Posts Tagged ‘dinosaur’

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stemmed from an email from a science journalist (Matt Kaplan) that, as is normal practice, shared a copy of the unpublished paper and asked for comments from me to potentially use in an article he was writing for the science journal Nature’s news site.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?

Read Full Post »

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.

Read Full Post »

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.

Read Full Post »


Keith Feinstein of Eureka Exhibits sent me this sketch he did, and when I expressed my reaction of hey-dude-this-is-awesome, he welcomed me to put it up on the blog. Well why the hell not? Awesome belongs here. Dinosaurs (especially space-tyrannosaurs) belong here. Astronauts go into space and space is cold– like an ultra-freezer? So there you are. Additional context: we’ve worked together on Eureka’s “Be the Dinosaur” simulation/exhibit and are now doing “Be the Astronaut.” I suppose this sketch foreshadows the next step: “Be The Astronaut Riding the Dinosaur in the Land of Badassedness”.

Stay tuned for a big post tomorrow…

Read Full Post »

Hey, Americans and others happening to be gobbling down Meleagris gallopavo today– don’t forget to practice your anatomy! Such a great opportunity. Dig in to that carcass and horrify/amaze your family and friends! This pic might help you get started (info below if you want it), and is my WIJF blog wish of happiness to you all, today.

Stomach-Churning Rating: 6 out of 10; a small picture of some fresh turkey leg muscles, but not that bad really.

Click to embiggen.

Wondering what’s shown here?

On the left: an ossified (turned into bone!) tendon, probably part of the M. flexor perforans et perforatus group (a wickedly complex set of muscles that go from the knee region to the toes, and act mainly to flex the knee, extend the ankle and (plantar)flex the toes; i.e curl the toes up). What’s particularly cool is that, towards the top, you can see the divisions where the pennate (angled) fibers of the short, meaty muscle belly sat. If you are eating a turkey drumstick, you will be picking some of these out of the meat, although many turkeys seem to have fewer bony tendons due to human breeding and young age at slaughter.

In the middle, top: a crude experiment where we hung a frozen turkey’s body in a few different orientations to determine its centre of mass, important for biomechanical calculations. Mad science, but simple science.

In the middle, bottom: the right hip joint of a turkey in lateral (side) view, showing a few of the key muscles of the thigh. The ITC is M. (abbreviated Latin for Musculus) iliotrochantericus caudalis. Practice saying that (ill-ee-oh-tro-kan-tare-ick-us caw-dahl-iss) to impress your friends. It sits in a depression in the ilium (top pelvic bone), in front of the hip joint. The ITC is also important for helping birds to support their weight, as Steve Gatesy and I discussed in our 2000 Paleobiology paper. The ITC leaves a lovely crescent-shaped scar on the top of the femur (thigh bone). Show off your culinary skills by noting to your dinner party that this muscle is the best bit of the bird, AKA the “oyster”. (A little tip is here for how to find it; in a chicken but the anatomy is almost the same in a turkey)

The OM is the obturatorius medialis (obb-turr-ahh-tor-ee-us mee-dee-ahl-iss), an antagonist to the ITC, used to swing the leg. It is mostly hidden inside the pelvis so you just see its tendon (dotted line), and especially in turkeys (seriously, they have very nicely visible muscle attachments on their leg bones, for any bird!), a little knobby bit of bone that helps guide the tendon to keep it in its little groove on the femur. Unless you’re very industrious and break open the body cavity to excavate into the pelvis, you won’t be eating this muscle.

The IFE; M. iliofemoralis externus (ill-ee-oh-fem-oh-rahl-iss ex-ter-nuss); arching over the ITC and OM tendons, is a vestigial muscle, often lost in birds, and having little major function but helping a bit to draw the leg away from the body (abduction). Even though it is a puny muscle, it still has a nice little pit for its insertion on the femur. Turkeys are just cool that way. But it’s not much in the way of eating.

And now you know three of the ~40 main muscles of the avian leg, well done! 

I love these muscles not only because I did a lot of my PhD (and later) research on them, but also because they leave great scars on bird and other dinosaurian bones that allow us to reconstruct how muscles evolved. I better stop here or I’ll be writing for days… don’t wind me up further! 🙂

On the right: the foot of a turkey in front and back views. Lots of ossified tendons are visible if you squint. Why do birds only have ossified tendons below their knee joints, and why only some muscles in some birds, and not so commonly in most other species of land animals? This is one of those cool mysteries that remain for people doing evolutionary or biomechanics research to sort out.

Hope you enjoyed a quick anatomy tour with our pal Meleagris!

Read Full Post »

Like other birds, ostriches are fluffy. Too fluffy for some anatomists– so fluffy, it’s hard imagining or estimating what they look like beneath all the feathers. A few years ago, we received an ostrich from a UK farmer. The male bird had been killed by a kick to the neck from another rival, and at the time was supposedly “Britain’s largest ostrich.” As the feathers were valuable to him, the farmer delivered the animal to us whole but plucked. I wanted to dissect it mainly to refresh my memory on ostrich anatomy while developing a biomechanical model of their limbs (see below). Taphonomy expert Jason Moore then buried it for his studies of how bodies decompose.

[Side note: ostriches and other ratites (flightless birds, members of the palaeognath group, whose evolution remains fascinatingly complex) are often brought up as uniquely dinosaur-like. That’s rather misleading; all birds are living dinosaurs, so all birds are descended from an ancestor that was equally ‘dinosaur-like’. What we see of them today is a snapshot that is biased by their recent evolutionary history. During their apparently multiple losses of flight, ratite birds increased in body size and “re-evolved” (or simply enhanced) some traits that were more marked in extinct dinosaurs than in the most recent common ancestor of living birds. Some of those more ‘primitive’ traits may be due to flightlessness, some due to large size, some due to their extreme running specializations; science hasn’t sorted all that out just yet. But the point is, ostriches and other ratites are far from the ancestral form that all birds sprung from, which was probably more like a small, flying tinamou-like animal. Their similarities are due to convergent evolution. And they’re still quite different from something like an “ostrich-mimic” dinosaur- which is a sad misnomer because it’s more that ostriches mimicked (in a naughty teleological sense) ostrich-mimic dinosaurs like Struthiomimus than the other way around; the ornithomimosaurs did it first (Huzzah!). Ratites have just gone back, in some ways but not others (e.g. no long tail or large arms) to a superficially more primitive body form. There have been some wacky ideas to the contrary before, such as the idea that ratites evolved entirely separately from other living birds from different dinosaur stock, but they’re so discredited now by multiple lines of evidence that I won’t glorify them by spending time discussing each. This tangent has gone on too long and must die.]

Anyway, back to the plucked ostrich in question. My first look at it really stunned me. It was a powerful example of just how ‘dinosaurian’ most of the anatomy of living birds is, for reasons noted above. I’d never seen a naked ostrich and now I’ll never look at them the same again. Maybe you won’t, either…

First, some images of the animal once it was brought into our dissection room (which you might recognize from the great Inside Nature’s Giants documentary).

The device near the top of the screen is a digital scale; we were weighing the bird before we cut in…

Close-up view of the hugely muscular legs (each leg is around 25% of the animal’s body weight, and mostly muscle; about 50% more bulky than our legs), and the arms (shown more below).

129 kg weight sans feathers; not bad! That’s about 284 pounds for those folks still mired in the medieval Imperial system of units. 🙂

The swollen, bloody region just below the head (on the left above) is where the mortal blow struck. Ouch!

I love the hands of ratite birds. Yes, those are little claws attached to the three vestigial fingers (thumb/first finger at top, long middle finger, and tiny third finger bound to it). Darren Naish covered some of this in a previous post, and let’s not forget SV-POW’s excellent series of “things to make and do” involving various critters including ostriches.

Ostriches and I go way back. Here I am from my less bald immature postdoctoral days at Stanford University in 2002, dissecting a smaller (female, 65kg) ostrich for some biomechanical modelling (still mostly unpublished; aaargh!).

And yes, I had a third hand back then; later lost during a tragic dissection incident involving a battleaxe and a bottle of tequila. I don’t want to talk about that.

Ostrich packed for transport. Just barely fit in the trunk of my little 1993 Toyota Tercel (R.I.P.)!

Once we complete dissections. we put everything together in some fancy biomechanical computer models (a subject of a future post), resulting in a nice, 3D,  poseable, anatomically-realistic model of the entire limb musculature, shown above. This is a right hindlimb in side view, with the individual muscle paths abstracted as red lines. More about this when it is finally published…

This is just a teaser showing off some of the cool external anatomy of ostriches-in-the-buff, and what we’ve done with the anatomical data we’ve gathered. I’ll do a post later showing what’s inside, which is also pretty amazing. Hope you enjoyed it!

Read Full Post »

« Newer Posts