But this post counts as my Freezermas post for 2016; it’s all I can manage. Old Freezermas posts are here.

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