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A Day in the Life of John

April 5, 2018 by John of the Freezers

As a person who has transitioned from the “simple life” (haha) of a grad student to postdoc to younger and then more experienced faculty member in academia/science, I constantly ponder how I spend my time. This is more so true lately, thanks to social media keeping me aware of how others spend their time (e.g. conversations about overwork and unrealistic expectations in academia/science), and thanks to my own experiences managing a moderate-to-large-sized group of 5-15ish scientists in the past ~10 years. I’ve had to learn to juggle a lot more than I did before and my life also has changed a lot (family, health, etc), some of which I’ve blogged about here before. Some of that excessive juggling is why there haven’t been so many blog posts here recently!

But today I want to turn the lens on the post’s title topic. What does a “typical” weekday in my life look like, with a focus on the academic/science aspects? There is no such “typical” ideal; every day is very different, but a Platonic abstraction will be heuristic. Let the clock tell the tale…

Stomach-Churning Rating: opinions may vary but I say it’s 0/10 (no gory photos).

0600-0700 I wake up and rush for the 2 big mugs of coffee that get and keep me moving, overcoming some huge side effects from medications I’m on. I feed the cats and check my email whilst having my coffee (and cereal + yoghurt). I deal with several simple messages from USA colleagues, or UK colleagues up late. Emails requiring more mindpower are saved for later. I tweet/retweet a little while skimming social media.

Nectar of the gods!

0730-0900 After shower etc. I begin my commute. 90 mins walk-train-train-walk (if no delays) and I can fit in another 60 mins or so of emails and some higher-functioning work (e.g. writing; editing papers; catching up on literature) on the train if I am feeling up for it. If I’m still too sluggish I listen to a (not-strictly-science but intellectual) podcast; e.g. RadioLab or Invisibilia; or (worst case) some rockin’ music.

0900-1000 Catching up on things in my office, with a few more emails, some organizing, quick chats with people around my office, and my day takes shape as I near my peak level of energy (and busy-ness).

1000-1200 Full steam ahead! I try to schedule my most demanding meetings to give them my full attention, or do my most challenging work if on my own.

1200-1230 John infamously gets hungry every ~5 hours and there is no stalling his need for fuel. Off to the campus restaurant he goes, for a hot meal and a little quiet time away from his office, to think/chat.

1230-1300 I like to leave this time as very flexible “me time”, whether spent on social media or whatever. I just do what suits me, maybe tidying up loose ends with smaller tasks, or just chilling (relatively) in contemplation.

1300-1400 A maybe less demanding meeting or a seminar (or a committee); in the latter case my powerful post-prandial somnolence becomes a battle now (and I don’t do caffeine >0800ish! Too sensitive). But I keep pushing on, and stuff gets done.

1400-1500 Another research-type meeting or data collection session, or writing, to fill some final, very valuable, on-campus time.

1500 Run for the train home, trying to stealthily escape campus without having any impromptu meetings that make me miss my train. My work day is not over but the commute is tiring so 6 hrs on campus and a bit more before and after are plenty!

1515-1645 Train ride and a bit of work where I feel able (50% of the time?).

1700-1800 Some catch-up emails (e.g. USA colleagues are waking up by now) and catch-up with family; juggling a lot. My activities vary a lot here: I may be inspired (even catching a second wind) to get some final work done or I may be totally wiped out and need a break. I listen to what my body tells me and also try to ensure I give myself time for non-work from here on.

1800-2100 Quality non-work time.

2100-2200  A bit of non-science reading before I fall asleep.

2200-0600 I need my 8 hrs sleep or I am a slow(er) grumpy John.

I’ve listed a “typical” day for non-teaching weeks. Currently my teaching load isn’t large by any measure, nor do I have many committee duties, and I am paid by my DAWNDINOS grant to spend 70% of my time (thru 2021) on that one project. So other than my October-November teaching I am mainly doing that 70% DAWNDINOS work, in various forms, plus a 30% that is some kind of science: a HUGE array of collaborations, some still stretching back to circa 2001 and still alive, some social media of course (although less these days than in ~2011-2012’s heyday, you may notice), and a potpourri of “other stuff”.

That “other” category is vast — travel to far-off places is a big time-sink lately, such as with 4 trips to the USA’s west coast in the past 4 months for seminars and conferences (although much of that involved DAWNDINOS presentations too). I am glad it’s all done, much as it was valuable science communication and meetings with friends/colleagues. Emails of sundry sorts fall into that “other” category too: I am not sure how many emails per day I field but I am the type of person that likes to handle a lot via email. Thereby I have a written record (my memory is patchy at times even though it can be excellent) that helps me organize my thoughts and actions. Maybe it’s 50 emails/day? Plus another 50 emails of fake conference/journal spam that seem to take more time deleting than they should (hello, spam filter)? Hosting visitors, talking on the phone/Skype with science writers, and certainly doing journal editorial/peer review duties are other big chunks. And so on; I won’t list it as most of it is normal academic life stuff. (Aside from the occasional elephant post-mortem)

Now, I got into academic life for what I feel are very good reasons, for me. A bit of context: I started working as a newspaper delivery boy at age 12, and continued that until I was maybe 15, then did odd jobs such as washing biochemistry dishes in my dad’s lab or fast food cashier/restaurant busboy & dishwasher until college. Then I kept up some intermittent part-time jobs like selling music CDs at Sam Goody, mixing margaritas as a “blender jockey” at Chi-Chi’s Mexican restaurant or tending snails at a marine ecology lab (thanks, Dianna Padilla!) until grad school. The point is, my parents had the wisdom to inculcate a work ethic into me, and that was VERY good, although I also got a strong taste of what it was like to work in a typical business, punching the clock in and out each day. And I HATED that clock-punching. It still provokes a deep visceral reaction from me. (Aside: ironically, that generous DAWNDINOS grant requires me to log my daily hours, and I hate that too but it must be done!)

In Sarasota, Florida where we spent winters with grandparents and I gleefully chased Anolis lizards (one blurry one here, I promise!).

To tie the story up, academic life attracted me (and I saw enough from my dad’s life as a professor to know) because it offered an escape from that punch-clock, 9-to-5 Monday-Friday life. The 9-to-5 strict schedule is just not for me, although I have plenty of respect those for whom it is; the world needs all kinds. I need flexibility; I need to be able to do science when Athena’s muse strikes me, not feeling chained to a rigid schedule and suffocating bookkeeping of how time is spent. In reality, in academia/science I feel now that it is impossible for me to realistically quantify how much time I spend on particular things – I may get a good idea while on the toilet, and that counts as science time doesn’t it? I am probably juggling a dozen things at once in my mind and efforts; work/other life/bullshit; at any one time, so partitioning my time is subjective nonsense. I prefer to be judged (when I must be judged) on what I do and its quality, and to be trusted to do this right by some “fair” standard rather than hours. To me, that’s what academia/science should be… (current reality be damned)

I blame the 80s.

That brings me to, how does a weekend look? In grad school I didn’t mind devoting some of my weekends – and plenty of late evenings – to work. Now, especially with a family, I do mind it. Living in Europe has helped me appreciate that quality-of-life mentality as well. It can still be a struggle within me, as I love science and sometimes I just want to do it; it may not matter if it is 6am on a Tuesday, 1pm on a Thursday or 7pm on a Saturday. Often I say “no” and don’t, and that can feel good, but sometimes I let myself enjoy after-hours work, because I live for enjoyment in all its forms in my life. That is a privileged position to be in and I do not forget that privilege. However, I’ve worked since 1989 to get here, so 29+ years of university life has to have been for some non-disposable purpose in my life. I’ve posted before about work-life integration and how I don’t personally recognize a rigid divide between these in my life, but with 24 hours in a day there is a real zero-sum game at play, so I prioritize what I do (or go with the moment).

In non-work mode: Reggie Regent (I’m the lion on the left; not the dog, who was beloved Daisy); high school mascot. A very sweaty one in that suit!

One failure I am working on is to return to fitting in ~2 gym workouts/week into my weekday schedule; that was good when I was doing it a couple of years ago. I have no great excuses for that. Nor would I rely on the “too busy” excuse for anything above — I find the “cult of busy” in academia to be tedious and repugnant (the post linked there is mainly about PhD students but at the faculty academic level such genitalia-sizing-up talk is rife). We all do what we can with our limited time, yet our life-goals are probably not identical, and we probably don’t understand what others do with their time or what constraints they work under.

Dealing with encroaching age and disability has thrown new challenges into my time-budgeting that I am still grappling with. I may want to work (or even need to, beyond the level of overcommitment I’m already in) but sometimes I simply do not have the energy. I don’t give myself guilt and grief for this if I can help it, while I expect that once I do have more energy I’ll devote it appropriately. I respect my limits, much as I confess I still don’t understand them.

As a lifelong learner, I am still learning how to live my life, one day at a time. Everyone lives their life differently. My life now is lived so incredibly differently from how I lived it 20 years ago as a young grad student that I can have a hard time recognizing myself in that scared, scarred, lost, naïve yet still very excited man.

One day that young grad student went into San Francisco, bought a huge teddy bear, and brought it home to cuddle with because he felt so alone. A blues musician on the street saw him carrying that bear and improvised a song mocking him, and he didn’t mind because it was the truth that was captured in that parody, and he was a student of the truth. It was a dark period in that man’s life—a void that was filled with work.

“How, then, can we fail to take the importance of factuality and reality seriously? How can we fail to care about truth? We cannot.”

But now my daughter has inherited that bear and it was worth every dime, every lonely tear, and every hour worked to become the person I am; the only person I can be at this moment, flawed yet ever in flux. Tomorrow will be another day and I will be grateful for those new hours, awake to their prospects and alert to their tribulations.

That was a condensed day in my scientific life and some backstory to it. Thanks for taking your time to read it.

We’ve been through a lot together.

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Posted in RANT | Tagged , , | 8 Comments »

Darwin the Human

February 12, 2018 by John of the Freezers

A personal story here for Darwin Day 2018. I knew about as much about Charles Robert Darwin as any typical science-interested student when I was growing up. But eventually I had the good fortune of taking a history of science class at the University of Wisconsin as an undergrad, and it inspired me with the story of Darwin as a human being, not just some clever scientist with a long argument that changed the world.

Stomach-Churning Rating: 0/10 unless you have Darwin’s gut-wrenching problems.

I devoured Desmond & Moore’s amazing biography of Darwin “the tormented evolutionist”, which was the transformative event for me. At the time I was experiencing the beginnings of some health problems that didn’t seem that far from problems Darwin suffered for much of his life, and then, as I read more about his life, I saw more features of this man that brought him vividly to life. I still think about those traits and how some parallel my life in certain ways (not that I am in any way a giant of science like him!!). And so this blog post was born, thusly:

I’m writing this post early on Darwin Day and entirely from memory, rather than doing my usual research into the post while I go; to keep the post more personal and less academic (e.g. just quick Wikipedia links below). I feel connected to Darwin’s life experience because, like him, I wandered about as a student, unsure about my direction in life and causing my parents some consternation early on. He tried medical school (Edinburgh; too bloody) and theology (Cambridge; faith just was not his thing) but found hunting for beetles on the heaths more exciting. In high school I played with ideas such as Hollywood screen-writing (too risky), radio DJ (I had no skills) and truant or criminal (I hung out with some shady characters even though I still had some morals; despite transgressions and convictions).

I then took a standardized “what is your best career fit?” test in biology class which conclusively told me that biology was best for me as a career; and that rang true. I’d always loved nature and so that was the idea I had when I went to undergrad. I signed up for the wrong college (Agriculture & Life Sciences, not Letters & Science; confusing divisions!) at the UW. I got some early research experience in that first college: I tried my hand at raising colonies of Indian mealmoths (Plodia interpunctella; I can still identify them!) and their parasitoid wasps. At that same agricultural lab I got to do my own experiments in a basement wind tunnel over my summer holiday, in which I released those pesky moths to fly down the tunnel toward various kinds of pheromone-based lures, finding that one kind seemed to work best. But I didn’t like that and frankly found agricultural science boring, for me. We didn’t connect, nor did some other lab experiences I had. But I grew from them and still value them (and respect the science and people involved) very much.

I took Evolution and also Functional Morphology courses, didn’t do great (I was young for the classes), and then finally took that history class—boom! Aha, scientists can be human! Not just hypothesis-robots! Darwin was a man of great privilege, having his estate and wealth handed down from his funky grandpa Erasmus and stern father Robert. But, in addition to his meanderings that eventually forced him (via his father’s impatient urgings) to become the Beagle’s naturalist for a five year voyage, he suffered in quite human ways throughout much of his life. The greater trials commenced during that voyage, with still-mysterious health problems and the fractious relationship with eccentric Captain Fitzroy. They continued with his marriage to cousin Emma Wedgwood (yes, of that pottery-famed lineage) in which they lost four of ten children at young ages (most critically, beloved Annie at 10 years old) and in which they struggled with Darwin’s diminishing faith and Emma’s stalwart beliefs.

Finally, Darwin struggled famously with his “big book” for >20 years, afraid of its impact and its reception, and of its need to have a watertight, evidence-based argument from many perspectives, with his hand forced by Alfred Russel Wallace’s converging ideas. Along the way, with his health and family problems, he had to contend with his mentors’ and peers’ reactions to his ideas—although one could call the acceptance of much of his main arguments to be a “happy ending” (the post-mortem eclipse of Darwinism, and its eventual resurrection + syntheses, aside). These trials that Darwin faced as a human are all relatable, and the more one learns about him the more complex, flawed, emotional and yes, tormented he becomes. He can be both a hero and a tragic figure or a cautionary tale.

When I get the chance, I like to teach students about this human side of Darwin. It is a way into the heart of the science, to show a person’s journey along with the wonder of discovery, and how such a journey is not necessarily a simple or even joyful one. I can feel the many facets of Darwin in my own life—the intensely curious, peripatetic, enthusiastic young man who loved experiencing nature in all its raw forms, the chronically suffering disabled person who sometimes could not enjoy the work or other aspects of life that he treasured, the family man who loved time at home, the explorer who treasured roaming the local heath or far-flung foreign terrain, the meticulous scientist who exhaustively gathered tiny bits of data in isolated studies to slowly build toward grander ideas, and much more.

But Darwin is a different human, too. We live in such different times, when there the world of science is far larger but the world feels far smaller, more interconnected. Naturalists today are not simply landed noblemen who can play with science in their luxurious spare time, nor do they work alone at their pursuits. Anyone can be a scientist, and a career scientist can, if they are fortunate and skilled enough, assemble their own laboratory in which they lead a team to tackle their big questions that captivate them. The individual questions in science tend to be smaller (more incremental and specialized) today, yet can overall (across career(s)) be bigger because we can tackle -and have tackled- some of the bigger ones; Darwin’s big questions being among the giant ideas we are now poised upon.

It’s not all about science, though. Darwin’s story, which I think about so often, reminds me of how we all struggle in our lives and amidst the joy of discovery in everyday life there can be considerable suffering and regret. It is a bittersweet story; an ever-so-human story. And today is a good day to reflect on that, and to celebrate life while we lament what has been lost.

Posted in Mad Science | Tagged , , , , | 4 Comments »

Jumbo Time

December 21, 2017 by John of the Freezers

Back in November 2016 I got an exciting email from colleague Dr. Richard Thomas, who was building a team of experts for a proposed documentary on Jumbo the elephant; the famed proboscidean of the Victorian era (and arguably most famous elephant of all time, first international celebrity animal, etc.). I knew him from social media and from our mutual interests in chicken anatomy and evolution. And that exciting email, for once, worked out! Over coming months I chatted with the film producers and they could see a place for me in the programme, contributing my expertise in elephant (postcranial) anatomy, locomotion, health/welfare etc. Lo and behold, in May 2017 I met Sir David Attenborough at Heathrow and we flew out to New York City to film with the skeleton at the American Museum of Natural History. And to cap it off, I got to meet another childhood science communication hero: Professor David Suzuki of CBC’s “The Nature of Things“– my adrenaline levels were sky high!

Brooklyn neighborhood by our hotel. Lots to do!

The show has aired in the UK and is coming very soon to Canada and the world (details below). Here’s my part of the story.

Stomach-Churning Rating: 3/10– bad bones but no blood.

We filmed from 15-19 May 2017 at the AMNH’s warehouse of mammalian skeletal remains, which is housed deep in the Brooklyn Army Terminal; a picturesque site in and of itself. And it is a site with a lot of history— WWI and II, Elvis and more.

It was a hectic week of the usual documentary stuff: repeat the same lines and motions again and again from different angles and with different paces and intonations (I cannot help in these cases but think about the Simpsons “Fallout Boy” episode), from ~9am-5pm, with plenty of downtime watching setup or other bits being filmed. I’m used to all that. But having the time to peer around the collection and chat to Richard and colleague Dr. Holly Miller (handling the tissue isotopes side of the story) about Jumbo’s skeleton was a lot of fun during downtime and filming itself. Not to mention the utter joy of studying one of the most famous museum specimens ever, and an animal widely held to be one of the largest of its kind, with much mystery surrounding its history despite its fame. (Wikipedia does a fair job of summarizing some of this)

Here are some photos to tell the story:

Photo of the team, courtesy of Infield Fly Productions (CBC production, “Jumbo: The Life of An Elephant Superstar”.

The Brooklyn Army Terminal, with a view of the harbour beyond.

Inside the terminal: old army staging area and an evocative wooden Liberty/tank artwork.

Army terminal cat. Shipping still comes through the terminal so I guess there are plenty of rats and handouts from cat-lovers to keep it going. I miss our cats when I travel so this moment was appreciated.

Whale skulls and other specimens inside the AMNH warehouse.

First view of Jumbo’s remains.

Photo opp with Sir David.

Photo opp with Prof Suzuki.

That’s the setup. I’ve done ~15 other documentary episodes/shows but this was like nothing else– simply an awesome experience.

Now the delivery: we set to studying those bones. We’d seen photos before, and Henry Fairfield Osborn had illustrated the specimen as his type of “Elephas africanus rothschildi” (Sudanese elephant; no longer valid but those were different times– it’s now just a nicely preserved Loxodonta africana africana), so we knew some of what to expect.

Looking at Osborn’s classic monograph. Oddly he didn’t address the GLARING MASSIVE PROBLEMS WITH THE TEETH!

Skull with terrible tooth pathologies– and let’s play spot Mumbo, my daughter’s toy elephant! He might even appear in some TV footage!

We had noted some serious issues with some bones (pathologies). I won’t spoil the message here but will show some images. I know some experts have voiced issues with how the tooth pathologies/growth were explained in some footage but I can’t address that here; it’s not my expertise. The important point to me is that the teeth are incredibly messed up and that can easily be linked to bad diet and other management/health issues, as the documentary explains.

Jumbo’s torso in left side view. Glorious preservation.

Right forelimb, showing that the “growth plates” (epiphyses”) were not all fused, consistent with Jumbo still growing– as expected for an African male elephant in his 20’s.

Right elbow with some pathologies consistent with degenerative joint disease.

Surprisingly, Jumbo’s feet were not in nasty condition in terms of pathologies. I’d expected to see that. They’d been painted and drilled for mounting, but were not riddled with arthritic changes that I could see.

Strange bony plaque on the left pelvis (hip) region; something I’d never seen before in any elephant (and I’ve seen many). Why? The programme offers a reasonable explanation.

Jumbo’s right hip, with bad erosion of the bone and thus presumably the overlying cartilage. Ouch!

Strange extra prong on one right rib in Jumbo- we didn’t figure that out. It could conceivably be natural variation.

So, poor Jumbo suffered some jumbo-sized problems, and in complex ways. That’s just scratching the surface of what his skeleton tells us, and there’s plenty more in the show plus plenty more we can say later– there’s real science that came out of this programme! I was surprised to find how little had been stated anywhere in the scientific literature about Jumbo’s pathologies.

Sad as Jumbo’s skeletal story is, the broader story of his life and death is sadder still. For purposes of time I don’t think any of the three versions of the show will get to delve into how Jumbo’s mother may have been slashed to death by a broadsword, as the story below describes was the ancient practice:

I’d hate to be “so pestered by a popinjay”, too.

Adding insult to injury, we can reflect on how Jumbo was taken from the Sudan to the east (across the Suez), then on boat to Italy and then overground to Paris, where he lived for a little while until the zoological garden sold him to London. Luckily Jumbo avoided becoming a meal to starving Parisians during the Prussian siege of 1870-1. So he did not become elephant consommé like some of his co-captives did. The more one learns about Jumbo’s life and the life of elephants in captivity in the 1800s, the more harrowing the tale becomes.

Jumbo is THE celebrity elephant. His name has come to mean ‘big’ and ‘bombastic’, from applications to jumbo jets to hot dogs and other (darkly ironic) forms of consumption and extravagance. He has had a jumbo effect on Western culture, but also symbolizes the complex human-elephant relationship, such as the inspiration for “Dumbo’s” own sad story. We love elephants but our fascination with them can also be their undoing, such as poaching for the ivory trade or mistreatment in captivity. Jumbo’s story writ large is also the story of elephants, and our story to learn from. If anything comes out of my participation in the Jumbo documentary for the public’s benefit, I hope it is increased empathy for how we interact with elephants. They are like us in many ways (maybe over-emphasized with anthropomorphism in many accounts), but also unlike us (maybe even unfathomable) in not only their size and anatomy but also in aspects of their prodigious intellect, emotions and social structure. Elephants aren’t just jumbo spectacles. They are jumbo responsibilities for humans now that we dominate the planet so much.

Want to catch a version of the Jumbo show? I’ll try to keep this list up to date:

BBC iplayer now: https://www.bbc.co.uk/iplayer/episode/b09jcxrj/attenborough-and-the-giant-elephant

BBC One: 5:05pm on January 31st

CBC: 8pm on January 7th– trailer is here:

http://www.cbc.ca/player/play/1115035715562

And the international version is coming soon, plus the above versions surely will circulate globally in some ways.

Have a jumbo time (in a good way) in the rest of 2017 and onwards into 2018!

-John

Posted in Frozen Mammals, Museums are Cool, When Anatomy Goes Bad | Tagged , , , , , , , | 2 Comments »

The Bird Knee Challenge

December 10, 2017 by John of the Freezers

An epiphysean Sispyhean task today: solve this mystery that has been bothering me for >15 years. It’s about bird knees. Read on.

Stomach-Churning Rating: 1/10- bones and brief words. Nothing to worry about.

Here is an ostrich. I was interviewing undergrads the other day and looked up to see it, then thought something like: “Oh yeah, that little bit of bone really bothers me. I cannot figure it out.” What little bit of bone?

Right leg, side view, ostrich…

This little bit of bone. Zooming in on that ostrich’s knee:

Who am I? (femur above; tibiotarsus below; “PTE” is the crest of bone with the white arrow on it)

The little bit of bone is not talked about much in the scientific literature on bird knees. But we know it’s there and it is part of the composite bone called the tibiotarsus (ancestral tibia, this bit of bone, and the proximal tarsal [ankle] bones on the other end; the astragalus and calcaneum of earlier dinosaurs).

What is it? We call it something like the proximal tibial epiphysis (PTE for short, here). An epiphysis is an end of a bone that fuses up with the shaft during growth, around the time of skeletal maturity; ultimately ending longitudinal (length-wise) growth of that bone. Mammals almost ubiquitously have them. So do lizards and tuataras. And some fossil relatives. Not much else– except birds, in this particular region (the two ends of the tibiotarsus; also in the foot region; the tarsometatarsus; which also has its share of mysteries such as the hypotarsus; I won’t go there today). You can see the PTE in mostly cartilaginous form if you take apart a chicken drumstick.

This PTE, like other well-behaving epiphyses, fuses with the tibiotarsus in mature birds, forming one bone. But the young ostrich’s knee above shows the PTE nicely; and other living birds show more or less the same thing.

It begs for explanations. I’ve talked about it in a few of my papers. But I’ve always punted on what it really means– does it have anything to do with the patella (they appear at similar times in evolution; we know that much, roughly)? Where does it come from, developmentally? (we sort of know that but more work is needed in different species and in high resolution) When did it evolve? What does it tell us? Why is it there in living birds and almost no other extinct birds/other dinosaurs? Does it have anything to do with why birds, during their evolution, seem to gradually increase the fusion of skeletal elements or ossify new ones (tendons, kneecaps, etc)? Why here and not in the femur or several other long bones of birds? How much do these PTEs vary between (or within) bird species?

This is the challenge in the post’s title. I present to you: solve this puzzle. Developmentally, biomechanically, evolutionarily, genetically, whatever– why does this PTE happen? There are hints– e.g. this paper proposes why growth rates of long bones favour the formation of “secondary centres of ossification” like this. But I’m unable to satisfy myself with any solutions I can find. Maybe you can complete The Bird Knee Challenge?

Have a go at it in the Comments below! There are plenty of papers or even a grant or something involved in sorting out this single mystery; one of the many basic mysteries about animal anatomy.

Posted in Anatomy Vignette | Tagged , , , , , , , | 9 Comments »

Papers Seen In 2017

November 25, 2017 by John of the Freezers

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Posted in Biomechanics, Croc-cicles, Exalting Archosauria, Two-Dog-Night Tetrapods | Tagged , , , , , , , , , | Leave a Comment »

You Thaw That, We Thaw These

November 23, 2017 by John of the Freezers

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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Experiencing the Irish Tetrapod Tracks

August 11, 2017 by John of the Freezers

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!

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