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This week we conducted wallaby leg dissections for a study of the kneecaps of marsupials (pouched mammals). Placental (non-pouched) mammals like us almost all have bony kneecaps but many marsupials do not. Kneecaps do important things, acting like gears around the knee joints (e.g. this old post), and yet it is unclear why some marsupials have lost, kept or even re-evolved them as bones. So we’re investigating that and already noticed that one of our wallabies has bony kneecap(s) whereas the other doesn’t, so we’re checking out why and taking tissue samples to do histology (sectioning for microscopic imaging of tissue composition and structure) on so we can see what the knee tendon/kneecap tissues are made of. Some marsupials turn their kneecaps into fibrocartilage rather than bone or tendon and that can be impossible to identify without histology.

The wallabies are small, about 20lbs or so and just take a day or so. Like a turkey. And it’s Thanksgiving today, so here I am with a post about thawing specimens for science, rather than for food. Maybe the title will make sense now.

Stomach-Churning Rating: 7/10; thawed wallaby bits from the get-go.

Thawed lower leg and foot of wallaby. The stickers are for an old study that would take too long to explain…

This post was directly inspired by journalist Jason Bittel’s inquiry to me about my tweet on the wallaby thawing; he wondered if there might be a fun story linking thawing-for-science with thawing-for-Thanksgiving. Some highfalutin editors didn’t agree, so no printed/online story came of this, but I am not so highfalutin, hence this blog post.

Thawed wallaby forelimbs. I’m also looking into the “false thumbs” that some marsupials have (“sixth fingers”), much as elephants and other mammals may have.

Thawing is second nature for our lab’s team; we do it all the time. Avid readers will be unsurprised to learn that just about everything I’ve worked on has been frozen at some time, and thus has been thawed out at some time(s). Normally we don’t freeze if we need live tissue or undistorted tissue, e.g. to measure physiology or very fine microstructure– freezing disrupts all of that. We would instead use physiological saline solution or else a preservative like formalin. And you can only freeze and then thaw a specimen for two times or so before it becomes too useless even for anatomical study.

A small specimen like this salamander can be thawed out simply by running it under warm water for a little while or leaving it out for an hour.

We just leave specimens in a cart, or on a table or sometimes in a cold-room shelving area, for slower thawing. Space heaters tend to overdo things. We don’t do any rough calculation from some sort of thermodynamic first principles of time-to-thaw vs. specimen size (I wish we were that smart!); just seat-of-pants guessing and checking (yes, poking specimens to check their thawedness is a method of choice). Cutting things in half along the way, or skinning them, may be used to accelerate the thawing process. But it’s about as unscientific a method as we use.

The hardest specimens to thaw of course have been the largest specimens. Elephant legs can be >2 metres long and hundreds of kilograms (especially when frozen). A week at room temperature tends to work OK for getting them to a dissectable state. One has to balance the outer deterioration with the inner frigidness. We’re not so concerned about microbe growth in most cases, as one would be with a thawing turkey, and not at all about consumption. We just want to be able to dissect it and make observations, mostly via eyeballing the specimens as we dissect them,

Left hindfoot of an Asian elephant. Still frozen; this was bandthawed- I mean bandsawed- to see its internal anatomy nice and clearly. You may see this specimen again somewhere else– stay tuned! 🙂

Moisture and fluids can be a challenge: generally the rooms we thaw in are low humidity so moisture may not be an issue once the ice melts away, and we have drains nearby. We try to remove ice first or have towels to wipe/soak fluids up as thawing progresses. But if a specimen is sitting in a cart or storage bag with too much ice early on, that can thaw first and then turn the specimen into a nasty slurry of the stuff you’re interested in and the less desirable muck. So we try to avoid that.

De-thawing too early is bad. The smell gets progressively worse– and once the interior of the specimen is thawed enough, then bacteria get in there and the interior becomes a brewing ground for heat production (rather than remaining a cooler region), which accelerates decay, so we don’t want that. We have to check on thawing specimens regularly and move them to cooler storage areas, or begin dissection earlier, if the decay process is noticeably getting excessive.

Any insulation affects thawing time- so scales, feathers, thick skin, shells, fat (for a short while until it decays), and other layers will slow thawing—and may keep heat inside, if there begins to be thawing of the core. So sometimes you open up a specimen that seems dry and clean on the outside and the inside is unpleasant. But with experience that is not hard to avoid.

Thawed wallaby patella prepared for histology.

The foulest specimen I’ve thawed by far was a monitor lizard… it was shipped to me in California from Arizona when I was a PhD student. This was in August’s heat and the box of the big lizard sat thawing at the post office for 2 weeks before they contacted me and asked why a smelly box was bleeding. I came and got it and brought it back to our department but the smell was so bad it set off our building health & safety person’s alarm bells (sorry, David!) and they emailed around a “toxic alert” warning, until I bashfully made it clear that my lizard was the cause, not some toxic chemical. I got in some trouble and was very ashamed. But we put the specimen into a big tank of brine solution and the smell was reduced—the specimen may well still be preserved there 20 years later; I do wonder! Anyway, that experience was so horrendous – and I have a strong stomach—that I regularly recall it and seek to avoid a repeat. It was the most disgusting thing I’ve ever experienced. I do not recommend it.

What we tend to want to get from thawed specimens is: (1) descriptive anatomy (what connects where), and maybe (2) quantitative measurements (laborious metrics of “muscle architecture”– how much does each muscle weigh, how long is it, etc; over and over again for many muscles…). These data not only serve to tell us what makes animals different (and how this evolved) but also the data are used to test questions such as how animals work. In the case of things like wallabies, ultimately we’d love to know what their kneecaps do if they are bony or not; what difference does it make and why might there be differences? We’d spotted one wallaby already that seemed to have a bony kneecap on one leg, and a non-bony one on the other leg, so that asymmetry got us excited.

What’s surprising to learn about thawing animals for science? Well, my first thought is that it’s beautiful. I don’t tend to think of it as gross. I’ve rhapsodized about this before. Animals are wonderful inside and out, and I regularly pause during a dissection to marvel at how amazing the anatomical specializations of animals are. Simple details- shapes, colours, configurations- can be gorgeous. (Often the blood is minimal, drained out early, so that doesn’t detract from or hide the detailed imagery) The gentle yet complex path of a tendon around a joint can yield profound visual enchantment in its elegance. This is all the more true once one ponders how these complex structures evolved, and how much diversity of form and function is out there to study—and how little we know about it! We still don’t know well how to fix many problems humans have with their anatomy, and that’s orders of magnitude worst for most animals, because we don’t understand how anatomy works, or even what the anatomy is like in some cases. So that keeps me busy discovering things. Every specimen is different with surprising little variations, or big ones—sometimes there is one muscle, sometimes it is clearly divided into two muscles, in the same species or even the left vs. right legs. I love seeing those intricacies and wondering about them.

Thawed wallaby shank sliced open to show lovely digital flexors and gastrocnemius muscles. So many questions are raised by this!

If you’re thawing for Thanksgiving, or thawing for science, or thawing out family relations during a gathering, or thawing yourself out from the winter’s cold– my best wishes to you! May we all enjoy what we thaw.

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We’d been wanting to do a family holiday in Ireland for years and so we finally did. I’d been to Dublin twice before for work visits and we wanted a more rural experience. On others’ recommendations, we started in the city of Cork. With some sleuthing and asking around, I realized that we weren’t far then from gorgeous Killarney National Park, and then it wasn’t far west from there to get to Valentia Island, where incidentally there is something amazing for palaeontology-lovers. There was no detering me at that point from visiting what I’d only read about. I’ll mainly let the images tell the story.

Stomach-Churning Rating: 0/10; fossils and scenery. Kick back and enjoy.

Island map- it really is that simple to get around! The harbour town of Portmagee is damned adorable.

Driving in (no I am the passenger; not taking photo while at the wheel!)- excitement level = 8 and building… “Tetrapod carpark” sign ratcheted up the excitement and was amusing.

Headed to the trail; excitement level = 9…

Looking down onto the site (on the right); excitement level = 9.5; beauty level = 9.5 too!

Now, the site of what is broadly accepted by experts as a ~Late Devonian tetrapod’s fossil trackway(s) was originally described by Stössel in 1995. To me, that feels like a recent discovery but it is 22 years ago. The only other well-preserved, widely-accepted, probably-terrestrial, Late Devonian tetrapod trackways are from the Genoa River site in Australia; described by Warren et al. in 1972. Those trackways even reveal some details of the fingers and toes; these do not. Other tracks are either isolated footprints of minimal scientific value/clarity, subaerial (i.e. underwater), not clearly tetrapod (or now argued to be arthropod or other origin), not Devonian, or controversial for reasons I won’t get into here. Clack and Lucas have reviewed the relevant evidence recently. So there are essentially two places in the world that you can visit to view tracks like these and it was a joy to go visit one set. (Easter Ross, Scotland may be a third site but it is reasonably disputed in age and maker)

There is a big “however,” however- Falkingham and Horner showed how lungfish can produce tracks (with fins and heads together) that look like these– so there is still uncertainty. Without finger and toe impressions, claims of discrete tetrapod tracks can be risky, and it would be wrong to say that the Valentia Island footprints are uncontroversially or 100% certainly tetrapod in origin, although they are Devonian and made by some sort of animal.

Stössel et al. also published a very recent update on these Valentia Island tracks with more information. I wish I’d come across that before I visited (oops!). That study reports on a total of nine(!) trackways from the area, adding to the 1995’s first one (the “Dohilla locality, Do 1”– see diagrams below), and describes them as Middle Devonian (with a radiometric dating of 385 million years old). I’m not enough of a geologist to evaluate that; prior reports had focused on Late Devonian or so.

Rippled sandstone example; near-shore preservation characteristic of the trackway area/Valentia Slate Formation. It’s an alluvial deposit (freshwater floodplain), interpreted to lie inland from the coastal marine deposits. Raindrop impressions and possible mudcracks on the plane of the tracks offer some support that the tracks were made on (moist) land.

The island has plenty of signs advertising the tracks as a tourist destination but happily(?) there are no knick-knack shops stocked with plush tetrapods, or other developments at or near the site. One simply winds down a very narrow road near a radio station and old lighthouse, and parks then walks to see the tracks. No fancy crap; just AWESOME sights to take in, and some good educational information.

Explanatory plaque at the viewing area. Pretty good!

Nice image of where Valentia Island was; although the 385 My age may be exaggerated. It’s not clear how old the tracks are but “Mid-to-Late Devonian” might suffice. Claims that they are the “oldest known” may still be contentious (see references above).

Explanatory signs on the peak above the shore. Given the likely tetrapod trackmakers like Acanthostega-style critters, the adult animal may have been able to breathe air with lungs and underwater with gills.

Enough exposition– let’s expose those tracks! (images can be clicked to enlarge)

My first close-up look at the tracks. Whoa! Small tracks are presumably hand (manus) impressions; larger ones are foot (pes). The tracks go in an alternating fashion (like a salamander’s walk) and the animal was probably going from the bottom-right toward the top-left. Moss and moisture obscured some of the prints that day, sadly. The tracks are oval, with the long axes perpendicular to the direction of travel. There are some pesky geological deformations of the trackway, faults, and other distortions. 145 footprints in total are reported from this one trackway!

Trackway as it turns to the left and gets harder to follow. John-shadow for ~scale. Frustratingly for me, a little rivulet was coming down the hill across the left side of the trackway and hiding much of the detail of the end.

Alternative view of the majority of the tracks; turned ~90 degrees from above two views.

Zoomed-in view of the tracks from head-on (opposite the view in other photos); i.e. western position looking east (ish). I added red and blue dots to roughly outline the right side of the main trackway (red) and the second one (blue), which crosses it and may have been made after it.

Even these nice trackways, viewed by an expert, take some unpacking. Here is some:

Diagram of known tracks at the site by Stössel et al. 2016.

Diagram at view site with extra tail (or body) drag trail crossing the main tracks; described later by Stössel.

I’m not at all a religious person and I don’t really like the term “spiritual” either, but this experience was emotional for me. Awe is certainly the best word to describe what I felt on viewing these tracks. The literature just doesn’t do them justice; nothing beats a first-person experience like this. We were lucky with excellent weather, too, and we were almost alone during the visit so there was pleasant silence in which to contemplate the tracks. I brought my copies of three papers on the trackways and, struggling with the wind, compared them with the visible tracks to understand what other scientists had seen. That amplified the experience enormously for me.

Even if they turn out to be non-tetrapod or younger or something less exciting (“sham-rock”?), it was thrilling to see the Valentia Island tracks and think about what happened >350 million years ago when they were made by our very distant cousins, along the land-water interface of space and time.

(I also feel bad for online reviewers that were disappointed with the site- it’s hard to grasp the scientific importance and/or accept the evidence, even with the decent information available on-site. Even if people know the nice fossil record of dinosaurs, they may not know how good the fossil record of early tetrapods is and how confidently we can figure out what happened in the Devonian emergence of tetrapods onto land. But some visitors clearly got it.)

And, looking at the site myself, I realized how many more tracks might be buried under the cliffs of the site- the first trackway emerges from under a cliff and thus must still be preserved for some distance underground, awaiting future exposure. What more might we learn about that single animal and others that made tracks around the same time? I hope to live to find out. I feel a personal connection now to these tracks, left pondering what story they preserve– and hide. I’m glad I’m able to share my own story with you, and encourage you to make the visit yourself!

Putting my morphologist hat back on today, I had an opportunity to dissect an Elegant-crested tinamou (Eudromia elegans) for the second time in my life. The last time was during my PhD work ~20 years ago. In today’s dissection I was struck by another reminder of how studying anatomy is a lifelong learning experience and sometimes it’s really fun and amazing even when it’s stinky.

Tinamou foot. I did know that tinamous don’t have a hallux; big “perching toe” (1st/”big toe” in us); true of ratites/palaeognaths more generally. Unlike a chicken or many other birds. Just the three main toes (2, 3 and 4) are here.

Stomach-Churning Rating: 7/10; you gotta have guts to learn about intestine-churning stuff.

Tinamous are neat little partridge-like ground birds but they are not close cousins of partridges or guineafowl at all. Their closest cousins are other ratites/palaeognaths such as ostriches and kiwis. And hence they are found in South America, especially Patagonia in Argentina. I’ve seen them there, much to my enjoyment.

Said tinamou.

What struck me today was that, as I delved into the digestive system of this bird, I saw features that were unfamiliar to me even after having dissected many species of birds from many lineages. The intestinal region was very lumpy, with little bud-like pockets full of dense droppings. Furthermore, on separating the tubes of the small and large intestines I realized that most of the intestinal volume itself was caecum (normally a modest side-pocket near the juncture of the small and large intestines). Indeed, that caecum was caeca (plural): it had two massive horns; it was a double-caecum, feeding back into the short rectum and cloaca. Birds have variable caeca and it is typical to see subdivision into two parts, but I’d never seen it to this degree.

Oh why not, here’s the gizzard/stomach showing its grinding pebbles and bits of food, plus the strong outer muscle layers (pink) for driving that grinding. Small intestine heads toward the bottom of the image. Yes, we do need a better dissection light…

I had to question my anatomical knowledge at this point, wondering if I was identifying things incorrectly—did I really screw up somehow and these were other organs, like giant ovaries? But no, they were clearly full of faecal matter; they were digestive organs. I finished the dissection, still puzzled, and hit the literature. Right away, Google-Scholaring for “tinamou caecum” I found the answer, here (free pdf link):

“at least one species (Elegant Crested Tinamou, [Eudromia elegans]), the ceca contain multiple sacculations, resulting in structures that look much like two bunches of fused grapes.”

The caeca in question.

OK buddy, those are the little lumpy buds I saw. Bunches of grapes—exactly.

And later:

“The paired ceca of the Elegant Crested Tinamou are extraordinary and probably unique within Aves (Fig. 3): long and wide (12.5-13.0 X 2.2- 2.5 cm; Wetmore 1926) and internally honeycombed by many small diverticula. These outpocketings gradually diminish in size and organization from the base to the tip of the organ, apically showing a more spiral form of internal ridges like ratite ceca. Externally, the basal diverticula protrude from the ceca as pointed lobes, gradually becoming flatter but still clearly apparent toward the organ’ s tip.”

Whoa! I never knew that! So I happened to be dissecting a bird, fairly common in its homeland, that has a really bizarre and singular form of caeca/ceca! That hit my morphologist sweet-spot so I was very pleased and decided to share with you. It is one of those many examples of times when you quickly go from confusion to illumination as a scientist, emerging with a neat fact about animal biology. And journal articles help you get there!

The bare “brood patch” on the back end of the tinamou’s belly; a nicely hotspot for keeping eggs warm. Perhaps for brooding bad puns, too.

Hi, sorry for the social media spam but this is important to me: I got EU money to study dinosaur movement and we made a website for the project. There will be some fun stuff posted there and nowhere else, such as new palaeo-art that we commissioned specifically for this project. Oh, and science, too! Five years of science!

So please have a look at it now that it is live!

https://dawndinos.com/

I love our logo (by Andrew Bourne) so I will spray paint it everywhere I can.

Work from the DAWNDINOS project won’t be featured here much, so either watch that new website or me on other social media to find out what’s up!

And coming up on John’s Freezer: another episode of “Better Know A Muscle”! Yeah, baby!

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

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

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

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

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

Ostrich knee with muscles as 3D objects.

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

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

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

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

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

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

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

FEA results! (click to embiggen)

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

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

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

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

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

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

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

A thread that has run through my various rants on this blog, usually more implicitly than explicitly, has been blame. Who or what is to blame for something undesirable? Blame is another name for causation (of a negative outcome). As conscious beings we’re drawn to find that causation and attribute it to agents, be they gods/spirits/the universe, governments, corporations, CEOs, supervisors, friends or ourselves. In my mid-forties I’ve become better at watching myself for situations involving blame/causation and pause when entering them, because everyone’s unconscious bias often is to seek very simple scenarios of blame. But, much as we’re trained as scientists to find parsimonious conclusions, Occam’s razor can balance a very complex scenario on its knife-edge when reality is indeed very complex. And the point of this post is to explore how that complexity is often very real, but that needn’t be stifling. That’s probably bloody obvious to everyone but maybe the exploration will be interesting—or at least, for me, cathartic.

Stomach-Churning Rating: 0/10- or blame me. I’m at best an amateur philosopher and psychologist!

I feel that a big part of my job as a responsible human, adult, parent, supervisor, colleague, scientist, etc. is to blame myself when I deserve it. “Responsible” encompasses that ability to attribute blame/causation correctly. I find that blaming myself comes easier now that I’m battle-scarred and wiser for it, and I am more able to watch for excessive self-blame and paralytic pummelling than I was when I was younger. Low self esteem makes it easier to find the simple solution that you’re entirely to blame, or that simply someone else is. Excessive self confidence/power makes it easier to deny personal culpability or hunker down until it blows over. Balance is hardest– and I fail all the time.

I’ve been in many situations, ranging from the more micro-scale (smaller, embarrassing/silly events) to more traumatic (e.g. long-term arguments, correction/retraction of papers), in which I’ve had to consider blame or something like it. Foremost in my mind are my health problems and personal relationships. I’ve explored some of those here before and there are others I’d love to write about publicly but, no.

Yet lately it seems that blame is everywhere; the “blame culture” we hear about. Watch the news and virtually every story is about blame. Blame is a symptom of an angry world. It can be informative (or even a fun game) to think over who/what is not blamed in those stories (a simpler narrative is convenient, or propaganda and/or paranoia). We should be looking inwards at those we don’t want to blame, too.

There are many ways to confront the issue of blame. On one side we can say “don’t sweat the small stuff—and it’s all small stuff”. I hate that shit. “Happy happy joy joy” and all that; Voltaire rotates in his crypt. To me, that attitude also means “existence is meaningless” and “we are utterly powerless and blameless”, which is in contradiction to my experience and philosophy. On another side we can try to micromanage everything around us (small and big stuff), dissecting all the levels of blame in every situation, and we’d go/be insane. A middle ground approach within this spectrum, as usual, is best. Don’t be ashamed of that blame; it’s a thing we can tame.

Purpose and meaning in existence are chosen based on the direction we want our life to go (and how our successors look back on it postmortem). We place blame on those causative agents that push us away from that vector, and credit those that aid us. The more neutral agents are harder to grasp (e.g. the indifference of the universe to our existence). Purpose comes from our consciousness — to me they are the same; although our purpose leaves a legacy that persists after consciousness departs. Consciousness arises gradually from the spectrum of life – a virus is somewhat alive but closer to a rock than we are in terms of its “purpose” (more mechanical, less choices to make), then as evolution added nervous systems and other bits to life, more choices and complexity piled on. Purpose could be said to exist throughout that spectrum, from “instinct” to “choice”, all of which involve some causation — and chance. Vast oversimplification here, yes, but please stay with me. I’m getting there.

To avoid the extreme ends of the blame spectrum, we have to pick our battles and choose what is right or wrong in our world view. Lately I’ve watched smaller-scale events like United’s awful treatment of a passenger (and inability to de-escalate, then terrible PR handling) and huge global events like the resurgence of anti-intellectualism/populism or the clusterf*@$ in Syria, and blame inevitably comes to mind. Those who had more power AND responsibility to amend these situations, like CEOs or politicians, often deserve more blame. But the more complex story is that blame can be spread around these situations, much as they rightly anger us.

On an even smaller scale, close to my own profession and direct experience, I read a story by a PhD supervisor that largely blamed their student for falling silent (“supervisor phobia”) and then having problems with their degree, while the supervisor “was too busy to notice for another six months.” That seemed to exhibit gross irresponsibility for apportionment of blame in a messy situation: the old-fashioned legacy of authoritative, hierarchical scientific culture when people ranging from the university, department, colleagues, supervisor and student were to blame. It’s also a learning opportunity for many of us, to see how a bad situation evolved and think about what could have been done differently—indeed, differently from what one participant judges post hoc.

The red flag of a silent student/staff member could mean many things: the person might be intimidated about poor progress– or they might have self-esteem sharing what is actually good progress, they might be totally inactive (too little training? Hard technical problems stopping them?), or more. The point is that time is vital and acting too late probably will only worsen the problem, adding more blame to the supervisor and upper echelons.

The overall, common-sense approach I’ve cultivated with figuring ways out of hard situations at work and elsewhere is to (1) watch for (potential) problems, (2) think them through – allowing for the conclusion to be that the situation is complex and requires a nuanced approach (e.g. openly accepting one’s own culpability, maybe not yet pointing fingers at others deserving blame), and then (3) take action to try to resolve them. “The system” (e.g. rules and regulations) may be part of the problem but it can also be part of the solution. Although the system’s carrot is far more pleasant to use than the stick, they are there for reasons, to be applied with empathy and patience. Being human, we can run out of those latter two things and their fuel levels need monitoring.

The hope is that, finally, action leads eventually to a better outcome with a lesson mutually learned and, eventually, greater peace of mind as we reconcile our worldview with reality. The distinct possibility, though, is that we can’t fix everything and sometimes we have to try to find contentment in an imperfect world. Some causes are mysterious and we might have to settle for that mystery. Or we can spiral into paranoia and conspiracy theories; all the rage today; which can be simple scenarios of blame or very elaborate ones. These scenarios deserve their own rational inspection for personal biases that lead toward them, and the desire for easy answers.

But we can still blame the fucked up shit, and that can be therapeutic. Even if we hold onto blame, we can forgive it. Maybe this holiday weekend is a good time to forgive someone that is blamed.

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

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

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

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

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

Front view of the ankle/foot of our specimen.

Back view of the ankle/foot of our specimen.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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