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Posts Tagged ‘RVC’

‘Full fathom five thy father lies, of his bones are coral made. Those are pearls that were his eyes. Nothing of him that doth fade, but doth suffer a sea-change into something rich and strange.’

(Shakespeare’s The Tempest Act 1, Scene 2)

Stomach-Churning Rating: 1/10- this time, tame images.

Five years have passed on this blog now, and this year with them passed Freezersaurus (soon to leave RVC’s campus; sob!). Indeed, the blog has changed, via the tempests I’ve weathered in my own life, which I lamented in last year’s summary. Regardless, the blog has been visited this year more than in any prior year, with >101,000 visits– thanks!

This year I’ll keep my annual retrospective shorter than usual, as I’m feeling healthier and more energetic but less self-indulgent.

I still got to have fun, like this ComicCon in NOLA. So, some self-indulgence.

I still got to have fun, like this ComicCon in NOLA. So, some self-indulgence.

I began the past year by blogging about why I blog, and how I feel that in a way I (and others) have long been blogging even if it wasn’t called that, and how I don’t see science communication such as blogging or tweeting as something distinct from science itself. Reading back on that post, I find some themes there that emerge again and again throughout this year’s posts, such as valuing diversity (in its diverse forms) and curiosity.

Like this? So much more is here!

Like this you do? So much more here there is!

Never tired of elephant feet will I be!

Those introspective posts included one that is very close to my heart, about how I notice my own decline (some of it since reversed, but some still lingering) and feel grief. It wasn’t long after that post that I wrote more about my experience as an epileptic; what it’s like to have a seizure. Another, more science-focused (but still very human) one laid out my views on what my team’s principles are. Then I returned a few posts later with some reflection on how time passes (too quickly!) and with it come publications (I reviewed some of my team’s latest), among other changes as a person living as an academic. I wrote then that “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.” Yep. Spot on. I’ve started a big new grant which has been a huge challenge, and I’ve rediscovered my health and some of my old self with it, rekindling some passion and hope. Later, on USA’s Thanksgiving, I typed in some musings about my appreciation for diversity in the human world. Again, with thoughts of disturbing recent political/social trends weighing heavily on me, I celebrated how the Women’s March inspired me, and how that relates to the importance of curiosity and empathy.

He ain't goin' nowhere.

He ain’t goin’ nowhere.

But there was plenty of time here to talk about freezers and anatomy and research, too! We published a paper that I think I’ll long regard as one of our better ones, on using dynamic computer simulations to study how ostriches control their walking and running gaits with their muscles. Throughout 2016, we worked hard to get our anatomical research out there to the public in person. So I posted about our presentations at the Cheltenham Science Festival (including a public cheetah dissection, which was a huge hit!), and “Team Cat” did a dissection of another cheetah (all zoo mortalities) at the RVC for a well-attended joint event with UCL/Grant Museum on “Wild Cats Uncovered: movement evolves“. UCL’s PhD student (soon Dr.) Marcela Randau wrote a great guest post about our paper on how size and ecology relate to the shapes of backbones in cats, which tied in nicely with those big cat dissection presentations. I also ruminated about how scientists balance testing big questions vs. getting very accurate data, using the big question (in my and others’ research) about how much more slowly big animals can move relative to smaller ones as an example. As a final anatomical post this blog-year, I wrote about the biceps muscle, and people seemed to like that, so I will do more of those.

Whale humeral epiphysis (joint) turned into a sculpture with walrus ivory teeth, at Point Vicente Museum, LA.

Whale humeral epiphysis (joint) turned into a sculpture with walrus ivory teeth, at Point Vicente Museum, LA.

In addition to being open about my (and my team’s) thoughts, experiences, dissections and publications, we put a lot of effort this year into making our scientific and anatomical data public. My blog posts about our huuuuuge open datasets on crocodile and tuatara 3D scans exemplify a deluge of data that is going to keep coming out. We’re going to push very hard on this, including an effort to release old data from prior publications of mine. I’m thrilled that we can finally deliver on these things; it is a great feeling!

Yale Peabody Museum specimen YPM57100: ilium (hip bone) and vertebrae of the Triassic archosaur Poposaurus. More about this later!

Yale Peabody Museum specimen YPM57100: right ilium (hip bone) and vertebrae of the Triassic archosaur Poposaurus. More about this later!

We enter year 6 of this blog with a new (temporary, maybe) freezer, which we failed to reach a conclusion on naming. I’m sure you’re on tenterhooks awaiting the final decision. I have a bunch of ideas for some blog posts to come soon (really fun anatomical papers en route), and I always welcome guest posts so let me know if you want to do one! In the meantime, I sprinkled some images from my 2016-7 travels here in this post. With good health comes more ability to go do fun things that I’ve put off while recovering, so hopefully 2017-8 will provide some new images to share.

A sunny Sceloporus fence lizard seen in LA.

A sunny Sceloporus fence lizard seen in LA. Meanwhile, the UK awaits some sunshine…

I doth not protest too much, methinks– there have been some good times this past year, and ides of March be damned, I look forward to sharing more science here for year 6!

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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

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

Labelled x-ray

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.

  1. 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.

  1. 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:

fig5-vonmises

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:

  1. 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:

fig6a-bates-sauropod-com-evol

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…

  1. 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…

fig2-randau-measurements

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

  1. 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!

mouse-mimics

  1. 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!

mouse-simm

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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Short post here– I have 4 jobs now opened on my team, 1 short-term one (~4 months or less) and 3 long-term ones (5 years; negotiable down to 2-3 minimum) as follows:

Stomach-Churning Rating: -10/10 Let’s do some SCIENCE!

  1. Research Technician in Vertebrate Anatomical Imaging; until ~1 December 2016 (some flexibility), on our Leverhulme Trust sesamoid bone grant. Lots of flexibility here and on a super fun, established project! Deadline to apply: 11 August (interviews will be 22 August)
  2. Part-time (50%) Research Administrator, on our ERC dinosaur evolution/locomotion grant until 2021. I’m hunting for someone that’s super organized and enthusiastic and not afraid of paperwork (it is EU funding, after all), but there is sure to be some involvement in science communication, too. Deadline to apply: 11 August  (interviews will be 31 August)
  3. Research Technician in Biomechanics; until 2021 as above. This post will not “just” be technical support but hands-on doing science. Some vital experience in biomechanics will be needed as the research will begin very quickly after starting. If the right person applies, we could agree for them to do a part-time PhD or MRes related to the grant research (but that’s not guaranteed in advance). Deadline to apply: 26 August (interviews will be 7/8 September)
  4. Postdoctoral Researcher in Biomechanics; until 2021 as above. This second postdoc on the project will join Dr. Vivian Allen and the rest of my team to push this project forward! I am keenest on finding someone who is good at biomechanical computer simulation, i.e., has already published on work in that general area. But the right person with XROMM (digital biplanar fluoroscopy), other digital imaging and biomechanics experience might fit. Deadline to apply: 23 August (interviews will be 7/8 September)

Update: all jobs have closed for applications.

Update 2: BUT not all the jobs are 5-year contracts. Some may open up again for new people in the future (but not very soon). Stay tuned…

Note that on the bottom of each page linked above, there are Person Specification and Job Description documents that explain more what the jobs are about and what skills we’re looking for in applicants. I strongly encourage any applicants to read these before applying. If those documents don’t describe you reasonably well, it is probably best not to apply, but you can always contact me if you’re not sure.

The project for jobs 2-4 is about testing the “locomotor superiority hypothesis”, an old idea that dinosaurs gained dominance in the Triassic-Jurassic transition because something about their locomotion was better in some way than other archosaurs’. That idea has been dismissed, embraced, ignored and otherwise considered by various studies over the past 40+ years but never really well tested. So in we go, with a lot of biomechanical and anatomical tools and ideas to try to (indirectly) test it! As usual for projects that I do, there is a healthy mix of empirical (e.g. experiments) and theoretical (e.g. models/simulations) research to be done.

Please spread the word if you know of someone right for any of these roles. I am casting a broad net. The next year (and beyond) is going to be a very exciting time on my team, with this big ~£1.9M ERC Horizon 2020 grant starting and lots of modelling, simulation, experiments, imaging and more. Non-EU/EEA/UK people are very welcome to apply– “Brexit” is not expected to affect this project. If you’re not familiar with my team, check out my “mission statement” for what we stand for professionally and as a team. Join us!

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I was inspired this week, after a stimulating conference, to put into writing what my team stands for. What do we have in common with other scientists, or what makes us different, or what should we all be doing together beyond the actual science itself? I’ve written advice for my team before, but not something like this, and with new staff/students coming soon, I want something ready for them to see what we’re about, and what we need to become more of, too. Not a rant, but a calm codification of our core beliefs. I presented this to my team later in the week for edits and ideas, and felt that it’s now ready for sharing. There’s no reason to keep it private; I personally like what’s here at the moment, and response from my team was positive, too. I am sure opinions will vary, and it’s my team to lead so I might not agree with some, but the fact that I’m posting this means that I expect it’s quite likely that this “mission statement” will improve if commenters pipe up.

No images this time, except for Jerry above. I want the emphasis to be on the thoughts.

Stomach-Churning Rating: wot? No, not that kind of post.

Here we outline my team’s fundamental principles and ethos for our scientific activities, beyond the rules of the RVC and other institutions (e.g. funders) that we adhere to, and basic common sense or morality, or elaborating on and emphasizing those in relation to our work. This is a document that will evolve as we learn from our experiences. We welcome input and discussion. It applies to all of Team Hutch’s staff and students (and Prof. John Hutchinson [JRH], too). The intent is positive: to remind us of our overarching scientific standards, to foster lively debate and to educate ourselves by challenging us to think about what we stand for. The motivation is to communicate the team’s ethos, benefiting from past lessons. The application is flexible, to accommodate the fact that everyone is different, although some of our ethos must be rigid.

While we are unified by research interests, we respect and value other aspects of science including teaching and administrative work. We consider science communication and public engagement to be part of research, too. Our focus is on the evolution of locomotor biomechanics in organisms and, to maintain a strength in this focus, we try to remain within it. However, “side projects” are enthusiastically supported as long as the main research foci of projects (including past work) remain the top priorities and on target.

We aim to conduct high quality research (and other scientific efforts), where possible setting and following gold standards, and acting in a professional leadership role. We are willing to slow our research progress in order to improve the quality of the work, although we also recognize that science is an imperfect human venture. “Minimal publishable units” are not a goal of our research but we fully recognize that early career scientists need to publish in order to move on in many careers.

We are scholars- we care deeply about communicating with each other, our colleagues, and the past and future of science via the literature. We try to keep up with progress in our fields. This is normal practice but we try to do even better than normal. We aim to publish all research we do; otherwise it is wasted effort.

We also treasure openness in science, from publishing our work in open access formats where feasible, to externally sharing open data and methods with the broader community and public, as quickly and comprehensively as possible.

Regular communication within the team and with collaborators is immensely valuable and so we respond promptly to it (sensibly—working or communicating out of normal working hours is not expected!). We participate in regular lab meetings as part of the team culture and communication. In socializing within and outside the team, we respect others, attempting to avoid offense caused by demeaning or other behaviour. Our team members should not be condescended to in discussions or otherwise made to feel stupid- speaking out should be cultivated, not repressed with aggression or egotism.

Quality of writing (and other communication such as oral presentations) in science is something that we aim to maximize, improving our own writing skills and products by pushing ourselves to learn to be better and by constructive critiques of others’ writing.

Ethical practice in all of our work is immensely valued. This includes diversity of people and skills, which broaden our perspectives and help us to transcend disciplinary boundaries that might otherwise blind us to broader insights. We are a team- we support each other in our work and careers, trying to eschew internal competition or territoriality. Mutual benefits from teamwork need to be raised above selfish individualism; focusing on one person’s need for career boosts may reduce others’ prospects.

One of the most treasured ethical principles that we cleave to is integrity. Among the worst scientific crimes that can be committed are fraud, intellectual property theft and plagiarism—no goal justifies those actions. We seek to be our own toughest critics, within reason, to minimize errors or worse outcomes in our science. We promptly correct our published research if we find errors needing amendment.

Ethical sourcing of and handling of data or specimens is important to us. Whether it is favouring publically accessible as opposed to privately held fossil (or other) specimens or cadaveric material that was obtained via traceable sources that maintain legal or optimal standards of animal welfare, we target the “high road” in obtaining material for study. If we conduct in vivo animal research we attempt to transcend the standards of the “three R’s” and set a high example, maximizing animal welfare and benefits from that research—as we are at a veterinary university, we involve vets and other health and welfare specialists in transferring knowledge from our work to improving the lives of animals.

We try to be inclusive in coauthorship of publications (following RVC rules) but especially do not tolerate “honorary coauthors” who contribute little or nothing to research. We value idea production, data collection and provision, analysis, writing and revision as ingredients that earn coauthorship.

[these next two paragraphs still feel too formal/negative to me, but they highlight something important that I’ve learned about; to a degree there must be hierarchy, and I’m the only one that will be in Team Hutch for as long as it lasts, so I have to be the enforcer of its long-term rules. It’s the aspect of this job that I probably enjoy least, but it looms there whether I like it or not.]

As per RVC intellectual property (IP) rules (as well as rules of funders etc.), all IP generated while working at the RVC remains its IP, managed by JRH. Such IP can and should be used by those generating it, and others that would benefit (including those who have since left the lab) but to ensure proper conduct, JRH must approve usage.

JRH is the leader of the team and as manager has final say in decisions, but encourages negotiation and reasonable disagreement to seek mutually acceptable solutions. JRH makes mistakes too and welcomes them being pointed out. JRH seeks to help his team succeed in whatever career goals they have and for long after they depart Team Hutch, but expects solid effort at work in return, and dedication to the principles outlined here.

We are human. We want fun, enjoyable lives including at work, and this pursuit of fun colours all that we do, because science is fun and so are scientists. We want that fun to radiate upon the world and echo through time.

=====

That’s as it stands right now. What do you think? I am certain that I have left things out, but it’s a start.

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Last year we finally, after about 14 years of slow work, released our biomechanical model of an ostrich’s hindleg. We showed how it informed us about the potential leverages (moment arms; contributions to mechanical advantage of the joints) of all of the muscles. It was a satisfying moment, to understate it, to finally publish this work from my postdoc at Stanford. Today, we begin to deliver on that model’s promise. And it only took 4 years or so, roughly? The journal Royal Society Interface has published our study of how we used this musculoskeletal model to simulate walking and running dynamics. Those simulations join an intimidatingly broad and complex literature using similar models to study human (and some other primate) locomotion or other functions at the level of individual muscles (for whole limbs/bodies) in vast detail and growing rigor. I have Dr. Jeffery Rankin, a research fellow finishing up his post with me after ~6 years of hard work on many projects, to thank for driving this work forward, and Dr. Jonas Rubenson (now at PennState) for his patient collaboration that has continued since the early 2000’s.

Stomach-Churning Rating: 2/10; computer models of muscle actions. The underlying anatomical data are goopy, as prior ostrich-dissection-focused posts show!

Our model; in right side view (on the left) and frontal view (on the right), with muscles in red and the leg's force as the blue arrow; frozen at the middle of a step.

Our model; in right side view (on the left) and frontal view (on the right), with muscles in red and the leg’s force as the blue arrow; frozen at the middle of a running step.

Simulations like these predict things that we can’t easily measure in living animals, such as how much force muscles and tendons generate, how quickly those tissues change length, how much mechanical energy they thus contribute to the joints, limbs and whole body, how much metabolic energy their actions cost, and much more. There are more ways to use these tools than I have space or time to explain, but simply put we forced our ostrich simulation to match experimental measurements of the motions and forces of a representative walking and running ostrich stride, from contact of one foot until the next time that foot hit the ground. It then used optimization methods (minimizing target criteria like muscle stress) to estimate how the muscles and tendons were used to generate those motions and forces. This is a ways ahead of some prior ostrich simulations such as this one that I recall from classes during my PhD studies.

Any modeller worth their salt knows that their models and simulations are wrong at some level. This is much as most science is “wrong”; i.e. a simplification of reality with some errors/noise introduced by assumptions, variation, methods and such. But generally these kinds of musculoskeletal dynamic simulations hold up pretty well against experimental data. A standard “validation” is to test how closely the simulations’ predictions of muscle activity match the “real” (measured in life, also with some uncertain error) activity of muscles. Science still lacks those data for ostriches, but fortunately measurements from other birds (by Steve Gatesy and colleagues) indicate that muscles tend to follow fairly conservative patterns. Grossly speaking, avian leg muscles tend to either be active mainly when the foot is on the ground (stance phase) or off the ground (swing phase). Some studies acknowledge that this is an oversimplification and other muscles do act across those two phases of a stride, either in multiple pulses or as “transitional” (stance-to-swing or swing-to-stance) switch-hitters in their activations. Our ostrich predictions matched the qualitative patterns for avian muscle activations measured to date, so that’s good. The results also reinforced the notion of transitional or multi-phasic muscle activation as still having some importance, which bears more study.

Yet what did the simulations with our ostrich model tell us that other ostrich experiments or other bird species didn’t? Three main things. First, we could calculate what the primary functions of muscles were; they can act as motors (generating energy), brakes (absorbing energy), springs (bouncing energy back and forth) or struts (just transmitting force). We could then sum up what whole muscle groups were doing overall. The image below shows how these broad functions of groups vary across the stance phase (swing phase is harder to condense here so I’ve left it out).

Positive work can speed things up; negative work can slow things down.

Positive work can speed things up; negative work can slow things down. Solid bars are running; striped bars are walking. (from our Fig. 13) You may need to click to em-broaden this image for the gory biomechanical details.

There’s a lot going on there but a few highlights from that plot are that the hip extensor (antigravity) muscles (biarticular hip/knee “hamstrings”) are acting like motors, the knee extensors (like our quadriceps) are mainly braking as in other animals and the ankle is fairly springy as its tendons (e.g. digital flexors; gastrocnemius) suggest. We often characterize birds as “knee-driven” but it’s more accurate biomechanically to say that their hips drive (power; i.e. act as motors) their motion, whereas their knees still act as brakes — in both cases as in many other land vertebrates. Thus in some ways bird legs don’t work so unusually. Birds like ostriches are, though, a little odd in how much they rely on their hamstring muscles to power locomotion (at the hip) rather than their caudofemoral muscles, which are reduced. Zooming in on some particular muscles such as parts of the hip or knee extensors, the functions sometimes weren’t as predictable as their similar anatomy might suggest. Some muscles had parts that turned on during swing phase and other parts used during stance phase. Neural control and mechanics can produce some unexpected patterns.

Second, we looked at one important methodological issue. Simulations of musculoskeletal dynamics can vary from simple static (assuming each instant of a motion is independent from the others; e.g. ignoring acceleration, inertia, tendon effects, etc.) to more complex grades of fully dynamic flavours (e.g. assuming rigid or flexible tendons). We looked across this spectrum of assumptions, for both walking and running gaits, with the expectation that more static assumptions would work less well (vs. more dynamic ones; by various criteria) for running vs. walking. This also showed us how much tendons influence our simulations’ estimates of muscle mechanics—a fully rigid tendon will make the muscle do all of the work (force times length change) whereas a flexible tendon can literally take up some (or even all) of that slack, allowing muscles to remain closer to their isometric (high force-generating, negligible length change) quasi-optimum.

Nicely, our predicted muscle functions weren’t influenced much by these methodological variations. However, static assumptions  clearly were in some ways less appropriate for running than for walking, as were flexible tendons. Somewhat surprisingly, making the simulations more dynamic didn’t lower the levels of activation (and thus presumably the metabolic costs) of muscles, but actually raised those levels. There are good reasons why this might be realistic but it needs further study. It does muddy the waters for the issue of whether assuming that rapid locomotion can be modelled as static is a “bad” thing such as for estimating maximal speeds—yes, tendons can do more (elastic energy storage, etc.) if more dynamic models are used, but co-contraction of antagonistic muscles against each other also brings in some added costs and might lead to slower speed estimates. We’ll see in future work…

Finally, one often overlooked (sometimes even undiscussed!) aspect of these simulations is that they may silently add in extra forces to help muscles that are struggling to support and move their joints. The justification is typically that these extra “reserve actuators” are passive tissues, bony articular forces and other non-muscular interactions. We found that the hip joint muscles of ostriches were very weak at resisting abduction (drawing the thigh away from the body) and this needed resisting during the stance phase, so our simulations had very high reserve actuators switched on there. That fits the anatomy pretty well and needs more investigation.

Want to know more? Happily, not only is the paper free for anyone to view but so are all of the data including the models (modified slightly from our last paper’s). So, although the software (Opensim) isn’t ideal for 4-year-olds to play with (it is fancy engineering stuff), if you have the interest and dilligence it is there to play with and re-use and all that. But also watch this space for future developments, as there is more to happen with our steadily improving models of ostriches and other beasties. Anyway, while this paper is very technical and challenging to explain I am not too bashful to say it’s one of the finer papers from my career; a big stride forward from what we’ve done before. I have been looking forward for a long time to us getting this paper out.

P.S. Our peer reviewers were splendid- tough but constructive and fair. The paper got a lot better thanks to them.

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Greetings Freezerinos, and Happy New Year! I have been quiet on this blog for health and other reasons but those will pass and there will be new posts in 2016. However, behind the scenes there have been super-cool things afoot. I am very happy to bring one of them to you now:

(but first: Stomach-Churning Rating: 6/10; video below shows a dissected sea turtle foot in motion)

We have just debuted our new social media “presence” (for lack of a better word) that is a sister blog to this one. It is called Anatomy To You (http://anatomytoyou.com/), as its intent is to bring a wide array of science about animal anatomy to “you”, the general public. This John’s Freezer blog will continue with it’s style of rambling longer posts targeted at a fairly geeky scientifically literate audience and focusing on my team’s research and my own disparate thoughts about science and related issues. Anatomy To You will bring you shorter posts, even just images, completely focused on celebrating the structure of organisms, and not just presenting my team’s research but also a wide array of anatomical science from around the globe. It will also be much more regular and frequent in its posts. We’ll welcome guest posts and I encourage you to get in touch with us if you want to jump on the bandwagon early, or have us feature your research for you!

More about the ATY blog is here, but there is also a Twitter feed and Facebook account. Our first major posts are on what skeletons are, and on a dissection of some sea turtles. Please follow us and join in the celebration of anatomy! My team’s scientific communicator/technician Dr. Lauren Sumner-Rooney is spearheading this ATY effort with me, so please follow her too!

Anatomy To You will continue to evolve over this coming year, so please stay with us and give us feedback; join in the morphological conversations with us. I am SUPER excited to see where this goes– it is an experiment that has a lot of potential, we think.

Sea turtle from our ATY dissection, foot muscles in action (found dead in the wild; don’t be ridiculous, we don’t kill sea turtles for our research)

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

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

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

The context

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

Starting the dissection at the RVC.

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

Hide.

Hide.

Fore- and hindlimbs.

Fore- and hindlimbs; comparative design for inspiring prosthetics.

Dissections!

Dissections on display!

Prototype goat-suits. Their mobility was too limited.

Prototype goat-suits. Their mobility was too limited.

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

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

Goat-suit shots.

Inhabited-goat-suit shots.

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

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

Thomas Thwaites with the goat-suit.

Thomas Thwaites with the goat-suit.

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

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

Showroom

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

Trip-trap-trip-trap...

Trip-trap-trip-trap… (but no trolls)

Goat-suit in action!

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

Acceptance?

Acceptance?

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

Do goats wish they were human?

Do goats wish they were human?

What are you looking at?

What are you looking at?

Close-up of goat head.

Close-up of goat head and shoulders.

Goat hooves-on-hips

Goat hooves-on-hips; a gruff pose.

So like us.

So like us.

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