Category Archives: Dinosaurs

How Fast was T. Rex?

Tyrannosaurus Rex is everyone’s favorite dinosaur, and we’ve all seen dozens of depictions of T. rex, and various more or less scientific reconstructions of its appearance and behavior.

One question has always been, “how fast did T. rex run?”

Experience from living land animals suggests that really large individuals are often slow-moving. On the other hand, T rex certainly looks like a fast runner, though it might have relied on surprise ambushes or even on harvesting carrion.

This month Sellers, William I published a study that uses mathematical models of the structure of the T rex skeleton, taking into account the strength of the bones [1]. The idea is that running stresses the body, and ultimately an animal cannot run so fast that it breaks its bones and joints.

There is a long history of biomechanica studies of living animals which has been applied to fossils including T. rex. These methods use the measurements of the skeleton along with plausible hypotheses about the muscles and other tissues to estimate the “locomotor performance” of the ancient animals. The authors report that these studies have given a range of estimates for how fast a T rex could move, from 5 to 15 m/s, including walking and running gaits.

The current study refines these estimates using two simulations, a mechanical model of the skeleton and a model of the stress on the bones.

Machine learning algorithms are used to generate the muscle activation patterns that simultaneously produce the maximum locomotor speed of a MBDA model of T. rex whilst maintaining defined skeletal safety factors.” ([1], p. 3)

These simulations were run driven by models of walking and running gaits. The detailed model involves all the muscle firings in the animal, so finding a stable gait is a huge computation. The system was run many times to search for maximum speed using the gaits. (See the paper for details.)

These computations indicate that the fast walking gait is consistent with bone stresses typically seen in living animals, which the running gaits often exceed typical stress levels. The authors argue that this indicates that adult T. rex did not run.

Considering the size of the animal, this isn’t a completely surprising conclusion. This fast walk may have been perfectly sufficient, given the size of their herbivore prey, which probably couldn’t run fast either.

The researchers are careful to point out that their simulations are simplified in order to make them computationally feasible. This method is effectively searching through all possible designs for a T. rex, which is a ludicrously large number of variables. In the future, more complete models may be possible, and the results may be refined.

They note that the behavior of a T. rex must have changed as it developed. The smaller young ones might have been fast runners, but reduced to walking as they grow enormous. But little is known about the developmental process.

The also note that their result overturned estimates based on analogy.

It is somewhat paradoxical that the relatively long and gracile limbs of T. rex—long argued to indicate competent running ability […]—would actually have mechanically limited it to walking gaits, and indeed maximised its walking speed. This observation illustrates the limitation of approaches that rely solely on analogy and the importance of a full biomechanical analysis when investigating animals with extreme morphologies such as T. rex.” ([1], p..13)

Cool.

Both dinosaurs and a neat example of multiphysics models, and an example of why HPC is relevant to lots of fields.


  1.  William I. Sellers, Stuart B. Pond, Charlotte A. Brassey, Philip L. Manning, and Karl T. Bates, Investigating the running abilities of Tyrannosaurus rex using stress-constrained multibody dynamic analysis. PeerJ, 5:e3420, 2017/07/18 2017. https://doi.org/10.7717/peerj.3420

Life After the Dinosaurs

Everyone knows about the mass extinction that ended the age of dinosaurs. This is often said to have opened the way for the age of mammals and eventually us.

Of course, it wasn’t exactly like that.

In the wake of the mass extinction, there was an explosive radiation of all the surviving species, not just mammals.

This month saw two articles about this exciting period.

First of all, the dinosaurs didn’t actually all die out. One whole wing of the family survived and thrived until today: the birds.

Ksepka, Daniel T., Thomas A. Stidham, and Thomas E. Williamson report on new findings which document the rapid diversification of birds after the extinction event.[2].  Specifically, they report a small bird that is dated from the very early Paleocene, i.e., soon after the end of the dinosaurs. They argue that dating this species implies that four major groups of birds arose soon after that.

The authors comment that this observation puts the diversification of birds on approximately the same time line as the expansion of mammals.


In a different study, Yan-Jie Feng and collagues analyzed DNA from 156 living species of frogs to construct a putative taxonimic history, anchored by 20 representative fossils [1]. The results suggest that “three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification” right after the end of the dinosaurs. ([1], p. 1)

They argue that the “mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities.” There is a very telling diagram in the full article, with a gigantic fan out of species just past the red line of the Cretaceous extinction event.

The researchers comment that their molecular study is important because the fossil record of frogs is sparse. This is one of the clearest pictures, albeit indirectly, that documents the evolutionary history of frogs during this period.

Again, this is the same time scale as mammals and birds, suggesting that there was a mad evolutionary scramble to fill the huge void left by the mass extinction at the end of the Cretaceous.

Cool!


After the Dinosaurs came not the “Age of Mammals” but the “Age of Pretty Much Everything Except Non-Avian Dinosaurs”! 🙂


  1. Yan-Jie Feng, David C. Blackburn, Dan Liang, David M. Hillis, David B. Wake, David C. Cannatella, and Peng Zhang, Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary. Proceedings of the National Academy of Sciences, July 3, 2017 2017. http://www.pnas.org/content/early/2017/06/26/1704632114.abstract
  2.  Daniel T. Ksepka, Thomas A. Stidham, and Thomas E. Williamson, Early Paleocene landbird supports rapid phylogenetic and morphological diversification of crown birds after the K–Pg mass extinction. Proceedings of the National Academy of Sciences, July 10, 2017 2017. http://www.pnas.org/content/early/2017/07/05/1700188114.abstract

 

Dinosaurs Rising From The Ashes

We’re all fascinated with the story of the end of the Dinosaurs, which corresponds with a really big impact, and possibly other catastrophes. The death of the dinosaurs is not only a puzzle, it is the event that made room for mammals and puny humans to evolve.

But there was also a mass extinction that cleared the way for the great adaptive radiation of dinosaurs. At the end of the Triassic period, about 200M years ago, there was a massive extinction of animals. The dinosaurs rose after this catastrophe.

This month a team of British scientists published new evidence that there was a huge sequence volcanic eruptions at that time, which would have been devastating for living things. This event has been suspected from other evidence of huge lava flows, global cooling (due to volcanic material in the atmosphere), and, of course, mass extinctions.

The new study uses a new techniques which measures mercury (Hg) in the rocks. This element is highly correlated with volcanic activity, which spews Hg into the air.  The mercury falsl out and is incorporated into rock, where it persists for long periods of time–hundreds of millions of years.

Careful measurements indicate high levels of mercury in the period between the extinctions at the end of the Triassic, and the beginning of the Jurassic. In other words, a very clear suggestion that the volcanic disaster caused the extinctions, and the end of the episode was followed by the rise of the dinosaurs.

A key aspect of this work is to trace mercury deposits to many locations around the world. Furthermore, the deposits should be temporally aligned, rising and falling at the same time.   These signatures are consistent with large volcanic “pulses”.

The researchers report that the “Hg excursions are recorded in five of the six sections studied”, and that “The onset of Hg enrichment occurred synchronously across the globe, coincident with the end-Triassic extinction and associated global carbon cycle perturbation.“ (p.5)

In other words, there is clear evidence of very widespread effects of volcanism at the precise time of the mass extinctions.

As Rebecca Morelle puts it, “The onset of Hg enrichment occurred synchronously across the globe, coincident with the end-Triassic extinction and associated global carbon cycle perturbation.

And, evidently, ancestors of the dinosaurs survived this catastrophe, and “once the volcanoes had simmered down, few of their competitors were left, allowing the age of the dinosaurs to begin.”

The dinosaur age began and ended in world-wide catastophe that wiped out most living species, clearing the way for another burst of speciation.

The “age of mammals” started with the catastrophe that killed off the dinosaurs.  It is ending now with the sixth extinction, and, most likely, a spike in global temperature.


  1. Rebecca Morelle, Volcanoes ‘triggered dawn of dinosaurs’, in BBC News: Science & Environment. 2017. http://www.bbc.com/news/science-environment-40333902
  2. Lawrence M. E Percival, Micha Ruhl, Stephen P. Hesselbo, Hugh C. Jenkyns, Tamsin A. Mather, and Jessica H. Whiteside, Mercury evidence for pulsed volcanism during the end-Triassic mass extinction. Proceedings of the National Academy of Sciences, June 19, 2017 2017. http://www.pnas.org/content/early/2017/06/13/1705378114.abstract

New Study: Tyrannosaurs Not Furry

One rule of thumb for blogging is, “when in doubt, go with Dinosaurs!”.  And, for preference, T. rex, of course.  🙂

As I have said, this is the great age of Dinosaur science. Aided in part by the opening of rich fossil beds in China, but also by better and better technology that lets us see much more from the fossils we find.

No controversy has been more controversial than the kerfluffle over feathered Dinosaurs. It’s not that many Dinosaurs couldn’t or shouldn’t have feathers—they did.  They are the ancestors of birds, after all.

But it’s very hard to accept a feathery T. rex. The very paragon of bad ass, top of the top predators, T. rex really should not be fluffy. I mean you’re dead anyway, but you don’t want to be saying, “ooh, look at that gorgeous thing” just as you are snarfed down by the most ferocious land animal ever. It’s just not dignified.

This month Phil Bell and colleagues from around the world published a new detailed study of the skin of Tyrannosaurus rex and family [1]. They conclude that T. rex was not feathered, though it might have had a some feathers on its back. It remains possible that baby rexes may have had features that shed as the animals matured. (We don’t know much at all about baby rexes.)

This finding makes sense form the point of view of thermoregulation. Large, active animals don’t really need a coat of feathers to keep warm. It also might indicate T. rex migrated to live a warmer climate, or out into hot open spaces.

Ancestors of T. rex definitely had a lot of hair-like feathers, and some of them grew to be fairly large, as large as some Tyrannosaurs. So there is still a lot to be learned about the evolution of these animals, and what may have influenced the evolution of feathers and scales.

It is important to note that this is one of the most comprehensive studies of fossils that preserve the skin, but it is nevertheless a pretty tiny dataset (a dozen or two samples). In addition, feathers are a lot less likely to be preserved than skin, so the absence of fossil feathers isn’t necessarily evidence of absence [2].

But for now, I’m not going to visualize T. rex as being fluffy.


  1. Phil R. Bell, Nicolás E. Campione, W. Scott Persons, Philip J. Currie, Peter L. Larson, Darren H. Tanke, and Robert T. Bakker, Tyrannosauroid integument reveals conflicting patterns of gigantism and feather evolution. Biology Letters, 13 (6) 2017. http://rsbl.royalsocietypublishing.org/content/13/6/20170092.abstract
  2. Helen Briggs, Study casts doubt on the idea of ‘big fluffy T. rex’, in BBC News – Science & Environment. 2017. http://www.bbc.com/news/science-environment-40172587

 

Study Proposes New Family Tree For Dinosaurs

There is quite a bit of buzz this week about Matthew Barron and colleagues report on a new classification of dinosaurs [1].

The researchers amassed a very large dataset of dinosaur fossils, the largest and most comprehensive known collection. The data include specimens from 74 taxa which were scored on 457 traits. (While Dinosaurian in comparison to earlier studies, in this age of Big Data this dataset is still pretty puny.   As the press reports noted, it took years to round up the data by hand, and five minutes to run the program.)

The resulting family tree is considerably different from text book consensus up to now. As it should be. The overthrown classifications were based on small datasets and quite a few untested assumptions and intuitions. Since the new analysis doesn’t include these assumptions, the results are different.

From: Figure 1: Phylogenetic relationships of early dinosaurs. From A new hypothesis of dinosaur relationships and early dinosaur evolution Matthew G. Baron, David B. Norman & Paul M. Barrett Nature 543, 501–506 (23 March 2017) doi:10.1038/nature21700

Of course, this sort of analysis needs to be taken carefully. This dataset is big enough and broad enough that it is worth taking seriously, but we still need to remember the limitations of the method.

First of all, the data are based mainly on skeletal remains, which are only a partial picture of the animals in question. We know only too well that skeletal analysis can mislead.

In addition, this kind of analysis can be quite sensitive to the exact sample used. Adding or omitting some traits, or additional fossils could rearrange the results, possibly quite a bit.   This means that future contributions might well produce different results.

The researchers point out some aspects of the classification that seem to add face validity to the results. In this tree, the earliest taxa seem to be small and omnivorous, which makes sense. Gigantic size and specialized diets would seem to be evolved from more moderate sized and general animals.

One conclusion that is particularly interesting is that in this taxonomy, “the supinated, grasping hands seen in some early taxa are interpreted as the primitive dino- saurian condition.” (p. 505) In other words, early dinosaurs had grasping front pawa. As they say, this might have been a key evolutionary advantage, and might also have been a precursor to development of bipedalism.

Cool.


  1. Matthew G. Baron, David B. Norman, and Paul M. Barrett, A new hypothesis of dinosaur relationships and early dinosaur evolution. Nature, 543 (7646):501-506, 03/23/print 2017. http://dx.doi.org/10.1038/nature21700

What A Dinosaur Looked Like

Yet more cool dinosaur science!

We are discovering more and more fossils which preserve traces of soft tissues that help us reconstruct the bodies and life of ancient dinosaurs and birds. (Feathers, a whole tail, more feathers, a larynx, blood vessels)

A new study reports on a technique that can bring out additional traces of soft tissues even when they are not visible to the unaided eye.

Xiaoli Wang and Michael Pittman and their colleagues used Laser-stimulated fluorescence (LSF) imaging to reveal traces of flesh, skin, and feathers in fossils of Anchiornis, an ancestor of modern birds that lived approximately 150 million years ago [2].

I’m not familiar with the LSF technique in any detail, but it works by zapping a fossil with a laser, and then recording the varying glow from the different minerals. The images reveal faint traces of tissues that were present then the fossil formed.

Of course, like any fossil evidence there is an element of luck. Not every fossil has such traces. In the case of Anchiornis, though, there are hundreds of fossils to survey, seeking fortunate cases.

Following this strategy, the investigators used nine different fossils, all from Shandong Tianyu Museum of Nature in Pingyi, China (recognized as the largest collection of dinosaur fossils in the world). These fossils include views of front and rear legs, and the tail. Combining evidence from these multiple samples gives the “Best ever’ view of what a dinosaur really looked like”, as Dr Stephen Brusatte told the BBC.

The new study gives more evidence for imaginative reconstructions such as offered by BBC.

Anchiornis: A feathered dinosaur from China. BBC
Anchiornis: A feathered dinosaur from China. (BBC)

We know that this animal had feathers and wings. In fact, it had four wings, arms and legs, as well as a feathered tail. Did it fly and/or glide? We don’t know, though it seems likely that it could at least glide.

Cool!


  1. Helen Briggs, ‘Best ever’ view of what a dinosaur really looked like. BBC News.March 1 2017, http://www.bbc.co.uk/news/science-environment-39126987
  2. Xiaoli Wang, Michael Pittman, Xiaoting Zheng, Thomas G. Kaye, Amanda R. Falk, Scott A. Hartman, and Xing Xu, Basal paravian functional anatomy illuminated by high-detail body outline. Nature Communications, 8:14576, 03/01/online 2017. http://dx.doi.org/10.1038/ncomms14576

Dinosaur protein observed

In recent years the study of dinosaurs has been awash in exciting new finds coming out of Western China. These rich beds have yielded dozens of new species, and a stream of exceptionally preserved specimens including soft tissues, which are very rare.

Last month Yan-Chang Lee and colleagues report yet another remarkable find: evidence of preserved collagen from the early Jurassic [2]. If confirmed, this would be the oldest known sample of a protein, and opens the possibility of studies much farther into the past.

The article actually focuses on the very careful microscopy that was required. The details are beyond my own humble understanding, but the a principle challenge is to establish that the detected chemicals are from the original animal, and not from bacteria or other intrusions.

In this case, they showed traces of collagen inside preserved blood (rich in iron), suggesting a fossilization process that could plausibly surround and contain the protein, and preserve it for 200 million years.

Perhaps future studies will be able to analyze such traces to infer genetic histories of dinosaurs and other animals. That would be cool!

Nice work.


  1. Helen Briggs ‘Startling’ dinosaur protein discovery.January 31 2017, http://www.bbc.com/news/science-environment-38810065
  2. Yao-Chang Lee, Cheng-Cheng Chiang, Pei-Yu Huang, Chao-Yu Chung, Timothy D. Huang, Chun-Chieh Wang, Ching-Iue Chen, Rong-Seng Chang, Cheng-Hao Liao, and Robert R. Reisz, Evidence of preserved collagen in an Early Jurassic sauropodomorph dinosaur revealed by synchrotron FTIR microspectroscopy. Nature Communications, 8:14220, 01/31/online 2017. http://dx.doi.org/10.1038/ncomms14220