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Darwin Day 2019: Some Papers In Evolutionary Biomechanics

February 12, 2019 by John of the Freezers

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.

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Posted in Biomechanics, Exalting Archosauria, Freezermas, Frozen Mammals, Two-Dog-Night Tetrapods | Tagged , , , , , , , , , | 1 Comment »

Learning by Serving

January 14, 2019 by John of the Freezers

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

Stomach-Churning Rating: 0/10

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

wink-wink musical interlude 1

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

Second, service should be done because:

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

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

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

wink-wink musical interlude 2

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

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

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

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

More links of interest:

DVM-DCB Twitter feed

DVM Facebook page (members+affiliates)

SPDAC Facebook page (anyone!)

SPDAC Twitter feed

Posted in Conference | Tagged , , , | 2 Comments »

Pre-Submission Manuscript Scrutiny

November 26, 2018 by John of the Freezers

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)

Posted in RANT | Tagged , | 4 Comments »

Busy Bodies

November 13, 2018 by John of the Freezers

A heads-up: dead people are in this blog post. Yes, I visited a Bodyworlds exhibition again (second link: human exhibit on Flickr) and here is some of what I saw. But first:

Stomach-Churning Rating: 10/10 may be too high (it’s all plastinated anatomy; not gooey bloody stuff) but I’m being wary. There are graphic images of humanity and opinions will vary on the tastefulness; I think they are beautiful. (And to me, Bodyworlds plastination leaves specimens looking more like puppets or statues than disturbing undead) There are images of reproductive anatomy that are not appropriate for children unless parental guidance is along for a “birds and the bees” chat. Got it? OK.

Continue Reading »

Posted in Museums are Cool | Tagged , , , , | 1 Comment »

Guest Post: Brittle Star Arms Are Weird

October 25, 2018 by John of the Freezers

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 species– Ophioderma 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!

Posted in Guestsicle | Tagged , , , , , | 2 Comments »

The Evolving Museum Revisited

July 22, 2018 by John of the Freezers

I had a spare hour in Cambridge this weekend so I dared the crowds in the revamped UMZC’s upper floor. In my prior visit and post I’d experienced and described the lower floor, which is almost exclusively mammals. This “new” floor has everything else that is zoological (animal/Metazoa) and again is organized in an evolutionary context. And here is my photo tour as promised!

Inviting, soft lighting perfuses the exhibits from the entryway onwards.

All images can be clicked to mu-zoom in on them.

Stomach-Churning Rating: 5/10 for spirit animals, by which I mean dissected/ghostly pale whole specimens of animals in preservative fluids.

The exhibits are on a square balcony overlooking the lower floor, so you can get some nice views. It does make the balcony crowded when the museum is busy, so take that in mind if visiting. Strollers on this upper floor could be really difficult. But the ceiling is very tall so it is not cramped in a 3D sense. The lower floor is more spacious.

Like phylogenies? You got em! Tucked away at the beginning of each major group; not occupying huge valuable space or glaringly obvious like AMNH in NYC but still noticeable and useful. To me, it strikes a good balance; gives the necessary evolutionary context for the displayed specimens/taxa.

Introductory panels explain how names are given to specimens, how specimens are preserved and more.

The exhibits give due focus to research that the UMZC is doing or has been famous for. Hey I recognize that 3D tetrapod image in the lower left! 🙂

There is ample coverage of diversity throughout Metazoa but my camera tended to be drawn to the Vertebrata. Except in some instances like these.

Some larger chelicerates.

Some smaller, shadowy sea scorpion (eurypterid) fossils.

Watch here for more about ophiuroids (brittlestars) in not too long!

A BIG fish brain! Interesting!
Before I go through specimens in evolutionary “sequence”, I will feature another thing i really liked: lots of dissected spirit-specimens that show off cool anatomy/evolution/adaptation (and technical skills in anatomical preparation). Mostly heads; mostly fish.

Salps and other tunicates! Our closest non-vertebrate relatives- and some insight into how our head and gut came to be.

Salp-reflection.

Lamprey head: not hard to spot the commonalities with the salps; but now into Vertebrata.

Hagfish head: as a fellow cyclostome/agnathan, much like a lamprey but never forget the slime glands!

Shark head. Big fat jaws; all the better to bite prey with!

Lungfish (Protopterus) head showing the big crushing tooth plates (above).

Sturgeon vertebrae: tweak some agnathan/shark bits and here you are.

Worm (annelid) anatomy model, displaying some differences from/similarities to Vertebrata. (e.g. ventral vs. dorsal nerve cord; segmentation)

Dissected flipper from a small whale/other cetacean. Still five fingers, but other specializations make it work underwater.

Wonderful diversity of tooth and jaw forms in sharks, rays and relatives. I like this display a lot.

More of the above, but disparate fossil forms!

On with the evolutionary context! Woven throughout the displays of modern animals are numerous fossils, like these lovely placoderms (lineage interposed between agnathans, sharks and other jawed fish).

Goblin shark head.

I seem to always forget what ray-finned fish this is (I want to say wolffish? Quick Googling suggests maybe I am right), but see it often and like its impressive bitey-ness.

Bichir and snakefish; early ray-finned fish radiations.

Armoured and similar fish today.

Armoured fish of the past; some convergent evolution within ray-fins.

Convergence- and homology- of amphibious nature in fish is another evolutionary pattern exemplified here.

Gorgeous fossils of ray-finned fish lineages that arose after the Permian extinctions, then went extinct later in the Triassic.

Note the loooooong snout on this cornetfish but the actual jaws are just at the tip.

Flying fish– those ray-fins are versatile.

Diversity of unusual ray-finned fish, including deep-water and bottom-dwelling forms.

Can you find the low-slung jaws of a dory?

Recent and fossil perch lineage fish.

It’s hard to get far into talking about evolution without bringing up the adaptive radiation of east African cichlid fish, and UMZC researchers are keen on this topic too.

Lobe-fins! Everybody dance!

Rhizodonts & kin: reasons to get out of Devonian-Carboniferous waters.

A Cretaceous fossil coelacanth (skull); not extremely different from living ones’.

Let’s admire some fossil and modern lungfish skulls, shall we? Big platey things  (here, mainly looking at the palate) with lots of fusions of tiny bones on the skull roof.

Eusthenopteron fossils aren’t that uncommon but they are still great to see; and very important, because…

OK let’s stop messing around. The UMZC has one of the best displays of fossil stem-tetrapods in the world! And it should.

Another look at the pretty Acanthostega models.

Acanthostega vs. primate forelimb: so like us.

Ichthyostega parts keep Acanthostega company.

A closer look at the “Mr. Magic” Ichthyostega specimen, which takes some unpacking but is incredibly informative and was a mainstay of our 2012 model. Back of skull, left forelimb, and thorax (from left to right here).

Eucritta, another stem-tetrapod.

Closer look at Eucritta‘s skull.

Weird stem-tetrapod Crassigyrinus, which we’re still trying to figure out. It’s a fabulous specimen in terms of completeness, but messy “roadkill” with too many damn bones.

The large skull of Crassigyrinus, in right side view.

Early temnospondyl (true amphibian-line) skulls and neck.

Nectrideans or the boomerangs of the Palaeozoic.

Cool fossil frogs.

Giant Japanese salamander!

Fire salamanders: not as colourful as the real thing, but here revealing their reproductive cycle in beautiful detail.

Closeup of oviduct in above.

Sexual dimorphism in Leptodactylus frogs: the males have bulging upper arms to (I am assuming) help them hold onto females during amplexus (grasping in mating competitions).

Did I forget that Leptodactylus has big flanges on the humerus in males, to support those muscles? Seems so.

An early stem-amniote, Limnoscelis (close to mammals/reptiles divergence); cast.

Grand sea turtle skeleton.

One of my faves on display: a real pareiasaurian reptile skeleton, and you can get a good 3D look around it.

Details on above pareiasaurian.

Mammals are downstairs, but we’re reminded that they fit into tetrapod/amniote evolution nonetheless.

Let there be reptiles! And it was good.

Herps so good.  (slow worm, Gila monster, glass lizard)

A curator is Dr Jason Head so you bet Titanoboa is featured!

Crocodylia: impressive specimens chosen here.

It ain’t a museum without a statuesque ratite skeleton. (There are ~no non-avian dinosaurs here– for those, go to the Sedgwick Museum across the street, which has no shortage!)

Avian diversity takes off.

Glad to see a tinamou make an appearance. They get neglected too often in museums- uncommon and often seemingly unimpressive, but I’m a fan.

I still do not understand hoatzins; the “cuckoo” gone cuckoo.

Dodo parts (and Great Auk) near the entrance.

Wow. What an oilbird taxidermy display! :-O

There we have it. Phew! That’s a lot! And I left out a lot of inverts. This upper floor is stuffed with specimens; easier there because the specimens are smaller on average than on the lower floor. Little text-heavy signage is around. I give a thumbs-up to that– let people revel in the natural glory of what their eyes show them, and give them nuggets of info to leave them wanting more so they go find out.

Now it’s in your hands– go find out yourself how lovely this museum is! I’ve just given a taste.

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Year Six of Johns Freezer

July 7, 2018 by John of the Freezers

I’m a few months late on the six-year anniversary of this blog but finally found some time. (For year 5 go here) It was seemed to be another quiet year on the blog because it was not a quiet year for work or other aspects of life. The DAWNDINOS project got into full swing and there will be a lot more about that soon on that website and maybe here, too.

Freeezersaurus 2 has been mostly vacated now; and Freezersaurus 3 is in place, with the contents shifted– and a mad rush in action to get rid of (boil down + varnish bones of) as many specimens as I can! I have way too many… of course, mostly elephant bits. Here are the last big bits left in Freezersaurus 2; we are intimidated to move them…

Stomach-Churning Rating: 3/10 until the opossum-digested-by-gator at the end, then 9/10, so hang tight!

Year 6 began with a post about a new paper! We published a big synthesis of data on what mammals turn their kneecaps into bone (or not), and how those states evolved. The story turned out pretty interesting and we are still pursuing some angles that it inspired, so stay tuned! Otherwise, the kneecap project (i.e. Leverhulme grant) has ended and staff/students have moved on (but published all their papers on it– well done, Sophie, Kyle and Viv!!), so it will fall quiet on that topic for a while.

Then we published another paper, and it happened to involve more sesamoid-y stuff! But with birds and their ankles, and some tantalizing evidence of soft tissue and organic biomolecular preservation. I’m still a bit amazed this paper happened and am pleased we got to collaborate on it.

Next, I got to ramble on a bit, about another serious topic related to science– this time, on blame.  I had forgotten about that post, and now on re-reading it it has fresh new relevance to me. All the more reason to keep blogging!

Smaller but better: Freezersaurus 3, part of a proud dynasty!

But then, what do you know, we published another kneecap paper! And on ostriches! With some simple but ambitious finite element analysis. We are meaning to get back to this approach… it just scratched the surface of some super cool “mechanobiology” that could shed light on “evo-devo”.

And next, BOOM! The dinosaurs dawned. By which I mean my current ERC grant “DAWNDINOS” began. Do take a look– the website now has some lovely NEW palaeo-art by Bob Nicholls, John Conway and Scott Hartman, with more to come! This project’s inception led to an inspection of caeca in tinamous; the following post.

I managed to have some summer holiday in the midst of the year, and that made an extremely memorable “pilgrimage” to a fossil site possible– “Experiencing the Irish Tetrapod Tracks” was the blog post that emerged from the waters. (That post needs a little revamp in light of some other literature; I will get around to that soon)

DAWNDINOS got a nice new 3D printer and we’re gradually printing up some archosaurs to show.

Holiday ended and back to the freezer I went, to post about how we thaw specimens (and how odd wallaby legs can be). Then we published three papers in quick succession and I played catchup posting about them (Mussaurus forelimbs; mouse vs. human hindlimb simulations; and tetrapod forelimb musculature).

Speaking of mouse hindlimb simulations, I didn’t blog about this related paper that we published earlier in 2018, but it’s very relevant. And GIF-worthy!

But I couldn’t stay away from bird legs for long, and so soon enough I posted “The Bird Knee Challenge“, which still stands.

Jumbo the elephant loomed into view at Christmas-time (plus a documentary about T. rex with Chris Packham, and another about Hannibal’s elephant excursion over the Alps– the latter also playing on PBS in USA); all featuring cameos with me, so I posted about the Jumbo/Attenborough one. That’s another life experience I will treasure.

Next, back to musing about science and humanity– and who’s a more big-name, very relatable human scientist than Darwin? Well, we could debate that endlessly but I posted about Darwin’s human nature for Darwin Day.

That takes me through to March 2017. I’ve posted a little more since then but that counts as Year 7 of this blog, so we’ll catch up with that then. Looking back on ~2017, I posted more blog posts than I thought I did! Maybe it’s just that 2018 feels very quiet to me blog-wise. We’ll see how it shapes up though.

Years ago, my team dissected an alligator (for Allen et al. 2010,2014 papers if you are keeping track) that had an opposum in its stomach, during winter when feeding wasn’t supposed to be happening much. So that came up again this year; and hopefully it does not make anything come up from your stomach. But this is real anatomy in action.

 

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