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Jason Anderson, vertebrate paleontologist and anatomist at the University of Calgary (Canada), shared these two intriguing photos with me, and agreed for me to share them with you. Yay, thanks Jason! Good timing for a badly needed Mystery Dissection post:

What are they (species ID) *AND* from what region of the body?

(they are the same region, same specimen, same animal)

RULE: Your answer must be in the form of a winter holiday song (at least four lines)!

If you’ve been following some of my recent tweets, I’ve been tweeting about the “joys” of increased academic paperwork around holiday-time; e.g. this one:

As always, you can score extra points for creativity.

Remember: the scoreboard is here.

Difficulty: Integumentary

Stomach-Churning Rating: 6/10; if beauty is only skin deep, then ugly is, too?

Here they are…

(more…)

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Here, I give you a long-planned post on the patella (“kneecap bone”) of birds, which was my Royal Society Senior Research Fellowship sabbatical project for 2012-13. This is only a brief introduction to the anatomical issues at hand, err, I mean at knee…

Stomach-Churning Rating: 6/10; mostly skeletons/fossils, but there are a few images of the dissection of a guineafowl, which is fresh and meaty.

Archaeopteryx, the Berlin specimen. Helluva fossil, but nary a patella!

Archaeopteryx, the Berlin specimen. Helluva fossil, but nary a patella!

The question I am exploring, first of all, is simply how the patella evolved, because it seems to be present in almost all living birds. However, it is absent in all non-avian dinosaurs, and indeed most Mesozoic birds, too. There is barely a hint of any precursor structure (a “patelloid”) in other reptiles, but lizards evolved their own patella that is quite different (a flattened lozenge, not a rectangular structure lying tightly confined in a “patellar groove” on the femur as it is in birds). Mammals evolved the knobbly, hemispherical kind of kneecap that we’re familiar with, possibly on several occasions (a different story!). So the patella evolved at least three times in the lizard, mammal and bird lineages– and possibly more than once in each of these groups. And that’s about it for almost 400 million years of tetrapod evolution, except for a few very rare instances in fossils and sort-of-patella-like things in some frogs or other weirdos.

Fossil birds exhibit no clear presence of a patella until we come very close to modern birds on the avian stem of the tree of life (see below). And then, suddenly in modern birds, there is a lot of variation and not much good documentation of what kind of patella exists. This makes it challenging to figure out if the patella is ancient for modern birds or if it evolved multiple times, or how it changed after it first evolved– let alone bigger questions of what the patella was “for” (performance benefits, functional consequences, etc.; and developmental constraints) in the birds that first evolved it.

Considering that the patella is such an obvious bone in some birds, and certainly affects the mechanics of the knee joint (forming a lever for the muscles that cross it; homologous to our quadriceps muscles) and hence locomotion, it is a compelling research topic for me.

What follows is a pictorial guide to the patella of some birds, in sort of an evolutionary/temporal sequence (see my earlier post for a recap of some major groups), with a focus on animals I’ve studied more intensively so far (with >10,000 species, there is a lot that could be done):

Gansus, IVPP V15080
The early Cretaceous bird Gansus (from the IVPP in Beijing), represented by many beautifully preserved specimens, all of which lack a patella. This absence is characteristic of other stunningly preserved fossil Chinese birds, indicating that this is almost certainly an ancestral absence of a patella, until…

The famed Cretaceous diving (flightless) bird Hesperornis, from Wikipedia/Smithsonian.  Note the massive, conical/crested patella in front of the  knee (jutting up and overlapping the ribs/vertebrae close to the pelvis; see also below). That elongate patella is characteristic of many diving birds that use foot-propelled swimming; it has evolved many times in this fashion. Other hesperornithiform birds show some transformational states in their anatomy toward this extreme one.
Hesp-patella

Check this out! More Hesperornis (cast), with the femur on the left and the patella on the right. The bloody patella is almost as long as the femur! That’s nuts. With kind permission from the Natural History Museum, London.

Exhibited ostrich skeleton in left side view showing the patella (white arrow).
Exhibited ostrich (Struthio camelus) skeleton in left side view showing the patella (white arrow), on exhibit atThe Natural History Museum at Tring, Hertfordshire, UK. Ostriches are remarkable in that they have this elongate patella (actually a double patella; there is a smaller, often-overlooked second piece of bone) and yet are rather basal (closer to the root of the modern avian family tree)– however, they obviously are specialized in ways other than this double patella, most notably their very large size, flightlessness, and elongate legs. So the unusual patella is more likely linked to their odd lifestyle than a truly primitive trait, at least to some degree (but stay tuned: what happened with the patella in other members of their lineage, the ratites/palaeognaths, is much less well understood!).
Note that ostriches and Hesperornis together hint that the presence of a patella might have been an ancestral trait for living birds, but their patellae are so different that the ancestral state from which they evolved must have been different, too; perhaps simpler and smaller. Hence we need to look at other birds…
Skinned right leg of guineafowl, Numida meleagris.
Skinned right leg of a Helmeted Guineafowl, Numida meleagris, above. That whitish band of tissue in the middle of the screen, on the front of  the knee, is part of what is concealing the patella. That is an aponeurosis (connective tissue sheet, like a thin tendon) of the muscles corresponding to our “quads” or our tensor fascia latae, detailed more below. Guineafowl are fairly basal and well-studied in terms of their bipedal locomotion, so they are an important reference point for avian form and function.
Right guinefowl leg, with patella semi-exposed.
Right guineafowl leg, with patella exposed. Here I’ve peeled away that white band of tissue  and associated muscles, which have been reflected toward the bottom of the screen (AIL and PIL labels corresponding to the anterior and posterior parts of the Iliotibialis lateralis muscle). The tip of the scalpel is contacting the patella. It’s not much to see, but lies atop the bright yellow fat pad that cushions it against the femur. You should be able to see a groove in the end of the femur just above that fat pad, which is where the patella sits and slides up and down as the knee moves/muscles contract. This is called the patellar groove, or sulcus patellaris.
Left leg of a guineafowl (with right tibiotarsus behind it) showing both patellae in articulation; in medial (inside) view. The  patella is the little rectangular bit of bone in the top middle of the screen, interposed between femur and tibiotarsus.
Left leg of another guineafowl (with right tibiotarsus behind it, on the left) showing the patellae in articulation; in medial (inside) and cranial (front) views, respectively. The patella is the little rectangular bit of bone in the top middle of the screen, interposed between femur (thigh) and tibiotarsus (shank). With kind permission from the Natural History Museum, London.  
Penguin-patella
Right leg of a Cape Penguin (Spheniscus demersus) from the University Museum of Zoology in Cambridge, showing the big lumpy patella in this wing-propelled diver. They still walk long distances on land, so presumably a patella plays some role in their gait, helping to explain its large size, which like the ostrich and Hesperornis seems to be a novel trait. Notice the groove across the patella, made by the tendon of the ambiens (like our sartorius/”tailor’s muscle”), which crosses from the inside to the outside of the leg via this route. This groove is often considered a useful phylogenetic character in modern birds, as its contact with the patella (sometimes via a hole, or foramen) varies a lot among species.
Buceros skeleton UMZC
A hornbill, Buceros sp., from the UMZ Cambridge museum as well. This displays the possibly-more-typical, little rounded patellar nubbin that many birds have. See below for more.

Buceros knee closeupCloseup of the knee/patella of the hornbill, Buceros sp., from above. Not much to squawk about, patella-wise, but it’s there.

And so we complete our quick tour of the avian patella, in its grand variation and humble beginnings.

Why does an ostrich have a patella and a Tyrannosaurus, Edmontosaurus or Triceratops did not? Why were birds the only bipedal lineage to evolve a patella (mammals and lizards gained a patella as small quadrupeds), and why did some bipeds like kangaroos “lose” (reduce to fibrous tissue, apparently) their patella?

These are the kinds of mysteries my group will now be tackling, thanks to a generous Leverhulme Trust grant on sesamoid bone ontogeny, mechanics and evolution.  My group is now Dr. Vivian Allen as the postdoc, Sophie Regnault as the PhD student, and Kyle Chadwick as the technician and MRes student, along with numerous collaborators and spin-off projects. We’re looking forward to sharing more! But for now, I hope that I’ve engendered some appreciation for the avian patella, as the silly title indicates (“fella” used in the general sense of anyone!). This work is all unpublished, but some of this should be out in not too long, in much more lavish detail! Much as the patella is the “forgotten lever “of the avian hindlimb, it is the fulcrum about which a substantial part of my research group’s activity now pivots.

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Well lookie here… it’s a new Mystery CT slice challenge! And it’s appearing while Society of Vertebrate Paleontology members are busy drinking and eating at the conference’s welcome reception– how naughty of me!

What is it, what species, etc.– tell me what you can.

RULE: Your answer must involve excessive alliteration!!!

Prodigious perambulations of appropriate prose promise to procure prodigious points!

Remember: the scoreboard is here.

Difficulty: lumpy + alliteration + possible intoxication if you are an SVP attendee (John whistles innocently).

Stomach-Churning Rating: 1/10 unless you have lump-associated PTSD.

Proceed, plucky puzzle ponderers!

Mystery CT 10

EDIT: These images give the answer and show some cool features. It’s an Asian elephant skull, NHMUK 1984.516, of a juvenile animal (probably a UK zoo animal). Gotta love that pneumaticity!
Elephant skull _Se1_Im002

And another view:

Elephant skull _Se1_Im001

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At this writing (17 October, 2013), I am headed home after a 10-day trip to China as part of an RVC delegation participating in a London Universities International Partnership (LUIP) event (celebrating London innovations, especially those developed with Chinese input) as part of a broader UK/London-China trade mission. I am still processing what has been an astonishing, exhausting, exhilarating, chaotic, lavish, smog-ridden, and inspiring visit. As a simple scientist, I’ve found myself in the midst of major global politics, business and science policy, with little time to assimilate what has happened but still learning plenty about how the bigger world, way beyond my lab, operates. I thought I’d share that experience, by way of pictures illustrating key – or just unusual or interesting – events and places from my journey. It was surreal, in so many ways…

Stomach-Churning Rating: 0/10 except for a couple of odd statues. No squat-toilets; I will spare you those.

Odd sight above entrace to the art gallery building that housed the LUIP event.

Odd decoration above entrance to the art gallery building that housed the LUIP event.

Several months ago the RVC selected me to help RVC Access director Nina Davies and colleagues set up an exhibit, as part of the LUIP event, featuring the work that my team has done, and is still doing, with Chinese collaborators at the IVPP in Beijing (exemplified by this past post). Dinosaurs and 3D computer modelling were thought to be a good potential draw for the public (ya think?) as opposed to more controversial subjects such as avian flu, with which the RVC also has research strengths and Chinese collaborations. I saw it as a great chance to go spend time at the IVPP’s spectacular fossil collection and develop ongoing collaborations with scientists there like Drs. Zhou Zhonghe and Xu Xing. Subsequently, I learned that it was a small enough event that I’d probably be meeting Boris Johnson (Mayor of London) there as well, possibly even presenting our research to him.

Hallway lined with art galleries, one of which is the Yang Gallery.

Hallway lined with art galleries, one of which is the Yang Gallery, which the event was held in.

The preparations for the exhibit were full of surprises, as you might expect a long-distance interaction between UK and Chinese people to be, especially if you’ve spent time in China and know some of the broad-brush cultural differences (e.g. “Yes” can mean no, and “maybe” usually means no). There were many cooks involved! Artists, policymakers, scientists, universities… and then the Mayor’s office got thrown into the action, and then it snowballed, with UK Higher Education and Science minister Rt Hon MP David Willetts coming to the LUIP event, and UK Foreign Chancellor George Osborne then scheduling a related trip to China at the same time. Meanwhile, I just supplied some images (courtesy of Luis Rey) and a video (by Vivian Allen and Julia Molnar) from our past paper to illustrate what we’re doing with Chinese collaborators.

There wasn’t time to prepare a fancy exhibit with lots of bells and whistles, but I was pleasantly surprised by what the LUIP organizers cooked up from what we provided, as photos below show. The addition of four great casts of fossils on loan from the IVPP was crucial and made us stand out from all the other exhibits in a big way! The event was held in the trendy 798 Art District in eastern Beijing, which is an old industrial area converted to a surprisingly bohemian, touristy area that still sports its rusting old industrial infrastructure, but bedecked with modern art! That really worked for me as a setting. This was my third visit to Beijing/China but my first time in this gritty area of the city, which I recommend spending an afternoon in sometime if you visit– the streets are lined with cafes and art galleries.

Boris bike and nice design of exhibits (placed on/around the giant letters LONDON) .

Boris bike and nice design of exhibits (placed on/around the giant letters LONDON). The back wall sports a Communist slogan, partly painted over, exhorting the workers to give their full effort for the glory of Chairman Mao or something (seriously). The building was once a weapons factory, I was told.

All the work we put into this event was a big deal to me, but as the event developed, and the schedule for my 10 day visit shifted almost daily as various political factions shuffled the LUIP and UK trade mission plans, I became aware of the vastly broader issues at play, and humbled by their scope. Sure, studying the 3D changes of dinosaur body shape across >225 million years is truly awesome to conduct, but the socio-political issues around the LUIP event boggled and baffled me. Issues like “How do we get more Chinese students to come study at London universities?”, “How do Chinese parents feel about their students studying to become veterinarians?” and “What are the key obstacles limiting UK-Chinese collaborations and how can they be resolved?” gradually eclipsed the technical, scientific issues in my mind, and I started to feel lost. I learned a lot from this eye-opening experience.

These two news stories here (with video; me speaking at ~01:15) and here (with pic of me w/exhibit) give a good idea of the scale and potential importance of the events.

The rest of his post is mostly a photo blog to illustrate the goings-on, but I consider some psychological/philosophical matters toward the end.

The London innovation event lighting gets tested out-- and looks sweet.

The London innovation event lighting gets tested out– and looks sweet.

Boris arrives, and proceeds to tour the exhibits rather than give his speech as planned. But it worked out OK in the end; he had 2 exhibit tours and a speech in the middle.

Boris arrives, and proceeds to tour the exhibits rather than give his speech as planned. But it worked out OK in the end; he had two exhibit tours and a speech in the middle.

Minister Willetts arrives and prepares to speak about UK higher education for Chinese students.

Minister Willetts arrives and prepares to speak about UK higher education for Chinese students.

I give Minister Willetts a tour of our fabulous fossil casts.

I give Minister Willetts a tour of our fabulous fossil casts.

Left to right = back in time through avian evolution, represented by Yixianornis, Pengornis, Jeholornis and Microraptor casts courtesy of the IVPP.

Left to right = back in time through avian evolution, represented by Yixianornis, Pengornis, Jeholornis and Microraptor casts, courtesy of the IVPP.

Arguably one of the most important fossil finds, the "four-winged" dinosaur Microraptor.

Arguably one of the most important fossil finds (ever?), the “four-winged” dinosaur Microraptor.

Added benefit of thaw in UK-Chinese relations: Microraptors for everyone!!! Well, for me anyway. And a cast, not a real one. But still pretty damn cool, and now it’s in my office for comparative research and teaching. See?

Darwin greets Microraptor in my office.

Darwin greets Microraptor in my office.

Like I said at the start, I don’t have a profound insight from this trip, not yet if ever. But it has obviously made a strong impression on me. It has reinforced some thoughts about Big Life Stuff. With the jetlag, the big geopolitical issues, the foreign country, the opulence, and my research thrown into that heady brew (ahem, along with some Tsingtao beer), I became lost. And I liked it, even though I was totally clueless at times, just looking around wide-eyed at the events unfolding and hearing about the political manoeuvring behind the scenes (e.g. how would big figures like Boris and Willetts share the limelight? And the news media was playing up the question of whether Boris’s or Osborne’s contingents were “winning” in some sense of some struggle, even though ostensibly they are on the same Tory team).

But we’re all clueless; we’re all lost. In some ways that’s a good thing. We have work to do; broad landscapes to explore whether evolutionary or socioeconomic or whatnot. There are big questions left, and no easy answers sometimes. That’s a bad thing, too; if we were less lost in major issues like climate change or habitat destruction or gross imbalance in wealth/power, the world would be a better place.

Quite apropos! Rockin' artwork found in the 798 art district surrounding the Yang Gallery.

Quite apropos! Rockin’ artwork found in the 798 art district surrounding the Yang Gallery.

I find it helpful at times to ground myself in the knowledge that I am lost just like everyone else. There are different ways we can get lost: such as in pondering how dinosaur anatomy and physiology transformed over the Mesozoic era, or in throwing ourselves into weighty issues of business and diplomacy in the real world. To pretend we’re not lost risks becoming foolhardy; to exemplify the Dunning-Kruger effect.

It might be helpful for others to remind themselves of this sense of being lost, and that we all feel it or at least should at times. Students may sometimes look to their professors and think they have some monopoly on wisdom, but they’re lost too, and surely in some ways more lost than any of their students.

Smaller scale dino art.

Smaller scale dino art in a local shop.

Boris got a bit lost, too, when he came to my exhibit – pondering the dinosaur-bird fossils, he pondered out loud “There’s some bone that birds and reptiles both have that shows they’re related… the, umm, the ischium?” Not understanding what he meant by this (all tetrapods have an ischium), I redirected him, along with a reassuring comment that he’d done his homework. I did this a bit clumsily as the multitude of news cameras and lights and boom-mikes hovered around us in eager anticipation of Something Interesting Happening, and as his minders began to urge him to move onward through the LUIP exhibit. I noted the wrist of a dinosaur like Microraptor and how it already had the unusual wing-folding mechanism that modern birds now use during flapping flight or to keep their feathers off the ground when standing. He seemed to sort of like that, then shook my hand and said something like “very impressive, well done” and moved on to the next exhibit. (Willetts fared a bit better and stayed longer, but science is his business)

funky statue (4)

Random artwork from the Yang Gallery and around the 798 Art District follows… I liked the style. My kind of funky art. The statue above combines childlike toy aspects with sinister jingoistic imagery. And the next one, well… see for yourself.

In that brief, frantic conversation, we were both lost, and I think none the less of Mayor Johnson for it. He’d come off the plane, rushed to hotel and to the LUIP event, gave an impassioned speech about London and China, and then was whisked around between a dozen or so exhibits, pursued all the while by a throng of media and minders and gawkers- was he expected to know all the sundry details of maniraptoran evolution at that point? No. But we had some fun and smiled for the cameras and then it was all over as we spun off, reeling into our different orbits. I wouldn’t be surprised if, from time to time, a politician like Boris pinches himself and thinks privately, “Wow, these issues I am embroiled in are so convoluted. I am totally, utterly lost.” I think that’s a healthy thing, and I enjoyed repeated doses of that feeling during my trip. funky statue (2) In science, we often deal with a sense of awe or wonder—that is the sunny side of being lost. The other side, which can coexist sometimes in duality with awe/wonder, is the more fearful/anxious side, like when you’re stuck in a foreign city far from your hotel; surrounded by alien, fantastic scenery; and night is falling but no taxis are around to take you back, and the locals are starting to watch you to see if you’ll do something stupid (this was me, briefly, after doing some evening mall-shopping in Shanghai). How we react to that duality is, in some way, our choice. I point to a scientist studying evolution and a creationist freaking out about the subject as a good example of two polar opposites in how an awesome topic in science can evoke very different reactions within that duality. A seasoned traveller who likes to throw themselves into a city and experience blissful, unpredictable immersion, and a worrisome tourist who can’t stray far from their tour group provide analogous examples. But I digress; this post is in danger of becoming lost… Enjoy some cool statues as the denouement. funky statue (3) Get lost in the comments—what makes you have that sense of awe, or being lost, and how do you deal with it? funky statue (1)

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Hey, Christofer Clemente sent me these photos of a ~10cm long skull found by a student on a beach in Perth, Australia ( sent to Chris by Christine Cooper from ECU in Perth). What is it?

I figured I’d feed it to our mystery anatomy gurus for some fun, and see what comes up. You must justify your answer to get points. Convincing us with links to other photos/images will help. I have my ideas what it is, but they kind of suck, because I suck at skull anatomy.

Bonus points for incorporating Australian slang into your answer or beachy imagery/jokes.

No rhyming, unless the rhyming is using silly Australian-ish lingo like adding “-idoo” to the end of a word, or making up Dr-Seussian Oz-ish words.

Remember the scoreboard is here.

Difficulty: skull…

Stomach-Churning Rating: 1/10 super tame and evocative of lovely antipodean beaches, sigh…. (looks out window at grey English vista)

Go!

mystery-spec (4) mystery-spec (3) mystery-spec (2) mystery-spec (1)

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I love doing sciencey road trips with my team when I can. Last week, we got a treat: four of us got a behind-the-scenes tour of the fairly new Crocodiles of the World facility near Oxford; just over 90 minutes west of our lab, nestled in the pictureseque Cotswolds region. We were not disappointed, so you get to share in the joy! In photo-blog format. Pics can be clicked to emcrocken.

In the midst of an unpreposessing industrial estate lies: AWESOME!

In the midst of an unpreposessing industrial estate lies: AWESOME!

If you want to bone up on your croc species, go here and here. I won’t go into details. This is an eye candy post!

Reasonably accurate description that caught my eye.

Reasonably accurate description that caught my eye. My scientific interest in crocodiles starts here, and with their anatomy/relationship with dinosaurs, but I’ve loved crocs since I was an infant (one of my first words, as I may have written here before, was “dock-a-dile”, for my favourite stuffed animal at the time [R.I.P.]).

Siamese crocodiles. They were apart when we entered, then got snuggly later, as I've often seen this species do.

Siamese crocodiles. The large male is “Hugo.” They were apart when we entered, then got snuggly later, as I’ve often seen this species do. Heavily endangered (<300 in the wild?), so any breeding is a good thing!

The above photo brings me to one of my general points. Crocodiles of the World seems genuinely to be a centre that is breeding crocodiles for conservation purposes (and for education, entertainment and other zoo-like stuff). Essentially every crocodile enclosure had a mated pair, and several were breeding. Such as…

Yes, that is a Dwarf African crocodile, Osteolaemus, and it is a female on her nest-mound. Which means...

Yes, that is a Dwarf African crocodile, Osteolaemus, and indeed it is a female on her nest-mound. Which means…

Eggs of said Osteolaemus.

Eggs of said Osteolaemus.

And babies of said Osteolaemus!

And babies of said Osteolaemus! As if the adults aren’t cute enough with their short snouts and doglike size/appearance! These guys have striking yellow colouration, too. I’d never seen it in person before.

That’s not all!

Male American Alligator warming up. Smaller female partner lives in same enclosure.

Male American Alligator “Albert” warming up. Smaller female partner “Daisy” lives in same enclosure. Plenty of babies from these guys, too! Daisy comes when called by name, and Albert is learning to do so.

~1 meter long juvenile Nile crocodiles, bred at the facility.

~1 meter long juvenile Nile crocodiles, bred at the facility.

But then crocodile morphological diversity (colours, textures) and behaviour is just too cool not to focus on a bit, so here are some highlights from our visit!

Endearing shot of a crocodylian I seldom get to see anywhere: Paleosuchus trigonatus, the Cuvier's Dwarf Caiman. Spiny armoured hide and quite terrestrial; poorly known in many ways. Some more info is here- http://crocodilian.com/paleosuchus/description.html (note its tortured taxonomy)

Endearing shot of a crocodylian I seldom get to see anywhere: Paleosuchus trigonatus, the Schneider’s Dwarf Caiman. Spiny armoured hide and quite terrestrial; poorly known in many ways. Some more info is here (note its tortured taxonomy)

Black caiman, Melanosuchus niger, showing some interest in us.

Black caiman, Melanosuchus niger, showing some interest in us.

Cuban crocodiles cooling off by exposing their mouths.

Cuban crocodiles (Crocodylus rhombifer; pound for pound the most badass croc in my experience; badassitude that this photo captures nicely) cooling off by exposing the well-vascularized soft tissues of the mouth region.

But it’s not just crocs there, either, and some of the highlights were non-croc surprises and memorable encounters:

A surprisingly friendly and tame Water monitor (14 yrs old; does kids parties). Note person for scale.

A surprisingly friendly and tame Water monitor (14 yrs old; does kids parties). Note person for scale. Was about 2 meters long, 20 kg or so.

Business end of nice Water monitor, with tongue engaged.

Business end of nice Water monitor, with tongue engaged.

And we got a nice farewell from an African spur-thigh tortoise (Geochelone sulcata) with an oral fixation (action sequence thereof):

tortoise-nom (1)
tortoise-nom (2)

tortoise-nom (3)
tortoise-nom (4)

tortoise-nom (5)

Chowmp!

If someone visits this facility and leaves without being converted to a croc-lover, they must be from a different planet than me. It is a celebration of crocodiles; the owner, Shaun Foggett, is the real deal. He sold his home and quit his job as a carpenter to care for crocodiles, and it seems to be a great success– about to get greater, as they have plans to move to a new, bigger, proper site! They are seeking funding, so if you can contribute go here.

Right then… UK residents and visitors: you need to go here! Badly! Get off the blog and go now. If it is a Saturday/Sunday (the cramped industrial estate location only allows the public then).

Otherwise just stew and imagine how much fun you could be having checking out crocodiles. I cruelly posted this on a Tuesday to ensure thorough marination of any croc-geeks.

Muhaha!  😉

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What a week!

My team had a new technician arrive, Kyle Chadwick from Uni. Virginia, and NSF Postdoctoral Research Fellow, Dr. Ashley Heers (see here for an example  of new stuff she’s starting here at the RVC!), started working with me at the RVC, and then these guys showed up…

Salamanders!

Woo hoo!

First a tiger salamander (Ambystoma) paid a visit, for filming an episode of the Windfall Films/PBS documentary “Your Inner Fish” (a la the famous book):

So cute! Tiger salamander, soon to be a TV celebrity.

So cute! Tiger salamander, soon to be a TV celebrity.

Dr. Stephanie Pierce (who was also a coauthor on a great open access croc paper in Proc Roy Soc B this week) was filmed with Prof. Jenny Clack to recap some of our past work on tetrapod locomotion. Watch out for the 3-part series!

And that gorgeous salamander was a star performer in strutting his stuff for the camera to demonstrate the locomotion of modern tetrapods, including some lovely slo-mo footage from our lab cameras:

(if that’s too slow for you, try the normal-speed footage. I’ll admit, salamanders don’t really need slo-mo video for normal walking, but I like it)

So cool!

But then we got a special package… with three frozen fire salamanders (Salamandra salamandra) from colleagues in Germany!

Three new occupants of the freezers, for planning our studies of salamander locomotion

Three new occupants of the freezers, for planning our studies of salamander locomotion

This marks the start of an exciting new period in my team’s work in the lab. I’ve always liked salamanders and newts, and we’ve scanned and modelled plenty (e.g. this old post), but now we’re going to work with live fire salamanders (a first for me)! We are using the dead ones to plan the new studies with the live ones– these new studies will involve lots of high speed videos and force platform analysis (as shown above), in conjunction with XROMM (biplanar fluoroscopy/3D skeletal motion analysis) and other techniques including computer simulations. We got initial approval this week to work with these salamanders, and found a reputable source this week too, so it was definitely Salamander Week in my group!

This research all will feed into our upcoming studies of extinct tetrapods: we’re using salamanders to figure out how salamanders move and what limits their speed and gait, and then we’re using the same sorts of computer tools to try to estimate how extinct tetrapods may have moved and how locomotion evolved, in much more specific detail than our prior work had done, which was mainly about using 3D reconstructions of anatomy to show what those animals could not do. More about the project here.

Watch this space for more scampering salamanders!

UPDATE: And here’s one! Not quite scampering, but…

Setting up our two fluoroscopes for a test run of our gait studies-- but with one of the deceased salamanders. Gotta get a good image  before any live animal work!

Setting up our two fluoroscopes for a test run of our gait studies– but with one of the deceased salamanders. Gotta get good images before any live animal work begins!

An example of the kind of footage we’re aiming for (single 2D fluoroscope view from Nadja Schilling’s team’s research; see XROMM website for more details on the methodology)

UPDATE 2:

I did a CT scan with a normal medical grade CT scanner at the highest resolution we can manage (0.625 mm slices). Check out the results below, which amuse me:

Looks like a toy; too crude resolution. But we can see major structures, and we can very nicely see the “microchip” (which looks HUGE) that was placed in this animal’s back when in captivity, and then another structure is visible near the pelvis which might be another chip or else remains of some food, pathology, or a really odd pelvis– I am not totally sure!

So this is why we tend to use microCT, which can go down to as low as ~5 micron resolution, to get 3D anatomy of animals this small. It’s no surprise to me, but it is fun to see how far we could push our normal CT machine. The results aren’t horrid but wouldn’t have much scientific value for us. They did confirm for us that this specimen is heavily ossified, so the faint images of bone that we are getting in our x-ray fluoroscopes (above) are due to something going wrong with our camera system, not the animal’s immature skeleton. Stay tuned for more updates as the science happens!

UPDATE 3:

20 wonderful adult Fire Salamanders have joined our team and are relaxing over the coming week before we start taking them for walks. Here is one exploring its new home:

Fire salamanderUPDATE 4:

August 11-15, 2014 we are in Jena, Germany using their fancy biplanar radiography system (“x-ray video”) to study our salamanders, at last! Follow the tweets starting here, for more information as it happened! https://twitter.com/JohnRHutchinson/status/500187568416518144

and this video of “Jabba” the corpulent salamander walking-

with a top view, too-

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Greetings, freezerinos! WIJF has been on hiatus this summer because my life has been freaking insane! ICVM conference with 3 talks (See earlier post), then grant deadlines, camping trip, packing and moving house, hiring new staff and inducting them into my team, breathing, and other activities (ranging from essential to trivial and/or infuriating) in addition to Actually Doing Some Science have been to blame. But WIJF is coming back like a bad rash! It cannot be defeated by bureaucracy, by my current lack of home internet connection, or even by the end of the universe! I have grand plans, muhahaha… This is just a teaser to give me some blog-writing momentum so I can finish some of those bigger posts sooner or later.

Stomach-Churning Rating: 3/10 — unless you are the goldfish in question, whose stomach has already been duly churned.

So I mentioned house-moving above, and we’ve finished that over the previous week. I had two ponds at my old home, full of >200 fish and (during breeding season; tweeted under #FrogCount) >200 frogs and toads, among other critters, documented on occasion in my Flickr photostream/set. Our new abode just has one pond, but a decent one at that, and we inherited some new fish that I am getting to know. Here is a peculiar goldfish, whose unusual anatomy inspired me to catch it, take a photo, and blog about it. Consider this:

The fish in question.

The fish in question. Not your standard sleek, hydrodynamic specimen of Carassius auratus auratus!

I’ve done some Googling and confirmed my suspicions that this is not a pregnant goldfish but is some other condition that we could loosely term as pathological. It has been feeding reasonably well and seems not too perturbed– as much as a fish’s degree of perturbation can be read from its behaviour– by its rotund morphology. It has some problems controlling its inertia in rolling and pitching, which makes for some amusing viewing as well as easy capture.

But what’s up with this fish? It does not have dropsy, a nasty condition fish get that leaves the scales in a “pinecone” sort of extruded orientation. It may have a gut infection or other air sac problem. I’m certainly not a vet and don’t know and fishy vets. But I wanted to share the photo to stimulate discussion of fishy fish physiognomy. What’s your diagnosis, doctor internet?

Also, if this fish takes a turn for the worse, it very well may end up in my freezer and thence into an internal anatomy WIJF post (“What’s In John’s Goldfish?”). We shall see. But I’ve grown fond of this unnamed fish (soliciting suggestions for names below in the Comments), so I’ll see how long I can keep it out of that situation.

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Yesterday I encountered the question that, as a scientist who has studied a certain chunky Cretaceous carnivore a lot, most deflates me and makes me want to go study cancer therapeutic methods or energy sources that are alternatives to fossil fuels (but I’d be useless at either). I will explain why this is at the end of the post.

The question stems from a new discovery, reported in Proceedings of the National Academy of Sciences (PNAS) and thus expected to be one of the more important or exciting studies this year (no, I’m not going to get into the issue here of whether these “high impact” journals include the best scientific research or the most superficial or hyped “tabloid” science; they publish both, and not in mutual exclusivity). It’s a broken Tyrannosaurus rex tooth embedded in a duckbill dinosaur’s tail bone, which healed after the injury, showing that the animal survived the attack.

If you’re with me so far, you might be making the logical leap that this fossil find is then linked to the hotbed of furious controversy that still leaves palaeontology in crisis almost 100 years after Lambe suggested it for the tyrannosaur Gorgosaurus. If the hadrosaur survived an attack from a T. rex, then T. rex was a habitual predator and OMG JACK HORNER AND OTHERS BEFORE HIM WERE WRONG!

And you’d be right.

My encounter with the question stemmed from an email from a science journalist (Matt Kaplan) that, as is normal practice, shared a copy of the unpublished paper and asked for comments from me to potentially use in an article he was writing for the science journal Nature’s news site. Here, then, was my off-the-cuff response:


“Ooh. I do have a pretty strong opinion on this. Not sure if you’d want to use it but here goes. I may regret it, but this hits my hot buttons for One of the Worst Questions in All of Palaeobiology!

The T. rex “predator vs. scavenger” so-called controversy has sadly distracted the public from vastly more important, real controversies in palaeontology since it was most strongly voiced by Dr Jack Horner in the 1990s. I find this very unfortunate. It is not like scientists sit around scratching their heads in befuddlement over the question, or debate it endlessly in scientific meetings. Virtually any palaeontologist who knows about the biology of extant meat-eaters and the fossil evidence of Late Cretaceous dinosaurs accepts that T. rex was both a predator and scavenger; it was a carnivore like virtually any other kind that has ever been known to exist.

While the discovery is nice evidence, it is not particularly exciting in a scientific sense and is only one isolated element from species that lived for hundreds of thousands of years, which to me changes nothing and allows no generalizations about the biology of any species, only the statement that at one point in time a Tyrannosaurus bit a hadrosaur that survived the encounter. There is no real substance to the controversy that T. rex was “either” a predator or scavenger. It is just something that scientists drum up now and then to get media attention. I hope that soon we can move on to more pressing questions about the biology of extinct animals, but the media needs to recognize that this is just hype and they are being played in a rather foolish way; likewise scientists that still feel this is an exciting question need to move on. Maybe this specimen will allow that. But somehow my cynical side leads me to suspect that this “controversy” will just persist because people want it to, regardless of logic or evidence. (bold font added; see below)

Great galloping lizards, I am so tired of this nonsense. Maybe there is educational value in showing how science deals with provocative half-baked ideas about celebrity species, but scientists in the community need to speak up and say what the real science is about. It’s not about this “controversy”. Modern palaeontology is so much better than this.

Sorry for the rant. Maybe it’s too extreme but I’m just fed up with this non-issue! I suspect a huge proportion of our field feels similarly, however.”


(I later redacted a bit of it where I got a little too excited and used the word “curmudgeon”; a mistake, as that could be seen as ad hominem rather than a term of endearment, and this issue is about the science and not the people, per se. That bit is redacted here, too. I’ve also redacted a sentence in which I made an opinion on whether the paper should have been published in PNAS; that is mostly irrelevant here. I was not a reviewer, and authors/reviewers/editors have to make that decision. This would be a massive tangent away from what this blog post is intended to be about! I know some of the authors and don’t want to offend them, but this is about the science and how it is represented to the world, not about these particular authors or even this paper itself.)

Importantly, Kaplan’s story did include my skeptical quote at the end. I am curious to see how many other news stories covering this paper go that far.

Would a T. rex prey on, or just scavenge, a giant chicken? (art by Luis Rey)

Would a T. rex prey on, or just scavenge — or have a great time racing — a giant chicken? (art by Luis Rey)

I will stop right here and acknowledge that I’ve published a lot on a somewhat related topic: how fast a T. rex could run or if it could run at all. To me, that’s a great scientific question that has consequences not only for the predator/scavenger false dichotomy, but also for general theories of locomotor biomechanics (can an animal the size of a large elephant run as well as or better than said elephant? What are the thresholds of size and maximal running/jumping/other athletic abilities and how do they vary in different evolutionary lineages? And so on.). I’ll defend the validity of that question to the bitter end, even if it’s a question I’ve grown a little (but only a little) tired of and generally feel is about as well settled as these things can be in palaeontology (see my review here). I’ll also defend that it has been a real controversy (I have plenty of old emails, formal rebuttals submitted by colleagues, and other discourse as evidence of this) since I tackled it starting in 2002 and sort of finishing by 2011. I am sensitive about the issue of hyping my research up– this is something I’ve been careful about. I set a reasonable bar of how much is too much, check myself continuously with reflective thought, and I do not feel I have ever really crossed that bar, away from science-promotion into darker realms. This is partly why I’ve stopped addressing this issue in my current work. I feel like the science we’ve done on this is enough for now, and to keep beating the same drum would be excessive, unless we discovered a surprising new way to address the questions better, or a very different and more compelling answer to them.

T. rex: scavenger or predator?” was controversial back  in 1994 when Horner published “The Complete T. rex”, where he laid out his arguments. Brian Switek covered this quite well in his post on it, so I will not review that history. There was a big Museum of the Rockies exhibit about it that toured the USA, and other media attention surrounding it, so Horner’s name became attached to the idea as a result. Other such as Lambe and Colinvaux had addressed it before, but their ideas never seemed to gain as much currency as Horner’s did. But this post is not about that.

What this post is about is a consideration of why this is still an issue that the media report on (and scientists publish on; the two are synergistic of course), if most scientists aware of past debates are in good agreement that a T. rex was like most other carnivores and was opportunistic as a switch-hitting scavenger-predator, not a remarkably stupid animal that would turn down a proper meal that was dead/alive. Indeed, the Nature news piece has a juicy quote from Horner that implies (although I do not know if it was edited or if important context is missing) that he has been in favour of the opportunistic predator-scavenger conclusion for some time. Thus, as Switek’s article notes, even the strongest advocates of the obligate scavenger hypothesis(?) have changed their minds; indeed, that 2011 blog post intimates that this had already happened at least 2 years ago.

For many years, nothing has been published in the main peer-reviewed literature that favours that extreme “obligate scavenger” hypothesis. If I am wrong and there is a scientific debate, where are the recent papers (say within the past 5 years) that are strong, respectable arguments in favour of it? I contend that it is a dead issue. And if it is just about the middle ground; i.e. what percent of its time did a T. rex spend hunting vs. scavenging; we have no clue and may never know, and it’s not a very interesting question.

But who then is feeding off of this moribund equine; this defunct tyranno-parrot?

In thinking about my reply to the journalist over the past 2 days, I am reminded again of my general feeling that this is no longer a question of scientific evidence; the important bit in bold font above. Maybe we just like this “hypothesis” or the “controversy”, or maybe we’re lazy and don’t want to have to hunt for real debates in science.

But who are “the people?” I do not feel that The Public should be blamed; they are the people that The Scientists and The Media ostensibly are seeking to inform about what the state of modern knowledge and uncertainty is in science. So when I get asked about the controversy after a public lecture, I always try to go into detail about it. I don’t sigh and say “go Google it”. Nor do I do this to a journalist. Indeed, I’ve generally headed this issue off at the pass and added a blurb to press releases/webpages explaining my T. rex research to explain how it relates to the non-controversy; example here.

I have to begin turning my finger of accusation away from scientists and toward some of the media, because they must play a huge role in the shennanigans. Yes, scientists should know better then to play this up as a valid, heated, modern controversy. That is true. Yet I have a feeling that the balance of blame should also fall heavily on the side of media (general and science news) that continue to report on this issue uncritically as a real controversy. Thus the general public thinks it still is, and scientists/journals keep issuing papers/press releases that it is, leading to more reporting on this “controversy”, and the beast refuses to die. Switek’s article is a good counter-example of balanced coverage with clear application of critical thinking.

This is trivially different from other non-controversies in palaeontology such as whether birds evolved from a subgroup of theropod dinosaurs and hence are dinosaurs by virtue of descent (consensus = yes). So it is reflective of a broader problem of not calling a spade a spade.

And it’s embarassing, to a scientist, as my quote above expressed, to see dead controversies trotted out again and again, feeding the public perception that they are not dead.

That’s what leaves me frustrated. When do the shennanigans end?

I am reminded of a quote from a Seinfeld episode:

“Breaking up is like knocking over a Coke machine. You can’t do it in one push. You gotta rock it back and forth a few times, and then it goes over.”– Jerry, from the episode “The Voice”.

But this predator/scavenger relationship-from-hell leaves me, as a specialist working in this general area, feeling like I am trapped under that fridge. Help!

That’s why I started off this long post talking about feeling deflated, or disappointed, when asked this question. I do feel that way. I have to admit, I sometimes even feel that way when a sweet young kid asks me that question. Deep inside, I wish they wondered about something else. I wish that science had reached them with a deeper, more contemporary question. But when a journalist asks me how I feel about a new paper that revisits the “controversy”, I feel embarassed for palaeontology. Can’t we get past this? It makes us look so petty, mired in trivial questions for decades. But we’re not like that. This is a dynamic, exciting, modern field, but every news story about non-issues in palaeontology just perpetuate bad elements of palaeontology’s image.

To the scientists— why don’t we put our foot down more and say enough is enough, this is a dead issue? We have a role not only in peer review, but also in communicating our views about published work to the media when asked (AND when not asked, as in this blog post). But if you call them on it, do they listen? Which brings me to…

To the media (science/general journalists etc; I know this is a huge category and please don’t think I am blaming 100% of journalists or assuming they are all the same; they are not!)– if scientists tell you that a “controversy” is not such, at what point do you accept their judgement and kill the story, or at least use that quote? Does that ever happen? In what way are you at the mercy of senior editors/others in such issues? What power do you have? Is a shift in the balance of editorial power needed, or even achievable, in your case or in good exemplar cases? I’d really like to hear your experiences/thoughts. I am sure there is a lot I am not understanding, and I know many journalists are in a tough situation.

To the public— You’re often being misinformed; you are the losers in this issue. How do you feel about all it? (While this post focuses on a very tiny issue, the T. rex scavenger/predator unending drama, it is also about a broader issue of how the media perpetuates controversies in science after they have already gone extinct.)

What did this post have to do with freezers? Nothing. I’m just (H)ornery. Although I was once filmed for a planned Discovery Channel film about scientists who find a frozen tyrannosaur in polar regions and have to decide what to do with it before it slips into a chasm and is lost forever. Probably better that this never aired; it was cancelled. Segue to this post.

The Berkeley cast of the Wankel (MOR555) specimen of T. rex. Will we ever see the end of the predator/scavenger non-issue?

The Berkeley cast of the Wankel (MOR555) specimen of T. rex. Will we ever see the end of the predator/scavenger non-issue?

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Hotel Fira Palace: view of the city

Hola from Barcelona, where 500ish of us are telling each other about the latest research in the field of morphology (like anatomy, but broader, deeper, more explanatory; but if you prefer to think of it as anatomy that’s OK by me)!

#ICVM and #ICVM2013 (favoured) are the hashtags, and http://icvm2013.com/ is the website, and there’s Facebook and all that too! You can read the full programme and abstracts here. It’s the best damn conference in the universe and I am not remotely biased. It happens every 3 years somewhere in the world and is always chock full of 5 days of glorious new information on animal form and function and much more, with just too many interesting talks to ever be able to take it all in.

I am speaking a few times and want to share a talk that is about sharing the glory of morphology in public.

Morphology research, that is; please put your clothing back on!

It’s a text-heavier talk than my rules-of-conference-talks normally would allow, but I’m going for it, as that makes it better for sharing because my dulcet tones will not accompany the version I am sharing online. Someday in the future, at a conference venue  that is better set up for reliably live-broadcasting a talk (this is NO FAULT of the excellent organizing committee of ICVM/ISVM!), I would just do it live, but not today, not here.

The point of the talk should be obvious from the first slide (as in my last post). But I’ll presage it by saying that another subtext, which might not come through so strongly in the slides as opposed to my spoken words, is that we need to tell people that we’re doing morphology/anatomy research! We should not be shy of that label because deans or geneticists or conventional wisdom or what/whomever might say (very, very wrongly!) that it is a dead or obsolete science.

While natural history, evolution, palaeontology and other fields allied to morphology do pretty well in the public eye, I don’t see people often reminded that what they are being told about in science communication is a NEW DISCOVERY IN ORGANISMAL MORPHOLOGY and that we are still discovering such new things about morphology all the freaking time! (e.g. my team’s research on elephant false sixth toes, or Nick Pyenson‘s team’s research on whale chin sense organs to name just 2 such studies, both published on the same day in Science!)

Indeed, many of those discoveries such as new fossils/exotic living things with cool features, cool developmental mechanisms that produced complex structures, or insights into how organisms are able to do amazing things are implicitly morphological discoveries, but the fanfare too often goes to natural history, palaeontology, evo-devo or some other area rather than explicitly to morphology.

In contrast, I too often hear people poo-pooing anatomical research as yesterday’s science.

Vesalius's classic skeleton, which is great but to me also conjures misleading connotations of anatomy as a  defunct discipline.

Vesalius’s classic skeleton (from Wikipedia), which is great but to me also conjures misleading connotations of anatomy as a defunct discipline that old dead dudes did.

We need to sell ourselves better not only in that regard, of a renaissance of discoveries and insights in our field, but also in the sense of being in a renaissance that is driven by TOTALLY AWESOME TECHNOLOGICAL AND METHODOLOGICAL ADVANCES, especially computerized tools. We’re just as fancy in terms of techy stuff as any other biologists, but we don’t shout it from the rooftops as much as other disciplines do.

We’re not just primitive scientists armed only with scalpels and maybe a ruler now and then, although that simple approach still has its sublime merits. We’re building finite element models, running dynamic computer simulations, taking high-resolution CT or synchotron scans, manipulating embryos, digging up fossils, sequencing genes– you name it, morphologists may be doing it! (For similar views see Marvalee Wake’s recent review of herpetology & morphology; I’m by far not the first person to make the arguments I’m making in my talk, but I am putting a personal spin on them)

And of course, as the talk is being delivered by me, you might rightly expect that I’ll say that we need to do more of this kind of cheerleading where we have maximal visibility and interaction, which includes online via social media, etc. I’ll discuss one other venue which has featured prominently here on this blog, too: documentaries. Oh I’m not done with that hobby horse, no sirree, not by a long shot!!

ICVM intro

Anyway I should get back to preparing my talk but here is the link to the slideshow (props to Anne Osterrieder for the inspiration to put my slides up here):

Please discuss anything related to this topic in the Comments– I’d love to hear what you think!

I am happy to clarify what my shorthand notes in the slide text mean if needed. There are links in the talk to other sites, which you can click and explore.

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