Posts Tagged ‘publication’

Today is the 210th anniversary of Charles R. Darwin’s birthday so I put together a quick post. I’d been meaning to blog about some of our latest scientific papers, so I chose those that had an explicit evolutionary theme, which I hope Chuck would like. Here they are, each with a purty picture and a short explainer blurb! Also please check out Anatomy To You’s post by Katrina van Grouw on Darwin’s fancy pigeons.

Stomach-Churning Rating: 1/10 science!

First, Brandon Kilbourne at the Naturkunde Museum in Berlin kindly invited me to assist in a paper from his German fellowship studying mustelid mammals (otters, weasels, wolverines, badgers, etc.; stinky smaller carnivorous mammals). Here we (very much driven by Brandon; I was along for the ride) didn’t just look at how forelimb bone shape changes with body size in this ecologically diverse group. We already knew bigger mustelids would have more robust bones, although it was cool to see how swimming-adapted and digging-adapted mustelids evolved similarly robust bones; whereas climbing ones had the skinniest bones.

The really exciting and novel (yes I am using that much-abused word!) aspect of the paper is that Brandon conjured some sorcery with the latest methods for analysing evolutionary trends, to test how forelimb bone shapes evolved. Was their pattern of evolution mostly a leisurely “random walk” or were there early bursts of shape innovation in the mustelid tree of life, or did shape evolve toward one or more optimal shapes (e.g. suited to ecology/habitat)? We found that the most likely pattern involved multiple rates of evolution and/or optima, rather than a single regime. And it was fascinating to see that the patterns of internal shape change deviated from external shape change such as bone lengths: so perhaps selection sometimes works independently at many levels of bone morphology?

Various evolutionary models applied to the phylogeny of mustelids.

Then there, coincidentally, was another paper originating in part from the same museum group in Berlin. This one I’d been involved in as a co-investigator (author) on a Volkswagen (yes! They like science) grant back about 8 years ago and since. There is an amazing ~290 million year old fossil near-amniote (more terrestrial tetrapod) called Orobates pabsti, preserved with good skeletal material but also sets of footprints that match bones very well, allowing a rare match of the two down to this species level. John Nyakatura’s team had 3D modelled this animal before, so we set out to use digital techniques to test how it did, or did not, move—similar to what I’d tried before with Tyrannosaurus, Ichthyostega and so forth. The main question was whether Orobates moved in a more “ancestral” salamander-like way, a more “derived” lizard-like way (i.e. amniote-ish), or something else.

The approach was like a science sledgehammer: we combined experimental studies of 4 living tetrapods (to approximate “rules” of various sprawling gaits), a digital marionette of Orobates (to assess how well its skeleton stayed articulated in various motions), and two robotics analysis (led by robotics guru Auke Ijspeert and his amazing team): a physical robot version “OroBOT” (as a real-world test of our methods), and a biomechanical simulation of OroBOT (to estimate hard-to-measure things in the other analyses, and matches of motions to footprints). And, best of all, we made it all transparent: you can go play with our interactive website, which I still find very fun to explore, and test what motion patterns do or do not work best for Orobates. We concluded that a more amniote-like set of motions was most plausible, which means such motions might have first evolved outside of amniotes.

OroBOT in tha house!

You may remember Crassigyrinus, the early tetrapod, from a prior post on Anatomy To You. My PhD student Eva Herbst finished her anatomical study of the best fossils we could fit into a microCT-scanner and found some neat new details about the “tadpole from hell”. Buried in the rocky matrix were previously unrecognized bones: vertebrae (pleurocentra; the smaller nubbins of what may be “rhachitomous” bipartite classic tetrapod/omorph structure), ribs (from broad thoracic ones to thin rear ones), pelvic (pubis; lower front), and numerous limb bones. One interesting trait we noticed was that the metatarsals (“sole bones” of the foot) were not symmetrical from left-to-right across each bone, as shown below. Such asymmetry was previously used to infer that some early tetrapods were terrestrial, yet Crassigyrinus was uncontroversially aquatic, so what’s up with that? Maybe this asymmetry is a “hangover” from more terrestrial ancestry, or maybe these bones get asymmetrical for non-terrestrial reasons.

The oddly asymmetrical metatarsals of Crassigyrinus.

Finally, Dr. Peter Bishop finished his PhD at Griffith University in Australia and came to join us as a DAWNDINOS postdoc. He blasted out three of his thesis chapters (starting here) with me and many others as coauthors, all three papers building on a major theme: how does the inner bone structure (spongy or cancellous bone) relate to hindlimb function in theropod dinosaurs (including birds) and how did that evolve? Might it tell us something about how leg posture or even gait evolved? There are big theories in “mechanobiology” variously named Wolff’s Law or the Trajectorial Theory that explain why, at certain levels, bony struts tend to align themselves to help resist certain stresses, and thus their alignment can be “read” to indicate stresses. Sometimes. It’s complicated!

Undaunted, Peter measured a bunch of theropod limb bones’ inner geometry and found consistent differences in how the “tracts” of bony struts, mainly around joints, were oriented. He then built a biomechanical model of a chicken to test if the loads that muscles placed on the joints incurred stresses that matched the tracts’ orientations. Hmm, they did! Then, with renewed confidence that we can use this in the fossil record to infer approximate limb postures, Peter scanned and modelled a less birdlike Daspletosaurus (smaller tyrannosaur) and more birdlike “Troodon” (now Stenonychosaurus; long story). Nicely fitting many other studies’ conclusions, Peter found that the tyrannosaur had a more straightened hindlimb whereas the troodontid had a more crouched hindlimb; intermediate between the tyrannosaur and chicken. Voila! More evidence for a gradual evolution of leg posture across Mesozoic-theropods-into-modern-birds. That’s nice.

Three theropods, three best-supported postures based on cancellous bone architecture.

If you are still thirsty for more papers even if they are less evolutionary, here’s the quick scoop on ones I’ve neglected until now:

(1) Former PhD student Chris Basu published his thesis work w/us on measuring giraffe walking dynamics with force plates, finding that they move mostly like other quadrupeds and their wobbly necks might cost them a little.

(2) Oh, and Chris’s second paper just came out as I was writing this! We measured faster giraffe gaits in the wilds of South Africa, as zoo giraffes couldn’t safely do them. And we found they don’t normally go airborne, just using a rotary gallop (not trot, pace or canter); unlike some other mammals. Stay tuned: next we get evolutionary with this project!

(2) How do you safely anaesthetize a Nile crocodile? There’s now a rigorous protocol (from our DAWNDINOS work).

(3) Kickstarting my broad interest in how animals do “extreme” non-locomotor motions, we simulated how greyhounds stand up, finding that even without stretchy tendons they should, barely, be able to do it, which is neat. Expect much more about this from us in due time.

(4) Let’s simulate some more biomechanics! Ashley Heers, an NSF research fellow w/me for a year, simulated how growing chukar birds use their wing muscles to flap their way up steeper inclines (“WAIR” for devotees), and the results were very encouraging for simulating this behaviour in more detail (e.g. tendons seem to matter a lot) and even in fossil species; and finally…

(5) Hey did you ever think about how bone shape differs between hopping marsupials (macropods) and galloping artiodactyl (even-toed) mammals? We did, in long-the-making work from an old BBSRC grant with Michael Doube et al., and one cool thing is that they mostly don’t change shape with body size that differently, even though one is more bipedal at faster speeds—so maybe it is lower-intensity, slower behaviours that (sometimes?) influence bone shape more?

So there you have the skinny on what we’ve been up to lately, messing around with evolution, biomechanics and morphology.


Read Full Post »

Pre-Submission Manuscript Scrutiny

This one goes out to the scientists. These days perhaps more than ever we live and die, career-wise, by the publication. Right or wrong as “publish or perish” may be, personally I enjoy writing papers– it hits my creative and intellectual buttons in fun ways. I also like to read and think about ways to write better papers, and am always improving (and making mistakes to learn from). Here are some I’ve come up with over the years, especially relating to the digital era and other aspects of modern science publishing but also to focus on the “forgotten fringes” of preparing a paper for submission to a journal. These are details that I find many authors forget, or do at the last minute, or don’t consult coauthors on, that matter and should be more of a focus. I won’t focus on good writing style or other important aspects of prose, or many things I’ve covered in my “mission statement” or elsewhere. The points I’ll make here are more specifically tactical and technical.

Stomach-Churning Rating: 0/10; the only anatomy here is that of a manuscript submission. Maybe that will excite you too?

So you’ve analysed some cool data and come up with a good story to encapsulate it, you chose a journal that suits it (and your belief system), and you’re closing in on clicking that serotonin-inducing “Submit” button. Did you think of these things yet?

  • Coauthor order: Did you discuss it earlier when doing the work? Oh dear, you should! Assuming you’re doing a multi-authored manuscript, that’s vital, and I’ve been burned by forgetting to do it properly until too late in the game before. It’s best to establish (1) who is doing what in terms of the research (all the way through writing up and submitting), and (2) who thus is where in author order, before having any draft of a manuscript at all. That may change as the research evolves, but it should be an explicit discussion with all involved—including, perhaps, those *not* listed as coauthors (but acknowledged, or even not), if there is reason they might be expecting otherwise. Yes, these days we all win by collaborating and co-author order may not matter for some coauthors, but it does not hurt to discuss it openly whereas it can lead to ill will if skipped. Think about details like: who’s the corresponding author(s)? You can have 2 at many journals, so maybe spread that around. Who’s the senior author? (that tradition may vary in different countries and fields) Again, you can even explicitly list ~2 senior authors (with asterisks by their names). Credit should be given where it is due; that’s all. Which leads very directly to…
  • Author contributions: This is a huge neglected area. And it matters tremendously, not just in terms of the above socio-political issues (or ego) but in terms of responsibility. If something seems wrong with a paper these days, we must turn to the “Author contributions” section to see who needs to explain what happened; although blame can be far from a simple issue. In cases of accusations of scientific error or misconduct that is vital. More positively, this section, thoughtfully considered, spreads credit around and shows potential employers who has the skills that paid the bills on that paper; or on grant/award applications/nominations who was/were the mastermind(s). If the journal oddly doesn’t have such a section online/in the manuscript format guidelines, add it to the end of the MS anyway! In tandem with item #1 above, this should be openly laid out, discussed, and explicitly agreed on before any submission—and the earlier in the process of research, the better. Detail not just who originated the idea, collected and analysed the data, and wrote the paper but the nitty-gritty of every step (“XX did CT scans… XX did segmentation of the scans…”), if space allows. The author contributions should make sense in terms of item #1, too. Minimally the senior author should be involved in conceiving the study (which IS important!) and editing + approving the final text; otherwise they probably should not be an (senior) author at all. Honorary coauthors, well, I’ve said plenty about those here before and they still make me grind my teeth.
  • Data availability/accessibility: If you’re active in science now you must know about the principles of Open Science, and all journals worth their salt are changing rapidly to adjust to evolving perspectives on this issue. You should be thinking about how you’ll share your data while you collect it. This is “Good Research Practice”. Metadata are data too, and should follow with their data. It takes time and that’s annoying perhaps, but think of this: what is someone going to do if they want to use the data from this paper 50 years from now? If it’s not in the Supplementary/Supporting Information online, or in a big database like Figshare/Dryad/OSF/etc, one may have cause to worry that it will vanish within 5 years. We all still see “data are available on request” in papers these days (that was the old way), and I won’t get into that debate here, but the writing is on the wall that the old ways are fading. Hence evolving one’s research practice to make sharing data part of one’s philosophy and publication practice, AND (here’s the clincher) promoting its value in other aspects of science (e.g. CVs, hiring, promotion, awards…) are only going to be looked back upon fondly by future scientists. We do also need top-down leadership for this sea-change to happen; and it will have a big impact when it settles in.
  • Funding: This is massively important. Be sure to ask all coauthors to specify if anyone needs to be thanked for funding the work. Double-check it for your own funders, and thank whomever did directly or indirectly contribute to the research; even if small amounts. (They all like being thanked, regardless of why they are being thanked, if they deserve it) Many funders don’t allow you to credit a paper to the grant (thus showing productivity) unless they are explicitly thanked here or in the Acknowledgements section. And on that note:
  • Acknowledgements: “Thank broadly!” Slow down and brainstorm here: did you get advice, tools or data from colleagues, undergraduate helpers (who didn’t quite make coauthorship—but we should try to help them get there!), or anyone else? Did you amend your reviewed paper to thank reviewers (or pre-print commenters)? Did you thank museums and other institutions (or even websites) that helped with resources? Be creative in this section because hey, it’s nice to see yourself thanked. I think this section is really important as human beings. Extra little tip: get rid of “We would like to thank” here; just “We thank”. No need to ask for permission or waffle with thanks.
  • Paper keywords: Most journals ask for some keywords to include with the paper, often during the submission process (as with item #2 above). So it is easy for the corresponding author to be the only one involved in this, which is not ideal. I try to add keywords to the manuscript draft (between authors and abstract, as usual) in the early editing process, to consider with the rest of the paper. While database searching is sophisticated these days, a good general strategy still is to choose words that aren’t in the title or strongly featured in the abstract. Broader terms, to draw in readers from overlapping research areas or questions, should be used; e.g. I tend to throw in “biomechanics” or “scaling” or “anatomy” and so on. Keywords should not be an afterthought.
  • References/Bibliography: A lot of people writing papers don’t check their references at all (I forget sometimes too)—errors easily creep in here, especially from naughty reference managers that corrupt formatting or even page numbers and years. I try to clear my head/eyes and skim the references in a near-final draft to add italics where needed, double-check journal details, and tidy up other formatting. Some journals do this for you later, but some do not. It’s wise to ensure it’s done as well as you can; messy references can lead one to doubt other aspects of care that went into the science.
  • Reviewers: Editors have a sucky job, to be honest. Finding and chasing down reviewers is not fun, but it is the service that editors provide, often for free. Please help them and, where feasible, recommend ~5 reviewers (include current emails) without conflicts of interest who can evaluate your paper. Do that in the online submission, or in the cover letter if there isn’t a spot for it there. Always do it; don’t leave it open to editors (even though they may not use any of them!). Rarely, you might have cause to ask for an excluded reviewer(s) if they won’t give you a fair shake or you otherwise have evidence to indicate they have a conflict of interest, so note that on submission and maybe justify it directly (without libel!). Excluded reviewer requests are almost always followed. All of these things should be discussed with coauthors well in advance to agree on them. Google-Scholaring around might find some names you forget. And as you build your list, think about selecting (1) non-white male status quo (i.e. not me), (2) early career researchers, and (3) scientists from outside the USA+UK. Think outside the box—maybe someone from slightly outside your field, with complementary expertise, could give a good perspective? Aim for some fair diversity; like item #3 above, this is increasingly becoming Good Practice, and rightly so.
  • Cover letter: As an editor and author, I don’t like them. Maybe I should more, but I think they tend to be overwrought and/or redundant these days. I don’t think the authors, title, journal, abstract (or even bite-sized summary, perhaps), or anything else mentioned elsewhere in the manuscript submission (e.g. recommended reviewers) should be in a cover letter, usually. The goal is brevity. You may not need to do a cover letter at all; check the journal to see if it is mandatory. The best usage is to explain why the paper fits the journal criteria; and perhaps nothing else. That may not be sufficiently clear in the paper itself. Keep in mind that editors reading cover letters are busy and do not want a 2-page screed about how awesome your paper is; but may want help (~1 succinct paragraph; plain English; very different from the Abstract or don’t bother) deciding if it is right for review. But if the cover letter doesn’t seem necessary, skip it. Get co-author input though, if unsure.
  • Pre-prints: Hey, that’s a new thing for us non-physicists! I don’t have a problem with them; some people do. I also haven’t gotten much out of them before, but that might be my fault or bad luck. But who cares what I think? You should think about them. Maybe try submitting your paper with one and trying it out; disseminate it via social media and see what happens? Almost all journals now allow pre-prints to be submitted before/with the manuscript. There may be little to lose in using them, but as I keep repeating, ensure you talk about it with coauthors first.

Those are some things I keep thinking of as I write, edit and review papers. What else? (the focus here is on the “bookends” surrounding the Abstract/Introduction and the Discussion/Conclusions)

Read Full Post »

Our special guest post this week comes from Dr. Liz Clark of Yale University (you may have heard of it?) in New Haven, Connecticut, USA. She is bringing some biomechanics-fu to echinoderms– the weird marine critters like seastars and sea urchins. Did you see her 9-awesome-things-about-echinoderms blog post on Anatomy to You? You should. And you should check this out– and check out our new paper on this topic, which just came out! Remember: all images below can be clicked to zoom in. That’s so fun!

Eversible Stomach-Churning Rating: 2/10; no Uni sushi here.

I remember the first time I saw one. I was at the Duke Marine Lab staring at a chunk of dredged-up oyster shells in a glass dish, when all of a sudden a mass of big, black spines obscured my view. I looked up from the microscope to see a creature with a round body the size of a nickel and a flurry of long, skinny, spiny arms skulking hurriedly across the dish. It wasn’t quite a spider- the five-fold symmetry gave its echinoderm affinity away- but it wasn’t quite a starfish, either. Starfish appear graceful as their tiny tube-feet make hurried and unseen movements underneath them to transport them slowly across the sand- appearing nearly motionless to the naked eye. This animal, on the other hand, was making rapid, whip-like strikes with its arms so that it clambered forward, rapidly and fearlessly scaling the uneven terrain of the shells in a bold attempt to escape the dish. I was hooked. I had to know who this monster was, and learn as much about it as I could.

Brittle star arm set up to study its ossicle-joint mobility with CT scanning (below).

That was the day I was introduced to the brittle star. The name “brittle star” is a bit of a misnomer, since they are really anything but. Brittleness implies rigidity and stiffness, suggesting they have a delicate nature with the impossibility of repair or to adapt, which couldn’t be farther from the truth. Their long arms are incredibly flexible, each made of around 100 tiny segments that allow them to bend in any direction or loop them around in circles. I bet that their name comes from the ease at which they can cast off their arms, which they do intentionally to escape predators or pesky researchers trying to grab them, which deceitfully suggests fragility when in fact their arms are incredibly sturdy and packed with powerful muscles. They can flawlessly regenerate their arms, and, in the meantime, even after they lose several of them, they adjust their strategy for locomotion so that they keep prowling across the seafloor unphased. Their physical flexibility and ability to repair and adapt in the face of damage makes them anything but brittle. The Japanese name for brittle star roughly translates to “spider-human-hand,” which I think much more accurately captures the ethos of this group.

Brittle stars have internal skeletons, and each segment of their arms are made of a cluster of small skeletal elements (ossicles). Researchers in the past have made the assumption that differences in the shape of these ossicles between species change how they move, but I wasn’t so sure. So, John and I decided to work together to figure it out.

We didn’t dive into the freezer for this one- sorry to disappoint all of the diehard fans of John’s freezer out there (but in my defense can you imagine how tough it would have been to even find them in the sea of rhinos, giraffes, and crocs?!). [JOHN: awwwwwww!! It’s more of a wall keeping in the wildlings, than a sea right now though!] Instead we ordered some brittle stars off the internet! The first thing we did was make some measurements of how flexible the arms of brittle stars are when they’re alive. Then we digitized their skeletons by micro-CT scanning them so we could see the articulations between the ossicles and the segments in 3D. We scanned them in a few different positions so we could see the articulations between the ossicles as their arms bend. Then we incorporated all of that data into a 3D model that allowed us to visualize what’s going on in the inside of brittle star arms as they move them around.

We made several different models using this strategy to see if different ossicle shapes change how their arms move. We looked at the differences between arm ossicles in two different speciesOphioderma brevispina and Ophiothrix angulata, which represent two of the three different major morphologies of brittle star arms.  We also looked at the difference in the movement mechanics at the tip and base of the arms in O. brevispina, since the ossicles at the tip are thin and elongated compared to wide and flat at the base.

We found that the tip of the arm of Ophioderma brevispina was more flexible than the base due, at least in part, to the shape of the ossicles. We also found several major differences between the two species, including the location of their joint center and the degree to which they could laterally flex. However, none of these differences were easily attributable to any specific morphological feature that set Ophiothrix angulata and O. brevispina apart, which cautions against making assumptions of brittle star functional capabilities by only looking at the shape of the ossicles. We also found that some of the smaller ossicles within each segment shift their position to accommodate arm flexion, when they were originally thought to limit the motion of the arm! We only looked at a few individuals of two species, but the methods for model-building we developed provide a framework to incorporate a broad sample of brittle star species in the future. We’re curious if the results we found stand when more brittle stars are brought into the mix!

It was incredible to take the journey from initially being surprised and captivated by the movement of these animals to eventually building 3D digital models to discover how they are able to do so. It made me realize that opportunities to be inspired by the natural world are around every corner, and that there are so many interesting questions out there that are still unanswered. Thanks to John and our other team members Derek Briggs, Simon Darroch, Nicolás Mongiardino Koch, Travis Brady, and Sloane Smith for making this project happen!

Read Full Post »

If you’re in London, you still have almost one week left to hurry to the Valence House in Dagenham and see a great exhibit on Ray Harryhausen’s dinosaurs and other cool “Dynamation” stop-motion models and art!

This blog post is a photo tour of what I saw, in case you cannot go.

Like it? Click it. Bigger pic.

Stomach-Churning Rating: 1/10 nice stop-motion animation models. Medusa won’t hurt you here.

I loooooooooooove Ray Harryhausen’s work, ever since I was a child and saw “Jason and the Argonauts” and many other films, plus “Clash of the Titans” once it came into theatres. There is the attention to detail in anatomy and locomotion, and the wondrous fantastic nature of even the more mundane creatures he animated, and the rich mythology that he drew from to inspire his creations. Modern CGI is great in a different way, but nothing I can think of in recent special effects truly beats (1) the skeleton battle in ‘Jason, and (2) the Medusa encounter in ‘Clash (to name what might be my top two faves). And so when I learned that several of the original (restored) models from those films were on exhibit in northeastern London, I requested to go there with my family for Fathers Day. Results:

Boom! Ole’ stony-gazed, snaky-haired gorgon of yore.

No deadly bow here, but the rattlesnake tail is.

Medusa concept art by Harryhausen; the “bra” was there for American censors but Ray thought it looked wrong and removed it in the final version.

Look out, Jason! Here come the Children of the Hydra! Yep, original (restored) articulated models. Joints are visible. They look ready to kick some Iolcusian butt!

Context of the exhibit- local chap befriended Harryhausen and convinced him to let him restore his models; and so here we are. On with the dinosaurs! (and other palaeo-things)

Gwangi model made in resin; non-poseable but made around time of the “Valley of Gwangi” film to help design the poseable models.

Gwangi climactic scene in church; concept art by Harryhausen.

Other ‘Gwangi characters: “Eohippus” (Hyracotherium), Ornithomimus and boy.

Cowboy lassoing an Ornithomimus as per the movie scene in ‘Gwangi? Yes please. (Harryhausen original)  Jurassic Park had its T. rex lurching out of a forest to grab a Struthiomimus, intentionally mirroring the scene in ‘Gwangi where the titular AllosaurusTyrannosaurus hybrid chomps the Ornithomimus.

Poseable “Eohippus” original- with real fur! Great Dynamation too; very lifelike in the film.

Original Harryhausen concept art of the “Eohippus” show demo.

Suddenly, Ceratosaurus! (from “One Million Years BC”)

Styracosaurus original resin model. (from “One Million Years BC”)

Old school Polacanthus art by Alan Friswell. SPIKEY!

Old school Iguanodon art by Alan Friswell. MUSCLEY!

Panoply of archosaurs by Alan Friswell: pterodactyl, Tenontosaurus (made for the Frame Store special effects company in 2001) and tyrannosaur head (made at age 9).

Pterodactyl made at age 12, so don’t laugh.

Back to the fantastic beasts– original poseable hydra from ‘Jason!

Original Pegasus from ‘Clash! What a seamless blend of fur and feathers.

Original R2, I mean Bubo, from ‘Clash!

I forget the scene (the 1-eyed fates in ‘Clash?) but I like it. Original Harryhausen concept art.

Lunar leader from “First Men in the Moon.” (original)

Non-original (but based thereon) model by Alan Friswell, of nautiloid thingy from “Mysterious Island”.

Fiji mermaid by Alan Friswell.

“Hand of Glory” by Alan Friswell.

Pithecanthropus by Alan Friswell. Very Harryhausen in spirit.

Oddly, but somehow appropriately, there are ?350 year old whale bones on display in the hall next door, with a mysterious history.

WW2 bomb shelter in a “Victory Garden” outside the House. And the house is supposedly haunted. So take care when you visit…

What can I say? I loved it! Almost a religious experience; like seeing holy relics. Awesome in every sense of awesome.

Downside: you cannot grab the precious Dynamation models and play with them hands-on. I wanted to enact a furious Hydra-Gwangi battle. But alas, only in my imagination…

Read Full Post »

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Read Full Post »

Uh oh, a “why?” question in biology! There are many potential, and not mutually exclusive, answers to such questions. Ultimately there is a historical, evolutionary answer that underpins it all (“ostriches evolved two kneecaps because…”). But we like ostrich knees and their funky double-kneecaps (patellae; singular = patella) so we wanted to know why they get so funky. One level of addressing that question is more like a “how?” they have them. So we started there, with what on the surface is a simple analysis. And we published that paper this week, with all of the supporting data (CT, MRI, FEA).

Stomach-Churning Rating: 6/10 because there is a gooey image of a real dissection later in the post, not just tidy 3D graphics.

First author Kyle Chadwick was my research technician for 2 years on our sesamoid evolution grant, and we reported earlier on the detailed 3D anatomy of ostrich knees (this was all part of his MRes degree with me, done in parallel with his technician post). Here, in the new paper with Sandra Shefelbine and Andy Pitsillides, we took that 3D anatomy and subjected it to some biomechanical analysis in two main steps.

Ostrich (right) knee bones. The patellae are the two knobbly bits in the knee.

First, we used our previous biomechanical simulation data from an adult ostrich (from our paper by Rankin et al.) to estimate the in vivo forces that the knee muscles exert onto the patellar region during moderately large loading in running (not maximal speed running, but “jogging”). That was “just” (Kyle may laugh at the “just”– it wasn’t trivial) taking some vectors out of an existing simulation and adding them into a detailed 3D model. We’ve done similar things before with a horse foot’s bones (and plenty more to come!), but here we had essentially all of the soft tissues, too.

Ostrich knee with muscles as 3D objects.

Second, the 3D model that the muscular forces were applied to was a finite element model: i.e., the original 3D anatomical model broken up into a mesh, whose voxels each had specific properties, such as resistance to shape change under loading in different directions. The response of that model to the loads (a finite element analysis; FEA) gave us details on the stresses (force/area) and strains (deformations from original shape) in each voxel and overall in anatomical regions.

Finite element model setup for our study. If you do FEA, you care about these things. If not, it’s a pretty, sciencey picture.

The great thing about a computer/theoretical model is that you can ask “what if?” and that can help you understand “how?” or even “why?” questions that experiments alone cannot address. Ostriches aren’t born with fully formed bony kneecaps; indeed those patellae seem to mature fairly late in development, perhaps well after hatching. We need to know more about how the patellae form but they clearly end up inside the patellar (knee extensor) tendon that crosses the knee. So we modelled our adult ostrich without bony patellae; just with a homogeneous patellar tendon (using the real anatomy of that tendon with the bony bits replaced by tendon); and subjected it to the loading environment for “jogging”.

The right knee of an ostrich hatchling. The patellae have yet to form; indeed there is little bone around the knee region at all, yet.

We then inspected our FEA’s results in light of modern theory about how tissues respond to loading regimes. That “mechanobiology” theory, specifically “tissue differentiation”, postulates that tendon will tend to turn into fibrocartilage if it is subjected to high compression (squishing) and shear (pushing). Then, the fibrocartilage might eventually be reworked into bone as it drops the compression and shear levels. So, according to that theory (and all else being equal; also ignoring the complex intermediate states that would happen in reality), the real ostrich’s kneecaps should be located in the same positions where the FEA, under the moderately large loads we applied, predicts the homogeneous tendon to have high compression and shear. But did the real anatomy match the mechanical environment and tissue differentiation theory’s predictions?

Tissue differentiation diagram displaying the theoretical pathways for transformation of tissues. If tendon (red) experiences high shear (going up the y-axis) and high compression (going toward the left), it should turn into fibrocartilage (purple). Transformation into bone (diagonally to the bottom right) would reduce the shear and compression.

Well, sort of. The image below takes some unpacking but you should be able to pick out the red areas on the bottom row where the patellae actually are, and the yellow shaded regions around some of those patellar regions are where the compression and shear regimes are indeed high and overlapping the actual patellar regions. The upper two rows show the levels of compression (or tension; pulling) and shear, but the bottom row gets the point across. It’s not a bad match overall for the first (“real”; common to all living birds) patella, located on top of the upper knee (femur). It’s not a good match overall for the second (unique to ostriches) patella, located below the first one (and attached to the tibia bone).

FEA results! (click to embiggen)

Kyle says, “Being a part of this project was exciting because of the application of engineering concepts to interesting biological (including evolutionary) questions. Also, it never gets old seeing people’s reactions when I tell them I study ostrich knees.

The study had a lot of nuances and assumptions. We only looked at one instant in slow running and only at one adult ostrich, not at the full development of ostrich anatomy and loading. That’s harder. We started simple. The tissue differentiation theory is used more for fracture healing than for sesamoid bone formation but there’s some reason to suspect that similar mechanisms are at play in both. And there’s much more; if you want the gory details see the paper.

So did we solve why, or how, ostriches have two kneecaps? We felt that the mechanical environment of our FEA was a good theoretical explanation of where the first patella forms. We originally expected the second patella, which evolved more recently and might be more mechanically sensitive as a result, to be a better match than the first one, but it was the opposite. C’est la science!

Enough models, let’s have some reality! I warned you this post would get messy, and here it is. Left leg (skinned) of an ostrich showing the muscles around the knee. The patellar region would be in the gloved hand of the lucky individual shown.

This study, for me, was a fun experience in moving toward more fusion of “evo-devo” and biomechanical analyses, a research goal of mine lately– but there’s still a ways to go with the “how?” and “why?” questions even about ostrich kneecaps.

We felt that the best conclusion supported by our analyses was that, rather than have homogeneous stresses and strains throughout their knee tissues (e.g. the patellar tendon), ostriches have a lot of regional diversity in how those tissues are loaded (in the condition we modelled, which is adequately representative of some athletic exertion). Look at the complex FEA coloured results above again, the top two rows: there are a lot of different shades of compression/tension and shear; not homogeneous strains. That diversity of regional loading sets those tissues up for potential transformation throughout growth and development. And thus ONE of the reasons why ostriches might have two kneecaps is that the heterogeneous loading of their knee tendon favours formation of heterogeneous tissue types.

Another, compatible, explanation is that these different tissues might have consequences for how the muscles, tendon and joint operate in movement behaviours. In due time there will be more about that. In the meantime, enjoy the paper if this post makes you want to know more about the amaaaaaazing knees of ostriches!

Read Full Post »

A Confuciusornis fossil; not the one from our study but prettier (more complete).

Today almost three years of collaboration come together in a publication that is a fun departure from my normal research, but also makes sense in light of it. Professor Baoyu Jiang from Nanjing University in China has been being working on the taphonomy of the Early Cretaceous Jehol biota from northeastern China (Manchuria) for a while, and he found a lovely Confuciusornis (early bird) fossil; one of thousands of them; from the volcanic pyroclastic flow-based lake deposits there.

Although at first glance the skeletal remains of that fossil are not fabulous compared with some other Confuciusornis, what makes this one lovely is that, on peering at it with multiple microscopic and other imaging techniques, he (and me, and a China-UK collaboration that grew over the years) found striking evidence of very well-preserved fossil soft tissues. Our paper reporting on these findings has gone live in Nature Communications so I can blog about it now.

Reference: Jiang, B., Zhao, T., Regnault, S., Edwards, N.P., Kohn, S.C., Li, Z., Wogelius, R.A., Benton, M., Hutchinson, J.R. 2017. Cellular preservation of musculoskeletal specializations in the Cretaceous bird Confuciusornis. Nature Communications 8:14779. doi: 10.1038/NCOMMS14779

Stomach-Churning Rating: 3/10; gooey, but fossil gooey, except for some colourful, gastrically-tolerable histology of bird tissue.

Front view of the ankle/foot of our specimen.

Back view of the ankle/foot of our specimen.

What has been fun about this collaboration is that, for one, it fits in perfectly with my prior work. Ever since my PhD thesis I’d been wondering about odd bones in the legs of birds, including a very puzzling and very, very neglected bit of bone called the tarsal sesamoid, on the outside of the upper end of the ankle joint. Furthermore, a tunnel of tissue called the tibial cartilage sits next to that sesamoid bone, and then across the ankle joint there is a bony prominence with grooves and tunnels that vary highly among bird species; that is called the hypotarsus. These structures are all known in living birds and, to a degree, in extinct fossil cousins. Our specimen seems to reveal an earlier stage in how these little features of bird ankles originated, which we concluded to be a step along the transition to the more crouched legs that modern birds have.

This study has also challenged me to broaden my horizons as a scientist. Although this was a big collaboration and thus we had several specialists to apply supercharged technological techniques to our fossil, I had to learn something about what all that meant. My kind colleagues helped me learn more about tissue histology, scanning electron microscopy, synchrotron mapping, FTIR and mass spectrometry and more. I won’t go through all of these techniques but there are some pretty pictures sprinkled here and in the paper, and a lot more detail in the paper for those who want the gory techno-detail. Basically we threw the kitchen sink of science at the fossil to crack open some of its secrets, and what we found inside was nifty.

Scanning electron micrograph image of probable tendon or ligament fibres (arrow) in cross-section, from near the ankle joint.

We found preserved cells and other parts of connective tissues including tendons and/or ligaments, fibrocartilage (the tougher kind) and articular cartilage (the softer joint-padding kind). That’s great, although not unique, but the kitchen sink also flushed out even more reductionist data: those tissues included some organic residues, including what appear to be bits of proteins (amino acids); particularly the collagen that makes up tendons.

Fibrocartilage (“fc”) from the ankle joint region.

Hopefully we’re right, and we included as much of the data as we could manage so that others can look at our findings. The specimen is crushed into nearly two dimensions, like all Jehol biota organisms, so its anatomy was hard to interpret but we think we got it right. All of the other kitchen-sinky tools have their own nuances and pitfalls but we did our best with a superb team of experts. We’ve had to wait 125 million years to uncover this specimen and a few more years to find out if we’ve looked at the right way is no greater test of patience.

I thank my coauthors, especially Baoyu Jiang for the kind invitation to participate and the very fun experience of collaborating. I think I’ll remember this study for a long time because, for me, it takes a step beyond just describing Another Case of Jaw-Dropping Fossilization (can you hear the hipsters recounting the excitement and cynicism of the 1990s when this all was dawning? I was there and maybe now I’m one of them). By combining all of those methods we learned new things about the palaeobiology of birds and the evolution of traits within birds. Confuciusornis, not shockingly, had ankles that should have functioned in ways intermediate between those of bog-standard non-avian theropods and modern birds.

Same anatomical regions in an extant bird as in the main fossil specimen. Left distal tibiotarsus (TT; below) and proximal tarsometatarsus (TMT; above) from an adult helmeted guineafowl (Numida meleagris) after formalin fixation. (from our paper’s Supp Info)

I’m hopeful that more synthesis of molecular/cellular, imaging, biomechanical and other tools (not to mention good old palaeontology and anatomy!) can wash away some more of this mystery. And it was fun to be a part of a study that adds to overwhelming evidence that was heretical ~25 years ago: some hardy biomolecules such as collagen and keratin can survive hundreds of millions of years, not just thousands. Pioneers such as Prof. Mary Schweitzer led the original charge that made reporting on discoveries like ours much easier today.

I know how the birds fly, how the fishes swim, how animals run. But there is the Dragon. I cannot tell how it mounts on the winds through the clouds and flies through heaven. Today I have seen the Dragon.“– Confucius, ca. 500 BCE.

Let’s finish with some images of a living bird’s ankle region, by co-author and PhD student Sophie Regnault. We considered these for inclusion in the paper but they didn’t fit quite right. I love them anyway so here they are:

Patchwork of histology slide images, from a guineafowl’s ankle (as per photo above). The numbered squares correspond to zoomed-in images below. The tibiotarsus is on the proximal end (bottom left); the tarsometatarsus is on the distal end (right side); and the enigmatic tarsal sesamoid is at the top. Magnification: 20x overall.

Region 1. nice (fibro)cartilage-bone inferface at ligament insertion.

Region 2: longitudinal slice through ligaments connecting the tibiotarsus to the tarsometatarsus across the ankle joint.

Region 3: front (bottom) of the tibiotarsus/upper ankle.

Region 4: tendon fibres in longitudinal section; on the back of the tibiotarsus. Some show mineralization into ossified tendons (“metaplasia”); another curious feature of modern birds.

Region 5: muscle attachment to the back of the upper tarsometatarsus bone. Small sesamoid fragment visible.

Read Full Post »

Older Posts »