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Posts Tagged ‘crocodile’

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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Seeking adaptations for running and swimming in the vertebral columns of ancient crocs

A guest post by Dr. Julia Molnar, Howard University, USA (this comes from Julia’s PhD research at RVC with John & colleagues)

Recently, John and I with colleagues Stephanie Pierce, Bhart-Anjan Bhullar, and Alan Turner described morphological and functional changes in the vertebral column with increasing aquatic adaptation in crocodylomorphs (Royal Society Open Science, doi 10.1098/rsos.150439). Our results shed light upon key aspects of the evolutionary history of these under-appreciated archosaurs.

Stomach-Churning Rating: 5/10; a juicy croc torso in one small photo but that’s all.

Phylogenetic relationships of the three crocodylomorph groups in the study and our functional hypotheses about their vertebrae. * Image credits: Hesperosuchus by Smokeybjb, Suchodus by Dmitry Bogdanov (vectorized by T. Michael Keesey) http://creativecommons.org/licenses/by-sa/3.0

Phylogenetic relationships of the three crocodylomorph groups in the study and our functional hypotheses about their vertebrae. * Image credits: Hesperosuchus by Smokeybjb, Suchodus by Dmitry Bogdanov (vectorized by T. Michael Keesey) http://creativecommons.org/licenses/by-sa/3.0

As fascinating as modern crocodiles might be, in many ways they are overshadowed by their extinct, Mesozoic cousins and ancestors. The Triassic, Jurassic, and early Cretaceous periods saw the small, fast, hyper-carnivorous “sphenosuchians,” the giant, flippered marine thalattosuchians, and various oddballs like the duck-billed Anatosuchus and the aptly named Armadillosuchus. As palaeontologists/biomechanists, we looked at this wide variety of ecological specializations in those species, the Crocodylomorpha, and wanted to know, how did they do it?

Of course, we weren’t the first scientists to wonder about the locomotion of crocodylomorphs, but we did have some new tools in our toolbox; specifically, a couple of micro-CT scanners and some sophisticated imaging software. We took CT and micro-CT scans of five fossil crocodylomorphs: two presumably terrestrial early crocodylomorphs (Terrestrisuchus and Protosuchus), three aquatic thalattosuchians (Pelagosaurus, Steneosaurus, and Metriorhynchus) and a semi-aquatic modern crocodile (Crocodylus niloticus). Since we’re still stuck on vertebrae (see, e.g., here; and also here), we digitally separated out the vertebrae to make 3D models of individual joints and took measurements from each vertebra. Finally, we manipulated the virtual joint models to find out how far they could move before the bones bumped into each other or the joints came apart (osteological range of motion, or RoM).

 

Our methods: get fossil, scan fossil, make virtual fossil and play with it.

Our methods: get fossil (NHMUK), scan fossil, make virtual fossil and play with it.

Above: Video of a single virtual inter-vertebral joint from the trunk of Pelagosaurus typus (NHMUK) showing maximum osteological range of motion in the lateral direction (video). Note the very un-modern-croc-like flat surfaces of the vertebral bodies! (modern crocs have a ball-and-socket spinal joint with the socket on the front end)

While this was a lot of fun, what we really wanted to find out was whether, as crocodylomorphs became specialized for different types of locomotion, the shapes of their vertebrae changed similarly to those of mammalian lineages. For example, many terrestrial mammals have a lumbar region that is very flexible dorsoventrally to allow up-and-down movements during bounding and galloping. Did fast-running crocodylomorphs have similar dorsoventral flexibility? And did fast-swimming aquatic crocodylomorphs evolve a stiffer vertebral column like that of whales and dolphins?

Above: Video of how we modelled and took measurements from the early crocodylomorph Terrestrisuchus gracilis (NHMUK).

Our first results were puzzling. The Nile croc had greater RoM in side-to-side motions, which makes sense because crocodiles mostly use more sprawling postures and are semi-aquatic, using quite a bit of side-to-side motions in life. The part that didn’t make sense was that we found pretty much the same thing in all of the fossil crocodylomorphs, including the presumably very terrestrial Terrestrisuchus and Protosuchus. With their long limbs and hinge-like joints, these two are unlikely to have been sprawlers or swimmers!

So we started looking for other parts of the croc that might affect RoM. The obvious candidate was osteoderms, the bony scales that cover the back. We went back to John’s Freezer and got out a nice frozen crocodile to measure the stiffness of its trunk and found that, sure enough, it was a lot stiffer and less mobile without the osteoderms. If the fairly flexible arrangement of osteoderms in crocodiles had this effect on stiffness, it seemed likely that (as previous authors have suggested; Eberhard Frey and Steve Salisbury being foremost amongst them) the rigid, interlocking osteoderms running from head to tail in early crocodylomorphs would really have put the brakes on their ability to move their trunk in certain ways.

Testing stiffness of crocodile trunks to learn the effects of osteoderms, skin, muscles, and ribs. We hung metric weights from the middle of the trunk and measured how much it flexed (Ɵ), then removed bits and repeated.

Testing the stiffness of (Nile) crocodile trunks to learn the effects of osteoderms, skin, muscles, and ribs. We hung metric weights from the middle of the trunk and measured how much it flexed (Ɵ), then removed bits and repeated. Click to em-croccen.

Another cool thing we found was new evidence of convergent evolution to aquatic lifestyles in the spines of thalattosuchians. The more basal thalattosuchians, thought to have been near-shore predators, had stiffness and RoM patterns similar to Crocodylus. But Metriorhynchus, which probably was very good at chasing down fast fish in the open ocean, seems to have had greater stiffness. (The stiffness estimates come from morphometrics and are based on modern crocodiles; see here again, or just read the paper already!) A stiff vertebral column can be useful for a swimmer because it increases the body’s natural frequency of oscillation, and faster oscillation means faster swimming (think tuna, not eel). The same thing seems to have happened in other secondarily aquatic vertebrate lineages such as whales, ichthyosaurs, and mosasaurs.

So, our results were a mixed bag of adaptations particular to crocs and ones that seem like general vertebrate swimming specializations. Crocodylomorphs are important because they are the only group of large vertebrates other than mammals that has secondarily aquatic members and has living members with a reasonably similar body plan, allowing us to test hypotheses in ways that would arguably be impossible for, say, non-avian dinosaurs and birds. The take-home message: crocodylomorphs A) are awesome, and B) can teach us a lot about how vertebrates adapt to different modes of life.

Another take on this story is on our lab website here.

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Even nine years later, I still keep thinking back to a day, early in my career as an academic faculty member based in England, that traumatized me. Today I’m going to share my story of that day. I feel ready to share it.

Stomach-Churning Rating: hmm that’s a tough call, but I’ll say 1/10 because it’s just photos of live crocs and such.

This day was part of a research trip that lasted a couple of weeks, and it was in Florida, not England, and little of that trip went well at first. It transpired almost exactly 9 years ago today; around 20 August 2005. I took two 2nd/3rd year undergraduate students and our lab technician with me to Florida, meeting up with Dr. Kent Vliet, an experienced crocodile specialist, to study the biomechanics of crocodile locomotion, a subject I’ve been slowwwwwwly working on since my PhD days (see recent related blog post here). We were funded by an internal grant from my university that was supposed to be seed money to get data to lay groundwork for a future large UK research grant.

Cuban crocodile adult relaxing in a nearby enclosure. Pound-for-pound, a scary croc, but these acted like puppies with their trainers.

Cuban crocodile adult relaxing in a nearby enclosure. Pound-for-pound, a scary croc, but these acted like puppies with their trainers.

I’m interested in why only some crocodylian species, of some sizes and age classes, will do certain kinds of gaits, especially mammal-like gaits such as bounding and galloping. This strongly hints at some kind of size-related biomechanical mechanism that dissuades or prevents larger crocs from getting all jiggy with it. And at large size, with few potential predators to worry about and a largely aquatic ambush predator’s ecology, why would they need to? Crocodiles should undergo major biomechanical changes in tune with their ecological shifts as they grow up. I want to know how the anatomy of crocodiles relates to these changes, and what mechanism underlies their reduction of athletic abilities like bounding. That’s the scientific motivation for working with animals that can detach limbs from your body. (The crocodiles we worked with initially on this trip were small (about 1 meter long) and not very dangerous, but they still would have done some damage if they’d chosen to bite us, and I’ve worked with a few really nasty crocs before.)

Me putting motion capture markers onto an uncooperative young Siamese crocodile.

Me putting motion capture markers onto an uncooperative young Siamese crocodile.

We worked at Gatorland (near Orlando) with some wonderfully trained crocodiles that would even sit in your lap or under your chair, and listened to vocal commands. The cuteness didn’t wear off, but our patience soon did. First, the force platform we’d borrowed (from mentor Rodger Kram’s lab; a ~$10,000 piece of useful gear) and its digital data acquisition system wouldn’t work to let us collect our data. That was very frustrating and even a very helpful local LabView software representative couldn’t solve all our problems. But at least we were able to start trying to collect data after four painstaking days of debugging while curious crocodiles and busy animal handlers waited around for us to get our act together. The stress level of our group was already mounting, and we had limited time plus plenty of real-life bugs (the bitey, itchy kind; including fire ants) and relentless heat to motivate us to get the research done.

Adorable baby Cuban crocodile.

Adorable baby Cuban crocodile.

Then the wonderfully trained crocodiles, as crocodiles will sometimes do, decided that they did not feel like doing more than a slow belly crawl over our force platform, at best. This was not a big surprise and so we patiently tried coaxing them for a couple of sweltering August days. We were working in their caged paddock, which contained a sloping grassy area, a small wooden roofed area, and then at the bottom of the slope was the crocodiles’ pond, where they sat and chilled out when they weren’t being called upon to strut their stuff for science. We didn’t get anything very useful from them, and then the weather forecast started looking ugly.

Hybrid Siamese crocodile in its pond in our enclosure, waiting to be studied.

Hybrid Siamese crocodile in its pond in our enclosure, waiting to be studied.

We’d been watching reports of a tropical storm developing off the southeastern coast of Florida, and crossing our fingers that it would miss us. But it didn’t.

When the storm hit, we were hoping to weather the edge of the storm while we packed up, because we decided we’d done our best but our time had run out and we should move to our next site, the Alligator Farm and Zoological Park in St Augustine, where I’d worked a lot before with other Crocodylia. But the storm caught us off guard, too soon, and too violently.

To give some context to the situation, for the previous several days the local croc handlers had told us stories of how lightning routinely struck this area during storms, and was particularly prone to hitting the fences on the park perimeter, which we were close to. There was a blasted old tree nearby that vultures hung out in, and they related how that blasting had been done by lightning. One trainer had been hit twice by (luckily glancing) blows from lightning hitting the fences and such.

Ominous onlooker.

Ominous onlooker.

The storm came with pounding rain and a lot of lightning, much of it clearly striking nearby- with almost no delay between flashes and thunder, and visible sky-to-ground bolts. We debated taking our forceplate out of the ground near the crocodile pond, because sensitive electrical equipment and rain don’t go well together, but this would take precious time. The forceplate was covered with a tarp to keep the rain off. I decided that, in the interest of safety, we needed to all seek shelter and let the forceplate be.

I’ll never forget the memory of leaving that crocodile enclosure and seeing a terrible sight. The crocodile pond had swiftly flooded and engulfed our forceplate. This flooding also released all the (small) crocodiles which were now happily wandering their enclosure where we’d been sitting and working before.

Another subject awaits science.

Another subject awaits science.

At that point I figured there was no going back. Lightning + deepening floodwater + electrical equipment + crocodiles = not good, so I wagered my team’s safety against our loaned equipment’s, favouring the former.

We sprinted for cars and keepers’ huts, and got split up in the rain and commotion. As the rain calmed down, I ventured out to find the rest of the team. It turned out that amidst the havoc, our intrepid lab technician had marshalled people to go fetch the forceplate out from the flooded paddock, storm notwithstanding. We quickly set to drying it out, and during some tense time over the next day we did several rounds of testing its electronics to see if it would still work. Nope, it was dead. And we still had over a week of time left to do research, but without our most useful device. (A forceplate tells you how hard animals are pushing against the ground, and with other data such as those from our motion analysis cameras, how their limbs and joints function to support them)

We went on to St Augustine and got some decent data using just our cameras, for a wide variety of crocodiles, so the trip wasn’t a total loss. I got trapped by remnants of the storm while in Washington, DC and had to sleep on chairs in Dulles Airport overnight, but I got home, totally wrecked and frazzled from the experience.

That poorly-timed storm was part of a series of powerful storms that would produce Hurricane Katrina several days later, after we’d all left Florida. So we had it relatively easy.

I’m still shaken by the experience- as a tall person who grew up in an area with a lot of dangerous storms, I was already uneasy about lightning, feeling like I had a target on my back. But running from the lightning in that storm, after all the warnings we’d had about its bad history in this area, and how shockingly close the lightning was, leaves me almost phobic about lightning strikes. I’m in awe of lightning and enjoy thunderstorms, which I’ve seen few of since I left Wisconsin in 1995, but I now hate getting caught out in them.

The ill-fated forceplate and experimental area.

The ill-fated forceplate and experimental area.

Moreover, the damage to the forceplate- which we managed to pay to repair and return to my colleague, and the failure of the Gatorland experiments, truly mortified me. I felt horrible and still feel ashamed. I don’t think I could have handled the situation much differently. It was just a shitty situation. That, and I wanted to show our undergrads a good time with research, yet what they ended up seeing was a debacle. I still have the emails I sent back to my research dean to describe what happened in the event, and they bring back the pain and stress now that I re-read them. But then… there’s a special stupid part to this story.

I tried to lighten the mood one night shortly after the storm by taking the team out to dinner, having a few drinks and then getting up to sing karaoke in front of the restaurant. I sang one of my favourite J Geil’s Band tunes– I have a nostalgic weakness for them- the song “Centerfold“. I not only didn’t sing it well (my heart was not in it and my body was shattered), and tried lamely to get the crowd involved (I think no one clapped or sang along), but also in retrospect it was a bad choice of song to be singing with two female undergrads there– I hadn’t thought about the song’s meanings when I chose to sing it, I just enjoyed it as a fun, goofy song that brought me back to innocent days of my youth in the early 1980’s. But it is not an innocent song.

So ironically, today what I feel the most embarrassed about, thinking about that whole trip and the failed experiment, is that karaoke performance. It was incredibly graceless and ill-timed and I don’t think anyone enjoyed it. I needed to unwind; the stress was crushing me; but oh… it was so damn awkward. I think I wanted to show to the team “I’m OK, I can still sing joyfully and have a good time even though we had a disastrous experiment and maybe nearly got electrified or bitten by submerged crocodiles or what-not, so you can relax too; we can move on and enjoy the rest of the trip” but in reality I proved to myself, at least, that I was not OK. And I’m still not OK about that experience. It still makes me cringe. Haunted, it took me many years to feel comfortable singing karaoke again.

It should have been a fun trip. I love working with crocodiles, but Florida is a treacherous place for field work (and many other things). I can’t say I grew stronger from this experience. There is no silver lining. It sucked, and I continually revisit it in my memory trying to find a lesson beyond “choose better times and better songs to sing karaoke with” or “stay away from floods, electricity and deadly beasts.”

So that wins, out of several good options, as the worst day(s) of my career that I can recall. I’ve had worse days in my life, but for uncomfortable science escapades this edges out some other contenders. Whenever I leave the lab to do research, I think of this experience and hope that I don’t see anything worse. It could have been much worse field work.

(Epilogue: the grants we’ve tried to fund for this crocodile gait project all got shot down, so it has lingered and we’ve done research on it gradually since, when we find time and students… And one of the students on this trip went on to do well in research and is finishing a PhD in the Structure & Motion Lab now, so we didn’t entirely scare them off science!)

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I visited the British Museum a while ago with my daughter and was struck by some of the animal imagery in the loot on display– particularly, as an archosaurophile, the crocodiles (Crocodylia, crocodylians, etc.; no alligatoroids to show in this post). So I decided to go back and photograph some of them for a blog post about the more obscure and rare animals that sometimes appear in human art and design.

It’s easy to think of horses, lions, dogs, eagles and other familiar, domestic or prized beasts in human decorations. Yet what roles do less common animals play? This post is the first of two on the unsung beasties of human artwork, as represented in the British Museum.

Stomach-Churning Rating: 1/10. Tame art and a dried crocodile skin.

Wherever humans and crocodiles coexist, the primeval appearance and dangerous potential of crocodiles are sure to impress themselves upon our psyche. Hence they will manifest themselves in art. This should especially apply in the early days of a civilization, before we extirpate local crocodiles or exclude them to the hinterlands, or in cases in which crocodylians become revered and protected.

Much of Western culture lacks such an emphasis, because it developed in more temperate climes where crocodiles were long since absent. It’s fun to think about what our culture would be like if it had developed with crocodiles as a prominent aspect, as in Egypt, which is the natural place to begin our tour, featuring mummies of course!

All images can be clicked to emcroccen them.

Small Nile crocodile mummy from >30 B.C, El Hiba, Egypt

Small Nile crocodile mummy from >30 B.C, El Hiba, Egypt

Second small Nile crocodile mummy from >30 B.C, El Hiba, Egypt

Second small Nile crocodile mummy from >30 B.C, El Hiba, Egypt

Those mummies remind me of a recent scientific study that used such mummies to reveal the history of the “cryptic” species Crocodylus suchus, a close relative of the Nile croc C. niloticus, and one that seems to be more threatened.

We proceed on our tour with a box showing an example of shabti, or doll-like funeral offerings of “enchanted” mummified figurines:

This shabti box was for a noble daughter, Neskshons, in Thebes, from around 650 B.C.

This shabti box was for a noble daughter, Neskshons, in Thebes, from around 650 B.C.

A crocodile deity receives the shabti from the departed soul, accompanied by  serpent god as well as a more human, ankh-bearing divinity.

A crocodile deity receives the shabti from the departed soul, accompanied by serpent god as well as a more human, ankh-bearing divinity.

Next, some amazingly preserved papyrus scrolls:

This papyrus is from around 900 B.C., with short blurbs about the woman Tentosorkon, part of a new style of funeral provisions in the 22nd Dynasty of Egypt.

This papyrus is from around 900 B.C., with short blurbs about the woman Tentosorkon, part of a new style of funeral provisions in the 22nd Dynasty of Egypt.

Crocodile featured in the story of Tentosorkon.

Crocodile featured in the story of Tentosorkon. What’s it doing? Why is a feathered snake-thing touching its butt? I wish I knew.

The "Litany of Ra", from around 1000 B.C., which is a style like that of the previous 22nd Dynasty papyrus and would have decorated a tomb's wall, dedicated to the lady Mutemwia. Ra, the sun god, is shown in his different manifestations, including a crocodile form, called Sobek-ra: http://www.princeton.edu/~achaney/tmve/wiki100k/docs/Sobek.html

The “Litany of Ra”, from around 1000 B.C., which is a style like that of the previous 22nd Dynasty papyrus and would have decorated a tomb’s wall, dedicated to the lady Mutemwia. Ra, the sun god, is shown in his different manifestations, including a crocodile form, called Sobek-ra (AKA Sebek); a protector and comforter of the dead:

egypt croc 1But crocodiles also feature prominently in other cultures around the world– I was hoping to find some in Thai, South American, or other cultures’ art (especially east/western Africa). However, the museum didn’t exhibit any I could find. I did find these, though, starting with this fantastic Roman armour with a great backstory (and hard to take photos of; argh!):

croc armour caption croc armour 1 croc armour 2 croc armour 3

Roman soldiers in a Sobek cult, running around Egypt while wearing badass armour and getting into all kinds of Bronze Age trouble: I DEMAND TO SEE A SWORD-AND-SANDALS MOVIE FEATURING THIS!

I searched for this next one but did not see it:

A crocodile mask from Mabuiag island near Australia- for some cool details, see this page where the image comes from (I didn’t get to see the original).

There were more tenuous links to crocodiles– surely some dragon images throughout the world relate at least partly to crocodiles, such as this one which seems very crocodylian to me:

A water spirit figure called a belum, from Sarawak, Malaysia, 18/1900s. Belief among  the Melanau people  was that these dragons would wrap their tails around someone's body to protect or drown them. Possibly inspired by saltwater or Phillipine crocs that they lived near.

A water spirit figure called a belum, from Sarawak, Malaysia, 18/1900s. Belief among the Melanau people was that these dragons would wrap their tails around someone’s body to protect or drown them. Possibly inspired by saltwater or Phillipine crocs that they lived near.

And that’s it- all I managed to find, but not a bad haul from this huge museum.  I looked for the Aztec croc-god Cipactli to no avail. If you have £850 to spare you might like to walk away with this one from the museum. I gladly accept donations of such things to my, err, research.

That’s just one museum’s view of crocodylians’ role in our culture. What crocodile imagery from human art around the world do you fancy?

 

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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

Xray

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.

morphometrics

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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I love doing sciencey road trips with my team when I can. Last week, we got a treat: four of us got a behind-the-scenes tour of the fairly new Crocodiles of the World facility near Oxford; just over 90 minutes west of our lab, nestled in the pictureseque Cotswolds region. We were not disappointed, so you get to share in the joy! In photo-blog format. Pics can be clicked to emcrocken.

In the midst of an unpreposessing industrial estate lies: AWESOME!

In the midst of an unpreposessing industrial estate lies: AWESOME!

If you want to bone up on your croc species, go here and here. I won’t go into details. This is an eye candy post!

Reasonably accurate description that caught my eye.

Reasonably accurate description that caught my eye. My scientific interest in crocodiles starts here, and with their anatomy/relationship with dinosaurs, but I’ve loved crocs since I was an infant (one of my first words, as I may have written here before, was “dock-a-dile”, for my favourite stuffed animal at the time [R.I.P.]).

Siamese crocodiles. They were apart when we entered, then got snuggly later, as I've often seen this species do.

Siamese crocodiles. The large male is “Hugo.” They were apart when we entered, then got snuggly later, as I’ve often seen this species do. Heavily endangered (<300 in the wild?), so any breeding is a good thing!

The above photo brings me to one of my general points. Crocodiles of the World seems genuinely to be a centre that is breeding crocodiles for conservation purposes (and for education, entertainment and other zoo-like stuff). Essentially every crocodile enclosure had a mated pair, and several were breeding. Such as…

Yes, that is a Dwarf African crocodile, Osteolaemus, and it is a female on her nest-mound. Which means...

Yes, that is a Dwarf African crocodile, Osteolaemus, and indeed it is a female on her nest-mound. Which means…

Eggs of said Osteolaemus.

Eggs of said Osteolaemus.

And babies of said Osteolaemus!

And babies of said Osteolaemus! As if the adults aren’t cute enough with their short snouts and doglike size/appearance! These guys have striking yellow colouration, too. I’d never seen it in person before.

That’s not all!

Male American Alligator warming up. Smaller female partner lives in same enclosure.

Male American Alligator “Albert” warming up. Smaller female partner “Daisy” lives in same enclosure. Plenty of babies from these guys, too! Daisy comes when called by name, and Albert is learning to do so.

~1 meter long juvenile Nile crocodiles, bred at the facility.

~1 meter long juvenile Nile crocodiles, bred at the facility.

But then crocodile morphological diversity (colours, textures) and behaviour is just too cool not to focus on a bit, so here are some highlights from our visit!

Endearing shot of a crocodylian I seldom get to see anywhere: Paleosuchus trigonatus, the Cuvier's Dwarf Caiman. Spiny armoured hide and quite terrestrial; poorly known in many ways. Some more info is here- http://crocodilian.com/paleosuchus/description.html (note its tortured taxonomy)

Endearing shot of a crocodylian I seldom get to see anywhere: Paleosuchus trigonatus, the Schneider’s Dwarf Caiman. Spiny armoured hide and quite terrestrial; poorly known in many ways. Some more info is here (note its tortured taxonomy)

Black caiman, Melanosuchus niger, showing some interest in us.

Black caiman, Melanosuchus niger, showing some interest in us.

Cuban crocodiles cooling off by exposing their mouths.

Cuban crocodiles (Crocodylus rhombifer; pound for pound the most badass croc in my experience; badassitude that this photo captures nicely) cooling off by exposing the well-vascularized soft tissues of the mouth region.

But it’s not just crocs there, either, and some of the highlights were non-croc surprises and memorable encounters:

A surprisingly friendly and tame Water monitor (14 yrs old; does kids parties). Note person for scale.

A surprisingly friendly and tame Water monitor (14 yrs old; does kids parties). Note person for scale. Was about 2 meters long, 20 kg or so.

Business end of nice Water monitor, with tongue engaged.

Business end of nice Water monitor, with tongue engaged.

And we got a nice farewell from an African spur-thigh tortoise (Geochelone sulcata) with an oral fixation (action sequence thereof):

tortoise-nom (1)
tortoise-nom (2)

tortoise-nom (3)
tortoise-nom (4)

tortoise-nom (5)

Chowmp!

If someone visits this facility and leaves without being converted to a croc-lover, they must be from a different planet than me. It is a celebration of crocodiles; the owner, Shaun Foggett, is the real deal. He sold his home and quit his job as a carpenter to care for crocodiles, and it seems to be a great success– about to get greater, as they have plans to move to a new, bigger, proper site! They are seeking funding, so if you can contribute go here.

Right then… UK residents and visitors: you need to go here! Badly! Get off the blog and go now. If it is a Saturday/Sunday (the cramped industrial estate location only allows the public then).

Otherwise just stew and imagine how much fun you could be having checking out crocodiles. I cruelly posted this on a Tuesday to ensure thorough marination of any croc-geeks.

Muhaha!  ;-)

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Models of a basal dinosaur and bird, showing methods and key differences in body shape.

Our 3D computer models of a basal dinosaur and bird, showing methods and key differences in body shape. The numbers at the bottom are museum specimen numbers.

At about the moment I’m posting this, our Nature paper (our more formal page here, and the actual article here) embargo is ending, drawing a 14+ year gestation to a close. The paper is about how dinosaur 3D body shape changed during their evolution, and how that relates to changes in hindlimb posture from early dinosaurs/archosaurs to birds; “morpho-functional evolution” sums up the topic. We used the 3D whole-body computational modelling that I, Allen and Bates (among others) have developed to estimate evolutionary changes in body dimensions, rather than focusing on single specimens or (as in our last study) tyrannosaur ontogeny. We’ve strongly supported the notion (dating back to Gatesy’s seminal 1990 Paleobiology paper) that the centre of mass of dinosaurs shifted forwards during their evolution, and that this shift gradually led to the more crouched (flexed) hind leg posture that characterizes living birds. Here is a movie from our paper showing how we did the modelling:

And here is a summary of our 17 computer models of archosaur bodies, shown as one walks along the tips of the phylogeny shown in the video (the models are not considered to be ancestral to one another; we used a common computer algorithm called squared-change parsimony to estimate ancestral state changes of body dimensions between the 16 numbered nodes of the tree):

But we’ve done much more than just put numbers on conventional wisdom.

We’ve shown, to our own surprise, that the shift of the centre of mass was largely driven by evolutionary enlargements of the forelimbs (and the head and neck, and hindlimbs, to a less strong degree), not the tail as everyone including ourselves has assumed for almost 25 years. And the timing of this shift occurred inside the theropod dinosaur group that is called Maniraptora (or Maniraptoriformes, a slightly larger group), so the change began in animals that were not flying, but not long before flight evolved (depending on whom you ask, what taxonomy they favour and what evidence one accepts, either the smaller clade Eumaniraptora/Paraves or the bird clade Aves/Avialae).

Now, if you don’t like the cliche “rewriting the textbooks”, do have a look through texts on dinosaur/early avian palaeobiology and you probably will find a discussion of how the tail shortened, the centre of mass moved forwards as a consequence, the caudofemoral musculature diminished, and theropod dinosaurs (including birds) became more crouched as a result. We did that to confirm for ourselves that it’s a pretty well-accepted idea. Our study supports a large proportion of that idea’s reasoning, but modifies the emphasis to be on the forelimbs more than the tail for centre of mass effects, so the story gets more complex. The inference about caudofemoral muscles still seems quite sound, however, as is the general trend of increased limb crouching, but our paper approximates the timing of those changes.

Figure 3 from our paper, showing how the centre of mass moved forwards (up the y-axis) as one moves toward living birds (node 16); the funny dip at the end is an anomaly we discuss in the paper.

Figure 3 from our paper, showing how the centre of mass moved forwards (up the y-axis) as one moves toward living birds (node 16); the funny dip at the end is an anomaly we discuss in the paper.

A final implication of our study is that, because the forelimbs’ size influenced the centre of mass position, and thus influenced the ways the hindlimbs functioned, the forelimbs and hindlimbs are more coupled (via their effects on the centre of mass) than anyone has typically considered. Thus bipedalism and flight in theropods still have some functional coupling– although this is a matter of degree and not black/white, so by no means should we do away with helpful concepts like locomotor modules.

And in addition to doing science that we feel is good, we’ve gone the extra mile and presented all our data (yes, 17 dinosaurs’ worth of 3D whole body graphics!) and the critical software tools needed to replicate our analysis, in the Dryad database (link now working!), which should have now gone live with the paper! It was my first time using that database and it was incredibly easy (about 1 hour of work once we had all the final analysis’s files properly organized)– I strongly recommend others to try it out.

That’s my usual general summary of the paper, but that’s not what this blog article is about. I’ll provide my usual set of links to media coverage of the paper below, too. But the focus here is on the story behind the paper, to put a more personal spin on what it means to me (and my coauthors too). I’ll take a historical approach to explain how the paper evolved.


This paper’s story, with bits from the story of my life:

Embarassing picture of me before I became a scientist. Hardee's fast food restaurant cashier, my first "real job."

Embarassing picture of me before I became a scientist. Hardee’s fast food restaurant cashier, my first “real job”, from ~1999- no, wait, more like 1986. The 1980s-style feathered (and non-receding) hair gives it away!

Rewind to 1995. I started my PhD at Berkeley. I planned to use biomechanical methods and evidence to reconstruct how Tyrannosaurus rex moved, and started by synthesizing evidence on the anatomy and evolution of the hindlimb musculature in the whole archosaur group, with a focus on the lineage leading to Tyrannosaurus and to living birds. As my PhD project evolved, I became more interested and experienced in using 3D computational tools in biomechanics, which was my ultimate aim for T. rex.

In 1999, Don Henderson published his mathematical slicing approach to compute 3D body dimensions in extinct animals, which was a huge leap for the field forward beyond statistical estimates or physical toy models, because it represented dinosaurs-as-dinosaurs (not extrapolated reptiles/mammals/whatever) and gave you much more information than just body mass, with a lot of potential to do sensitivity analysis.

I struggled to upgrade my computer skills over the intervening years. I was developing the idea to reconstruct not only the biomechanics of T. rex, but also the evolutionary changes of biomechanics along the whole archosaur lineage to birds– because with a series of models of different species and a working phylogeny, you could do that. To me this was far more interesting than the morphology or function of any one taxon, BUT required you to be able to assess the latter. So Tyrannosaurus became a “case study” for me in how to reconstruct form and function in extinct animals, because it was interesting in its own right (mainly because of its giant size and bipedalism). (Much later, in 2007, I finally finished a collaboration to develop our own software package to do this 3D modelling, with Victor Ng-Thow-Hing and F. Clay Anderson at Honda and Stanford)

Me and a Mystery Scientist (then an undergrad; now a successful palaeontologist), measuring up a successful Cretaceous hypercarnivore at the UCMP; from my PhD days at Berkeley, ~2000 or so.

Me and a Mystery Scientist (then an undergrad; now a very successful palaeontologist!), measuring up a successful Cretaceous hypercarnivore at the UCMP; from my PhD days at Berkeley, ~2000 or so.

In all this research, I was inspired by not only my thesis committee and others at Berkeley, but also to a HUGE degree by Steve Gatesy, a very influential mentor and role model at Brown University. I owe a lot to him, and in a sense this paper is an homage to his trailblazing research; particularly his 1990 Paleobiology paper.

In 2001, I got the NSF bioinformatics postdoc I badly wanted, to go to the Neuromuscular Biomechanics lab at Stanford and learn the very latest 3D computational methods in biomechanics from Prof. Scott Delp’s team. This was a pivotal moment in my career; I became partly-an-engineer from that experience, and published some papers that I still look back fondly upon. Those papers, and many since (focused on validating and testing the accuracy/reliability of computer models of dinosaurs), set the stage for the present paper, which is one of the ones I’ve dreamed to do since the 1990s. So you may understand my excitement here…

Stanford's Neuromuscular Biomechanics Lab, just before I left in 2003.

Stanford’s Neuromuscular Biomechanics Lab, just before I left in 2003.

But the new paper is a team effort, and was driven by a very talented and fun then-PhD-student, now postdoc, Dr Vivian Allen. Viv’s PhD (2005-2009ish) was essentially intended to do all the things in biomechanics/evolution that I had run out of time/expertise to do in my PhD and postdoc, in regards to the evolution of dinosaur (especially theropod) locomotor biomechanics. And as I’d hoped, Viv put his own unique spin on the project, proving himself far better than me at writing software code and working with 3D graphics and biomechanical models. He’s now everything that I had hoped I’d become by the end of my postdoc, but didn’t really achieve, and more than that, too. So huge credit goes to Viv for this paper; it would never have happened without him.

We also got Karl Bates, another proven biomechanics/modelling expert, to contribute diverse ideas and data. Furthermore, Zhiheng Li (now at UT-Austin doing a PhD with Dr Julia Clarke) brought some awesome fossil birds (Pengornis and Yixianornis) from the IVPP in Beijing in order to microCT scan them in London. Zhiheng thus earned coauthorship on the paper — and I give big thanks to the Royal Society for funding this as an International Joint Project, with Dr Zhonghe Zhou at the IVPP.

That’s the team and the background, and I’ve already given you the punchlines for the paper; these are the primitive and the derived states of the paper. The rest of this post is about what happened behind the scenes. No huge drama or anything, but hard, cautious work and perseverance.

Me shortly after I moved to the RVC; video still frame from a dinosaur exhibit I was featured in. Embarassingly goofy pic, but I like the blurb at the bottom. It's all about the evolutionary polarity, baby!

Me shortly after I moved to the RVC; video still frame from a dinosaur exhibit (c. 2004) I was featured in. Embarassingly goofy pic, but I like the blurb at the bottom. It’s all about the evolutionary polarity, baby!

The paper of course got started during Viv’s PhD thesis; it was one of his chapters. However, back then it was just a focus on how the centre of mass changed, and the results for those simple patterns weren’t very different from those we present in the paper. We did spot, as our Nature supplementary information notes,  a strange trend in early theropods (like Dilophosaurus; to a lesser degree Coelophysis too) related to some unusual traits (e.g. a long torso) and suggested that there was a forward shift of centre of mass in these animals, but that wasn’t strongly upheld as we began to write the Nature paper.

On the urging of the PhD exam committee (and later the paper reviewers, too), Viv looked at the contributions of segment (i.e. head, neck, trunk, limbs, tail) mass and centre of mass to the overall whole body centre of mass. And I’m glad he did, since that uncovered the trend we did not expect to find: that the forelimb masses were far more important for moving the centre of mass forwards than the mass (or centre of mass) of the tail was– in other words, the statistical correlation of forelimb mass and centre of mass was strong, whereas changes of tail size didn’t correlate with the centre of mass nearly as much. We scrutinized those results quite carefully, even finding a very annoying bug in the 3D graphics files that required a major re-analysis during peer review (delaying the paper by ~6 months).

The paper was submitted to Nature first, passing a presubmission inquiry to check if the editor felt it fit the journal well enough. We had 3 anonymous peer reviewers; 1 gave extensive, detailed comments in the 3 rounds of review and was very fair and constructive, 1 gave helpful comments on writing style and other aspects of presentation as well as elements of the science, and 1 wasn’t that impressed by the paper’s novelty but wanted lots more species added, to investigate changes within different lineages of maniraptorans (e.g. therizinosaurs, oviraptorosaurs). That third reviewer only reviewed the paper for the first round (AFAIK), so I guess we won them over or else the editor overruled their concerns. We argued that 17 taxa were probably good enough to get the general evolutionary trends that we were after, and that number was ~16 more species than any prior studies had really done.

Above: CT scan reconstruction of the early extinct bird Yixianornis in slab conformation, and then Below: 3D skeletal reconstruction by Julia Molnar, missing just the final head (I find this very funny; Daffy Duck-esque) which we scaled to the fossil’s dimensions from the better data in our Archaeopteryx images. Yixianornis reconstruction There is also the concern, which the reviewers didn’t focus on but I could see other colleagues worrying about, that some of the specimens we used were either composites, sculpted, or otherwise not based on 100% complete, perfectly intact specimens. The latter are hard to come by for a diversity of extinct animals, especially in the maniraptoran/early bird group. We discussed some of these problems in our 3D Tyrannosaurus paper. The early dinosauromorph Marasuchus that we used was a cast/sculpted NHMUK specimen based on original material, as was our Coelophysis, Microraptor and Archaeopteryx; and our Carnegie ??Caenagnathus??Anzu (now published) specimen was based more on measurements from 1 specimen than from direct scans, and there were a few other issues with our other specimens, all detailed in our paper’s Supplementary Information.

But our intuition, based on a lot of time spent with these models and the analysis of their data, is that these anatomical imperfections matter far, far less than the statistical methods that we employed– because we add a lot of flesh (like real animals have!) outside of the skeleton in our method, the precise morphology of the skeleton doesn’t matter much. It’s not like you need the kind of quality of anatomical detail that you need to do systematic analyses or osteological descriptive papers. The broad dimensions can matter, but those tend to be covered by the (overly, we suspect) broad error bars that our study had (see graph above). Hence while anyone could quibble ad infinitum about the accuracy of our skeletal data, I doubt it’s that bad– and it’s still a huge leap beyond previous studies, which did not present quantitative data, did not do comparative studies of multiple species, or did not construct models based on actual 3D skeletons as opposed to artists’ 2D shrinkwrapped reconstructions (the “Greg Paul method”). We also did directly measure the bodies of two extant archosaurs in our paper: a freshwater crocodile and a junglefowl (CT scan of the latter is reconstructed below in 3D).

One thing we still need to do, in future studies, is to look more carefully inside of the bird clade (Aves/Avialae) to see what’s going on there, especially as one moves closer to the crown group (modern birds). We represented modern birds with simply 1 bird: the “wild-type chicken” Red junglefowl, which isn’t drastically different in body shape from other basal modern birds such as a tinamou. Our paper was not about how diversity of body shape and centre of mass evolved within modern birds. But inspecting trends within Palaeognathae would be super interesting, because a lot of locomotor, size and body shape changes evolved therein; ostriches are probably a very, very poor proxy for the size and shape of the most recent common ancestor of all extant birds, for example, even though they seem to be fairly basal within that whole lineage. And, naturally, our study opens up opportunities for anyone to add feathers to our models and investigate aerodynamics, or to apply our methods to other dinosaur/vertebrate/metazoan groups. If the funding gods are kind to us, later this year we will be looking more closely, in particular, at the base of Archosauria and what was happening to locomotor mechanics in Triassic archosaurs…

Clickum to embiggum:

Australian freshwater crocodile, Crocodylus johnstoni; we CT scanned it in 3 pieces.

Australian freshwater crocodile, Crocodylus johnstoni; we CT scanned it in 3 pieces while visiting the Witmer lab in Ohio.

A Red junglefowl cockerel, spotted in Lampang, Thailand during one of my elephant gait research excursions there. Svelte, muscular and fast as hell.

A Red junglefowl cockerel, spotted in Lampang, Thailand during one of my elephant gait research excursions there. Svelte, muscular and fast as hell. This photo is here to remind me to TAKE BLOODY PICTURES OF MY ACTUAL RESEARCH SPECIMENS SO I CAN SHOW THEM!

I’d bore you with the statistical intricacies of the paper, but that’s not very fun and it’s not the style of this blog, which is not called “What’s in John’s Software Code?”. Viv really worked his butt off to get the stats right, and we did many rounds of revisions and checking together, in addition to consultations with statistics experts. So I feel we did a good job. See the paper if that kind of thing floats your boat. Someone could find a flaw or alternative method, and if that changed our major conclusions that would be a bummer– but that’s science. We took the plunge and put all of our data online, as noted above, so anyone can do that, and that optimizes the reproducibility of science.

What I hope people do, in particular, is to use the 3D graphics of our paper’s 17 specimen-based archosaur bodies for other things– new and original research, video games, animations, whatever. It has been very satisfying to finally, from fairly early in the paper-writing process onwards, present all of the complex data in an analysis like this so someone else can use it. My past modelling papers have not done this, but I aim to backtrack and bring them up to snuff like this. We couldn’t publish open access in Nature, but we achieved reasonably open data at least, and to me that’s as important. I am really excited at a personal level, and intrigued from a professional standpoint, to see how our data and tools get used. We’ll be posting refinements of our (Matlab software-based) tools, which we’re still finding ways to enhance, as we proceed with future research.

Velociraptor-model-min Dilophosaurus-model-min00

Above: Two of the 17 archosaur 3D models (the skinny “mininal” models; shrinkwrapped for your protection) that you can download and examine and do stuff with! Dilophosaurus on the left; Velociraptor on the right. Maybe you can use these to make a Jurassic Park 4 film that is better, or at least more scientifically accurate, than Hollywood’s version!😉 Just download free software like Meshlab, drop the OBJ files in and go!

Now, to bring the story full circle, the paper is out at last! A 4 year journey from Viv’s PhD thesis to the journal, and for me a ~14 year journey from my mind’s eye to realization. Phew! The real fun begins now, as we see how the paper is received! I hope you like it, and if you work in this area I hope you like the big dataset that comes with it, too. Perhaps more than any other paper I’ve written, because of the long voyage this paper has taken, it has a special place in my heart. I’m proud of it and the work our team did together to produce it. Now it is also yours. And all 3200ish words of this lengthy blog post are, as well!

Last but not least, enjoy the wonderful digital painting that Luis Rey did for this paper (another of my team’s many failed attempts to get on the cover of a journal!); he has now blogged about it, too!

Dinosaur posture and body shape evolving up the evolutionary tree, with example taxa depicted.

Dinosaur posture and body shape evolving up the evolutionary tree, with example taxa depicted. By Luis Rey.

 


News stories about this paper will be added below as they come out, featuring our favourites:

1) NERC’s Planet Earth, by Harriet Jarlett: “Dinosaur body shape changed the way birds stand

2) Ed Yong on Phenomena: “Crouching  bird, hidden dinosaur

3) Charles Choi on Live Science: “Crouching bird, hidden evolutionary purpose?

4) Brian Handwerk on Nat Geo Daily News: “Birds’ “Crouching” Gait Born in Dinosaur Ancestors

5) Jennifer Viegas on Discovery News: “Heavier dino arms led evolution to birds

6) Puneet Kollipara on Science News: “Birds may have had to crouch before they could fly

And some superb videos- we’re really happy with these:

1) Nature’s “Crouching Turkey, Hidden Dragon

2) Reuters TV’s “3D study shows forelimb enlargement key to evolution of dinosaurs into birds

Synopsis: Decent coverage, but negligible coverage in the general press; just science-specialist media, more or less. I think the story was judged to be too complex/esoteric for the general public. You’d think dinosaurs, evolution, computers plus physics would be an “easy sell” but it was not, and I don’t think we made any big errors “selling” it. Interesting– I continue to learn more about how unpredictable the media can be.

Regardless, the paper has had a great response from scientist colleagues/science afficionados, which was the target audience anyway. I’m very pleased with it, too– it’s one of my team’s best papers in my ~18 year career.

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