Posts Tagged ‘buddies’

Freezermas continues with track 3 of our rockin’ anatomy concept album! The number of the beast today is 5 (five days to go in Freezermas!), and I will deviate from the rock/metal theme to embrace the other side of the tracks: hip hop and rap. The Beastie Boys and I go way back: their “Licensed to Ill” album was the second cassette tape I bought (I remember proudly showing it off in Geometry class, circa 1986/7), and still ranks as one of my favourite albums ever. Everyone should own a copy of that, and of this next album…

The Five Felids, featuring KC

If only MCA were still alive to do this follow-up album…

The Beastie Boys’ superb, old school rap NYC-style (and themed) “To The Five Boroughs” (2004) satisfies my search for a #5-themed concept album/song. No track has that title, so I’m going with this one, “Triple Trouble” (song 3; day 3 of Freezermas… c’mon this is all just an excuse for me to talk about music I like and celebrate the concept album/freezers anyway!), as an introduction to a collaborative cat (felid) project we’ve started; and to continue the felid theme from Sunday (also be sure to check out the Snow Leopard dissection I posted on earlier!):

If You If You 
Wanna Know Wanna Know 
The real deal about the cats
Well let me tell you 
We’re felid funded ya’ll 
We’re gonna bring you some mad facts

(yes, that’s painful, I know… be relieved, I tried working some rap jargon into this post’s text but it just looked wack)

Dodgy-looking bagged-up skinned jaguar (bag-uar?) after delivery from Scotland.

Dodgy-looking bagged-up skinned jaguar (bag-uar?) after delivery from Scotland.

Anjali Goswami at University College London, myself, and Stephanie Pierce have teamed up to join the former’s skills in mammalian evolution, morphometrics, evo-devo and more together with our RVC team’s talents in biomechanics, evolution and modelling, and to apply them to resolving some key questions in felid evolution. We’ve hired a great postdoc from Bristol’s PhD programme, soon-to-be-Dr. Andrew Cuff, to do a lot of the experimental/modelling work, and then we have the marvellous Marcela Randau as a PhD student to tackle more of the morphometrics/evo-devo questions, which we’ll then tie together, as our Leverhulme Trust grant’s abstract explains:

“In studying the evolution of vertebrate locomotion, the focus for centuries has been on limb evolution. Despite significant evolutionary and developmental correlations among the limbs, vertebrae, and girdles, no biomechanical studies have examined the entire postcranial skeleton or explicitly considered the genetic and developmental processes that underly morphological variation, which are captured in phenotypic correlations. We propose to conduct experimental and geometric morphometric analyses of living and fossil cats, including the only large, crouching mammals, to study the evolution of locomotion, the mechanical consequences of size-related morphological evolution, and the evolution of correlations (modularity) in the postcranial musculoskeletal system.”

Above: snow leopard (headless) reconstructed and taken for a spin

Our study will integrate some prior studies from Anjali’s group, on modularity for example, and from my group, on the apparent lack of postural change with increasing size in felids (most other birds and mammals get more straight-legged as size increases, to aid in support, cats don’t– paper forthcoming). How does the neglected vertebral column fit into these limb-focused ideas? We’ll find out!

And it’s all very freezer-based research, using a growing stock of specimens that we’ve collected from zoo/park mortalities, many of which are kindly being supplied by Dr. Andrew Kitchener from the National Museums Scotland. We’ll be scanning, dissecting, measuring and modelling them and then returning the skeletons to be curated as museum specimens. This page features five sets of felid specimens involved in the research. We’ll be presenting plenty more about this research on this blog and elsewhere as it continues!

Above: ocelot from Freezermas day 1, now in 3D!

The Bag-o-Cats: whole specimens of a black-footed cat (Felis nigripes), juvenile cheetah, and juvenile snow leopard. I think. Sometimes you get a bag-o-cats and are not sure.

The Bag-o-Cats: x-ray CT slice showing whole specimens of a black-footed cat (Felis nigripes), juvenile cheetah, and juvenile snow leopard. I think. Sometimes you get a bag-o-cats and are not sure.

Panthera atrox (large American lion) from the NHM in LA. Oh yes we'll be applying our insights to strange extinct cats, too!

Panthera atrox (large American lion; “Naegele’s giant jaguar”) from the NHM in LA. Oh yes we’ll be applying our insights to strange extinct cats, too!


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Hey, a short post here to say go check this new blog out! I love it. The first main post-introductory post is a dissection of a snow leopard, documenting a real vet case attempting to figure out why it died. The “Veterinary Forensics blog” is going cool places, and it is a kindred spirit to this blog. You might, as I do sometimes when walking into a veterinary pathology/postmortem facility, see surprising and rare stuff– like in this photo of urban foxes:

troop of foxes


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Today, to help thaw you poor Americans out of that Arctic Vortex, we have a guest post bringing the heat, by my PhD student Sophie Regnault! This relates to some old posts about rhinos, which are a mainstay here at the WIJF blog- I’ve posted a lot about the rhino extinction crisisfeet, skin, big and bigger bones, and more, but this is our first rhinoceros-focused, actual published scientific paper! Take it away, Sophie! (We’re planning a few more “guest” blog posts from my team, so enjoy it, folks!)

Almost a year ago to the day, I submitted my first paper written with John Hutchinson and Renate Weller at the RVC and it has (finally!) just been published. To celebrate, I have been allowed to temporarily hijack ‘What’s in John’s Freezer?’ for my first foray into the world of blogging. I started the paper back as an undergraduate veterinary student. It was my first experience of proper research, and so enjoyable that I’m now doing a PhD, studying sesamoid bones like the patella!

We wanted to discover more about the types of bony disease rhinos get in their feet, of which there isn’t much known. Rhinos, of course, are big, potentially dangerous animals – difficult enough to examine and doubly difficult to x-ray clearly because of their thick skin. Unlike diseases which are fairly easy to spot (like abscesses or splitting of the nails and footpad), there is hardly anything out there in the scientific literature on bony diseases in rhino feet. It’s no small issue, either. When your feet each need to support over 900kg (typical for a large white rhino), even a relatively minor problem can be a major pain. Progressing unseen under their tough hide, lesions in the bone can eventually become so serious than the only solution is euthanasia, but even mild conditions can have negative consequences. For example, foot problems in other animals are known to have knock-on effects on fertility, which would be a big deal for programs trying to breed these species in captivity.

Hidden treasures abound!

Hidden treasures abound! (Photos can be clicked to embiggen)

Data gathering was a blast. I got to travel to Cambridge, Oxford, and London during one of England’s better summers, and these beautiful old museums were letting me snoop around their skeleton collections. I’d been there often as a visitor, but it was anatomy-nerd-heaven to go behind the scenes at the Natural History Museum, and to be left alone with drawers and drawers of fantastic old bones. Some of the specimens hadn’t been touched for decades – at Cambridge University Museum of Zoology, we opened an old biscuit tin filled with the smallest rhinoceros foot bones, only to realise they were wrapped in perfectly preserved 1940’s wartime Britain newspaper.

rhino-feet (2)

rhino-feet (4)

rhino-feet (3)

Osteomyelitis… (3 clickable pics above) the toe’s probably not meant to come off like that!

In addition to my museum studies, I had another fun opportunity to do hands-on research.  John (of course!) had freezers full of rhino legs (looking disconcertingly like doner kebabs, but maybe that’s just me!), which we CT scanned to see the bones. Although it is a pretty standard imaging technique, at this point I had only just started my clinical studies at the vet hospital, and being able to flick through CT scans felt super badass. Most vet students just get to see some horse feet or dog/cat scans, at best.

Another osteomyelitis fracture, visible in a CT scan.

Another osteomyelitis fracture, visible in a CT scan reconstruction.

We expected to find diseases like osteoarthritis (a degenerative joint disease) and osteomyelitis (bone infection and inflammation). Both had previously been reported in rhinoceroses, although it was interesting that we saw three cases of osteomyelitis in only 27 rhinos, perhaps making it a fairly common complication. It’s an ugly-looking disease, and in two of the cases led to the fat, fluffy bones fracturing apart.

We also had several unexpected findings, like flakes of fractured bone, mild dislocations, tons of enthesiophytes (bone depositions at tendon/ligament attachments) and lots of holes in the bones (usually small, occasionally massive). For me, writing up some of these findings was cool and freaky paranoid in equal measures. They hadn’t been much described before, and we were unsure of their significance. Was it normal, or pathological? Were we interpreting it correctly? Discussions with John and Renate (often involving cake) were reassuring, as was the realisation that in science (unlike vet school at the time, where every question seemed to have a concrete answer) you can never be 100% sure of things. Our study has a few important limitations, but has addressed a gap in the field and found some neat new things. Six months into my PhD, I’m enjoying research more than ever, and hoping that this paper will be the first of many (though I promise I won’t keep nicking John’s blog for my own shameless self-promotion if that happens!  EDIT BY JOHN: Please do!).

Nasty osteoarthritis wearing away the bone at the joint surface. Most cases occurred in the most distal joint.

Nasty osteoarthritis wearing away the bone at the joint surface. Most cases occurred in the most distal joint.

Deep holes in some of the bones: infection, injury?

Deep holes in some of the bones: infection, injury?

The paper:
Sophie Regnault, Robert Hermes, Thomas Hildebrandt, John Hutchinson, and Renate Weller (2013) OSTEOPATHOLOGY IN THE FEET OF RHINOCEROSES: LESION TYPE AND DISTRIBUTION. Journal of Zoo and Wildlife Medicine: December 2013, Vol. 44, No. 4, pp. 918-927.

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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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Today I’m doing something a bit unusual for this blog, but which very comfortably fits within its theme. Enough talking about my papers and media appearances and such. Too much self-indulgence, I feel. I want to talk about someone else. And then I will get back to the usual business of this blog: sharing the joy of cool anatomy, with a Mystery Dissection/Image post that is long overdue. Yet first, I wish to share the joy of knowing a cool anatomist– and artist.

One of my great shames as a scientist is that I never cultivated some decent artistic skills that I had as a young boy. And now as an anatomist I feel that my work often suffers from a lack of artistic talent (e.g. the image below, which still makes me hang my head in shame). In addition to scientific know-how, anatomy, when done best, demands the eyes and the hands of an artist. I might have the eyes but I definitely lack the hands. I envy people that have both; Julia Molnar from my team is but one example. And for me, encountering them is always a special delight. What follows is my personal perspective on one of the shining stars in the field.

Right ischium (hip bone) of an adult ostrich in side view, showing some muscle origins and stuff, with a 1cm scale bar. Cringe. My amateurish line drawing. I hate it and wish I'd done better.

Right ischium (hip bone; pelvis/synsacrum) of an adult ostrich in side view, showing some muscle origins and stuff, with a 1cm scale bar. Cringe. My boring, amateurish, pixelly line drawing from a paper on pelvic evolution. I hate it and wish I’d done better.

Mieke Roth is a scientific illustrator from the Netherlands, with a Masters degree from the prestigious and hallowed halls of Wageningen University Her homepage has the tagline “Complex processes beautifully revealed”. This is a wonderfully succinct and eloquent way to describe the magic that she is able to conjure with her skills in scientific illustration. Her “Ultimate Croc Anatomy” project will be the greatest weaving of that sorcery yet. That project is described and will be documented on this page, and has an Indiegogo crowdfunding page here. Mieke describes its goals best:

“I will meticulously dissect a Nile crocodile and document it. I will share the dissection in text, illustrations and video via my website. I will process the data I gathered and each time build a new part of the digital crocodile. From there I will adapt the model for illustrations, books, animations and apps.”

I first became a happy victim of the artistic spells that Mieke casts when I saw her blog entry “How to make an octopus,” which you absolutely must read if you have not already or else you’ll be firmly spanked and sent away from this blog with only lumps of coal in your freezer for Freezermas (what’s Freezermas? Find out soon, and in the meantime be nice– or else!). In her post, Mieke didn’t just look up a picture of an octopus somewhere and redraw it in an abstract, schematic, flat and deceptively simplified way. She went and did her own hands-on research by dissecting an octopus, and then described the steps in converting those observations into a brilliantly novel set of digital illustrations that really brought octopus anatomy to life.

Octopus image by Mieke Roth

Octopus image by Mieke Roth

Part of what first mesmerized me is that this whole investigative and creative process was lovingly documented on her blog. In doing this, Mieke played the roles of both scientist and artist, by displaying the mundane-but-wonderful labour she did to come up with her final, gorgeous results, and the passion, dedication, scholarship and originality that make her stand head and shoulders above so many gifted scientific or medical illustrators. This thrilled me at both visceral and intellectual levels. It literally gave me chills to witness how good the final product was. As I write this and look back on that blog again, months later, I still feel the magic.

So then I started browsing around her homepage and became punch-drunk from repeated blows of amazement—again and again and again the quality and novelty and thoroughness leaped off the computer screen. Images of nature that I thought I knew well, such as the growth of a chick into a chicken (really great blog here documenting this with sketches), were conveyed in a way that made me see them as if for the first time, with joy and wonder. In the space of a day, I became a huge Mieke Roth fan.


Young chicken sketched by Mieke Roth

And now Mieke is taking it not just a notch, but a huge step, to spend a year documenting the anatomy of the Nile crocodile—how cool is that!?! As an expert in the postcranial anatomy of the Crocodylia, I can confidently state that the available scientific literature on the subject is patchy in coverage and often poor in quality by modern standards. There are big flashes of excellence here and there, such as Larry Witmer’s and Chris Brochu’s teams’ very thorough work on head and neck anatomy, or Colleen Farmer’s and Emma Schachner’s studies of lung morphology. But then I glance at some scholarly books (to avoid offending, I will not cite them here) that are supposed to be key references on the complete anatomy of Crocodylia and I frankly am left cold. While there is some superb work from the 1800s (Gadow, Fürbringer and others come immediately to mind), it is in the flat, often colourless style which the printing technology of that age imposed upon those great masters of anatomy. And while there is superb work by Romer, a tome on the Chinese alligator and a few others, again they tend to be limited to line drawings or spotty coverage of various anatomical systems. We need a visionary with both the scientific and artistic skill to make a subject that could seem dry or arcane become miraculous and accessible. I think you can guess whom I have in mind.

I can think of no one better suited to the ambitious goals and demands of the Ultimate Croc Anatomy project than Mieke Roth. She combines the attention to anatomical detail of a classical 19th century anatomist with the technical wizardry of a modern digital artist. She will have a supportive team of experts to ensure the content is exceptional and up-to-date. I’ll be one of them (and the crocs will come from my freezer), because of my enthusiasm for  the project, and I’ve been helping to recruit others. So I urge you not just to join in her crowdfunding effort to carry out a very worthy and exciting project that the world can share, but also to share the joy I had in discovering her work by browsing her online collection of awesomeness. I predict that many of you will feel the power of her spell and become Mieke Roth fans, too, if you are not fortunate enough to be one yet.


Squirrel monkey drawing by Mieke Roth

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At the Structure and Motion Laboratory, we’re not boring scientists who robotically focus only on writing grants and publishing papers, much as senior management might want us to pretend. We’re human. We like fun. And we like Halloween. And brainssss! What follows is some good, jolly, Halloweenerly, spooky, sciencey fun that we came up with yesterday (in between writing grants and papers, ahem).

First, our surreal B-movie extravaganza: It Came From the Biomechanics Laboratory. See if you can piece together the plot:

(subtitle: Open John’s freezer… if you dare!!!)

And in case you want more of the ritual sacrifice of the pumpkin at beginning, here are two versions in glorious slo-mo, from our AOS high-speed digital video cameras:


Finally, an outtake from the film, in which Gary, the RHex robot from Andrew Spence’s Spencelab, takes his gory vengeance on a hapless cameraman, and then turns on his masters!

Thanks to our brave participants: Miguel Lamas (who compiled the first video), Luis “Demon Emu” Lamas and his squad of brave –but now devoured– emu-wranglers from the RVC, Andrew “Robo Arrigato” Spence, Jeff “Giraffe Leg” Rankin (nice acting, Jeff!), Olgascoob Panagiotopoulou-doo, Becky “Schrodinger’s Evil Cat” Fischer, Rich “Sit, Stand, KILL!” Ellis,  Hazel Halliday, and finally that unnamed plucky, cute little kitty-girl (lone survivor and heroine of our story)!

Happy Halloween… muhahahahaaaaaa!!!

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

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

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

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

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

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

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