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Posts Tagged ‘science story’

Recent Papers.

Posted in Biomechanics, Reviews, tagged anatomy, dem bones, evolution, fossilicious, publication, science story on July 7, 2024| 1 Comment »

Stomach-Churning Rating: 1/10 unless I change my mind and add some unsavoury images (which I did not).

A most un-creative title for a most un-creative post topic. I’ve been short on new ideas for the blog for a long time, and short on energy for them. Furthermore, I’ve been more busy trying to get specimens out of my freezers and reduced to bones, rather than getting new specimens and doing new anatomical work on them, which might otherwise be good fodder for blog posts. I’d love to do a new “Better Know a Muscle” post, but that is hard work. Yet a good old standby post, a summary of stuff I’ve coauthored lately that grabs my immediate fancy, is fine. So here is that summary; most recent papers first.

1. Hutchinson, J.R., Pringle, E.V. 2024. Footfall patterns and stride parameters of Common hippopotamus (Hippopotamus amphibius) on land. PeerJ 12:e17675. https://doi.org/10.7717/peerj.17675

This one got a ton of media attention, much more than I expected. And in a week that was far from slow news (UK election, ever-crazier USA politics, so on). I think the media liked a fun distraction that reminds us how the natural world still has its wonders and how scientists are still doing goofy stuff. I’ve long wanted to do a study of hippo locomotion, as part of my opus on how giant land animals move, so I recruited vet undergrad Emily Pringle to go film hippos at Flamingo Land Resort in North Yorkshire (who’ve been immensely supportive of our research). She set up GoPro cameras and filmed what she could over 2 days. It wasn’t much. The two hippos just walked slowly in and out of their night-time barn now and then. But we had a cunning plan. Emily also searched the internet (mostly Youtube) for more videos showing a wider range of speeds, and I added some more after her project. The upshot is, hippos only use trotting gaits (diagonal limbs moving in near-unison) from slow to fast speeds (walking trots to running trots), and at fast speeds they go airborne for substantial periods of time. That’s cool for two reasons: (1) it’s odd for a (large) mammal to just trot and not use the usual walk-trot-canter-gallop series of gaits; and (2) it wasn’t known (or even asked, much) in scientific literature if hippos did go airborne or not.

My favourite sequence, of a really fast trot with many airborne periods.

I cringe a little at how simple this work is, but there’s still great value in observation and a “data paper” as I regarded this one. Still, I like it and it fills a lacuna in our understanding, and takes my research a step further toward what I’d like to know (e.g., what constraints influence locomotion at giant sizes, and how those evolved in particular lineages). I’ve never written a paper so quickly. It took maybe a week from start to submission. It’s not rocket science, but it’s useful. It has gotten me more motivated to expand this hippo research into some novel directions. A little more about the paper on Twitter.

Speaking of data, here are some. Duty factor (DF; fraction of stride cycle that a given foot is in contact with the ground; i.e., 1 means the feet never ever leave the ground; 0 means that the animal never touches the ground and thus is truly flying) on the x-axis, and stride frequency (SF; stride cycles per second) on the y-axis. So trotting hippos swing their limbs <1 cycle/second at low DFs (~slow speeds), then can get up to impressive frequencies as they break into a run (e.g., DF<0.5 means there is an airborne phase in a trot). Some of them breached 3 strides/second, which is swinging those stubby limbs awfully quickly!

2. von Baczko, M.B., Zariwala, J., Ballentine, S.E., Desojo, J.B., Hutchinson, J.R. 2024. Biomechanical modelling of musculoskeletal function related to the terrestrial locomotion of Riojasuchus tenuisceps (Archosauria: Ornithosuchidae). Anatomical Record 25528. https://doi.org/10.10 02/ar.25528

A new DAWNDINOS grant paper; #41 published so far from that project (since 2017), with many many more to come. I enjoyed writing this one, quite a bit. The subject is a member of a small clade of very strange crocodile-line archosaurs (ornithosuchids) from the Triassic period. They have a long history (>100 years) of study and ideas about them have roamed widely, such as what they were more closely related to (theropod dinosaurs? No. Early dinosaurs and pterosaurs? No.). And how they moved: bipedally and/or quadrupedally? Sprawling to erect limb posture? Plantigrade (flat-footed) or digitigrade (tip-toed)? We did our standard approach of scanning the skeletal remains of Riojasuchus tenuisceps, making a 3D musculoskeletal model, and then using that to address lingering questions like those I’ve mentioned. We found the evidence for/against bipedalism to be wonderfully ambiguous, which might sound strange to say, but I like that Riojasuchus tenuisceps remains a conundrum. It is weird. But we were convinced that it used quite erect and plantigrade postures. There’s a lot more to the paper such as consideration of the evolution of hindlimb musculature but that gets really technical. We’ll be doing more with this model, involving deeper biomechanical analysis, in the near future. Here, again, an RVC undergrad, Sarah Ballentine, got involved in the early stages of modelling. A little more about the paper on Twitter.

The model, in the (digital) flesh above, with centre of mass as a green sphere, and just the skeleton below. It’s in our “reference pose”, which is a non-biological straight-limbed orientation having all joint angles at 0 degrees.

3. Etienne, C., Houssaye, A., Fagan, M., Hutchinson, J.R. 2024. Estimation of the forces exerted on the limb long bones of a White Rhinoceros (Ceratotherium simum) using musculoskeletal modelling and simulation. Journal of Anatomy, published online. https://doi.org/10.1111/joa.14041

Much as I’ve long wanted to study hippos as one of the “big four” clades of giant land mammals, I’ve wanted to do so with rhinos; and this is my fifth such study. Here, we (led by French PhD student Cyril) use the same kind of 3D musculoskeletal modelling process as paper #2 above, but including real data from dissections of muscles from a white rhino, and usage of those data in a simple static simulation to estimate how the muscles might be activated to support a quiet standing pose, and what the corresponding muscle and joint forces might be. Surely because it supports more weight, the forelimb had greater muscle activations and forces; especially from some lower limb muscles such as the ulnaris lateralis (an elbow extensor) and digital flexors; and the humerus experienced the greatest forces, reflecting its robust morphology. This is a step toward other kinds of modelling such as finite element analysis of bone stresses. Cyril put in a huge effort to build a nice model and conduct careful analyses with complex input and output data, and he cleverly designed some nice figures of those data.

4. Pintore, R., Hutchinson, J.R., Bishop, P.J., Tsai, H.P., Houssaye, A. 2024. The evolution of femoral morphology in giant non-avian theropod dinosaurs. Paleobiology, 1-22. https://doi.org/10.1017/pab.2024.6

A dinosaur paper, imagine that! This one came from 1st author Romain’s PhD and some data we collected during the DAWNDINOS grant; and quite a bit of data that he wrangled during the COVID pandemic lockdowns. The data are 3D scans of 68 specimens from 41 species of Mesozoic theropods, then subjected to 3D geometric morphometrics shape analysis, to see what features related to giant body size or to other things (e.g., more “birdlike” traits). Each time theropods reached giant (>1000 kg) body sizes, their femora (thigh bones) attained many similar aspects of shape, but also more of those “birdlike” traits kept accumulating (and convergently evolving) along the theropod family tree, and even in some giant forms, and especially in “miniaturised” theropods. I like how this paper ties together two of my big research themes, how giant size influences form and function, and how archosaurian/dinosaurian locomotion evolved; and in the context of rich 3D anatomy. And Romain did some stellar work assembling a huge dataset with very rigorous analyses — and gorgeous figures in the paper!

5. Kurz, M.J., Hutchinson, J.R. 2023. Visual feedback influences the consistency of the locomotor pattern in Asian elephants (Elephas maximus). Biology Letters 20230260. https://dx.doi.org/10.1098/rsbl.2023.0260

Hippos, then rhinos, and now elephants! How grand. This paper feels like it was ages ago, and the data collection was — we did the experiments involved back in 2006! Co-author Max Kurz and I wondered, how much would the slow walking patterns of elephants be disrupted if we removed their capacity to see? This question ties into how elephants maintain “stability” (a fraught term in science). Stability is clearly of great importance to giant land animals following “the bigger you are, the harder you fall” principle. Compared to walking with vision, blindfolded elephants were able to keep the duration of each stride close to the average (in one way remaining “stable”) but the noisiness (“consistency”) of their stride decayed across multiple strides, so they tended to take slower or faster strides as they walked across their paddock. This decay would increase the chances of a stumble or fall as blind elephants moved over longer periods. Thus it shows how vision removes that risk, aiding these giant animals in maintaining “stability”. It’s a neat little experiment. We had the paper all written back in 2010 but held back, then in 2023 I decided to go for it and submit what we had; and I am glad we did that. A little more about the paper on Twitter.

A friendly elephant leading an experimental subject, bearing blindfold, belly-mounted GPS unit (to measure speed) and toe-mounted accelerometers (to measure foot on/off timings for determining stride durations).

6. Lacerda, M.B.S., Bittencourt, J.S., Hutchinson, J.R. 2023. Macroevolutionary patterns in the pelvis, stylopodium and zeugopodium of megalosauroid theropod dinosaurs and their importance for locomotor function. Royal Society Open Science 10230481230481 http://doi.org/10.1098/rsos.230481

and

7. Lacerda, M.B.S., Bittencourt, J.S., Hutchinson, J.R. 2023. Reconstruction of the pelvic girdle and hindlimb musculature of the early tetanurans Piatnitzkysauridae (Theropoda, Megalosauroidea). Journal of Anatomy 244:557-593. https://doi.org/10.1111/joa.13983

Brazilian PhD student Mauro Lacerda joined my lab for a sustained period back in 2022, to collaborate on learning how to reconstruct the hindlimb musculature of theropod dinosaurs and use such data in 3D biomechanical modelling. It has been a really fun and productive collaboration, with at least two more papers yet to come. Mauro had been focussing on the “intermediate” theropods (not ‘early’ ones like coelophysoids and ceratosaurs; not ‘late’ ones like carnosaurs and coelurosaurs, but in a hazy in-between phylogenetic position), called Megalosauroidea. As the name indicates, this clade includes the oldest named dinosaur, Megalosaurus (happy 200th birthday!). Many members are Jurassic forms from around the world, often of medium-large size and rather robust build; but also the celebrity dinosaurs, Spinosauridae, are embedded within Megalosauroidea. We set out to first characterise how key skeletal traits of the hindlimbs of these animals evolved, building a nice pictorial and phylogenetic “atlas” of sundry bumps and squiggles on the bones, and mapping how the distribution of those traits compares across groups of early theropods in a “morphospace”. It’s detailed work that should be a helpful reference for all of those working on this interesting clade of theropods and their relatives.

The second study built on the first, by applying methods and evidence I’ve formalised for reconstructing the (hind)limb muscles of theropods and other archosaurs/tetrapods. We estimated where the muscles of three megalosauroids (Condorraptor, Marshosaurus, and Piatnitzkysaurus in order of improved fossil preservation) originated from and inserted onto, where possible. Some bones or regions of bone were unpreserved, limiting what we could estimate, but this is an aspect of the study that I like, as it is a comparative exercise in how much taphonomy influences what we can infer about soft tissues and their evolution across extinct lineages. And it makes possible the usual kinds of 3D biomechanical analyses that my group does — stay tuned for that.

So there you have it. Hippos, early archosaurs, rhinos, earlier and later theropod dinosaurs, and elephants. Lots of locomotor anatomy, biomechanics and evolution. This pretty much sums up my research career and current foci. The variety is part of what makes my job so fun, but the central issues keep it chugging along to push the boundaries of knowledge forwards in my little corner of science. Moreover, it’s a lot of collaboration, around the world and with researchers at different career stages and in varied disciplines from biology to palaeontology to engineering. I love that variety, too. I’m particularly pleased in this set of papers that I’ve included some undergrads, which I’ve been trying to get better at, but which takes some careful planning of studies and persistence (and time!) to get the papers out the door after the students move on.

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Thank You

Posted in in all seriousness, tagged in all seriousness, science story on May 10, 2023| 11 Comments »

Today the official news came out that represents a highlight of my scientific career. After seven years of intense internal and external review and scrutiny, I’ve been elected as a Fellow of the Royal Society (of the United Kingdom) (“‘FRS” title), the oldest scientific society in the world; since 1660 C.E. “For British scientists, a fellowship to the Royal Society is the equivalent of a lifetime achievement Oscar.” It has included eminent scientists from Newton and Darwin to Boyle, Faraday, Einstein, Turing, Hodgkin, Peter and Rosemary Grant, Tickle, and personal scientific hero Alexander. And… Elon Musk. The Royal Society’s broad announcement is here, and the RVC’s press release about me [pending] is here.

Stomach-Churning Rating: 0/10; no anatomy, or even images, here.

I got the initial e-mail message (then a formal letter) from the Council back on 22 March 2023, and when I opened it I screamed repeatedly in joy and surprise, for about an hour. I barely could breathe. I could not believe it, even though this process had been going on for so long. I’d trained myself not to expect it, as I knew it was incredibly selective. It was a spectacular feeling that I’ll treasure forever. And it came at a very dark time, when I was full of doubts about myself and my future, with old feelings of ‘imposter syndrome’ resurfacing against a backdrop of terrible health problems plaguing me more intensely for about 2 years. It has tremendously uplifted my mood. It has been weird to hold back any sharing of the news for almost 2 months.

I’ve openly written here at great length about my troubles with becoming disabled, and then my strategies for managing a complex team, handling the issue of blame, how I enjoy and reflect on success while remaining vulnerable, a typical day in my working life, condemnation of game-playing in paper co-authorship, and more such introspection. This post is a positive one that focusses on what I am grateful for (mainly, who I am grateful to) that has enabled me to get to this point, where I have the privilege of an award that means a lot to me.

First and foremost, the most important thing is that I thank my family. Most immediately, I would never have had this privileged position without the constant, loving support of my wife before and during raising our daughter (who gave me new delights of fatherhood). We’ve shared some great times. I learned a lot about life and myself. I wasn’t alone; I had someone wonderful to trust and confide in. I can’t put into words how much this helped me, day after day through over 25 years now. And I can’t mention this without mentioning the terrible burden we experienced when my epilepsy struck in 2014, and since then. There were depths of despair that my wife helped me through. I’ve never spoken or written about this particular thing before, but around 2016, when I was having a terrible time getting the right drug to stave off my clonic-tonic “grand mal” seizures, one drug gave me side effects amplifying thoughts and urges to commit suicide to escape the suffering. It was an indescribably scary feeling, and fortunately we switched drugs and now seem to have found a combination that at least temporarily is working for me. That’s but one example. I share it also because suicide is a huge issue that impacts so many others, and I hope my example might be a light of hope, however small it might be. More generally, I have needed a lot of help from my wife, and I got it. Thank you, so much.

My parents gave me a middle-class upbringing that was quick to praise intellectual ability and academic success; my sisters and I all flourished in different ways. I benefitted from excellent resources and experiences with the natural world, from reading library books to visiting museums and exploring the great outdoors near home and during travels; often to my grandparents’ homes in Ohio and Florida, with different nature to investigate. I received a solid education and went to a good university where my intellectual life flowered. I didn’t always excel, and sometimes truly disappointed (cough that ‘D’ in one semester of chemistry, cough), but that was on me. I had fun, too. Too much fun.

Second, I had influential academic mentors. In undergraduate education and research at the University of Wisconsin, from Wendell Burkholder in agricultural entomology, to my own dad’s lab (as a Professor in microbial genetics, to Dianna Padilla’s lab in molluscan marine ecology, to Dana Geary’s and Klaus Westphal’s expertise in (again, mainly invertebrate) palaeontology; and all of their teams. Grad school at the University of California in Berkeley (Integrative Biology department) was marvelous. It transformed the life of my mind and my career. My supervisory committee Kevin Padian, Rodger Kram, Bob Full and Tony Keaveny (and other faculty such as Marvalee Wake, David Lindberg and Bill Clemens) gave me so, so much support and constructive criticism. I struggled for 3 of my 6 PhD years and they got me to my feet. Finally then, I realised what my career trajectory and goals were; I wanted to weave together evolutionary biology/palaeontology (with a morphological foundation) and biomechanics more strongly into the emerging discipline of evolutionary biomechanics. That epiphany has guided my whole career and identity as a scientist. It was a challenging journey but my mentors got me through it, and I had great external role models/mentors; Steve Gatesy at Brown University most prominently amongst them. Next, I was massively fortunate to get an NSF Bioinformatics postdoc to learn more biomechanics and cutting-edge biomedical engineering methods (musculoskeletal modelling and simulation) with Scott Delp at Stanford. This opened up the academic path that I’d dreamed of, giving me the vital technical foundation that I still use today. All of the teams of these people, and fellow graduate students/postdocs, were a fantastic peer group, even more role models, and educators for me.

Third, I’ve had an enormous panoply of collaborators in my own team and externally. I’ve had the opportunity to mentor and work with about 24 postdocs/fellows, 12 technicians and an administrator, 14 Masters students, 12 main and 26 co-supervised PhD students, and lots of undergraduate research projects. I tried to do good for them, too, but I had my share of failures, mistakes and mis-judgements. There has never been a one-way flow of benefits from me to them. I have always prospered from these experiences, crucially by learning new things (e.g., skills; knowledge; understanding of interpersonal relationships) from this interdisciplinary group. I’ve not just benefitted from publishing papers with them, although I love doing that. The same goes for the countless collaborators I’ve had outside of my team. I don’t know how to begin acknowledging all of these wonderful people, but my publications and grants are concrete evidence of their help.

Finally, the RVC has had my back for almost 20 years now. They believed in me enough to give me a job straight out of my first, 2-year postdoc. The aid I got goes from our amazing Structure & Motion Lab (led by Alan Wilson, FRS), which welcomed me into the ‘ground floor’ to help begin building it in 2003 and raising it to global prominence in our fields, to other faculty that became friends and inspirations, to upper management that created a near-perfect environment for me. I always was told to just do good work, in whatever form. They set me free to decide what was best and to just do it, and they gave me (and the rest of us in the SMLab) tremendous, world-class resources (space, funding, infrastructure and more) enabling it. I’d never have had the success I had in getting grant funding without all of this. And I know this kind of situation is a rare privilege. I can’t say I suffered from any biases or other major obstacles that held me back. It was all up to me in the end, to take advantage of what was available. “Onward and upward” was the saying I heard, and what happened.

There’s much more to thank, such as the friends and colleagues, the helpers I never may have fully been aware of, the medical care I got since I first became chronically ill in the mid-1990s (and via NHS since then), and then there’s money, and other concrete support that came from family. I lost my parents in early 2011. They passed on an inheritance that has helped us to prevent lean times. I’m not a financial whiz, and without this money the stress would have been so much harder to bear. Man, do I ever wish my parents were here today. My sisters took care of my parents during their illnesses, and I was in the UK unable to really help. That made a big difference.

But I can’t end without thanking who first nominated me for this Fellowship. I feel very emotional about this. It dredges up profound feelings and memories of good and bad times. Jenny Clack, FRS, came to the RVC to give a college seminar sometime around 2015(?), during our second NERC grant on early tetrapod locomotion. That was another collaboration that gave my career a big boost, and I’ve had a lot of fun with it. I drove Jenny back home after the seminar, and she was in contemplation at one point, carefully asking me something like “What do you think your effect on the field has been?” I came up with an OK answer; I think she might have been satisfied. Not long thereafter, she nominated me for the Fellowship. I didn’t understand the process, but gradually learned and got some guidance through the years. But Jenny died from cancer in 2020, just as the Covid-19 pandemic was about to truly kick off. This occurred during a year that was awful beyond my capacity to express, in innumerable ways; breaking my heart, my mind and my body; from which I’ve not recovered. Losing her deeply wounded me. She was a great friend and mentor. I have enormous respect for her, and I miss her. I wouldn’t have received this award now without her faith in me. Mike Benton kept the ball rolling with the nomination process after she passed, and I thank him too. Whoever else; Fellows or external reviewers; that gave me the thumbs-up during this process, wow, thank you too.

No one pulls themselves up by their bootstraps or is self-made. That’s a stupid myth that serves the privileged.

Now it’s all up to me. I see this moment in my career as a challenge to me. What do I do with this new privilege? Yes, it’s a highlight of my CV and all that, and I can bask in this honour for a while. I will enjoy that. It will be really fun to see what it is like being a Fellow and rubbing elbows with the others in this august academy. Quite a few Fellows have been disabled people, which is a meaningful fact to me, and for which I wrote about in a Fellow nomination section “As a disabled person, Hutchinson has made himself visible to the community as a potential role model and inspiration (see CV), and a major new goal of his career is to maximize the societal benefits from this opportunity.” I’ve thrown down the gauntlet to myself on that. This blog has been a place I’ve done that since 2012; it taught me to do so. Before then, my health troubles had been a more private issue. I’m still thankful that I am, as I’ve mused here before, “not dead yet“. If anyone is seeking to talk with a disabled scientist, either on a smaller scale or publicly, please reach out to me.

What comes next will be exciting new pages for my career and life, and I look forward to that. Blogs haven’t been the same since 2016, but I’ll keep using this one to document my journey, as I like it. Thank you again to the people above, and the many deserving folks that I have not explicitly thanked. This blog has given me the chance to share the joy and pain of life as a scientist, and I am pleased to share this one. I’ll keep sharing.

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Year 10.5 of John’s Freezer: WTF?

Posted in Freezermas, tagged in all seriousness, publication, science story on August 20, 2022| 3 Comments »

2021-2022: “over and over again & again” sums it up. I do love this band I “discovered” in 2021 though. Finding new music has been a joy for me through these tough recent years.

The pandemic goes on; my life goes on; but it has been another rough 1+ years. I have hardly done any hands-on anatomy as I’m hardly on campus at all, and my team’s work has mostly shifted into digital modelling for now (more about that below; it is not a bad thing though). My main news for 2021-2022 falls into the categories of Life Stuff, and Work Stuff to summarise here. “WTF” sums it up as it has been a… strange time; very challenging at a personal level, due to the Life Stuff.

Stomach-Churning Rating: stuff is weird, but nothing truly stomach-churning is here

Life Stuff: It’s been about the same as 2020-2021; summarised here. Thankfully, no major grief from losing people/pets close to me, this time. But my heath has been really awful instead — my epilepsy returned in May 2021, much to our surprise, after 2 years of remission. I suspect dehydration was a cause, as I later found out that I’d been chronically dehydrated, which came as a shock. I’ve since learned to step up my hydration routine, and I feel better. Right now I’m >5 months seizure-free, after a very hard time of monthly seizures for ~5 months in a row, including a scary one after a flight from Phoenix-London, in which I woke up in a toilet stall at Heathrow baggage claim, very disoriented and alone, eerily with no one in that large men’s loo area. My taxi driver was wondering why I was so late… I am glad I didn’t fall and hurt myself with no one around. Fingers crossed that doesn’t happen again. But on top of that, I’ve been fighting a longstanding chronic illness (details are not necessary) at the same time, and that got very bad in April 2022, sending me to hospital with severe internal infection; very life-threatening, painful and frightening. Again, right now I feel that I’m in recovery, and grateful for some good (overall) care from the NHS. Owing to these health problems though, plus the pandemic and financial challenges, I’ve not been travelling and don’t foresee much of that for my near future. Which also means not enough real holiday; “staycations” in my house just aren’t enough, as I’ve been here for ~2.5 years. I’m starting to do more fun things, finally, again, and that led to this blog post (first one in almost one year). I feel I have some energy to do things that I enjoy again.

Walking tinamou bird XROMM animation

Work Stuff: Mostly that has been pretty good, with a caveat. The DAWNDINOS project still dominated my work life, much to my pleasure. Indeed, just this week I tied the final ribbon on that, formally, with submission of my final grant report to the EU/ERC. The grant ended on March 31, 2022 and I was VERY, VERY sad to have to bid farewell to my team, who I hugely enjoyed working with for those 5.5 years. Now comes the caveat to “work is good”, which is that suddenly I have no funding (feast-to-famine) and “just” one PhD student (Vittorio LaBarbera; reinforcement learning simulations of locomotion); MRes student Georgia Wells just finished; and a Research Fellow (Dr. Masaya Iijima). It looks like I’ll be doing more undergrad research projects than postgrad for awhile, but we’ll see. The grant funding lottery can be hard to predict. Regardless, there’s a lot of fun science going on! With DAWNDINOS, since last summary we’ve cranked out a bunch of cool papers on archosaur locomotor biomechanics — find them here. #25-31 are the newer ones I haven’t blogged about anywhere yet; #25, 28 and 30 are blogged about by Dr. Ashleigh Wiseman here; and #30 (which is, in part, a summary of DAWNDINOS to date) got SICB conference coverage here.

Muscle-bound Euparkeria hindlimbs from our DAWNDINOS paper #28; picture by Oliver Demuth.

DAWNDINOS paper #26 with DAWNDINOS postdoc Dr. Delyle Polet was a serendipitous one inspired by him giving a seminar to our lab when he first came to the UK, and it struck me that his method for using biomechanical simulations with the “Murphy number” (related to pitch moment of inertia; MOI) to test how animals move would work really well with a long-bodied, hefty Triassic pseudosuchian (= large pitch MOI) such as Batrachotomus, whose results we could compare with known fossil trackways of similar archosaurs (e.g., Isocheirotherium). We found evidence for it using at least two running gaits, which was pretty surprising.

Walking/running Batrachotomus 2D simulation, matching tracks (blue+red).

And just this week we published another “spin-off” paper (also see van Beesel primate shoulder-modelling studies #17,#29) adapting our 3D digital modelling methods to another taxon. This one came out of left field for me (I’d never expected I’d work on sharks!) but actually fits very well with my research interests in giant animals, biomechanics and palaeontology. We reconstructed the giant shark Otodus megalodon from the best fossils available (including a Belgian vertebral column somewhat neglected since the 1860s), finding that it was ~16m long and >60,000 kg; but this is not the largest it could get, as a vertebra ~50% larger is known! This paper got a LOT of nice press attention, and the video below is perhaps the best science communication release I’ve been involved with (all kudos go to Catalina Pimiento and the animation team she commissioned). Very importantly, the key data are free to use.

Explanatory video by @cookedillustra, Ian Cooke-Tapia

LATE ADDITIONS: But it wasn’t all #DAWNDINOS-related research! I was very pleased to have Dr. Chris Basu’s PhD work with me on giraffid locomotor biomechanics published in PNAS. We showed, with experiments and computer simulations, that Giraffa has unusually low overall leverage (“effective mechanical advantage”; EMA) for its forelimbs during walking (and presumably all gaits/speeds); and even its cousin Okapia does, to a degree; and the extinct giant giraffid Sivatherium too. This is because of its long limbs, which one might look at and call it “cursorial adaptation” but our analysis reveals the tradeoffs of that; as limb length goes up, EMA goes down, and that negatively impacts athletic abilities. All the more reason to be wary of simplistic length-speed conclusions from extinct animals (calling T. rex!). This, with the similar paper on elephant EMA we published in 2010, is one of my papers I’m proudest of; even though neither (curiously) got much (if any) media/other attention. So it goes.

Above: OpenSim simulation of left forelimb of Giraffa during walking; in ~real-time, representing one ground-contact (stance) phase. Green arrow = ground-reaction force (GRF); red lines = major muscle lines of actions (the simulation activated/deactivated them, producing forces to counter the GRF). EMA is the ratio of the muscles’ leverage vs. GRF leverage around joints; it is ~0.3 in a giraffe vs. ~1.0 in a horse. EMA tends to be larger in larger mammals, up to horse-sized, then it gets weird in really big animals.

We also scienced the hell out of salamanders. Four papers, all involving Fire salamanders Salamandra salamandra! Three stemmed from my past PhD student Eva Herbst’s work: one explaining a new method to measure joint mobility; another applying that to walking salamanders in vivo and ex vivo; and the third comparing similar data to the Permian ‘giant’ salamander-relative Eryops, showing that its hip and knee joints were about as mobile as a Fire salamander’s. The fourth paper used video analyses of Fire salamanders in a theoretical model and simulation (with other animals) to demonstrate how multi-legged locomotion is controlled. It’s great to have these studies (partly from my old NERC grant on tetrapod locomotor evolution) out after ?5+ years; now Fire salamanders are among the salamanders whose locomotion we understand best. And we have more data still…

Above: Hindlimb configurations in S. salamandra (A) from rotoscoping of in vivo walking, during (B) mid-swing, (C) toe-on,(D) mid-stance, and (E) just before toe-off. These limb configurations were recreated in E. megacephalus (F) with three different knee spacing options: (G–J) tight knee spacing; (K–N) intermediate knee spacing; and (O–R) larger knee spacing, based on the amount of knee spacing present in the rotoscoped salamander at the null pose. S. salamandra configurations in (B–E) were scaled to E. megacephalus knee B.

Oh and I did some science consulting! “Prehistoric Planet” rocked the casbah; glad to see it out ~3 years after I began offering some critiques on the animations. I hope one scene I commented on eventually sees the light of day, as it wasn’t in the final programme. Similarly, “Dinosaurs: The Final Day” did well, and I gave the same kind of input. My experiences with these shows have inspired me to blog someday about how to become, and do, science consulting for documentaries, so watch for that. I may work in some commentary on what it means to be an invisible minority in that context, as I have thoughts.

Blink and you’ll miss me waving my arms about how Carnotaurus might have waved its arms!

There’s a lot of fun science to come, and that keeps me going. We’ve finished initial biomechanical models of 13 extinct archosaurs for DAWNDINOS, and those will become papers on modelling and simulating locomotor function, ultimately testing how performance differed between Pseudosuchia and Dinosauriformes/Dinosauria; and how locomotion evolved (e.g., bipedalism). Some examples in progress are below; these don’t show the muscles or external dimensions reconstructed. Stay tuned in 2022 and beyond for all that! Beyond this, time will tell what I’ll be doing, but DAWNDINOS is going to keep me very busy for plenty of years, and that is good fun for me.

Top image: top to bottom = *Postosuchus* (pseudosuchian), *Heterodontosaurus* (ornithischian dinosaur), *Riojasuchus* (pseudosuchian), *Silesaurus* (dinosauriform); Bottom image: *Gracilisuchus* (pseudosuchian), *Lago/Marasuchus* (dinosauriform), *Coelophysis* (theropod dinosaur). These are from ongoing studies with DAWNDINOS team members and collaborators around the world. All use 3D scans of the actual fossil material of one main specimen, wherever possible.

See you in 2023!?

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Simulating Dinosaur Locomotion And Wrestling With Scepticism

Posted in Biomechanics, Exalting Archosauria, tagged DAWNDINOS, dinosaur, fossilicious, modelling, muscle, publication, science story, simulation on September 22, 2021| 6 Comments »

We released a publication that, for me, comes full circle with research that started my career off. Back in 1995 when I started my PhD, I thought it would be great to use biomechanical models and simulations to test how extinct dinosaurs like Tyrannosaurus rex might have moved (or not), taking Jurassic Park CGI animations (for which the goal was to look great) into a more scientific realm (for which the goal is to be “correct”, even at the cost of beauty). “It would be great”, or so I thought, haha. I set off on what has become a ~26 year journey where I tried to build the evidence needed to do so, at each step trying to convince my fairly sceptical mind that it was “good enough” science. For my PhD I mainly focused on reconstructing the hindlimb muscles and their evolution, then using very simple “stick figure”, static biomechanical models of various bipeds to test which could support fast running with their leg muscles, culminating in a 2002 Nature paper that made my early career. I since wrote a long series of papers with collaborators to build on that work, studying muscle moment arms, body/segment centre of mass, and finally a standardized “workflow” for making 3D musculoskeletal models. And gradually we worked with many species, mostly living ones, to simulate walking and running and estimate how muscles controlled observed motions and forces from experiments. This taught us how to build better models and simulations. Now, in 2021, our science has made the leap forward I long hoped for, and the key thing for me is that I believe enough of it is “good enough” for me, which long held me back. This is thus my personal perspective. We have a press release that gives the general story for public consumption; here I’ve written for more of a sciencey audience.

Skeleton of the extinct theropod *Coelophysis* in a running pose, viewed side-on. Image credit: Scott Hocknull, Peter Bishop, Queensland Museum.

Stomach-Churning Rating: 1/10: just digital muscles.

Earlier in 2021, we simulated tinamou birds in two papers (first one here), the second one revealing our first ever fully predictive simulations, of jumping and landing; detailed here and with a nice summary article here. That research was led by DAWNDINOS postdoc Peter Bishop and featuring new collaborators from Belgium, Dr. Antoine Falisse and Prof. Friedl De Groote. Thanks to the latter duo’s expertise, we used what is called direct collocation (optimal control) simulation; which is faster than standard “single-shooting” forward dynamic simulation. The simulations also were fully three-dimensional, although with some admitted simplifications of joints and the foot morphology; much as even most human simulations do. The great thing about predictive simulations is that, unlike tracking/inverse simulations (all of my prior simulation research), it generates new behaviours, not just explaining how experimentally observed behaviours might have been generated by neuromuscular control.

OK, so what’s this new paper really about and why do I care? We first used our tinamou model to predict how it should walk and sprint, via some basic “rules” of optimal control goals. We got good results, we felt. That is the vital phase of what can be called model “validation”, or better termed “model evaluation”; sussing out what’s good/bad about simulation outputs based on inputs. It was good enough overall to proceed with a fossil theropod dinosaur, we felt.

Computer simulation of modern tinamou bird running at maximum speed. Grey tiles = 10 cm.

And so we returned to the smallish Triassic theropod Coelophysis, asking our simulations to find optimal solutions for maximal speed running. We obtained plausible results for both, including compared against Triassic theropod footprints and our prior work using static simulations. Leg muscles acted in ways comparable with how birds use them, for example, and matching some of my prior predictions (from anatomy and simple ideas of mechanics) of how muscle function should have evolved. The hindlimbs were more upright (vertical; and stiff) as we suspect earlier theropods were; unlike the more crouched, compliant hindlimbs of birds.

TENET: Thou shalt not study extinct archosaur locomotion without looking at extant archosaurs, too!

Computer simulation of extinct theropod dinosaur Coelophysis running at maximum speed. Grey tiles = 50 cm.

We observed that the simulations did clever things with the tail, swinging it side-to-side (and up-down) with each step in 3D; and in-phase with each leg: as the leg moved backward, the tail moved toward that leg’s side. With deeper analyses of these simulations, we found that this tail swinging conserved angular momentum and thus mechanical energy; making locomotion effectively cheaper, analogous to how humans swing their arms when moving. This motion emerged just from the physics of motion (i.e., the “multi-body dynamics”); not being intrinsically linked to muscles (e.g. the big caudofemoralis longus) or other soft tissues/neural control constraints (i.e., the biology). That is a cool finding, and because Coelophysis is a fairly representative theropod in many ways (bipedal, cursorial-limb-morphology, big tail, etc.), these motions probably transfer to most other fully bipedal archosaurs with substantial tails. Curiously, these motions seem to be opposite (tail swings left when right leg swings backward) in quadrupeds and facultatively bipedal lizards, although 3D experimental data aren’t abundant for the latter. But then, it seems beavers do what Coelophysis did?

Tail swings this-a-way (by Peter Bishop)

Computer simulation of extinct theropod dinosaur Coelophysis running at maximum speed, shown from behind to exemplify tail lateral flexion (wagging). Grey tiles = 50 cm.

The tail motions, and the lovely movies that our simulations produce, are what the media would likely focus on in telling the tale of this research, but there’s much more to this study. The tinamou simulations raise some interesting questions of why certain details didn’t ideally reflect reality: e.g., the limbs were still a little too vertical, a few muscles didn’t activate at the right times vs. experimental data, the foot motions were awkward, and the forces in running tended to be high. Some of these have obvious causes, but others do not, due to the complexity of the simulations. I’d love to know more about why they happen; wrong outputs from such models can be very interesting themselves.

Computer simulation of modern tinamou bird (brown) and extinct theropod dinosaur Coelophysis (green) running at maximum speed. Grey tiles = 10 cm for tinamou, 50 cm for Coelophysis.

Speaking of wrong, in order to make our Coelophysis walk and run, we had to take two major shortcuts in modelling the leg muscles. The tinamou model had standard “Hill-type” muscles that almost everyone uses, and they’re not perfect models of muscle mechanics but they are a fair start; it also had muscle properties (capacity for force production, length change, etc.) that were based on empirical (dissection, physiology) data. Yet for our fossil, because we don’t know the lengths of the muscle fibres (active contractile parts) vs. tendons (passive stretchy bits), we adopted a simplified “muscle” model that combined both into one set of properties rather than more realistically differentiating them. It was incredibly important, then, that we try this simple muscle model with our tinamou to see how well it performed; and it did OK but still not “perfect”, and that simple muscle model might not work so well in other behaviours. That was the first major shortcut. Second, again because we don’t know the detailed architecture of the leg muscles in Coelophysis, we had to set very simple capacities for muscular force production: all muscles could only produce at most 2.15 body weights of force. This assumption worked OK when we applied it to our simulation of sprinting in the tinamou (vs. average 1.95 body weights/muscle in the real bird), so it was sufficiently justifiable for our purposes. In current work, we’re examining some alternative approaches to these two shortcuts that hopefully will improve outputs while maximising realism and objectivity.

Computer simulation of extinct theropod Coelophysis running at maximum speed, shown alongside running human (at 4 m/s) for scale and context. Image credit: Peter Bishop.

If you pay close attention, our simulations of Coelophysis output rather high leg-forces, and it’s unclear if that’s due to the simple muscle model, the simple foot modelling, or is actually realistic due to the more vertical (hence stiff) hindlimbs; or all of these. Another intriguing technical finding was that shifting the body’s centre of mass forwards slowed down the simulation’s running speed, as one might expect from basic mechanics (greater leg joint torques), but unlike some prior simulations by other teams.

Computer simulation of extinct theropod Coelophysis shown alongside running human for scale and context. Shown from above to illustrate tail wagging behaviour. Image credit: Peter Bishop.

Users of models and simulations are very familiar with catchphrases like “all models are wrong, but some are useful” or the much more cynical (or ignorant) “garbage in, garbage out”; or the very dangerous attitude that “if the mathematics is correct, then the models can’t be that wrong” (but if the biology is wrong, fuggedaboutit!). These are salutary cautionary tales and catechisms that keep us on our toes, because the visual realism that realistic-looking simulations produce can seduce you into thinking that the science is better than it is. It’s not a field that’s well-suited for those fearful of being wrong. I’ll never think these outputs are perfect; that is a crazy notion; but today I feel pretty good. This was a long time coming for me, and it is satisfying to get to this stage where we can push forwards in some new directions such as comparing simulations of different species to address bigger evolutionary questions.

The wrestling with scepticism never ends, but we can make progress while the match goes on.

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The Forbidden Academic Tale

Posted in RANT, tagged in all seriousness, life/death, RVC, science story on August 10, 2019| 4 Comments »

I’ve written some soul-searching posts here before, but the topic I’ve long held back from addressing is the one that feels most forbidden as a senior-level academic. Today I’ve relented and written on it. Well, anyway I wrote this about 4 months ago and sat on it, and now’s the time. To hell with the forbidden — it is that nature which has been a torment. In academia we hear many stories, and are encouraged to talk openly about, the trials and tribulations of securing a permanent faculty (or similar; e.g. curator) post. I could write about my experience as an early career scientist, which wasn’t easy, but it wouldn’t be as contemporary or as fraught with emotion as this one is. This post is about the next step, one we hear so little about: attempting a mid-career transition between institutions.

I’ve bottled these thoughts up long enough but realized they are a teachable moment that others may benefit from, as I will loop back to at the end. The point of the post is not to seek pity or sympathy, or convey that doom and gloom about academia that pervades the internet, or even to hope for empathy, but to simply state this how it has been for me so far (SPOILER: it’s a story of failure), if one is headed down this path it might help, or at least the tale might be of interest in some other way, even having parallels with some non-academic careers.

Stomach-Churning Rating: me 10¹⁰/10; yours will vary

It is probably a good idea, and I don’t know the statistics but I imagine it is common, to move between institutions at least once in a scientist’s career, and not uncommonly twice; thrice enters a bad dimension and four or more times is either pathological or purposefully peripatetic (which might be fun!). Sooner or later one wants a change of pace: one may seek to move up the ladder to a better institution, more salary or other benefits, more desirable geographic location, escape poor working conditions for anything else, and/or other factors. New adventure, mid-life crisis, whatever. At mid-career, the temporal window is closing to find that place you finish your career at, hoping for ultimate stability and satisfaction. The pressure begins mounting, but while the opportunities to transition at assistant professor level are small (with much competition), the opportunities to do so at associate professor, let alone full professor level, approach the nadir. It varies among fields and geographic regions (and how choosy one is), but there may be only 1-2 jobs in one’s field in a year. Competition may be smaller than at junior level, or just hard to even compare, but a qualitatively different factor emerges.

Early career scientists (ECSs) are evaluated in job interviews for faculty-level posts in terms of their potential to grow to become what the institution needs; with evidence of already being on that trajectory important. But it’s less about who you are as how you convince the institution that you can become that dream academic they need most. At a mid-career level, everything is in plain sight. You have a track record. You probably know 1+ people in the institution or they might never give your application a second look. So as a known quantity, the question switches to how the person fits what is needed now and in the immediate future. They are less malleable. They probably won’t do a major pivot to change their research or other direction; that’s hard at a senior level (and an uphill battle to convince committees of). Once the few candidates have been interviewed, it’s probably clear to the search committee who fits their needs. There is less likely to be the “what if?” mystery with the ambiguous future of ECSs that may leave the committee more uncertain. It’s like being handed a puzzle to put together, vs. handed a batch of ingredients to cook freestyle.

Now begins my personal story. It’s maybe the worst-kept secret I have, I realize. And now I’m OK with that. When I came to the RVC, I was told that I’d probably remain for 5-7 years and then move back to the USA, and that was fine — even expected. I thought as much, too, and by the end of that time period I’d been applying for jobs to make that return voyage as prophesized. 10 years later, after almost 16 years, I’m still here. I’ve hit the wall of the mid-career transition and had to come to grips with its harsh reality. With few jobs and slim odds, I worry that I’m near an event horizon. I’m an academic straddling some fields that makes me somewhat of a square peg for many jobs. What am I? Do I fit into conventional labels and needs? This has been my career-long identity struggle — an evolutionary biomechanist is a weird mix. Having a large grant, too (the DAWNDINOS one), could be seen as an impediment as I’m still set on a major research project for 2 more years. Yet who knows… the rest is personal and remains uncertain.

Before I finish I must address the forbidden nature of such concerns. As mid-career academics, we’re enormously privileged. We have a job, perhaps a family, a home, relative stability and security, and so forth. ECSs might give anything for that! But we have our own lives to live, and the existential crisis of time-is-running-out only gets more intense. The prizes of tenure and other success may not come with happiness. We may feel “forbidden” to speak of our experiences not only because of such privilege, but also because of massively complex socio-political interactions that face us when trying to move institutions. I am fortunate that my institution has had my back throughout my process — others would not be so kind. I’ve heard of some universities that will sack their academics if they mention to senior administrators that they are contemplating a move! That’s just evil.

It can cause deep anxiety, uncertainty, political chicanery and other trouble for the news of seeking a mid-career transition to reach the wrong ears at the wrong time — particularly as it tends to be a prolonged, uncertain process. Seeking a job vs. moving with a signed contract are different things! Far, far, far apart on the spectrum of certainty are they. Moreover, the choice to seek to move jobs is a personal and private one. We may not want to become the topics of idle gossip, or even misinformation and undermining. These factors make the journey a lonely and unique one, and it would be a grotesque understatement to say that the personal (e.g. family, health) dynamics involved will compound the stresses. Together these can impact not just life outside of work but performance at and enjoyment of work itself.

The learning opportunity that I most want to share is this: if you’re on this kind of career track, plan to move early and get started early. Apply to jobs sooner (i.e. as an assistant professor) than later (i.e. tenure onwards) even if you’re not sure about wanting to move. Talk to your partner, peers or those that matter most about this; have a trusted, private support network and advice. Get some irons in the fire and see what opportunities arise. Expect that it may take much longer than you thought, so be strategic. Have a plan B, C and D; think about how flexible you can be. And, while you might do well getting interviews and hear nice things about how amazing you are (cold comfort at times), get used to the answer that you just don’t fit what a search committee was looking for. “Fit” is that Swiss army knife of words we use in such situations in academia, to embrace a wide range of reasons we don’t want to (or can’t, for HR/legal concerns) get into at the time for why a job decision is made. A lack of “fit” is a hard word to hear and accept, as we might see it otherwise, but it is the reality and we must accept it. By accepting such realities, perhaps the forbidden will become bearable.

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Learning by Serving

Posted in Conference, tagged admin, buddies, in all seriousness, science story on January 14, 2019| 3 Comments »

I had the privilege and pleasure of serving for the past 2 years as Chair of the Division of Vertebrate Morphology at the Society for Integrative and Comparative Biology, and that service just ended. So I had the showerthought to briefly post about the broader messages from that experience, with the hope that other scientists might benefit. But first, a little backstory.

Stomach-Churning Rating: 0/10

I’d only done some minor service before this, in scientific societies. At the time I ran for Chair-Elect 5 years ago, I felt it was time to try something new; to give back to science, as one should do. And so I did. It was a challenging and thus rewarding experience of learning the ropes- the Chair position is fairly open-ended to allow one to contribute what new things and leadership one envisions and can manage. In a short 2 years I felt I gained just enough momentum that I could have run the role more smoothly if I’d had a 3rd year, but that’s hindsight. The details don’t matter here but they lead to the messages of this post.

wink-wink musical interlude 1

First, the simple message that service, like the Holy Ghost, is the oft-forgotten third component of the trinity of professional science/academia; teaching and research being the other two (and science communication, to me, bridging all of these). As one moves along in one’s career, service tends to become increasingly expected—and the wisdom accumulated aids its conduct.

Second, service should be done because:

It’s the right thing to do
You learn things about your professional society, discipline, colleagues, leadership and self (skills and limits)
It’s not necessarily just boring bureaucracy (more about that below)
It will aid your career (CV, promotion, connections, future service, etc.) and you can aid others along the way

I think a common misconception is that service is boring. Yes, hearing the minutes of prior meetings read to you, or a long screed about minutia of health-and-safety, can be boring at times. But pay attention and find things that interest you and new vistas can open. This depends on the position one serves in and how it fits you. In my case, I found it a fun challenge to run meetings (i.e. try to follow the standard protocol of devising an agenda, checking minutes, etc.; standard bureaucracy) – especially the key activity of raising and voting on issues to consider taking the division in new directions. That allowed some creativity and made for energetic discussions on issues that mattered.

Another contrast to “boring” is resolving crises that arise (in my case, quite a few arose that felt serious to me). Yes, they’re stressful, but they also teach you things about how to handle crises, and you learn about your own ability to do so; and how others interface with that dynamic process. As I tend to emphasize on this blog, doing science is HUGELY about human interactions and foibles, and in service, as everywhere, such things are especially prominent and complex.

wink-wink musical interlude 2

Service comes in many forms. Students and postdocs can and should take part—many societies such as SICB tend to allow or encourage early career researcher participation. At a minimum, scientists should vote on elections (participation tends to be low among student/postdoc members) and attend their societies’ business or other meetings to see how the machine of a professional society works inside. It may even learn to serendipitous outcomes! And lessons learned will serve you well in many forms of future career.

One can do many other forms of service. Minimally in research, one is expected to participate in peer review; and that experience can lead to editor roles at journals, which I’ve found very interesting. Certainly in academic and other departments, there are numerous committee and other roles analogous to those in professional societies that are opportunities to serve.

I’ve surely left out other important lessons learned from serving. I’m still processing my experiences, reflecting and thinking forward. Now I’ve moved on to new service at SICB as Chair of the Student-Postdoc Affairs Committee, so there’s lots more for me to learn and share in that role.

What have you learned from serving? Do you have questions about service in science? Please chime in below.

A Day in the Life of John

Posted in RANT, tagged admin, in all seriousness, science story on April 5, 2018| 9 Comments »

As a person who has transitioned from the “simple life” (haha) of a grad student to postdoc to younger and then more experienced faculty member in academia/science, I constantly ponder how I spend my time. This is more so true lately, thanks to social media keeping me aware of how others spend their time (e.g. conversations about overwork and unrealistic expectations in academia/science), and thanks to my own experiences managing a moderate-to-large-sized group of 5-15ish scientists in the past ~10 years. I’ve had to learn to juggle a lot more than I did before and my life also has changed a lot (family, health, etc), some of which I’ve blogged about here before. Some of that excessive juggling is why there haven’t been so many blog posts here recently!

But today I want to turn the lens on the post’s title topic. What does a “typical” weekday in my life look like, with a focus on the academic/science aspects? There is no such “typical” ideal; every day is very different, but a Platonic abstraction will be heuristic. Let the clock tell the tale…

Stomach-Churning Rating: opinions may vary but I say it’s 0/10 (no gory photos).

0600-0700 I wake up and rush for the 2 big mugs of coffee that get and keep me moving, overcoming some huge side effects from medications I’m on. I feed the cats and check my email whilst having my coffee (and cereal + yoghurt). I deal with several simple messages from USA colleagues, or UK colleagues up late. Emails requiring more mindpower are saved for later. I tweet/retweet a little while skimming social media.

Nectar of the gods!

0730-0900 After shower etc. I begin my commute. 90 mins walk-train-train-walk (if no delays) and I can fit in another 60 mins or so of emails and some higher-functioning work (e.g. writing; editing papers; catching up on literature) on the train if I am feeling up for it. If I’m still too sluggish I listen to a (not-strictly-science but intellectual) podcast; e.g. RadioLab or Invisibilia; or (worst case) some rockin’ music.

0900-1000 Catching up on things in my office, with a few more emails, some organizing, quick chats with people around my office, and my day takes shape as I near my peak level of energy (and busy-ness).

1000-1200 Full steam ahead! I try to schedule my most demanding meetings to give them my full attention, or do my most challenging work if on my own.

1200-1230 John infamously gets hungry every ~5 hours and there is no stalling his need for fuel. Off to the campus restaurant he goes, for a hot meal and a little quiet time away from his office, to think/chat.

1230-1300 I like to leave this time as very flexible “me time”, whether spent on social media or whatever. I just do what suits me, maybe tidying up loose ends with smaller tasks, or just chilling (relatively) in contemplation.

1300-1400 A maybe less demanding meeting or a seminar (or a committee); in the latter case my powerful post-prandial somnolence becomes a battle now (and I don’t do caffeine >0800ish! Too sensitive). But I keep pushing on, and stuff gets done.

1400-1500 Another research-type meeting or data collection session, or writing, to fill some final, very valuable, on-campus time.

1500 Run for the train home, trying to stealthily escape campus without having any impromptu meetings that make me miss my train. My work day is not over but the commute is tiring so 6 hrs on campus and a bit more before and after are plenty!

1515-1645 Train ride and a bit of work where I feel able (50% of the time?).

1700-1800 Some catch-up emails (e.g. USA colleagues are waking up by now) and catch-up with family; juggling a lot. My activities vary a lot here: I may be inspired (even catching a second wind) to get some final work done or I may be totally wiped out and need a break. I listen to what my body tells me and also try to ensure I give myself time for non-work from here on.

1800-2100 Quality non-work time.

2100-2200 A bit of non-science reading before I fall asleep.

2200-0600 I need my 8 hrs sleep or I am a slow(er) grumpy John.

I’ve listed a “typical” day for non-teaching weeks. Currently my teaching load isn’t large by any measure, nor do I have many committee duties, and I am paid by my DAWNDINOS grant to spend 70% of my time (thru 2021) on that one project. So other than my October-November teaching I am mainly doing that 70% DAWNDINOS work, in various forms, plus a 30% that is some kind of science: a HUGE array of collaborations, some still stretching back to circa 2001 and still alive, some social media of course (although less these days than in ~2011-2012’s heyday, you may notice), and a potpourri of “other stuff”.

That “other” category is vast — travel to far-off places is a big time-sink lately, such as with 4 trips to the USA’s west coast in the past 4 months for seminars and conferences (although much of that involved DAWNDINOS presentations too). I am glad it’s all done, much as it was valuable science communication and meetings with friends/colleagues. Emails of sundry sorts fall into that “other” category too: I am not sure how many emails per day I field but I am the type of person that likes to handle a lot via email. Thereby I have a written record (my memory is patchy at times even though it can be excellent) that helps me organize my thoughts and actions. Maybe it’s 50 emails/day? Plus another 50 emails of fake conference/journal spam that seem to take more time deleting than they should (hello, spam filter)? Hosting visitors, talking on the phone/Skype with science writers, and certainly doing journal editorial/peer review duties are other big chunks. And so on; I won’t list it as most of it is normal academic life stuff. (Aside from the occasional elephant post-mortem)

Now, I got into academic life for what I feel are very good reasons, for me. A bit of context: I started working as a newspaper delivery boy at age 12, and continued that until I was maybe 15, then did odd jobs such as washing biochemistry dishes in my dad’s lab or fast food cashier/restaurant busboy & dishwasher until college. Then I kept up some intermittent part-time jobs like selling music CDs at Sam Goody, mixing margaritas as a “blender jockey” at Chi-Chi’s Mexican restaurant or tending snails at a marine ecology lab (thanks, Dianna Padilla!) until grad school. The point is, my parents had the wisdom to inculcate a work ethic into me, and that was VERY good, although I also got a strong taste of what it was like to work in a typical business, punching the clock in and out each day. And I HATED that clock-punching. It still provokes a deep visceral reaction from me. (Aside: ironically, that generous DAWNDINOS grant requires me to log my daily hours, and I hate that too but it must be done!)

In Sarasota, Florida where we spent winters with grandparents and I gleefully chased Anolis lizards (one blurry one here, I promise!).

To tie the story up, academic life attracted me (and I saw enough from my dad’s life as a professor to know) because it offered an escape from that punch-clock, 9-to-5 Monday-Friday life. The 9-to-5 strict schedule is just not for me, although I have plenty of respect those for whom it is; the world needs all kinds. I need flexibility; I need to be able to do science when Athena’s muse strikes me, not feeling chained to a rigid schedule and suffocating bookkeeping of how time is spent. In reality, in academia/science I feel now that it is impossible for me to realistically quantify how much time I spend on particular things – I may get a good idea while on the toilet, and that counts as science time doesn’t it? I am probably juggling a dozen things at once in my mind and efforts; work/other life/bullshit; at any one time, so partitioning my time is subjective nonsense. I prefer to be judged (when I must be judged) on what I do and its quality, and to be trusted to do this right by some “fair” standard rather than hours. To me, that’s what academia/science should be… (current reality be damned)

I blame the 80s.

That brings me to, how does a weekend look? In grad school I didn’t mind devoting some of my weekends – and plenty of late evenings – to work. Now, especially with a family, I do mind it. Living in Europe has helped me appreciate that quality-of-life mentality as well. It can still be a struggle within me, as I love science and sometimes I just want to do it; it may not matter if it is 6am on a Tuesday, 1pm on a Thursday or 7pm on a Saturday. Often I say “no” and don’t, and that can feel good, but sometimes I let myself enjoy after-hours work, because I live for enjoyment in all its forms in my life. That is a privileged position to be in and I do not forget that privilege. However, I’ve worked since 1989 to get here, so 29+ years of university life has to have been for some non-disposable purpose in my life. I’ve posted before about work-life integration and how I don’t personally recognize a rigid divide between these in my life, but with 24 hours in a day there is a real zero-sum game at play, so I prioritize what I do (or go with the moment).

In non-work mode: Reggie Regent (I’m the lion on the left; not the dog, who was beloved Daisy); high school mascot. A very sweaty one in that suit!

One failure I am working on is to return to fitting in ~2 gym workouts/week into my weekday schedule; that was good when I was doing it a couple of years ago. I have no great excuses for that. Nor would I rely on the “too busy” excuse for anything above — I find the “cult of busy” in academia to be tedious and repugnant (the post linked there is mainly about PhD students but at the faculty academic level such genitalia-sizing-up talk is rife). We all do what we can with our limited time, yet our life-goals are probably not identical, and we probably don’t understand what others do with their time or what constraints they work under.

Dealing with encroaching age and disability has thrown new challenges into my time-budgeting that I am still grappling with. I may want to work (or even need to, beyond the level of overcommitment I’m already in) but sometimes I simply do not have the energy. I don’t give myself guilt and grief for this if I can help it, while I expect that once I do have more energy I’ll devote it appropriately. I respect my limits, much as I confess I still don’t understand them.

As a lifelong learner, I am still learning how to live my life, one day at a time. Everyone lives their life differently. My life now is lived so incredibly differently from how I lived it 20 years ago as a young grad student that I can have a hard time recognizing myself in that scared, scarred, lost, naïve yet still very excited man.

One day that young grad student went into San Francisco, bought a huge teddy bear, and brought it home to cuddle with because he felt so alone. A blues musician on the street saw him carrying that bear and improvised a song mocking him, and he didn’t mind because it was the truth that was captured in that parody, and he was a student of the truth. It was a dark period in that man’s life—a void that was filled with work.

“How, then, can we fail to take the importance of factuality and reality seriously? How can we fail to care about truth? We cannot.”

But now my daughter has inherited that bear and it was worth every dime, every lonely tear, and every hour worked to become the person I am; the only person I can be at this moment, flawed yet ever in flux. Tomorrow will be another day and I will be grateful for those new hours, awake to their prospects and alert to their tribulations.

That was a condensed day in my scientific life and some backstory to it. Thanks for taking your time to read it.

We’ve been through a lot together.

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Darwin the Human

Posted in Mad Science, tagged Darwin, evolution, in all seriousness, life/death, science story on February 12, 2018| 4 Comments »

A personal story here for Darwin Day 2018. I knew about as much about Charles Robert Darwin as any typical science-interested student when I was growing up. But eventually I had the good fortune of taking a history of science class at the University of Wisconsin as an undergrad, and it inspired me with the story of Darwin as a human being, not just some clever scientist with a long argument that changed the world.

Stomach-Churning Rating: 0/10 unless you have Darwin’s gut-wrenching problems.

I devoured Desmond & Moore’s amazing biography of Darwin “the tormented evolutionist”, which was the transformative event for me. At the time I was experiencing the beginnings of some health problems that didn’t seem that far from problems Darwin suffered for much of his life, and then, as I read more about his life, I saw more features of this man that brought him vividly to life. I still think about those traits and how some parallel my life in certain ways (not that I am in any way a giant of science like him!!). And so this blog post was born, thusly:

I’m writing this post early on Darwin Day and entirely from memory, rather than doing my usual research into the post while I go; to keep the post more personal and less academic (e.g. just quick Wikipedia links below). I feel connected to Darwin’s life experience because, like him, I wandered about as a student, unsure about my direction in life and causing my parents some consternation early on. He tried medical school (Edinburgh; too bloody) and theology (Cambridge; faith just was not his thing) but found hunting for beetles on the heaths more exciting. In high school I played with ideas such as Hollywood screen-writing (too risky), radio DJ (I had no skills) and truant or criminal (I hung out with some shady characters even though I still had some morals; despite transgressions and convictions).

I then took a standardized “what is your best career fit?” test in biology class which conclusively told me that biology was best for me as a career; and that rang true. I’d always loved nature and so that was the idea I had when I went to undergrad. I signed up for the wrong college (Agriculture & Life Sciences, not Letters & Science; confusing divisions!) at the UW. I got some early research experience in that first college: I tried my hand at raising colonies of Indian mealmoths (Plodia interpunctella; I can still identify them!) and their parasitoid wasps. At that same agricultural lab I got to do my own experiments in a basement wind tunnel over my summer holiday, in which I released those pesky moths to fly down the tunnel toward various kinds of pheromone-based lures, finding that one kind seemed to work best. But I didn’t like that and frankly found agricultural science boring, for me. We didn’t connect, nor did some other lab experiences I had. But I grew from them and still value them (and respect the science and people involved) very much.

I took Evolution and also Functional Morphology courses, didn’t do great (I was young for the classes), and then finally took that history class—boom! Aha, scientists can be human! Not just hypothesis-robots! Darwin was a man of great privilege, having his estate and wealth handed down from his funky grandpa Erasmus and stern father Robert. But, in addition to his meanderings that eventually forced him (via his father’s impatient urgings) to become the Beagle’s naturalist for a five year voyage, he suffered in quite human ways throughout much of his life. The greater trials commenced during that voyage, with still-mysterious health problems and the fractious relationship with eccentric Captain Fitzroy. They continued with his marriage to cousin Emma Wedgwood (yes, of that pottery-famed lineage) in which they lost four of ten children at young ages (most critically, beloved Annie at 10 years old) and in which they struggled with Darwin’s diminishing faith and Emma’s stalwart beliefs.

Finally, Darwin struggled famously with his “big book” for >20 years, afraid of its impact and its reception, and of its need to have a watertight, evidence-based argument from many perspectives, with his hand forced by Alfred Russel Wallace’s converging ideas. Along the way, with his health and family problems, he had to contend with his mentors’ and peers’ reactions to his ideas—although one could call the acceptance of much of his main arguments to be a “happy ending” (the post-mortem eclipse of Darwinism, and its eventual resurrection + syntheses, aside). These trials that Darwin faced as a human are all relatable, and the more one learns about him the more complex, flawed, emotional and yes, tormented he becomes. He can be both a hero and a tragic figure or a cautionary tale.

When I get the chance, I like to teach students about this human side of Darwin. It is a way into the heart of the science, to show a person’s journey along with the wonder of discovery, and how such a journey is not necessarily a simple or even joyful one. I can feel the many facets of Darwin in my own life—the intensely curious, peripatetic, enthusiastic young man who loved experiencing nature in all its raw forms, the chronically suffering disabled person who sometimes could not enjoy the work or other aspects of life that he treasured, the family man who loved time at home, the explorer who treasured roaming the local heath or far-flung foreign terrain, the meticulous scientist who exhaustively gathered tiny bits of data in isolated studies to slowly build toward grander ideas, and much more.

But Darwin is a different human, too. We live in such different times, when there the world of science is far larger but the world feels far smaller, more interconnected. Naturalists today are not simply landed noblemen who can play with science in their luxurious spare time, nor do they work alone at their pursuits. Anyone can be a scientist, and a career scientist can, if they are fortunate and skilled enough, assemble their own laboratory in which they lead a team to tackle their big questions that captivate them. The individual questions in science tend to be smaller (more incremental and specialized) today, yet can overall (across career(s)) be bigger because we can tackle -and have tackled- some of the bigger ones; Darwin’s big questions being among the giant ideas we are now poised upon.

It’s not all about science, though. Darwin’s story, which I think about so often, reminds me of how we all struggle in our lives and amidst the joy of discovery in everyday life there can be considerable suffering and regret. It is a bittersweet story; an ever-so-human story. And today is a good day to reflect on that, and to celebrate life while we lament what has been lost.

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You Thaw That, We Thaw These

Posted in Frozen Mammals, Mad Science, tagged anatomy, Danger: Double Entendres, dissection, freezer love, patella, science story on November 23, 2017| Leave a Comment »

This week we conducted wallaby leg dissections for a study of the kneecaps of marsupials (pouched mammals). Placental (non-pouched) mammals like us almost all have bony kneecaps but many marsupials do not. Kneecaps do important things, acting like gears around the knee joints (e.g. this old post), and yet it is unclear why some marsupials have lost, kept or even re-evolved them as bones. So we’re investigating that and already noticed that one of our wallabies has bony kneecap(s) whereas the other doesn’t, so we’re checking out why and taking tissue samples to do histology (sectioning for microscopic imaging of tissue composition and structure) on so we can see what the knee tendon/kneecap tissues are made of. Some marsupials turn their kneecaps into fibrocartilage rather than bone or tendon and that can be impossible to identify without histology.

The wallabies are small, about 20lbs or so and just take a day or so. Like a turkey. And it’s Thanksgiving today, so here I am with a post about thawing specimens for science, rather than for food. Maybe the title will make sense now.

Stomach-Churning Rating: 7/10; thawed wallaby bits from the get-go.

Thawed lower leg and foot of wallaby. The stickers are for an old study that would take too long to explain…

This post was directly inspired by journalist Jason Bittel’s inquiry to me about my tweet on the wallaby thawing; he wondered if there might be a fun story linking thawing-for-science with thawing-for-Thanksgiving. Some highfalutin editors didn’t agree, so no printed/online story came of this, but I am not so highfalutin, hence this blog post.

Thawed wallaby forelimbs. I’m also looking into the “false thumbs” that some marsupials have (“sixth fingers”), much as elephants and other mammals may have.

Thawing is second nature for our lab’s team; we do it all the time. Avid readers will be unsurprised to learn that just about everything I’ve worked on has been frozen at some time, and thus has been thawed out at some time(s). Normally we don’t freeze if we need live tissue or undistorted tissue, e.g. to measure physiology or very fine microstructure– freezing disrupts all of that. We would instead use physiological saline solution or else a preservative like formalin. And you can only freeze and then thaw a specimen for two times or so before it becomes too useless even for anatomical study.

A small specimen like this salamander can be thawed out simply by running it under warm water for a little while or leaving it out for an hour.

We just leave specimens in a cart, or on a table or sometimes in a cold-room shelving area, for slower thawing. Space heaters tend to overdo things. We don’t do any rough calculation from some sort of thermodynamic first principles of time-to-thaw vs. specimen size (I wish we were that smart!); just seat-of-pants guessing and checking (yes, poking specimens to check their thawedness is a method of choice). Cutting things in half along the way, or skinning them, may be used to accelerate the thawing process. But it’s about as unscientific a method as we use.

The hardest specimens to thaw of course have been the largest specimens. Elephant legs can be >2 metres long and hundreds of kilograms (especially when frozen). A week at room temperature tends to work OK for getting them to a dissectable state. One has to balance the outer deterioration with the inner frigidness. We’re not so concerned about microbe growth in most cases, as one would be with a thawing turkey, and not at all about consumption. We just want to be able to dissect it and make observations, mostly via eyeballing the specimens as we dissect them,

Left hindfoot of an Asian elephant. Still frozen; this was bandthawed- I mean bandsawed- to see its internal anatomy nice and clearly. You may see this specimen again somewhere else– stay tuned! 🙂

Moisture and fluids can be a challenge: generally the rooms we thaw in are low humidity so moisture may not be an issue once the ice melts away, and we have drains nearby. We try to remove ice first or have towels to wipe/soak fluids up as thawing progresses. But if a specimen is sitting in a cart or storage bag with too much ice early on, that can thaw first and then turn the specimen into a nasty slurry of the stuff you’re interested in and the less desirable muck. So we try to avoid that.

De-thawing too early is bad. The smell gets progressively worse– and once the interior of the specimen is thawed enough, then bacteria get in there and the interior becomes a brewing ground for heat production (rather than remaining a cooler region), which accelerates decay, so we don’t want that. We have to check on thawing specimens regularly and move them to cooler storage areas, or begin dissection earlier, if the decay process is noticeably getting excessive.

Any insulation affects thawing time- so scales, feathers, thick skin, shells, fat (for a short while until it decays), and other layers will slow thawing—and may keep heat inside, if there begins to be thawing of the core. So sometimes you open up a specimen that seems dry and clean on the outside and the inside is unpleasant. But with experience that is not hard to avoid.

Thawed wallaby patella prepared for histology.

The foulest specimen I’ve thawed by far was a monitor lizard… it was shipped to me in California from Arizona when I was a PhD student. This was in August’s heat and the box of the big lizard sat thawing at the post office for 2 weeks before they contacted me and asked why a smelly box was bleeding. I came and got it and brought it back to our department but the smell was so bad it set off our building health & safety person’s alarm bells (sorry, David!) and they emailed around a “toxic alert” warning, until I bashfully made it clear that my lizard was the cause, not some toxic chemical. I got in some trouble and was very ashamed. But we put the specimen into a big tank of brine solution and the smell was reduced—the specimen may well still be preserved there 20 years later; I do wonder! Anyway, that experience was so horrendous – and I have a strong stomach—that I regularly recall it and seek to avoid a repeat. It was the most disgusting thing I’ve ever experienced. I do not recommend it.

What we tend to want to get from thawed specimens is: (1) descriptive anatomy (what connects where), and maybe (2) quantitative measurements (laborious metrics of “muscle architecture”– how much does each muscle weigh, how long is it, etc; over and over again for many muscles…). These data not only serve to tell us what makes animals different (and how this evolved) but also the data are used to test questions such as how animals work. In the case of things like wallabies, ultimately we’d love to know what their kneecaps do if they are bony or not; what difference does it make and why might there be differences? We’d spotted one wallaby already that seemed to have a bony kneecap on one leg, and a non-bony one on the other leg, so that asymmetry got us excited.

What’s surprising to learn about thawing animals for science? Well, my first thought is that it’s beautiful. I don’t tend to think of it as gross. I’ve rhapsodized about this before. Animals are wonderful inside and out, and I regularly pause during a dissection to marvel at how amazing the anatomical specializations of animals are. Simple details- shapes, colours, configurations- can be gorgeous. (Often the blood is minimal, drained out early, so that doesn’t detract from or hide the detailed imagery) The gentle yet complex path of a tendon around a joint can yield profound visual enchantment in its elegance. This is all the more true once one ponders how these complex structures evolved, and how much diversity of form and function is out there to study—and how little we know about it! We still don’t know well how to fix many problems humans have with their anatomy, and that’s orders of magnitude worst for most animals, because we don’t understand how anatomy works, or even what the anatomy is like in some cases. So that keeps me busy discovering things. Every specimen is different with surprising little variations, or big ones—sometimes there is one muscle, sometimes it is clearly divided into two muscles, in the same species or even the left vs. right legs. I love seeing those intricacies and wondering about them.

Thawed wallaby shank sliced open to show lovely digital flexors and gastrocnemius muscles. So many questions are raised by this!

If you’re thawing for Thanksgiving, or thawing for science, or thawing out family relations during a gathering, or thawing yourself out from the winter’s cold– my best wishes to you! May we all enjoy what we thaw.

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Time

Posted in Frozen Mammals, Museums are Cool, When Anatomy Goes Bad, tagged admin, anatomy, cool cats, dem bones, dinosaur, fossilicious, funky feet, museum, publication, rhinos, RVC, science story on October 21, 2016| 4 Comments »

It has been almost three months since my last post here, and things have fallen quiet on our sister blog Anatomy to You, too. I thought it was time for an update, which is mostly a summary of stuff we’ve been doing on my team, but also featuring some interesting images if you stick around. The relative silence here has partly been due to me giving myself some nice holiday time w/family in L.A., then having surgery to fix my right shoulder, then recovering from that and some complications (still underway, but the fact that I am doing this post is itself evidence of recovery).

Stomach-Churning Rating: 4/10; semi-gruesome x-rays of me and hippo bits at the end, but just bones really.

X-ray of my right shoulder from frontal view, unlabelled

Labelled x-ray

So my priorities shifted to those things and to what work priorities most badly needed my limited energy and time. I’ve also felt that, especially since my health has had its two-year rough patch, this blog has been quieter and less interactive than it used to be, but that is the nature of things and maybe part of a broader trend in blogs, too. My creative juices in terms of social media just haven’t been at their ~2011-2014 levels but much is out of my control, and I am hopeful that time will reverse that trend. Enough about all this. I want to talk about science for the rest of this post.

My team, and collaborators as well, have published six recent studies that are very relevant to this blog’s theme- how about we run through them quickly? OK then.

Panagiotopoulou, O., Pataky, T.C., Day, M., Hensman, M.C., Hensman, S., Hutchinson, J.R., Clemente, C.J. 2016. Foot pressure distributions during walking in African elephants (Loxodonta africana). Royal Society Open Science 3: 160203.

Our Australian collaborators got five African elephants together in Limpopo, South Africa and walked them over pressure-measuring mats, mimicking our 2012 study of Asian elephants. While sample sizes were too limited to say much statistically, in qualitatively descriptive terms we didn’t find striking differences between the two species’ foot pressure patterns. I particularly like how the centre of pressure of each foot (i.e. abstracting all regional pressures down to one mean point over time) followed essentially the same pattern in our African and Asian elephants, with a variable heelstrike concentration that then moved forward throughout the step, and finally moved toward the outer (3rd-5th; especially 3rd) toes as the foot pushed off the ground, as below.

African elephant foot COP traces vs. time in red; Asian elephant in orange. Left and right forefeet above; hindfeet below.

African elephant foot COP traces vs. time in red; Asian elephant in orange-yellow. Left and right forefeet above; hindfeet below.

Gradually, this work is moving the field toward better ability to use similar techniques to compare elephant foot mechanics among species, individuals, or over time– especially with the potential of using this method (popular in human clinical gait labs) to monitor foot (and broader musculoskeletal) health in elephants. I am hopeful that a difference can be made, and the basic science we’ve done to date will be a foundation for that.

Panagiotopoulou, O., Rankin, J.W., Gatesy, S.M., Hutchinson, J.R. 2016. A preliminary case study of the effect of shoe-wearing on the biomechanics of a horse’s foot. PeerJ 4: e2164.

Finally, about six years after we collected some very challenging experimental data in our lab, we’ve published our first study on them. It’s a methodological study of one horse, not something one can hang any hats on statistically, but we threw the “kitchen sink” of biomechanics at that horse (harmlessly!) by combining standard in vivo forceplate analysis with “XROMM” (scientific rotoscopy with biplanar fluoroscopy or “x-ray video”) to conduct dynamic analysis of forefoot joint motions and forces (with and without horseshoes on the horse), and then to use these data as input values for finite element analysis (FEA) of estimated skeletal stresses and strains. This method sets the stage for some even more ambitious comparative studies that we’re finishing up now. And it is not in short supply of cool biomechanical, anatomical images so here ya go:

Above: The toe bones (phalanges) of our horse’s forefoot in dorsal (cranial/front) view, from our FEA results, with hot colours showing higher relative stresses- in this case, hinting (but not demonstrating statistically) that wearing horseshoes might increase stresses in some regions on the feet. But more convincingly, showing that we have a scientific workflow set up to do these kinds of biomechanical calculations from experiments to computer models and simulations, which was not trivial.

And a cool XROMM video of our horse’s foot motions:

Bates, K.T., Mannion, P.D., Falkingham, P.L., Brusatte, S.L., Hutchinson, J.R., Otero, A., Sellers, W.I., Sullivan, C., Stevens, K.A., Allen, V. 2016. Temporal and phylogenetic evolution of the sauropod dinosaur body plan. Royal Society Open Science 3: 150636.

I had the good fortune of joining a big international team of sauropod experts to look at how the shapes and sizes of body segments in sauropods evolved and how those influenced the position of the body’s centre of mass, similar to what we did earlier with theropod dinosaurs. My role was minor but I enjoyed the study (despite a rough ride with some early reviews) and the final product is one cool paper in my opinion. Here’s an example:

The (embiggenable-by-clicking) plot shows that early dinosaurs shifted their centre of mass (COM) backwards (maybe related to becoming bipedal?) and then sauropods shifted the COM forwards again (i.e. toward their forelimbs and heads) throughout much of their evolution. This was related to quadrupedalism and giant size as well as to evolving a longer neck; which makes sense (and I’m glad the data broadly supported it). But it is also a reminder that not all sauropods moved in the same ways- the change of COM would have required changes in how they moved. There was also plenty of methodological nuance here to cover all the uncertainties but for that, see the 17 page paper and 86 pages of supplementary material…

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

Back in 2011, Stephanie Pierce, Jenny Clack and I tried some simple linear morphometrics (shape analysis) to see how pinniped (seal, walrus, etc) mammals changed their vertebral morphology with size and regionally across their backbones. Now in this new study, with “Team Cat” assembled, PhD student Marcela Randau collected her own big dataset for felid (cat) backbones and applied some even fancier techniques to see how cat spines change their shape and size. We found that overall the vertebrae tended to get relatively more robust in larger cats, helping to resist gravity and other forces, and that cats with different ecologies across the arboreal-to-terrestrial spectrum also changed their (lumbar) vertebral shape differently. Now Marcela’s work is diving even deeper into these issues; stay tuned…

Example measurements taken on felid vertebrae, from the neck (A-F) to the lumbar region (G-J), using a cheetah skeleton.

Charles, J.P., Cappellari, O., Spence, A.J., Hutchinson, J.R., Wells, D.J. 2016. Musculoskeletal geometry, muscle architecture and functional specialisations of the mouse hindlimb. PLOS One 11(4): e0147669.

RVC PhD student James Charles measured the heck out of some normal mice, dissecting their hindlimb muscle anatomy, and using microCT scans produced some gorgeous images of that anatomy too. In the process, he also quantified how each muscle is differently specialized for the ability to produce large forces, rapid contractions or fine control. Those data were essential for the next study, where we got more computational!

Charles, J.P., Cappellari, O., Spence, A.J., Wells, D.J., Hutchinson, J.R. 2016. Muscle moment arms and sensitivity analysis of a mouse hindlimb musculoskeletal model. Journal of Anatomy 229:514–535.

James wrangled together a lovely musculoskeletal model of our representative mouse subject’s hindlimb in the SIMM software that my team uses for these kinds of biomechanical analyses. As we normally do as a first step, we used the model to estimate things that are hard to measure directly, such as the leverages (moment arms) of each individual muscle and how those change with limb posture (which can produce variable gearing of muscles around joints). James has his PhD viva (defense) next week so good luck James!

The horse and mouse papers are exemplars of what my team now does routinely. For about 15 years now, I’ve been building my team toward doing these kinds of fusion of data from anatomy, experimental biomechanics, musculoskeletal and other models, and simulation (i.e. estimating unmeasurable parameters by telling a model to execute a behaviour with a given set of criteria to try to perform well). Big thanks go to collaborator Jeff Rankin for helping us move that along lately. Our ostrich study from earlier this year shows the best example we’ve done yet with this, but there’s plenty more to come.

I am incredibly excited that, now that my team has the tools and expertise built up to do what I’ve long wanted to do, we can finally deliver the goods on the aspirations I had back when I was a postdoc, and which we have put enormous effort into pushing forward since then. In addition to new analyses of horses and mice and other animals, we’ll be trying to push the envelope more with how well we can apply similar methods to extinct animals, which brings new challenges– and evolutionary questions that get me very, very fired up.

Here we are, then; time has brought some changes to my life and work and it will continue to as we pass this juncture. I suspect I’ll look back on 2016 and see it as transformative, but it hasn’t been an easy year either, to say the least. “Draining” is the word that leaps to mind right now—but also “Focused” applies, because I had to try to be that, and sometimes succeeded. I’ve certainly benefited a lot at work from having some talented staff, students and other collaborators cranking out cool papers with me.

I still have time to do other things, too. Once in a while, a cool critter manifests in The Freezers. Check out a hippo foot from a CT scan! It’s not my best scan ever (noisy data) but it shows the anatomy fairly well, and some odd pathologies such as tiny floating lumps of mineralized soft tissue here and there. Lots to puzzle over.

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