Posts Tagged ‘buddies’

As 2017 approaches its end, there have been a few papers I’ve been involved in that I thought I’d point out here while I have time. Our DAWNDINOS project has been taking up much of that time and you’ll see much more of that project’s work in 2018, but we just published our first paper from it! And since the other two recent papers involve a similar theme of muscles, appendages and computer models of biomechanics, they’ll feature here too.

Stomach-Churning Rating: 0/10; computer models and other abstractions.

Mussaurus patagonicus was an early sauropodomorph dinosaur from Argentina, and is now widely accepted to be a very close relative of the true (giant, quadrupedal) sauropods. Here is John Conway’s great reconstruction of it:

We have been working with Alejandro Otero and Diego Pol on Mussaurus for many years now, starting with Royal Society International Exchange funds and now supported by my ERC grant “DAWNDINOS”. It features in our grant because it is a decent example of a large sauropodomorph that was probably still bipedal and lived near the Triassic-Jurassic transition (~215mya).

In our new study, we applied one of my team’s typical methods, 3D musculoskeletal modelling, to an adult Mussaurus’s forelimbs. This is a change of topic from the hindlimbs that I’ve myopically focused on before with Tyrannosaurus and Velociraptor [in an obscure paper that I should never have published in a book! pdf link], among other critters my team has tackled (mouse, elephant [still to be finished…], ostrich, horse, Ichthyostega… dozens more to come!). But we also modelled the forelimbs of Crocodylus johnstoni (Australian “freshie”) for a key comparison with a living animal whose anatomy we actually knew, rather than reconstructed.

Mussaurus above; Crocodylus below; forelimb models in various views; muscles are red lines.

The methods for this biomechanical modelling are now standard (I learned them from their creator Prof. Scott Delp during my 2001-2003 postdoc at Stanford): scan bones, connect them with joints, add muscle paths around them, and then use the models to estimate joint ranges of motion and muscle moment arms (leverage) around joints. I have some mixed feelings about developing this approach in our 2005 paper that is now widely used by the few teams that study appendicular function in extinct animals. As a recent review paper noted and I’ve always cautioned, it has a lot of assumptions and problems and one must exercise extreme caution in its design and interpretation. Our new Mussaurus paper continues those ruminations, but I think we made some progress, too.

On to the nuts and bolts of the science (it’s a 60 page paper so this summary will omit a lot!): first, we wanted to know how the forelimb joint ranges of motion in Mussaurus compared with those in Crocodylus and whether our model of Mussaurus might be able to be placed in a quadrupedal pose, with the palms at least somewhat flat (“pronated”) on the ground. Even considering missing joint cartilage, this didn’t seem very plausible in Mussaurus unless one allowed the whole forearm to rotate around its long axis from the elbow joint, which is very speculative—but not impossible in Crocodylus, either. Furthermore, the model didn’t seem to have forelimbs fully adapted yet for a more graviportal, columnar posture. Here’s what the model’s mobility was like:

So Mussaurus, like other early sauropodomorphs such as Plateosaurus, probably wasn’t quadrupedal, and thus quadrupedalism must have evolved very close to in the Sauropoda common ancestor.

Second, we compared the muscle moment arms (individual 3D “muscle actions” for short) in different poses for all of the main forelimb muscles that extend (in various ways and extents) from the pectoral girdle to the thumb, for both animals, to see how muscle actions might differ in Crocodylus (which would be closer to the ancestral state) and Mussaurus. Did muscles transform their actions in relation to bipedalism (or reversal to quadrupedalism) in the latter? Well, it’s complicated but there are a lot of similarities and differences in how the muscles might have functioned; probably reflecting evolutionary ancestry and specialization. What I found most surprising about our results was that the forelimbs didn’t have muscles well-positioned to pronate the forearm/hand, and thus musculoskeletal modelling of those muscles reinforced the conclusions from the joints that quadrupedal locomotion was unlikely. I think that result is fairly robust to the uncertainties, but we’ll see in future work.

You like moment arms? We got moment arms! 15 figures of them, like this! And tables and explanatory text and comparisons with human data and, well, lots!

If you’re really a myology geek, you might find our other conclusions about individual muscle actions to be interesting—e.g. the scapulohumeralis seems to have been a shoulder pronator in Crocodylus vs. supinator in Mussaurus, owing to differences in humeral shape (specialization present in Mussaurus; which maybe originated in early dinosaurs?). Contrastingly, the deltoid muscles acted in the same basic way in both species; presumed to reflect evolutionary conservation. And muuuuuuch more!

Do you want to know more? You can play with our models (it takes some work in OpenSim free software but it’s do-able) by downloading them (Crocodylus; Mussaurus; also available: Tyrannosaurus, Velociraptor!). And there will be MUCH more about Mussaurus coming soon. What is awesome about this dinosaur is that we have essentially complete skeletons from tiny hatchlings (the “mouse lizard” etymology) to ~1 year old juveniles to >1000kg adults. So we can do more than arm-wave about forelimbs!

But that’s not all. Last week we published our third paper on mouse hindlimb biomechanics, using musculoskeletal modelling as well. This one was a collaboration that arose from past PhD student James Charles’s thesis: his model has been in much demand from mouse researchers, and in this case we were invited by University of Virginia biomechanical engineers to join them in using this model to test how muscle fibres (the truly muscle-y, contractile parts of “muscle-tendon units”) change length in walking mice vs. humans. It was a pleasure to re-unite in coauthorship with Prof. Silvia Blemker, who was a coauthor on that 2005 T. rex hindlimb modelling paper which set me on my current dark path.

Mouse and human legs in right side view, going through walking cycles in simulations. Too small? Click to embiggen.

We found that, because mice move their hindlimb joints through smaller arcs than humans do during walking and because human muscles have large moment arms, the hindlimb muscles of humans change length more—mouse muscles change length only about 48% of the amount that typical leg muscles do in humans! This is cool not only from an evolutionary (mouse muscles are probably closer to the ancestral mammalian state) and scaling (smaller animals may use less muscle excursions, to a point, in comparable gaits?) perspective, but it also has clinical relevance.

Simulated stride for mouse and human; with muscles either almost inactive (Act=0.05) or fully active (Act=1). Red curve goes through much bigger excursions (along y-axis) than blue curve), so humans should use bigger % of their muscle fibre lengths in walking. Too small? Click to embiggen.

My coauthors study muscular dystrophy and similar diseases that can involve muscle stiffness and similar biomechanical or neural control problems. Mice are often used as “models” (both in the sense of analogues/study systems for animal trials in developing treatments, and in the sense of computational abstractions) for human diseases. But because mouse muscles don’t work the same as human muscles, especially in regards to length changes in walking, there are concerns that overreliance on mice as human models might cause erroneous conclusions about what treatments work best to reduce muscle stiffness (or response to muscle stretching that causes progressive damage), for example. Thus either mouse model studies need some rethinking sometimes, or other models such as canines might be more effective. Regardless, it was exciting to be involved in a study that seems to deliver the goods on translating basic science to clinical relevance.

Muscle-by-muscle data; most mouse muscles go through smaller excursions; a few go through greater; some are the same as humans’.

Finally, a third recent paper of ours was led by Julia Molnar and Stephanie Pierce (of prior RVC “Team Tetrapod” affiliation), with myself and Rui Diogo. This study tied together a bunch of disparate research strands of our different teams, including musculature and its homologies, the early tetrapod fossil record, muscle reconstruction in fossils, and biomechanics. And again the focus was on forelimbs, or front-appendages anyway; but turning back the clock to the very early history of fishes, especially lobe-finned forms, and trying to piece together how the few pectoral fin muscles of those fish evolved into the many forelimb muscles of true tetrapods from >400mya to much more recent times.

Humerus in ventral view, showing muscle attachments. Extent (green) is unknown in the fossil but the muscle position is clear (arrow).

We considered the homologies for those muscles in extant forms, hypothesized by Diogo, Molnar et al., in light of the fossil record that reveals where those muscles attach(ed), using that reciprocal illumination to reconstruct how forelimb musculature evolved. This parallels almost-as-ancient (well, year 2000) work that I’d done in my PhD on reconstructing hindlimb muscle evolution in early reptiles/archosaurs/dinosaurs/birds. Along the way, we could reconstruct estimates of pectoral muscles in various representative extinct tetrapod(omorph)s.

Disparity of skeletal pectoral appendages to work with from lobe-fins to tetrapods.

Again, it’s a lengthy, detailed study (31 pages) but designed as a review and meta-analysis that introduces readers to the data and ideas and then builds on them in new ways. I feel that this was a synthesis that was badly needed to tie together disparate observations and speculations on what the many, many obvious bumps, squiggles, crests and tuberosities on fossil tetrapods/cousins “mean” in terms of soft tissues. The figures here tell the basic story; Julia, as usual, rocked it with some lovely scientific illustration! Short message: the large number of pectoral limb muscles in living tetrapods probably didn’t evolve until limbs with digits evolved, but that number might go back to the common ancestor of all tetrapods, rather than more recently. BUT there are strong hints that earlier tetrapodomorph “fishapods” had some of those novel muscles already, so it was a more stepwise/gradual pattern of evolution than a simple punctuated event or two.

Colour maps of reconstructed right fin/limb muscles in tetrapodomorph sarcopterygian (~”fishapod”) and tetrapod most recent common ancestors. Some are less ambiguous than others.

That study opens the way to do proper biomechanical studies (like the Mussaurus study) of muscle actions, functions… even locomotor dynamics (like the mouse study)– and ooh, I’ve now tied all three studies together, tidily wrapped up with a scientific bow! There you have it. I’m looking forward to sharing more new science in 2018. We have some big, big plans!


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A quick heads-up that we just posted on our sister blog Anatomy To You, about a new open-access paper we’ve published on the skeletal anatomy of the tuatara Sphenodon. Lots of cool images you can’t see anywhere else are there!

In focus: The big picture of little bones in tuatara

I give it a Stomach-Churning Rating of 3/10- some picked specimens of tuatara but they’re still cute, not nasty, I’d say.

AND, like the Cool-Whip or vanilla ice cream atop your leftover pumpkin pie, there’s an added delicious bonus: a huge dataset of microCT scans from 19 tuatara specimens, free to access here:


We are VERY pumped up about getting this paper and dataset released, so we are spreading the word as wide as we can!


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(Marcela with some furry friends; photo by Oliver Siddon)

(Marcela with some felid friends; photo by Oliver Siddon)

A guest post by Marcela Randau (m.randau@ucl.ac.uk)

Stomach-Churning Rating: 1/10; just bones and data plots!

It is often said that all cats are very similar in terms of their skeletal morphology (“a cat is a cat is a cat”). But is this really the case? It may be if only gross, qualitative anatomy is taken into consideration, i.e., if you just eyeball the skeletons of tigers and lions you might find yourself not knowing which one is which. But with huge advances in technology that allows for extracting detailed shape information off a structure (e.g., a skull) and for analysing this information (‘Geometric Morphometrics’), it has become more and more possible to distinguish between relatively similar forms – which may be from distinct species, separate sexes, or even just different populations of the same taxon.

And it is reasonable to think that cat skeletons might be a lot more different than what meets the eye, as for a lineage of apparently similarly built animals, with not that much variation in diet  (all cats are hypercarnivores) there is substantial variation in body mass (over 300-fold just in living species!) and in ecology across cat species. From the cursorial cheetah to the arboreal clouded leopard, felids present a wide range of locomotory adaptations. Yes, all cats can climb, but some do it better than others: think lion versus margay (yes, they do descend trees head-first). As hypercarnivores, all cats are meat specialists, but they also change with regards to how big their prey is, with a general and sometimes-not-so-black-and-white three-tier classification into small, mixed and large prey specialists. The rule of thumb is ‘if you are lighter than ~20-25 kg, hunt small stuff. If you are heavier than that, hunt BIG BIG things; bigger than yourself. And if you are in the middle ground, hunt some small-ish things, some big-ish things, and things about your size. Well, -ish’ – their prey size preference has a lot to do with energetic constraints (have a look at Carbone et al. 1999; and Carbone et al. 2007, if you’re interested in this). But the fun bit here is that form sometimes correlates quite strongly with function, so we should be able to find differences in some of their bones that carry this ecological signal.

Indeed, for a while now, we have known that the shape of the skull and limbs of felids can tell us a lot about how they move and how big their prey is (Meachen-Samuels and Van Valkenburgh 2009, 2009), but a large proportion of their skeleton has been largely ignored: we don’t know half as much about ecomorphology and evolution of the vertebral column. Well, it was time we changed this a bit! As the PhD student in the Leverhulme-funded ‘Walking the cat back’ (or more informally, “Team Cat”) project, I’ve spend a big chunk of my first two years travelling around the world (well, ok, mainly to several locations in the USA) carrying a heavy pellet case containing my working tool, a Microscribe, to collect 3-D landmarks (Fig. 1) across the presacral vertebral column of several cat species. And some of first results are just out! Check them out by reading our latest paper, “Regional differentiation of felid vertebral column evolution: a study of 3D shape trajectories” in the Organisms Diversity and Evolution journal (Randau, Cuff, et al. 2016).


Fig. 1: Different vertebral morphologies and their respective three-dimensional landmarks. Vertebral images are from CT scans of Acinonyx jubatus (Cheetah, USNM 520539)

Building from results based on our linear vertebral data from the beginning of the year (Randau, Goswami, et al. 2016), the 3-D vertebral coordinates carry a lot more information and we were able to describe how this complex shape-function relationship takes place throughout the axial skeleton (in cats at least) in much better detail than our prior study did. One of the difficulties in studying serial structures such as the vertebral column is that some clades present variation in vertebral count which makes it less straightforward to compare individual vertebrae or regions across species. However, mammals are relatively strongly constrained in vertebral count, and Felidae (cats; living and known fossils) show no variation at all, having 27 presacral vertebrae. So adaptation of the axial skeleton in mammals has been suggested to happen by modification of shape rather than changes in vertebral number.

Using a variety of geometric morphometric analyses, under a phylogenetically informative methodology, we have shown that there is clear shape and functional regionalisation across the vertebral column, with vertebrae forming clusters that share similar signal. Most interestingly, the big picture of these results is a neck region which is either very conservative in shape, or is under much stronger constraints preventing it from responding to direct evolutionary pressures, contrasting with the ‘posteriormost’ post-diaphragmatic tenth thoracic (T10) to last lumbar (L7) vertebral region, which show the strongest ecological correlations.

We were able to analyse shape change through functional vertebral regions, rather than individual vertebrae alone, by making a novel application of a technique called the ‘Phenotypic Trajectory Analysis’, and demonstrated that the direction of vertebral shape trajectories in the morphospace changes considerably between both prey size and locomotory ecomorphs in cats, but that the amount of change in each group was the same. It was again in this T10-L7 region that ecological groups differed the most in vertebral shape trajectories (Fig. 2).


Figure 2: Phenotypic trajectory analysis (PTA) of vertebrae in the T10 – L7 region grouped by prey size (A) and locomotory (B) categories.

So in the postcranial morphology of cats can be distinguished, changing its anatomy in order to accommodate the different lifestyles we see across species. But the distinct parts of this structure respond to selection differently. The next step is figuring out how that might happen and we are working on it.

While Team Cat continues to investigate other biomechanical and evolutionary aspects of postcranial morphology in this interesting family, we’ve been able to discuss some of these and other results in a recent outreach event organised by the University College of London Grant Museum of Zoology and The Royal Veterinary College. We called it “Wild Cats Uncovered: movement evolves”. Check how it went here: (https://blogs.ucl.ac.uk/museums/2016/11/17/cheetah-post-mortem/) and here (http://www.rvc.ac.uk/research/research-centres-and-facilities/structure-and-motion/news/wild-cats-uncovered), with even more pics here (https://www.flickr.com/photos/144824896@N07/sets/72157676695634065/).

References used here:

Carbone, C., Mace, G. M., Roberts, S. C., and Macdonald, D. W. 1999. Energetic constaints on the diet of terrestrial carnivores. Nature 402:286-288.

Carbone, C., Teacher, A., and Rowcliffe, J. M. 2007. The costs of carnivory. PLoS biology 5 (2):e22.

Meachen-Samuels, J. and Van Valkenburgh, B. 2009. Craniodental indicators of prey size preference in the Felidae. Biol J Linn Soc 96 (4):784-799.

———. 2009. Forelimb indicators of prey-size preference in the Felidae. Journal of morphology 270 (6):729-744.

Randau, M., Cuff, A. R., Hutchinson, J. R., Pierce, S. E., and Goswami, A. 2016. Regional differentiation of felid vertebral column evolution: a study of 3D shape trajectories. Organisms Diversity and Evolution Online First.

Randau, M., Goswami, A., Hutchinson, J. R., Cuff, A. R., and Pierce, S. E. 2016. Cryptic complexity in felid vertebral evolution: shape differentiation and allometry of the axial skeleton. Zoological Journal of the Linnean Society 178 (1):183-202.

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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Goat morphology is cool! (from work with local artist)

I posted the above photo once before, but didn’t explain any of the fun details of artist-designer Thomas Thwaites‘s visit to the RVC to dissect a goat with us. Now his show has just finished in London, celebrating the end of his project and the near-completion of his book about his experience trying to live life as a goat. This week, I went to his east side gallery and had some time to chat with Thomas about his transhuman experiences. Because the project has a strong biomechanics, anatomy, art and science theme to it, I’m posting a photo-blog post about all of that. It’s goat to be seen to be believed! I for one wouldn’t mind being a goat right now; I could use a break from my decrepit body…

Stomach-Churning Rating: Too late, there’s the goat pic above and more like it below. I’d give those a 8/10; no kidding. The puns make it worse, too.

The context

The context. Thomas never did get to gallop (sorry, spoiler!) but he did manage a trot, and some other capricious behaviours. I forgot to ask him if he’d tried the Goat Simulator. I have; it’s good for an hour of fun hircosity.

Starting the dissection at the RVC.

Starting the dissection at the RVC, to get inside a goat.



Fore- and hindlimbs.

Fore- and hindlimbs; comparative design for inspiring prosthetics.


Dissections on display!

Prototype goat-suits. Their mobility was too limited.

Prototype goat-suits. Their mobility was too limited.

The prototype in the foreground could not move without falling down.

The prototype in the foreground could not move without falling down.

Goat-suit shots.

Inhabited-goat-suit shots.

The Goat-Suit: custom made prothetics, a helmet, and some form-fitting casts.

The final Goat-Suit: custom prosthetics, a helmet, and some form-fitting casts.

Thomas Thwaites with the goat-suit.

Thomas Thwaites with the goat-suit.

The forelimb prosthesis. I was worried it would hurt his wrists but apparently it transferred the loads mainly to the forearms.

The forelimb prosthesis. I was worried it would hurt his wrists but apparently it transferred the loads mainly to the forearms. It was made by a prosthetics clinic up in Salford.


Photos from rambling around the Swiss Alps in the goat-suit with goats.


Trip-trap-trip-trap… (but no trolls)

Goat-suit in action!

Goat-suit in action! With Goat-Pro camera, I see.



And the goat that we had dissected, skeletonized at RVC and re-articulated by Thomas:

Do goats wish they were human?

Do goats wish they were human?

What are you looking at?

What are you looking at?

Close-up of goat head.

Close-up of goat head and shoulders.

Goat hooves-on-hips

Goat hooves-on-hips; a gruff pose.

So like us.

So like us.

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This is a follow-up post to my earlier one and also weaves into my post on “success” (with a little overlap). I am sharing my thoughts on this topic of research management, because I try to always keep myself learning about doing and managing research, and this blog serves as a set of notes as I learn; so why not share them too? I tried editing the old post but it clearly was too much to add so I started a new post. It’s easy to just coast along and not reflect on what one is doing, caught up in the steady stream of science that needs to get done. Mistakes and mis-judgements can snowball if one doesn’t reflect. So here are my personal reflections, freshly thawed for your consideration, on how I approach doing research and growing older as I do it, adapting to life’s changes along the way.

Stomach-Churning Rating: 0/10, just words and ideas.

I realized that a theme in these rant-y posts on my blog is to Know Yourself, and, in the case of mentoring a team, Know Your Team. That knowledge is a reward from the struggles and challenges of seeking whatever one calls success. I critique some traits or practices here that I’ve seen in myself (and/or others), and perhaps managed to change. And I seek to change my environment by building a strong team (which I feel I have right now!) and by finding the best ways to work with them (which I am always learning about!). I also realized a word to describe a large part of what I seek and that is joy. The joy of discovery in the study of nature; the joy from the satisfaction of a job well done; the joy of seeing team members succeed in their careers and broader lives. I want to know that multifarious joy; the ripening of fulfilment.

We’re all busy in one way or another. Talking about being busy can just come across as (very) boring or self-absorbed or insecure. Talk about what you’re doing instead of how much you’re juggling. That’s more interesting. Avoid the Cult of Busy. I try to. It’s any easy complaint to default with in a conversation, so it takes some alertness… which keeps you busy. 🙂  I remember Undergrad-Me sighing wistfully to my advisor Dianna Padilla “I’m SO busy!” and her looking at me like I was an idiot. In that moment I realized that I was far from the only (or most) busy person in that conversation. Whether she was truly thinking that I was naïve, my imaginary version of her reaction is right. It was a foolish, presumptuously arrogant thing for me to declare. There surely are more interesting things to talk about than implied comparisons of the magnitudes of each other’s busy-ness. And so I move on…

Don’t count hours spent on work. That just leads to guilt of too much/too little time spent vs. how much was accomplished. Count successes. A paper/grant submitted is indeed a success, and acceptance/funding of it is another. A handy rule in science is that everything takes so much more time than you think it does that even trying to predict how long it will take is often foolish and maybe even time that could be better spent on doing something that progresses your work/life further.

Becoming older can slow you down and make you risk-averse, so you have to actively fight these tendencies. Ageing as a researcher needn’t always mandate becoming slower or less adventurous. But life will change, inevitably. One has to become more efficient at handling its demands as life goes on, and force oneself to try new things for the sake of the novelty, to think outside the box and avoid slipping into dogma or routine. We don’t want to be that stereotype of the doddering old professor, set in their ways, who stands in the way of change. The Old Guard is the villain of history. Lately I’ve been examining my own biases and challenging them, potentially re-defining myself as a scientist. I hope to report back on that topic.

The tone of life can darken as one becomes a senior researcher and “grows up”, accumulating grim experiences of reality. Some of my stories on this blog have illustrated that. In an attempt to distract me from that gloaming on the horizon, I try to do things at work that keep it FUN for me. This quest for fun applies well to my interactions with people, which dominate my work so much– I am seemingly always in meetings, less often in isolation at my desk. The nicer those meetings are, the happier I am. So I try to minimize exposure to people or interactions that are unpleasant, saving my energy for the battles that really matter. This can come across as dismissive or curt but in the end one has little choice sometimes. These days, nothing to me is more negatively emotive than sitting in an unproductive meeting and feeling my life slipping away as the clock ticks. I cherish my time. I don’t give it away wantonly to time-vampires and joy-vandals. They get kicked to the kerb– no room (or time) for them on this science-train. Choo choo!

Moreover, the No Asshole Rule is a great principle to try to follow at work. Don’t hire/support the hiring of people that you can’t stand socially, even if they are shit-hot researchers with a hugely promising career trajectory. Have a candidly private moment with someone who knows them well and get the inside scoop on what they’re like to work with. Try to get to know people you work with and collaborate more with people that you like to work with. Build a team of team-players (but not yes-men and yes-women; a good team challenges you to know them and yourself; so there must be some tension!). That can help you do better science because you enjoy doing it more, and you prioritize it more because of that, and you have more energy because of all that. Hence your life gets better as a result. I prefer that to a constant struggle in tense, competitive collaborations. One of the highest compliments I ever got was when someone described me to their friend as a “bon vivant”. I felt like they’d discovered who I was, and they’d helped me to discover it myself.

I wondered while writing this, would I hire 2003-Me, from when I was interviewing for my current job 12 years ago? I suppose so, but I’d give myself a stern scolding on day one at the job. “Chill the fuck out,” I’d say. “Focus on doing the good science and finding the other kinds of joy in life.” I like the more mellowed-out, introspective, focused, compassionate 2015-Me, and I think 2003-Me would agree with that assessment.

There is a false dichotomy in a common narrative about research mentoring that I am coming to recognize: a tension between the fortunes of early career researchers and senior research managers. The dichotomy holds that once one is senior enough, ambition wanes and success is complete and one’s job is to support early career researchers to gain success (as recompense for their efforts in pushing forward the research team’s day-to-day science), and to step back out of the limelight.

The reality, I think, is that all these things are linked: early career researchers succeed in part because their mentors are successful (i.e. the pedigree concept; good scientists arise in part from a good mentoring environment), and research-active mentors need to keep seeking funding to support their teams, which means they need to keep showing evidence of their own success. Hence it never ends. One could even argue that senior researchers need to keep authoring papers and getting grants and awards and other kinds of satisfaction and joy in science that maintain reputations, and thus their responsibility to themselves and their team to keep pushing their research forward may not decrease or even may intensify. Here, a “team” ethos rather than an “us vs. them” mentality seems more beneficial to all—we’re in this together. Science is hard. We are all ambitious and want to achieve things to feel happy about. I don’t think the “it never ends” perspective is gloomy, either—if the false dichotomy were true, once one hit that plateau of success as a senior researcher, ambition and joy and personal growth would die. Now that’s gloomy. Nor does the underlying pressure mandate that researchers can’t have a “life outside of work”. I’ve discussed that enough in other posts.

Trust can be a big issue in managing research. If people act like they don’t trust you, it may be a sign that they’ve been traumatized by violated trust before. Be sensitive to that; gently inquire? And get multiple sides of the story from others if you can… gingerly. But it also might be a warning sign that they don’t deserve trust themselves. Trust goes both ways. Value trust, perhaps above all else. It is so much more pleasant than the lack thereof. Reputation regarding trustworthiness is a currency that a research manager should keep careful track of in themselves and others. Trust is the watchdog of joy.

Say “No” more often to invitations to collaborate as your research team grows. “Success breeds success” they say, and you’ll get more invitations to collaborate because you are viewed as successful — and/or nice. But everyone has their limits. If you say “Yes” too much, you’ll get overloaded and your stock as a researcher will drop– you’ll get a reputation for being overcommitted and unreliable. Your “Yes” should be able to prove its value. I try to only say “Yes” to work that grabs me because it is great, do-able science and with fun people that I enjoy collaborating with. This urge to say “No” must be balanced with the need to take risks and try new directions. “Yes” or “No” can be easy comfort zones to settle into. A “Yes” can be a longterm-noncommittal answer that avoids the conflict that a “No” might bring, even if the “No” is the more responsible answer. This is harder than it seems, but important.

An example: Saying “No” applies well to conference invitations/opportunities, too. I love going to scientific conferences, and it’s still easy enough to find funding to do it. Travel is a huge perk of academic research! But I try to stick to a rule of attending two major conferences/year. I used to aim for just one per year but I always broke that rule so I amended it. Two is sane. It is easy to go to four or more annual conferences, in most fields, but each one takes at least a week of your time; maybe even a month if you are preparing and presenting and de-jetlagging and catching up. Beware the trap of the wandering, unproductive, perennial conference-attendee if doing science is what brings you joy.

This reminds me of my post on “saying no to media over-coverage“– and the trap of the popularizer who claims to still be an active researcher, too. There is a zero-sum game at play; 35 or 50 hour work week notwithstanding. Maybe someday I’d want to go the route of the popularizer, but I’m enjoying doing science and discovering new things far too much. It is a matter of personal preference, of course, how much science communication one does vs. how much actual science.

The denouement of this post is about how research teams rise and fall. I’m now often thinking ahead to ~2016, when almost all of my research team of ~10 people is due to finish their contracts. If funding patterns don’t change — and I do have applications in the works but who knows if they will pan out — I may “just” have two or so people on my team in a year from now. I could push myself to apply like mad for grants, but I thought about it and decided that I’ll let the fates decide based on a few key grant submissions early in the year. There was too little time and too much potential stress at risk. If the funding gods smile upon me and I maintain a large-ish team, that’s great too, but I would also truly enjoy having a smaller, more focused team to work with. I said “No” to pushing myself to apply for All The Grants. I’ll always have diverse external collaborations (thanks to saying “Yes” enough), but I don’t define my own success as having a large research group (that would be a very precarious definition to live by!). I’m curious to see what fortune delivers.

Becoming comfortable with the uncertainty of science and life is something I’m finding interesting and enjoy talking about. It’s not all a good thing, to have that sense of comfort (“whatever happens, happens, and I’m OK with that”). I don’t want my ambition to dwindle, although it’s still far healthier than I am. There is no denying that it is a fortunate privilege to feel fine about possibly not drowning in grant funds. It just is what it is; a serenity that I welcome even if it is only temporary. There’s a lot of science left to be written about, and a smaller team should mean more time to do that writing.

Will I even be writing this blog a year from now? I hope so, but who knows. Blogs rise and fall, too. This one, like me, has seen its changes. And if I am not still writing it, it might resurface in the future anyway. What matters is that I still derive joy from blogging, and I only give in to my internal pressure to write something when the mood and inspiration seize me. I hope someone finds these words useful.

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Maybe it’s uncool to talk about heroes in science these days, because everyone is poised on others’ shoulders, but “Neill” (Robert McNeill) Alexander is undeniably a hero to many researchers in biomechanics and other strands of biology. Our lab probably wouldn’t exist without his pervasive influence- he has personally inspired many researchers to dive into biomechanics, and he has raised the profile of this field and championed its importance and principles like no other one individual. Often it feels like we’re just refining answers to questions he already answered. His influence extends not only to comparative biomechanics and not only around his UK home, but also –via his many, many books on biology, anatomy and related areas, in addition to his research, editorial work and public engagement with science– to much of the life sciences worldwide.

What does a kneecap (patella) do? Alexander and Dimery 1985, they knew. My team is still trying to figure that out!

What does a kneecap (patella) do? Alexander and Dimery 1985, they knew. 30 years later, my team is still trying to figure that out!

Sure, one could (and with great humility I’m sure Alexander would) mention others like Galileo and Marey and Muybridge and Fenn and Gray and Manter who came before him and did have a profound impact on the field. Alexander can, regardless, easily be mentioned in the same breath as luminaries of muscle physiology such as AV Hill and even Andrew + Julian Huxley. But I think many would agree that Alexander, despite coming later to the field, had a singular impact on this young field of comparative biomechanics. That impact began in the 1970s, when Dick Taylor and colleagues in comparative physiology were also exploding onto the scene with work at the Concord Field Station at Harvard University, and together biomechanics research there, in the UK, elsewhere in Europe and the world truly hit its stride, with momentum continuing today. I’m trying to think of some women who played a major role in the early history of biomechanics but it was characteristically a woefully male-dominated field. That balance has shifted from the 1970s to today, and my generation would cite luminaries such as Mimi Koehl as key influences. There are many female or non-white-male biomechanics researchers today that are stars in the field, so there seems to have been progress in diversifying this discipline’s population.

Hence, honouring Alexander’s impact on science, today our college gave Neill an honorary doctorate of science (DSc). Last year, I also helped organize a symposium at the Society for Vertebrate Paleontology’s conference in Berlin that honoured his impact specifically on palaeontology, too- compare his book “The Dynamics of Dinosaurs and Other Extinct Giants” to current work and you’ll see what fuelled much of that ongoing work, and how far/not far we’ve come since ~1989. Even 10 years later, his “Principles of Animal Locomotion“, with Biewener’s “Animal Locomotion“, remains one of the best books about our field (locomotion-wise; Vogel’s Comparative Biomechanics more broadly) , and his educational CD “How Animals Move“, if you can get it and make it work on your computer, is uniquely wonderful, with games and videos and tutorials that still would hold up well as compelling introductions to animal biomechanics. Indeed, I’ve counted at least 20 books penned by Alexander, including “Bones: The Unity of Form and Function” (under-appreciated, with gorgeous photos of skeletal morphology!).

1970s Alexander, with a sauropod leg.

1970s Alexander, with a sauropod leg.

And then there are the papers. I have no idea how many papers Neill has written –again and again I come across papers of his that I’ve never seen before. I tried to find out from the Leeds website how many papers he has, but they’re equally dumbfounded. I did manage to count 38 publications in Nature, starting in 1963 with “Frontal Foramina and Tripodes of the Characin Crenuchus,” and 6 in Science. So I think we can be safe in assuming that he has written everything that could be written in biomechanics, and we’re just playing catchup to his unique genius.

Seriously though, Alexander has some awesome publications stemming back over 50 years. I’m a big fan of his early work on land animals, such as with Calow in 1973 on “A mechanical analysis of a hind leg of a frog” and his paper “The mechanics of jumping by a dog” in 1974, which did groundbreaking integrations of quantitative anatomy and biomechanics. These papers kickstarted what today is the study of muscle architecture, which our lab (including my team) has published extensively on, for example. They also pioneered the integration of these anatomical data with simple theoretical models of locomotor mechanics, likewise enabling many researchers like me to ride on Alexander’s coattails. Indeed, while biomechanics often tends to veer into the abstract “assume a spherical horse”, away from anatomy and real organisms, Alexander managed to keep a focus on how anatomy and behaviour are related in whole animals, via biomechanics. As an anatomist as well as a biomechanist, I applaud that.

How do muscles work around joints? Alexander and Dimery 1985 figured out some of the key principles.

How do muscles work around joints? Alexander and Dimery 1985 figured out some of the key principles.

Alexander has researched areas as diverse as how fish swim, how dinosaurs ran, how elastic mechanisms make animal movement more efficient, how to model the form and function of animals (see his book “Optima for Animals” for optimization approaches he disseminated, typifying his elegant style of making complex maths seem simple and simple maths impressively powerful) and how animals walk and run, often as sole author. In these and other areas he has codified fundamental principles that help us understand how much in common many species have due to inescapable biomechanical constraints such as gravity, and how these principles can inspire robotic design or improvements in human/animal care such as prosthetics. Neill has also been a passionate science communicator, advising numerous documentaries on television.

~1990s Alexander, with model dinosaurs used to estimate mass and centre of mass.

~1990s Alexander, with model dinosaurs used to estimate mass and centre of mass.

Alexander’s “Dynamics of Dinosaurs” book, one of my favourites in my whole collection, is remarkably accessible in its communication of complex quantitative methods and data, which arguably has enhanced its impact on palaeontologists. Alexander’s other influences on palaeobiology include highly regarded reviews of jaw/feeding mechanics in fossil vertebrates (influencing the future application of finite element analysis to palaeontology), considerations of digestion and other aspects of metabolism, analysis of vertebral joint mechanics, and much more.  Additionally, he conducted pioneering analyses of allometric (size-related) scaling patterns in extant (and extinct; e.g. the moa) animals that continue to be cited today as valuable datasets with influential conclusions, by a wide array of studies including palaeontology—arguably, he helped compel palaeontologists to contribute more new data on extant animals via studies like these.

Neill Alexander did his MSc and PhD at Cambridge, followed by a DSc at the University of Wales, a Lecturer post at Bangor University and finally settling at the University of Leeds in 1969, where he remained until his retirement in 1999, although he maintains a Visiting Professorship there. I had the great pleasure of visiting him at his home in Leeds in 2014; a memory I will treasure forever, as I had the chance to chat 1-on-1 with him for some hours. He has been Secretary of the Zoological Society of London throughout most of the 1990s, President of the Society for Experimental Biology and International Society of Vertebrate Morphologists, long championing the fertile association of biomechanics with zoology, evolutionary biology and anatomy. More recently, he was a main editor of Proceedings of the Royal Society B for six years.

Many people I’ve spoken to about Neill before have stories of how he asked a single simple question at their talk, poster or peer review stage of publication, and how much that excited them to have attracted his sincere interest in their research. They tend to also speak of how that question cut to the core of their research and gave them a facepalm moment where they thought “why didn’t I think of that?”, but how he also asked that question in a nice way that didn’t disembowel them. I think that those recalling such experiences with Neill would agree that he is a professorial Professor: a model of senior mentorship in terms of how he can advise colleagues in a supportive, constructive and warmly authoritative, scholarly way. For a fairly recent example of his uniquely introspective and concise, see the little treasure “Hopes and Fears for Biomechanics”, a ~2005 lecture you can find here. I really like the “Fears” part. I share those fears- and maybe embody them at times…

My visit with RMcNeill Alexander in 2014.

My visit with RMcNeill Alexander in 2014.

Perhaps I have gushed enough, but I could go on! Professor RMcNeill Alexander, to summarise the prodigious extent of his research, is to biomechanics as Darwin is to biology as a whole. One could make a strong case for him being one of the most influential modern biologists. He is recognised for this by his status as a Fellow of the Royal Society (since 1987), and a CBE award, among many other accolades, accreditations and awards. And, if you’ve met him, you know that he is a gentle, humble, naturally curious and enthusiastic chap who instils a feeling of awe nonetheless, and still loves to talk about science and keeps abreast of developments in the field. And as the RVC is honouring Neill today, it is timely for me to honour him in this blog post. There can never be another giant in biomechanics like Alexander, and we should be thankful for the broad scientific shoulders upon which we are now, as a field, poised.

I hope others will chime in with comments below to share their own stories.



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