Posts Tagged ‘fossilicious’

At this writing (17 October, 2013), I am headed home after a 10-day trip to China as part of an RVC delegation participating in a London Universities International Partnership (LUIP) event (celebrating London innovations, especially those developed with Chinese input) as part of a broader UK/London-China trade mission. I am still processing what has been an astonishing, exhausting, exhilarating, chaotic, lavish, smog-ridden, and inspiring visit. As a simple scientist, I’ve found myself in the midst of major global politics, business and science policy, with little time to assimilate what has happened but still learning plenty about how the bigger world, way beyond my lab, operates. I thought I’d share that experience, by way of pictures illustrating key – or just unusual or interesting – events and places from my journey. It was surreal, in so many ways…

Stomach-Churning Rating: 0/10 except for a couple of odd statues. No squat-toilets; I will spare you those.

Odd sight above entrace to the art gallery building that housed the LUIP event.

Odd decoration above entrance to the art gallery building that housed the LUIP event.

Several months ago the RVC selected me to help RVC Access director Nina Davies and colleagues set up an exhibit, as part of the LUIP event, featuring the work that my team has done, and is still doing, with Chinese collaborators at the IVPP in Beijing (exemplified by this past post). Dinosaurs and 3D computer modelling were thought to be a good potential draw for the public (ya think?) as opposed to more controversial subjects such as avian flu, with which the RVC also has research strengths and Chinese collaborations. I saw it as a great chance to go spend time at the IVPP’s spectacular fossil collection and develop ongoing collaborations with scientists there like Drs. Zhou Zhonghe and Xu Xing. Subsequently, I learned that it was a small enough event that I’d probably be meeting Boris Johnson (Mayor of London) there as well, possibly even presenting our research to him.

Hallway lined with art galleries, one of which is the Yang Gallery.

Hallway lined with art galleries, one of which is the Yang Gallery, which the event was held in.

The preparations for the exhibit were full of surprises, as you might expect a long-distance interaction between UK and Chinese people to be, especially if you’ve spent time in China and know some of the broad-brush cultural differences (e.g. “Yes” can mean no, and “maybe” usually means no). There were many cooks involved! Artists, policymakers, scientists, universities… and then the Mayor’s office got thrown into the action, and then it snowballed, with UK Higher Education and Science minister Rt Hon MP David Willetts coming to the LUIP event, and UK Foreign Chancellor George Osborne then scheduling a related trip to China at the same time. Meanwhile, I just supplied some images (courtesy of Luis Rey) and a video (by Vivian Allen and Julia Molnar) from our past paper to illustrate what we’re doing with Chinese collaborators.

There wasn’t time to prepare a fancy exhibit with lots of bells and whistles, but I was pleasantly surprised by what the LUIP organizers cooked up from what we provided, as photos below show. The addition of four great casts of fossils on loan from the IVPP was crucial and made us stand out from all the other exhibits in a big way! The event was held in the trendy 798 Art District in eastern Beijing, which is an old industrial area converted to a surprisingly bohemian, touristy area that still sports its rusting old industrial infrastructure, but bedecked with modern art! That really worked for me as a setting. This was my third visit to Beijing/China but my first time in this gritty area of the city, which I recommend spending an afternoon in sometime if you visit– the streets are lined with cafes and art galleries.

Boris bike and nice design of exhibits (placed on/around the giant letters LONDON) .

Boris bike and nice design of exhibits (placed on/around the giant letters LONDON). The back wall sports a Communist slogan, partly painted over, exhorting the workers to give their full effort for the glory of Chairman Mao or something (seriously). The building was once a weapons factory, I was told.

All the work we put into this event was a big deal to me, but as the event developed, and the schedule for my 10 day visit shifted almost daily as various political factions shuffled the LUIP and UK trade mission plans, I became aware of the vastly broader issues at play, and humbled by their scope. Sure, studying the 3D changes of dinosaur body shape across >225 million years is truly awesome to conduct, but the socio-political issues around the LUIP event boggled and baffled me. Issues like “How do we get more Chinese students to come study at London universities?”, “How do Chinese parents feel about their students studying to become veterinarians?” and “What are the key obstacles limiting UK-Chinese collaborations and how can they be resolved?” gradually eclipsed the technical, scientific issues in my mind, and I started to feel lost. I learned a lot from this eye-opening experience.

These two news stories here (with video; me speaking at ~01:15) and here (with pic of me w/exhibit) give a good idea of the scale and potential importance of the events.

The rest of his post is mostly a photo blog to illustrate the goings-on, but I consider some psychological/philosophical matters toward the end.

The London innovation event lighting gets tested out-- and looks sweet.

The London innovation event lighting gets tested out– and looks sweet.

Boris arrives, and proceeds to tour the exhibits rather than give his speech as planned. But it worked out OK in the end; he had 2 exhibit tours and a speech in the middle.

Boris arrives, and proceeds to tour the exhibits rather than give his speech as planned. But it worked out OK in the end; he had two exhibit tours and a speech in the middle.

Minister Willetts arrives and prepares to speak about UK higher education for Chinese students.

Minister Willetts arrives and prepares to speak about UK higher education for Chinese students.

I give Minister Willetts a tour of our fabulous fossil casts.

I give Minister Willetts a tour of our fabulous fossil casts.

Left to right = back in time through avian evolution, represented by Yixianornis, Pengornis, Jeholornis and Microraptor casts courtesy of the IVPP.

Left to right = back in time through avian evolution, represented by Yixianornis, Pengornis, Jeholornis and Microraptor casts, courtesy of the IVPP.

Arguably one of the most important fossil finds, the "four-winged" dinosaur Microraptor.

Arguably one of the most important fossil finds (ever?), the “four-winged” dinosaur Microraptor.

Added benefit of thaw in UK-Chinese relations: Microraptors for everyone!!! Well, for me anyway. And a cast, not a real one. But still pretty damn cool, and now it’s in my office for comparative research and teaching. See?

Darwin greets Microraptor in my office.

Darwin greets Microraptor in my office.

Like I said at the start, I don’t have a profound insight from this trip, not yet if ever. But it has obviously made a strong impression on me. It has reinforced some thoughts about Big Life Stuff. With the jetlag, the big geopolitical issues, the foreign country, the opulence, and my research thrown into that heady brew (ahem, along with some Tsingtao beer), I became lost. And I liked it, even though I was totally clueless at times, just looking around wide-eyed at the events unfolding and hearing about the political manoeuvring behind the scenes (e.g. how would big figures like Boris and Willetts share the limelight? And the news media was playing up the question of whether Boris’s or Osborne’s contingents were “winning” in some sense of some struggle, even though ostensibly they are on the same Tory team).

But we’re all clueless; we’re all lost. In some ways that’s a good thing. We have work to do; broad landscapes to explore whether evolutionary or socioeconomic or whatnot. There are big questions left, and no easy answers sometimes. That’s a bad thing, too; if we were less lost in major issues like climate change or habitat destruction or gross imbalance in wealth/power, the world would be a better place.

Quite apropos! Rockin' artwork found in the 798 art district surrounding the Yang Gallery.

Quite apropos! Rockin’ artwork found in the 798 art district surrounding the Yang Gallery.

I find it helpful at times to ground myself in the knowledge that I am lost just like everyone else. There are different ways we can get lost: such as in pondering how dinosaur anatomy and physiology transformed over the Mesozoic era, or in throwing ourselves into weighty issues of business and diplomacy in the real world. To pretend we’re not lost risks becoming foolhardy.

It might be helpful for others to remind themselves of this sense of being lost, and that we all feel it or at least should at times. Students may sometimes look to their professors and think they have some monopoly on wisdom, but they’re lost too, and surely in some ways more lost than any of their students.

Smaller scale dino art.

Smaller scale dino art in a local shop.

Boris got a bit lost, too, when he came to my exhibit – pondering the dinosaur-bird fossils, he pondered out loud “There’s some bone that birds and reptiles both have that shows they’re related… the, umm, the ischium?” Not understanding what he meant by this (all tetrapods have an ischium), I redirected him, along with a reassuring comment that he’d done his homework. I did this a bit clumsily as the multitude of news cameras and lights and boom-mikes hovered around us in eager anticipation of Something Interesting Happening, and as his minders began to urge him to move onward through the LUIP exhibit. I noted the wrist of a dinosaur like Microraptor and how it already had the unusual wing-folding mechanism that modern birds now use during flapping flight or to keep their feathers off the ground when standing. He seemed to sort of like that, then shook my hand and said something like “very impressive, well done” and moved on to the next exhibit. (Willetts fared a bit better and stayed longer, but science is his business)

funky statue (4)

Random artwork from the Yang Gallery and around the 798 Art District follows… I liked the style. My kind of funky art. The statue above combines childlike toy aspects with sinister jingoistic imagery. And the next one, well… see for yourself.

In that brief, frantic conversation, we were both lost, and I think none the less of Mayor Johnson for it. He’d come off the plane, rushed to hotel and to the LUIP event, gave an impassioned speech about London and China, and then was whisked around between a dozen or so exhibits, pursued all the while by a throng of media and minders and gawkers- was he expected to know all the sundry details of maniraptoran evolution at that point? No. But we had some fun and smiled for the cameras and then it was all over as we spun off, reeling into our different orbits. I wouldn’t be surprised if, from time to time, a politician like Boris pinches himself and thinks privately, “Wow, these issues I am embroiled in are so convoluted. I am totally, utterly lost.” I think that’s a healthy thing, and I enjoyed repeated doses of that feeling during my trip. funky statue (2) In science, we often deal with a sense of awe or wonder—that is the sunny side of being lost. The other side, which can coexist sometimes in duality with awe/wonder, is the more fearful/anxious side, like when you’re stuck in a foreign city far from your hotel; surrounded by alien, fantastic scenery; and night is falling but no taxis are around to take you back, and the locals are starting to watch you to see if you’ll do something stupid (this was me, briefly, after doing some evening mall-shopping in Shanghai). How we react to that duality is, in some way, our choice. I point to a scientist studying evolution and a creationist freaking out about the subject as a good example of two polar opposites in how an awesome topic in science can evoke very different reactions within that duality. A seasoned traveller who likes to throw themselves into a city and experience blissful, unpredictable immersion, and a worrisome tourist who can’t stray far from their tour group provide analogous examples. But I digress; this post is in danger of becoming lost… Enjoy some cool statues as the denouement. funky statue (3) Get lost in the comments—what makes you have that sense of awe, or being lost, and how do you deal with it? funky statue (1)

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Yesterday I encountered the question that, as a scientist who has studied a certain chunky Cretaceous carnivore a lot, most deflates me and makes me want to go study cancer therapeutic methods or energy sources that are alternatives to fossil fuels (but I’d be useless at either). I will explain why this is at the end of the post.

The question stems from a new discovery, reported in Proceedings of the National Academy of Sciences (PNAS) and thus expected to be one of the more important or exciting studies this year (no, I’m not going to get into the issue here of whether these “high impact” journals include the best scientific research or the most superficial or hyped “tabloid” science; they publish both, and not in mutual exclusivity). It’s a broken Tyrannosaurus rex tooth embedded in a duckbill dinosaur’s tail bone, which healed after the injury, showing that the animal survived the attack.

If you’re with me so far, you might be making the logical leap that this fossil find is then linked to the hotbed of furious controversy that still leaves palaeontology in crisis almost 100 years after Lambe suggested it for the tyrannosaur Gorgosaurus. If the hadrosaur survived an attack from a T. rex, then T. rex was a habitual predator and OMG JACK HORNER AND OTHERS BEFORE HIM WERE WRONG!

And you’d be right.

My encounter with the question stemmed from an email from a science journalist (Matt Kaplan) that, as is normal practice, shared a copy of the unpublished paper and asked for comments from me to potentially use in an article he was writing for the science journal Nature’s news site. Here, then, was my off-the-cuff response:

“Ooh. I do have a pretty strong opinion on this. Not sure if you’d want to use it but here goes. I may regret it, but this hits my hot buttons for One of the Worst Questions in All of Palaeobiology!

The T. rex “predator vs. scavenger” so-called controversy has sadly distracted the public from vastly more important, real controversies in palaeontology since it was most strongly voiced by Dr Jack Horner in the 1990s. I find this very unfortunate. It is not like scientists sit around scratching their heads in befuddlement over the question, or debate it endlessly in scientific meetings. Virtually any palaeontologist who knows about the biology of extant meat-eaters and the fossil evidence of Late Cretaceous dinosaurs accepts that T. rex was both a predator and scavenger; it was a carnivore like virtually any other kind that has ever been known to exist.

While the discovery is nice evidence, it is not particularly exciting in a scientific sense and is only one isolated element from species that lived for hundreds of thousands of years, which to me changes nothing and allows no generalizations about the biology of any species, only the statement that at one point in time a Tyrannosaurus bit a hadrosaur that survived the encounter. There is no real substance to the controversy that T. rex was “either” a predator or scavenger. It is just something that scientists drum up now and then to get media attention. I hope that soon we can move on to more pressing questions about the biology of extinct animals, but the media needs to recognize that this is just hype and they are being played in a rather foolish way; likewise scientists that still feel this is an exciting question need to move on. Maybe this specimen will allow that. But somehow my cynical side leads me to suspect that this “controversy” will just persist because people want it to, regardless of logic or evidence. (bold font added; see below)

Great galloping lizards, I am so tired of this nonsense. Maybe there is educational value in showing how science deals with provocative half-baked ideas about celebrity species, but scientists in the community need to speak up and say what the real science is about. It’s not about this “controversy”. Modern palaeontology is so much better than this.

Sorry for the rant. Maybe it’s too extreme but I’m just fed up with this non-issue! I suspect a huge proportion of our field feels similarly, however.”

(I later redacted a bit of it where I got a little too excited and used the word “curmudgeon”; a mistake, as that could be seen as ad hominem rather than a term of endearment, and this issue is about the science and not the people, per se. That bit is redacted here, too. I’ve also redacted a sentence in which I made an opinion on whether the paper should have been published in PNAS; that is mostly irrelevant here. I was not a reviewer, and authors/reviewers/editors have to make that decision. This would be a massive tangent away from what this blog post is intended to be about! I know some of the authors and don’t want to offend them, but this is about the science and how it is represented to the world, not about these particular authors or even this paper itself.)

Importantly, Kaplan’s story did include my skeptical quote at the end. I am curious to see how many other news stories covering this paper go that far.

Would a T. rex prey on, or just scavenge, a giant chicken? (art by Luis Rey)

Would a T. rex prey on, or just scavenge — or have a great time racing — a giant chicken? (art by Luis Rey)

I will stop right here and acknowledge that I’ve published a lot on a somewhat related topic: how fast a T. rex could run or if it could run at all. To me, that’s a great scientific question that has consequences not only for the predator/scavenger false dichotomy, but also for general theories of locomotor biomechanics (can an animal the size of a large elephant run as well as or better than said elephant? What are the thresholds of size and maximal running/jumping/other athletic abilities and how do they vary in different evolutionary lineages? And so on.). I’ll defend the validity of that question to the bitter end, even if it’s a question I’ve grown a little (but only a little) tired of and generally feel is about as well settled as these things can be in palaeontology (see my review here). I’ll also defend that it has been a real controversy (I have plenty of old emails, formal rebuttals submitted by colleagues, and other discourse as evidence of this) since I tackled it starting in 2002 and sort of finishing by 2011. I am sensitive about the issue of hyping my research up– this is something I’ve been careful about. I set a reasonable bar of how much is too much, check myself continuously with reflective thought, and I do not feel I have ever really crossed that bar, away from science-promotion into darker realms. This is partly why I’ve stopped addressing this issue in my current work. I feel like the science we’ve done on this is enough for now, and to keep beating the same drum would be excessive, unless we discovered a surprising new way to address the questions better, or a very different and more compelling answer to them.

T. rex: scavenger or predator?” was controversial back  in 1994 when Horner published “The Complete T. rex”, where he laid out his arguments. Brian Switek covered this quite well in his post on it, so I will not review that history. There was a big Museum of the Rockies exhibit about it that toured the USA, and other media attention surrounding it, so Horner’s name became attached to the idea as a result. Other such as Lambe and Colinvaux had addressed it before, but their ideas never seemed to gain as much currency as Horner’s did. But this post is not about that.

What this post is about is a consideration of why this is still an issue that the media report on (and scientists publish on; the two are synergistic of course), if most scientists aware of past debates are in good agreement that a T. rex was like most other carnivores and was opportunistic as a switch-hitting scavenger-predator, not a remarkably stupid animal that would turn down a proper meal that was dead/alive. Indeed, the Nature news piece has a juicy quote from Horner that implies (although I do not know if it was edited or if important context is missing) that he has been in favour of the opportunistic predator-scavenger conclusion for some time. Thus, as Switek’s article notes, even the strongest advocates of the obligate scavenger hypothesis(?) have changed their minds; indeed, that 2011 blog post intimates that this had already happened at least 2 years ago.

For many years, nothing has been published in the main peer-reviewed literature that favours that extreme “obligate scavenger” hypothesis. If I am wrong and there is a scientific debate, where are the recent papers (say within the past 5 years) that are strong, respectable arguments in favour of it? I contend that it is a dead issue. And if it is just about the middle ground; i.e. what percent of its time did a T. rex spend hunting vs. scavenging; we have no clue and may never know, and it’s not a very interesting question.

But who then is feeding off of this moribund equine; this defunct tyranno-parrot?

In thinking about my reply to the journalist over the past 2 days, I am reminded again of my general feeling that this is no longer a question of scientific evidence; the important bit in bold font above. Maybe we just like this “hypothesis” or the “controversy”, or maybe we’re lazy and don’t want to have to hunt for real debates in science.

But who are “the people?” I do not feel that The Public should be blamed; they are the people that The Scientists and The Media ostensibly are seeking to inform about what the state of modern knowledge and uncertainty is in science. So when I get asked about the controversy after a public lecture, I always try to go into detail about it. I don’t sigh and say “go Google it”. Nor do I do this to a journalist. Indeed, I’ve generally headed this issue off at the pass and added a blurb to press releases/webpages explaining my T. rex research to explain how it relates to the non-controversy; example here.

I have to begin turning my finger of accusation away from scientists and toward some of the media, because they must play a huge role in the shennanigans. Yes, scientists should know better then to play this up as a valid, heated, modern controversy. That is true. Yet I have a feeling that the balance of blame should also fall heavily on the side of media (general and science news) that continue to report on this issue uncritically as a real controversy. Thus the general public thinks it still is, and scientists/journals keep issuing papers/press releases that it is, leading to more reporting on this “controversy”, and the beast refuses to die. Switek’s article is a good counter-example of balanced coverage with clear application of critical thinking.

This is trivially different from other non-controversies in palaeontology such as whether birds evolved from a subgroup of theropod dinosaurs and hence are dinosaurs by virtue of descent (consensus = yes). So it is reflective of a broader problem of not calling a spade a spade.

And it’s embarassing, to a scientist, as my quote above expressed, to see dead controversies trotted out again and again, feeding the public perception that they are not dead.

That’s what leaves me frustrated. When do the shennanigans end?

I am reminded of a quote from a Seinfeld episode:

“Breaking up is like knocking over a Coke machine. You can’t do it in one push. You gotta rock it back and forth a few times, and then it goes over.”- Jerry, from the episode “The Voice”.

But this predator/scavenger relationship-from-hell leaves me, as a specialist working in this general area, feeling like I am trapped under that fridge. Help!

That’s why I started off this long post talking about feeling deflated, or disappointed, when asked this question. I do feel that way. I have to admit, I sometimes even feel that way when a sweet young kid asks me that question. Deep inside, I wish they wondered about something else. I wish that science had reached them with a deeper, more contemporary question. But when a journalist asks me how I feel about a new paper that revisits the “controversy”, I feel embarassed for palaeontology. Can’t we get past this? It makes us look so petty, mired in trivial questions for decades. But we’re not like that. This is a dynamic, exciting, modern field, but every news story about non-issues in palaeontology just perpetuate bad elements of palaeontology’s image.

To the scientists– why don’t we put our foot down more and say enough is enough, this is a dead issue? We have a role not only in peer review, but also in communicating our views about published work to the media when asked (AND when not asked, as in this blog post). But if you call them on it, do they listen? Which brings me to…

To the media (science/general journalists etc; I know this is a huge category and please don’t think I am blaming 100% of journalists or assuming they are all the same; they are not!)– if scientists tell you that a “controversy” is not such, at what point do you accept their judgement and kill the story, or at least use that quote? Does that ever happen? In what way are you at the mercy of senior editors/others in such issues? What power do you have? Is a shift in the balance of editorial power needed, or even achievable, in your case or in good exemplar cases? I’d really like to hear your experiences/thoughts. I am sure there is a lot I am not understanding, and I know many journalists are in a tough situation.

To the public– You’re often being misinformed; you are the losers in this issue. How do you feel about all it? (While this post focuses on a very tiny issue, the T. rex scavenger/predator unending drama, it is also about a broader issue of how the media perpetuates controversies in science after they have already gone extinct.)

What did this post have to do with freezers? Nothing. I’m just (H)ornery. Although I was once filmed for a planned Discovery Channel film about scientists who find a frozen tyrannosaur in polar regions and have to decide what to do with it before it slips into a chasm and is lost forever. Probably better that this never aired; it was cancelled. Segue to this post.

The Berkeley cast of the Wankel (MOR555) specimen of T. rex. Will we ever see the end of the predator/scavenger non-issue?

The Berkeley cast of the Wankel (MOR555) specimen of T. rex. Will we ever see the end of the predator/scavenger non-issue?

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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 out 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 Londo. 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?? 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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If you want to see a new/reinvigorated, exciting direction that palaeoart is headed, check out the All Yesterdays book by Conway, Kosemen and Naish. This review is fully cognizant that I’m late to the party of hailing this book as part of a palaeoart renaissance. I confess I haven’t read any of the many reviews of this book; I just know it is highly regarded and popular, from excitement on social media sites I frequent. So if my review covers ground others have too, so be it; it’s purely my own thoughts but I expect that mine fall in line with many others’. I’m reviewing the book on this blog because I love the interface between science and art (which is very important in anatomy), and because anatomy, and how one infers it when it is unknown, is the fundamental theme of the book.

You can buy All Yesterdays for around £18 (ASIDE: oddly, used copies (“May not include CD, access code, or DJ”– ???) are around £42 on the same site; perhaps those are artist-signed??? I have no idea!). It is a good deal at that price. While you’re at it, get “Dinosaur Art: The World’s Best Paleoart” by White et al. (including Conway) for a similar price. My review will return to some comparisons between these two books, released just a few months apart.


All Yesterdays is about not only how we reconstruct dinosaurs and other prehistoric animals, but also about thinking outside-the-box in the ways we reconstruct them and thereby bucking some recent clichés and tropes. Some of those outside-the-box ideas might seem ludicrous, and some probably are. But one of the main points of All Yesterdays is that there is plenty about extinct animals, and even living animals, that we don’t know, even though the field of paleoart has matured into greater scientific rigor than in the days of Knight, Zallinger and others (1920s-1950s). There is a focus on uncertainties about integument (e.g. feathering, spines, colour/patterning, body contours) and behaviour (e.g. avoiding stereotypes like perpetually aggressive predators and frightened prey animals– amen to that!). And the capstone of the book, which in some ways I loved the most, is turning the issue on its head and pretending that we only had skeletons of extant animals, then proceeding to reconstruct those animals (elephants, whales, horses and swans stand out prominently in this section; some of these are shown below). I wish more scientists in my general area would practice this; e.g. validation of a methodology used to reconstruct extinct animals in science.

The ‘speculative zoology’ of All Yesterdays deserves favourable comparison to one of my favourite science-art books, 1981′s After Man by Dougal Dixon. I fell so in love with that book as a 10-year-old that I wouldn’t let my parents return it to the library and I made them pay the hefty lost-book-fee (yes, I was a little bastard!). I still have it, too. (Sorry, Sequoya Branch Public Library of Madison, WI!) Likewise, the whimsy of the Rhinogrades is evoked by this work, and of course Tetrapod Zoology blog readers will be no strangers to it, either.

The book begins with a clear, succinct (7 page) summary of the history and science of reconstructing animals, with a focus on paleoart’s approach rather than science’s. I would have found it interesting (but space constraints presumably precluded) to feature more of the interface/parallels with scientists at the same time, such as the careful reconstructions of musculature in A.S. Romer’s masterful work in the 1920s (e.g. below), or later efforts by palaeontologists like Alick Walker and Walter Coombs. Many of these luminaries sought not to reconstruct animals for artistic purposes, but for almost purely scientific ones: to understand what skeletal anatomy meant in terms of broader biology (e.g. comparative anatomy) and phylogeny (e.g. origin of birds or archosaur evolution). The quality of their own artistic representations as well as scientific interpretations varied a lot. Indeed, sometimes the choice of model organisms (crocodile for Romer; lizard for Walker; birds in the post-1960′s) reveals much about the author’s preconceptions about phylogeny, marshalled towards a favoured hypothesis (e.g. a crocodile origin of birds for Walker; or an avian origin amongst dinosaurs for Bakker, Paul and others), rather than a circumspect assessment of all relevant evidence.


Figure 6 from Romer, 1923; very crocodylian T. rex right hindlimb muscles.

But eventually the “model organism” approach to reconstructing extinct animals gave way to the extant phylogenetic bracket; very popular today; which itself is an adaptation of the outgroup method for polarity assessment in phylogenetic systematics (cladistics). I am sure many modern paleoartists explicitly consider the “EPB” in their reconstructions, although this leaves many ambiguities (e.g. integument of crocodiles and birds being totally different!) that they must overcome, whereas scientists might just give up. This interface of art and science is part of what make palaeontology so enjoyable.

The EPB mindset has been a big step forward for evolutionary morphology and palaeontology, but still some of the greatest questions (e.g. what were the actual sizes, colour patterns, or behaviours of extinct animals? How did novelties arise and which novelties did dinosaurs have that extant relatives lack?) are left ambiguous by the EPB. This is because either the EPB itself is ambiguous (crocodiles or other taxa do one thing; birds do something altogether different), or because features leave no osteological correlates (e.g. muscle/tendon/ligament scars) on fossils that can be compared with the EPB.  This quandary leads to the fun side of this book– filling in the huge gaps left by both basic anatomical interpretation and the restrictions imposed by the EPB, and then playing with the frontiers of anatomical, behavioural and ecological reconstruction, using informed speculation.

The extant phylogenetic bracket for archosaurs.

The extant phylogenetic bracket for archosaurs.

In addition to the startling, bizarre “All Todays” reconstructions at the end of the book, the highlights for me were the camouflaged Majungasaurus and plesiosaur, the “feathered mountain” (below) of a therizinosaur (can anyone illustrate a plausible therizinosaur and make it normal and boring? I wager not!) and the neck-swinging elasmosaurs engaged in “honest signalling” of their fitness. Many of the illustrations riff on notions popular in the modern palaeo-zeitgeist (and subject of many conversations at conferences, or even publications), such as evidence for the spiny integument of some ornithischians, fat ornithopods, Microraptor of somewhat-known-colouration, and so on. But plenty of other images riff on a “well why not?” theme, challenging the viewer to consider that extinct animals could have many surprises left in store for us with future discoveries, or else plausible features that we’ll never know of but might seem laughable or unfashionable to illustrate now. Each image has text explaining the logic behind it- this is not just a montage of pictures. This is a thinking person’s book- you should buy it for rumination, to challenge your preconceptions, not to have a flashy coffee table book. It’s not eye candy — it’s more like brain jerky.

John Conway's mountain-of-feathers therizinosaurs: eerily beautiful.

John Conway‘s mountain-of-feathers therizinosaurs: eerily beautiful.

I think this is a bold, fun (re)new(ed) direction for palaeoart. There’s always a place for rigorous, conservatively evidence-based, by-comparison-almost-uncreative scientific illustration of extinct organisms. The World’s Best Paleoart presents loads of this, often in vividly colourful, photo-realistic, lavish, glossy detail, whereas the approach in All Yesterdays tends toward a more soft, matte, informal style including sketches or abstractions, toning down the serious and intense (even cluttered?) approach that can characterize modern palaeoart, including The World’s Best Paleoart.  Sometimes those reconstructing life of the past (scientists included!) may emphasize that detailed realism too much and lose some of the joyful playfulness that palaeoart can revel in, at its best, most inspirational or thought-provoking. The former style might be considered the more “safe” or technical practice; the latter more risky or unconstrained.

Memo Kosemen's "All Todays" swans, with tadpolefish, might haunt your nightmares.

C.M. Kosemen‘s “All Todays” swans, with tadpolefish, might haunt your nightmares.

I’m not casting negative judgement on either style; both are absolutely wonderful — and valuable. I love both books! I’m glad we’re in a new age where the fun is waltzing back into palaeoart, that’s all. All Yesterdays doesn’t just waltz, either. It pounces into your field of view, wiggles its rainbow-coloured, mandrill-esque ankylosaurid bottom at you with a cheeky grin, and proceeds to make you smirk, be bemused, and even gasp at its adventurousness in rapid succession as you turn its pages. At 100 pages it doesn’t overstay its welcome either– that kaleidoscopic thyreophoran rump cartwheels off into the sunset at an opportune moment.

You won't forget Memo Kosemen's "All Todays" elephant.

You won’t forget C.M. Kosemen‘s “All Todays” elephant.

If All Yesterdays makes someone uncomfortable with its swashbucklerish daring, they’re probably taking palaeontology way too seriously– and maybe missing not only some good fun, but also some potential truths. Dogma is a terrible thing, and All Yesterdays slaughters it with delightful relish. Bring on the next installment! If you have  All Yesterdays too, what’s your favourite part? Or if you don’t have it, I’d be happy to answer queries in the Comments.

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…a daily picture of anatomy!

Welcome to Freezermas! In the dead of winter, the WIJF blog jumps down your internet to deliver mind-warming science, and images, and evolution! To celebrate Charles Darwin’s birthday (204th = tomorrow Feb 12, 2013), I’m bringing you one Anatomy Vignette each day this week (we’ll see if I can manage the weekend or not)! Let’s do this!

Stomach-Churning Rating: 2/10; just bones; one picture of them, and then a lot of discussion of muscle anatomy but no pictures of it.


The above image comes from one of my old, somewhat obscure anatomy papers (link to pdf here), from 2003. It’s possibly the first figure I made, entirely by myself, that I’m sort of proud of. It doesn’t totally suck compared with some of my other attempts. I did the stippled line drawing on the left, and on the right is one of my first usages of a digital photo in a paper (digital cameras were finally up to the task around that time; I used my new Nikon Coolpix 900, if memory serves). It was a greatly improved figure over what I’d submitted for this paper originally, which was a rushed, half-baked manuscript for a SICB conference symposium on tendons. I’ll never forget one of the peer reviews of the manuscript, which said something like “the text of this paper is a joy to behold, but the figures are a horror.” They were right, and luckily the images in the paper I submitted changed a lot in revision. (I’m still embarrassed by the incident, though!)

Anyway, the picture is of  the lower hind limb of two theropod dinosaurs: (a,c) an adult Tyrannosaurus rex, and (b,d) a wild turkey (Meleagris) from my personal collections of dissected-then-skeletonized animals (this turkey became a biomechanical model in a 2004 paper of mine, too!).  In both cases we’re looking at a right hind limb; in (a) and (b) from a caudal/posterior/rear view, and in (c) and (d) from a lateral/side-on/profile view.

If you’re having trouble visualizing these bones in the real animal, check this T. rex skeleton in rear and side views and try to find these bones. You can do it! You might also want to look back at my paroxysmic outburst of love for knee joint anatomy.

The thicker long bone is the tibia (your main shank bone; or in a lamb shank, chicken drumstick, etc); the thinner outer bone is the fibula. Together with some smaller bones, for brevity we can call them the tibiotarsus – but only in theropod dinosaurs, or you will anger the freezer gods.

The labels show some cool anatomical features, as follows:

CC” the cranial cnemial crest of the tibia (a projection of bone unique to the knees of birds);

CF” the crista fibularis; or fibular crest; of the tibia (more about this below);

FT” the fibular tubercle (insertion of the big hamstring/biceps muscle M. iliofibularis);

LC” the lateral cnemial crest of the tibia (a big arching swath of bone that both birds and non-avian theropods like Tyrannosaurus have; the CC is just pasted on top of this in birds); and

MF” which denotes a muscle fossa (depression) on the inner surface of the upper end of the fibula, which presumably housed a muscle (M. popliteus) binding the fibula to the tibia in earlier dinosaurs, but is vestigial in birds.

The CF, or fibular crest, is a feature that only theropod dinosaurs, among reptiles, develop like this. It evolved early in their history and thus was passed on to birds with other ancient features like hollow bones and bipedalism. It binds the fibula closely appressed to the tibia, making those bones act more like a single functional unit –and sometimes they even fuse together. The CF also transmits forces from the whopping big M. iliofibularis muscle’s insertion (the FT label) across the puny fibula onto the robust tibia. The MF once held a muscle that also helped keep those two bones together, but additionally it could have contracted to move them relative to each other a little bit, as in other living animals (many mammals and reptiles have a big M. popliteus and/or M. interosse[o]us). So these features all have a common functional, anatomical and evolutionary (and developmental; different story for evo-devo fans) relationship. By binding the fibula and tibia together, these structures helped early bipeds (the first theropods and kin) support themselves on one leg at a time during standing and moving, and also helped begin to reduce the limbs to lighten them for easier, faster swinging. So we can think of these features as specializations that helped theropod dinosaurs, and ultimately birds, get established as bipedal animals.

The CC and LC have a similar story to tell; for one, they are muscle attachments, again mainly for thigh muscles. And again, the LC dates back to early theropods (and some other dinosaurs had a version of it; usually smaller). These crests serve mainly as insertions for the “quadriceps” (in human/mammal terms) or triceps (in reptile/bird terms) muscle group’s major tendon, spanning from the pelvis/femur across the thigh and knee to this region. In birds, we call this structure of insertion the patellar tendon or (less appropriately) ligament. But dinosaurs had no patella, ever, so the triceps femoris tendon would be the proper technical term. Regardless, that crest (LC, and later LC too) helped the attached muscles to straighten the knee joint or support body weight during standing/moving, by giving them better leverage. So it would have been important for early bipeds, too, like the CF, MF and other features above. Your cnemial crest (tibial tuberosity) is pathetic by comparison. Don’t even look at it. Droop your knees in primate shame!

Bumps and squiggles on bones might seem puny details just for anatomists to study and describe in long, tedious monographs, but each is part of the great story of evolution, and each has a story to tell that fits into that story. Back in Darwin’s day, some of the world’s greatest scientists of the age (Richard Owen and Thomas Huxley being but two spectacular examples) pored over these seemingly innocuous features, and so they became part of nascent evolutionary theory even then. This week, I’ll be celebrating a lot of those details, which I still feel are important today, and the stories they help to tell.

Happy Freezermas! Sing it: “On the first day of Freezermas, this blo-og gave to me: a tibiotarsus with a CF and FT!”

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To kick off the New Year just right, our tetrapod team has a new paper in Nature, following up on last year’s Ichthyostega not-so-good-at-walking study (also see here). Yet this paper has a more anatomically descriptive — and also an “evo-devo” — twist to it. For brevity, I’ll let our press release tell the story, since I think it does a good job of it (like I always preach scientists should do, we worked with our PR company to write this together, so we’re happy with how the press release came out). In a nutshell, our study used some very fancy synchotron radiation techniques to image the 3D anatomy of the backbone in early land vertebrates. Our findings surprised even us, and ended up turning around palaeontology/comparative anatomy’s view of how the backbone evolved, giving us a new glimpse into our inner tetrapod.

Stick around for the videos at the end, which are the first four supplementary movies from the paper and are rather pretty (there are two more, for imaging/segmenting afficionados, but they are not as pretty or interesting for most of this blog’s readership). The final figure (Figure 1 from our paper) gives some extra visual context.

The paper is:

Pierce, S.E., Ahlberg, P.E., Hutchinson, J.R., Molnar, J.L., Sanchez, S., Tafforeau, P., Clack, J.A. 2013. Vertebral architecture in the earliest stem tetrapods. Nature, published online [here].

I should note that I’m just 3rd author, so I deserve only modest credit. But I helped. Even though no freezers were involved, or harmed, in the process.


Above image: Julia Molnar‘s illustration of Ichthyostega showing anatomical changes of its spine from front to back, with neural arch/spine in pink, twin pleurocentra in yellow, and intercentrum in green. These four parts, three kinds of bones, made up the backbone of the first land vertebrates. These parts evolved in different ways in later animals, but formed one main bone in all living lineages of vertebrates.


Scientists reassemble the backbone of life using a particle accelerator

Research published today (Sunday 13 January 2013) in the journal Nature documents, for the first time, the intricate three-dimensional structure of the backbone in the earliest four-legged animals (tetrapods).

The international team of scientists, led by Dr Stephanie E. Pierce from The Royal Veterinary College and Professor Jennifer A. Clack from the University of Cambridge, bombarded 360 million year old early tetrapod fossils with high energy synchrotron radiation. The resulting high resolution X-ray images allowed the researchers to reconstruct the backbones of the extinct animals in exceptional detail.

The backbone, also known as the spine or vertebral column, is a bony structure found in all tetrapods, along with other vertebrates such as fish. It is formed from many elements or vertebrae all connected in a row – from head to tail. Unlike the backbone of living tetrapods (e.g. humans), in which each vertebra is composed of only one bone, early tetrapods had vertebrae made up of multiple parts.

Lead author Dr Pierce says: “For more than 100 years, early tetrapods were thought to have vertebrae composed of three sets of bones – one bone in front, one on top, and a pair behind. But, by peering inside the fossils using synchrotron X-rays we have discovered that this traditional view literally got it back-to-front.”

For the analysis, the European Synchrotron Radiation Facility (ESRF) in France, where the three fossil fragments were scanned with X-rays, used a new protocol to reveal tiny details of the fossil bones buried deep inside the rock matrix.

Using this new technology, the team of scientists discovered that what was thought to be the first bone – known as the intercentrum – is actually the last in the series. And, although this might seem like a trivial oversight, this re-arrangement in vertebral structure has over-arching ramifications for the functional evolution of the tetrapod backbone. (see here for a now out-of-date image from Wikipedia)

Dr. Pierce explains: “By understanding how each of the bones fit together we can begin to explore the mobility of the spine and test how it may have transferred forces between the limbs during the early stages of land movement”.

But, the findings didn’t end there. One of the animals – known as Ichthyostega – was also found to have an assortment of hitherto unknown skeletal features including a string of bones extending down the middle of its chest.

Professor Clack says: “These chest bones turned out to be the earliest evolutionary attempt to produce a bony sternum.  Such a structure would have strengthened the ribcage of Ichthyostega, permitting it to support its body weight on its chest while moving about on land.”

This unexpected discovery supports recent work done by the same authors that showed Ichthyostega probably moved by dragging itself across flat ground using synchronous ‘crutching’ motions of its front legs – much like that of a mudskipper or seal.

Dr Pierce adds: “The results of this study force us to re-write the textbook on backbone evolution in the earliest limbed animals.”

The next step, the researchers say, is to understand how the backbone aided locomotion in these early tetrapods using sophisticated biomechanical analysis.

The study was funded by the Natural Environment Research Council.

Additional support was provided by the European Research Council and the ESRF, of which the Science and Technology Facilities Council (STFC) is the UK shareholder.


These are rotating images of the anatomy, colour-coded, of the four species of early tetrapod that we examined for this study. Each shows the same basic pattern of having a “reverse rhachitomous” (pleurocentra in the front, intercentrum in the back; trying to think of a mullet joke…) anatomy. This is opposite the pattern that essentially all studies since famed evolutionary biologist/palaeontologist Edward Drinker Cope coined the term “rhachitomous” in 1878 have portrayed these and related animals as having. And this realization forces a re-examination of how the backbone structures first evolved in tetrapods and which parts (intercentra? pleurocentra? And where?) formed the spines of later animals.

For once, as authors we all felt that this finding really deserved the painfully hackneyed “rewrite the textbooks” label. It changes a lot of what we thought we knew about this classic evolutionary transition of anatomy. Check a vertebrate palaeontology/comparative anatomy textbook and you’ll likely find rhachitomous vertebrae and/or changes of pleurocentra vs. intercentra told in a way that we now are pretty sure is wrong.

You can also see the “sternebrae” (sternal elements; parts of the sternum that evolved independently in later land animals) in the first movie.  This, to my knowledge, is by far the oldest such evidence. I know of ossified sternal plates in Early Permian mesosaurs like Stereosternum, but nothing earlier although perhaps in some synapsid I don’t know, or a basal diapsid of some kind? Chime in in the comments if you know of something I missed. Regardless, the sternebrae in Ichthyostega have nothing to do directly with those convergently evolved in lissamphibians, lepidosaurs, synapsids and archosaurs, although there may be some parallel developmental mechanisms involved and at least similar dermal tissues recruited into ossification patterns. Even so, these sternebrae are further evidence of how that taxon, at least, was beginning to make forays onto land, as they’d have helped it to support its belly on land and breathe.

The segmented PPC-SRµCT of Ichthyostega stensioi MGUH VP 6115 spinning in yaw and roll.

The segmented PPC-SRµCT of Ichthyostega eigili MGUH VP 29017a spinning in yaw and roll.

The segmented PPC-SRµCT of Acanthostega gunnari MGUH f.n. 1227 spinning in yaw.

The segmented µCT of Pederpes finneyae GLAHMS 100815 spinning in yaw.


Figure 1_Pierce et al

Above: (a,b) How we used to think the vertebrae were composed in early tetrapods like Ichthyostega. (c) How we found that Ichthyostega‘s posterior thoracic vertebrae actually tend to look. (d) Ichthyostega‘s anterior lumbar vertebral morphology. (e) Acanthostega according to Coates’s important description. (f) Our revision of the anatomy of Acanthostega (anterior dorsal). (g) Our new interpretation of Pederpes‘s morphology, from a posterior dorsal. Focus on the yellow vs. green elements. In a,b and e they are in different positions (reversed) compared with our new versions in c,d,f,g.

To put the above figure and movies into broader context, check this Wikipedia image. We think the red/pink bones (pleurocentra) are in the wrong place relative to the blue ones (intercentrum); the ones currently there in this image actually belong to the vertebral unit behind that one, so the pleurocentra should be moved to the front (left end) of each unit. But also look down toward the bottom of the figure. Some of those vertebrae may need to have their blue/pink bits re-examined and interpreted, too. Is it turtles intercentra all the way down?

There you have it! Welcome to your new, revised, irradiated, reverse-rhachitomous inner tetrapod’s vertebrae. Propagation phase-contrast X-ray synchrotron microtomography FTW!!!!

Science media articles arising from this study–

I like to keep track of media stories covering our research, using this blog, so here are some of the stories about this paper. It’s funny… this was one of the most broadly important papers I’ve ever been on, but the coverage was relatively scant. It was too technical. We knew that would be a problem, and really had a hard time putting into words why the study was so surprising even to us! Most writers wanted the “how did the animals move?” angle, which was not what the study was about. I still feel that this angle was not even needed; the study (and again I take minimal credit for it) is exciting without it. To comparative anatomy and evo-devo specialists, anyway. Well, that’s science for you; sometimes it is just too hard to explain its value to the outside world, even when you feel its importance in your very spine… And the press coverage was not terrible by any means; no sour grapes from me. Regardless, we’re glad it has been well received by specialist researcher colleagues we’ve spoken to, and that matters a lot.

NERC’s Planet Earth (nice story from our funder)- “Scientists had fossil backbone backwards”

BBC online (the only story aside from NERC’s that did more than read the press release) “Tetrapod anatomy: Backbone back-to-front in early animals”

Discovery News online- “First Land Animals Shuffled Like Seals” (good, but is sort of mixing up our this study, our 2012 one and Ahlberg et al’s 2005 seal-analogue study; latter two were more about movement. As often happens, a lot of other media stories basically copied this one’s headline/angle.)

Discover 80beats- “Paleontologists Use 3-D Models to Rewrite Evolution” (also in “top stories”)

Popsci- “Particle Accelerator Reveals That First Land Animals Walked Like Seals”

Daily FMail (nice pics)- “Astonishing 3D images reveal the first four-legged land animals in amazing detail – and overturn a century of research” (wins longest headline award)

Red Orbit- “Study Reveals First Ever Images Of Early Tetrapod Backbone And How It Helped In Land Evolution”

Examiner.com- “X-ray study rewrites tetrapod backbone evolution (Photos)”

Everything Dinosaur- “Ichthyostega Gets a Re-Think”

Business Standard- “Scientists recreate earliest quadraped’s backbone” (Proofread, editors! Quadruped.)

Geekosystem- “Early Land-Dwelling Animals Moved About Like Seals, Probably Didn’t Balance Balls on Their Noses” (scores some pts for humour)

…and the PR-copying, non-spellchecking fail of the week award goes to… Physorg! “Scientists reassemble the backbone of life with a particle acceleratorynchrotron [sic] X-rays”

Warming up the acceleratorynchrotron for our next study… :)

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