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My Kind of Palace

August 29, 2019 by John of the Freezers

If you go into central Lausanne, Switzerland, you’re likely to pass the Palais du Remine, and if you do, I recommend you go inside. I was happy I did while visiting Lausanne for the AMAM2019 conference. A luxurious palace has been given over to house five (!) free (!) museums on science and culture. These include the canton’s (~state’s) museums of palaeontology and zoology, which I’ll showcase here (also a little of geology and archaeology museums). Tripadvisor’s reviews were good but not as glowing as I’d make mine, so I will remedy that. I’m a sucka for old-school museums, and that’s what these are. So if that sounds right for you, journey onward!

It’s nice.

As you may be expecting by now if you’ve been here before, it’s time for another museum photo blog!

Stomach-Churning Rating: 5/10 for bones, preserved organs, taxidermy aplenty, and animal developmental deformities.

Nice cathedral nearby, w/great view of the city.

Nice interior architecture. There’s lots of nice to behold.

Posters That Get You Excited 101. But you must wait. Like I did.

Quadrupedal human at Zoology museum entry.

Tomistoma, false gharial.

Not a bad collection of taxidermied Crocodylia!

Visually arresting cobra display.

I’ve never seen three Draco gliding lizards on display together!

Bipedal lizard taxidermy displays, freezing the dynamic in the static, are no easy feat.

Plenty of stuffed animals like these raptors/other large birds. Classical zoology museum style. Minimal signage. Just specimen labels, mainly.

Coelacanth!

Sperm whale jaw.

Open space with big specimens. A ~4m long great white shark included.

Second zoology hall: bones!

Gorilla standing tall next to human.

Ostrich skeleton up close, amongst the mammalz.

Cassowary skeleton.

Emu shoulder/arm bones in right side view.

Walrus skeleton in what seems like an odd pose to me, but then they are odd on land.

Alligator skeleton in repose.

Giant anteater, “knuckle-walking”.

Pangolin skeleton! And mounted digging into a nest– very well done!

Bernard Heuvelmans display, about the (in)famous cryptozoologist. This was quite a surprise to me. I’m sure I’d read his English-translated book “On the Track of Unknown Animals” as a kid, during my long stint as an avid reader of much zoology, crypto- and otherwise. He bequeathed a lot of his work to the museum.

Bernard’s handwritten CV!? With a “sea serpent” sketch.

A “sea serpent” vertebra… but if you know any anatomy, it’s not a snake’s vertebra at all but a fish’s, such as a basking shark‘s.

Are you ready for more weirdness? How about some “mutants”- congenital deformities of animals? Fascinating errors of developmental anatomy… somehow this two-headed calf survived awhile. Plenty more where that came from, as follows:

And then there’s all kinds of wonderful comparative anatomy. To be a student of this subject in Lausanne would be a lucky thing, with this museum’s collection at hand. These are valuable specimens, made with love and skill.

Jaws

Fish head anatomy. Some vertebrae on the left, too.

Developmental regions of the head: a lovely wax(?) model of an Echidna skull. A treasure.

Brains: alligator vs. pigeon.

Salamander muscles.

Pigeon muscles.

More spotted felids than you can shake a jar of catnip at.

Another pangolin!

Giant armadillo.

Petaurus: flying phalanger (a gliding marsupial).

Second zoology hall open area: left side.

Second zoology hall open area: right side.

A final hall with a more new-fangled display, on the topic of evolution and extinction. Attractive phylogeny graphic here. Birds at the “top”, of course. Poor lowly mammals!

Taxidermied giant auk- not a common sight! (Extinct)

The extinct southern pig-footed bandicoot. Also a rare sight of a whole specimen- in a Swiss museum, too.

NOW ON TO THE FOSSILS!

You’ve been very patient. Here, have a Toblerone.

Palaeo museum entry. Already there are cool things visible. Inside, we find it just like I prefer my zoo/palaeo museums (as above): stuffed with specimens and leaving plenty for you to wonder about and investigate. Not frilly; a well-stocked museum that mostly lets its specimens speak for themselves.

Sauriermuseum (Aathal) specimen of Plateosaurus: sculpt/cast. A very good, big skeleton of this common dinosaur, rearing up.

Rear view of same.

Real bones of same; vertebrae and pelvic (this is the “Frick specimen”).

Metaxytherium (current name), an ancient and large fossil dugong/seacow. Skull is in left side view. (that may help, as their skulls are odd!)

Anthracotherium upper jaw: ancient hippo-cousin.

Prolagus: the “Sardinian hare” (recently extinct; old lineage).

Potamotherium: to some an early otter-like mammal, more recently thought to be an ancient seal.

“Broke-ulum”: a walrus broke its penis bone (baculum) and was surely not pleased about it, but lived to heal— physically if not mentally. Yeesh!

Glyptodont tail club and armour.

Aepyornis elephant bird legs!

A partial/reconstructed skeleton of the dodo.

Velociraptor preparing to pounce from above. It’s too late for you!

Rhamphorhynchus fossil (2D slab) and sculpt/cast coming alive in 3D– good stuff.

Anhanguera pterosaur watches the chaos from above, fish snagged in its teeth.

Not-shabby metriorhynchid marine croc fossils, from Britain.

Lovely 3D plesiosaur bones (flippers, neck, etc.) from near RVC: Peterborough!

Mesosaur; early reptile.

The museum clearly is proud of its excellent “Mammoth of Brassus” skeleton, essentially complete.

Ice Age elk/moose, a 10,000 year old skeleton in fine shape.

Cave bear skull rawr

Purty ammonites!

Spiky ammonite!

Cretaceous sponge colony from France. I hadn’t seen something like this before, so here it is.

Trilobites, brittlestars and friends.

Well I did wander through the geology and archaeology museums too, and while I liked them I did not take so many photos. My non-human organismal bias is apparent. But check these final ones out:

Splendid cross-section of the stratigraphy of the Alps around Lausanne. I gazed at this for quite a few minutes, trying to figure out what was where in the landscape I’d seen and how old, how deformed, etc.

Slab of “dinosaur” tracks but it was not clear to me what dinosaurs/archosaurs/whatever made them. I wish my French was better. Closeup below shows two footprints superimposed.

At last, the coup de grace! What museum would be complete without a diorama!? (I love them) This one, with a goat sacrifice and early Stone Age people praying to heathen deities/spirits at an elaborate petroglyph array rocked my world. And so it makes a perfect final image. Enjoy, and conduct the proper rites.  \m/

 

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Posted in Museums are Cool | Tagged , , , , , , , , | 5 Comments »

The Forbidden Academic Tale

August 10, 2019 by John of the Freezers

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

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

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

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

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

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

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

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

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

Posted in RANT | Tagged , , , | 3 Comments »

Zoology Museum: Take 3

August 4, 2019 by John of the Freezers

I heard that the UMZC has some new exhibits open, so back I went! For the prior posts see here (mammals/basement) and here (everything else). Another photo tour! There’s a special (art) exhibit, too, so stick around to the end.

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

Stomach-Churning Rating: 3/10 mainly skeletons, some preserved critters in jars.

The first new section is an elaborated display on reptiles.

Clevosaurus, a Triassic relative of the living tuatara reptile, Sphenodon. Nice fossil hindlimbs!

Tuataras (Sphenodon), skeletal and preserved.

Tuatara embryos!

Nice chameleon mount w/tongue extended.

Thorny devil (Moloch), de-thorned and in the flesh.

Skull (cast) of Ninjemys, the giant turtle.

Pipe snakes! Snakes with vestigial hindlegs.

Istiodactylus pterosaur snout-tip (real fossil) from the Isle of Wight, UK. Nice 3D fossil.

The gharial (Gavialis), male with protuberance on snout (mating-related).

I dub thee Dinosaur Corner! For dinosaurs, the Sedgwick Museum across the street (also free; also classic and awesome) is the place to go but this corner does a good job fighting for the scientific conclusion that birds are dinosaurs.

And now a change of pace. On to the special exhibit!

A nice surprise to see naturalist superstar Jonathan Kingdon‘s scientific illustrations and nature-inspired artwork displayed here. I’ve added photos of ones I liked the most.

As the caption explains, Kingdon used art to explain the value of nature; via realistic images of life, dissections, and creative abstractions drawn from them.

Hammerhead bats: even freakier when skinned.

Begone if ye find not joy in aardvarks!

White-toothed shrew looking extra-ghoulish with flensed face.

Skinned sengis in action.

More sengis (elephant shrews); with a note explaining that they are not rodents/insectivores but afrotheres, cousins of aardvarks, elephants and kin.

Bronze Jackson’s chameleon bust.

Asian barbet faces: this was fascinating. Kingdon used the paintings to explain how barbet faces vary across species as recognition devices to aid in territorial defense, especially of their nest-holes in trees, in which they face outwards to display their coloured faces. The middle image shows one lone species that has no such territorial competitors and has evolved back into brown colour, perhaps due to relaxed selective pressure for colour. Neat!

Oh my, this took my breath away! Mixed media depicting the varied forms of facial ornaments in vultures; soft tissues used in communcation. And here mounted on a butcher’s rack. Do vulture bits mimic their grisly food?

Posted in Museums are Cool, Two-Dog-Night Tetrapods | Tagged , , , , , | 5 Comments »

These Are A Few of Mon Préféré Things

March 3, 2019 by John of the Freezers

To me, there is no question that the Galerie de Paléontologie et d’Anatomie comparée of Paris’s Muséum national d’Histoire naturelle (MNHN) is the mecca of organismal anatomy, as their homepage describes. Georges Cuvier got the morphological ball rolling there and numerous luminaries were in various ways associated with it too; Buffon and Lamarck and St Hiliaire to name but a few early ones. It is easy to think of other contenders such as the NHMUK in London (i.e., Owen), Jena in Germany, the MCZ at Harvard (e.g. Romer) and so forth. But they don’t quite cut the dijon.

As today is John’s Freezer’s 7th blogoversary, and I was just at the MNHN in Paris snapping photos of their mecca, it’s time for an overdue homage to the magnificent mustard of that maison du morphologie. The exhibits have little signage and are an eclectic mix of specimens, but this adds to its appeal and eccentricity for me. I’ve chosen some of my favourite things I saw on exhibit on this visit, with a focus on things that get less attention (NO MESOZOIC DINOSAURS! sorry), are just odd, or otherwise caught my fancy. It’s a photo blog post, so I shall shut up now, much as I could gush about this place. I could live here.

Need plus-grand images? Clic!

Stomach-Churning Rating: 7/10 for some potentially disturbing anatomical images such as viscera, preserved bits, models of naughty bits etc.

Greetings. Note the stomach-churning rating above, please.

Right. We’ll get the amazing first view as one steps into the gallery done first. Mucho mecca. Anatomy fans simply must go here at least once in their life to experience it, and one cannot ever truly absorb all the history and profound, abundant details of morphology on exhibit.

Less-often-seen views from the balcony; one more below.

Indian Rhinoceros from Versailles’s royal menagerie; came to the MNHN in 1792.

Brown bear hindlimb bones.

Brown bear forelimb bones and pelvis.

Two baby polar bears; part of the extensive display of ontogeny (too often missing in other museums’ exhibits).

Asian elephant from Sri Lanka.

Lamb birth defect. Like ontogeny, pathology was a major research interest in the original MNHN days.

Wild boar birth defect.

Fabulous large Indian gharial skull + skeleton.

“Exploded” Nile crocodile skull to show major bones.

Let’s play name-all-the-fish-skull-bones, shall we?

Rare sight of a well-prepared Mola mola ocean sunfish skeleton.

Diversity of large bird eggs.

Asian musk deer (male), with tooth roots exposed.

Freaky gorilla is here to say that now the really odd specimens begin, including the squishy bits.

Freaky tamandua, to keep freaky gorilla company. Displaying salivary glands associated with the tongue/pharynx. These are examples of anatomical preparations using older analogues of plastination, such as papier-mâché modelling. I’m not completely sure how the preservation was done here.

Tamandua preserved head, showing palate/tongue/pharynx mechanism.

Chimp ears. Because.

Why not add another chimp ear?

Many-chambered ruminant stomach of a sheep.

Simpler stomach of a wolf. Not much room for Little Red Riding Hood, I’m afraid.

Expansive surface area of a hippo’s stomach; but not a multi-chambered ruminant gut.

Cervical air sacs of a Turquoise-fronted Amazon parrot.

Heart and rather complex pulmonary system of a varanid lizard.

It’s pharynx time: Keratinous spines of a sea turtle’s throat. All the better to grip squids or jellies!

Pharynx convergent evolution in a giraffe: keratinous spines to help grip food and protect the pharynx from spiny acacia thorns while it passes down the long throat.

Tongue/hyoid region of the pharynx of a varanid, showing the forked tongue mechanism.

Palaeontological awesomeness on the upper floor (the 2nd part of the gallery’s name). Here, the only Siberian woolly mammoth, I’m told, to have left Russia for permanent display like this. Frozen left side of face, here, and 2 more parts below.

Mammuthus primigenius freeze-dried lower ?left forelimb.

Skeleton that goes with the above 2 parts. It’s big.

But “big” is only relative- my large hand for scale here vs. a simply ginormous Mammuthus meridionalis; full skeleton below.

Four-tusked, moderate-sized Amebelodon elephantiform.

Naked woolly rhinoceros Coelodonta.

Extinct rhino Diaceratherium, with a pathological ankle (degenerative joint disease). I love spotting pathologies in specimens- it makes them stand out more as individuals that lived a unique life.

Glyptodont butt and thagomizer, to begin our tour of this business-end weaponry.

Eutatus leg bones, from a large fossil armadillo; Argentina. Really odd morphology; Xenarthrans are so cool.

Giant ground sloth (Megatherium) foot; ridiculously weird.

Giant ground sloth hand is full of WTF.

Metriorhynchus sea-crocodile from the Cretaceous: hind end.

Odobenocetops one-tusked whale that I still cannot get my head around, how it converged so closely on the morphology of a walrus.

Thalassocnus, the large marine sloth… few fossils are so strange to me as this one. But modern sloths swim well enough so why not, evolution says!

Rear end of the sea-sloth.

Megaladapis, the giant friggin’ lemur! Not cuddly.

A basilosaurid whale Cynthiacetus, one of the stars of the show, as the denouement of this post. Plan your visit now!

Posted in Museums are Cool, Voyages | Tagged , , , , , , , , , | 5 Comments »

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.

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

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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)

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