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Posts Tagged ‘science story’

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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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.

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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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It has been almost three months since my last post here, and things have fallen quiet on our sister blog Anatomy to You, too. I thought it was time for an update, which is mostly a summary of stuff we’ve been doing on my team, but also featuring some interesting images if you stick around. The relative silence here has partly been due to me giving myself some nice holiday time w/family in L.A., then having surgery to fix my right shoulder, then recovering from that and some complications (still underway, but the fact that I am doing this post is itself evidence of recovery).

Stomach-Churning Rating: 4/10; semi-gruesome x-rays of me and hippo bits at the end, but just bones really.

X-ray of my right shoulder from frontal view, unlabelled

X-ray of my right shoulder from frontal view, unlabelled

Labelled x-ray

Labelled x-ray

So my priorities shifted to those things and to what work priorities most badly needed my limited energy and time. I’ve also felt that, especially since my health has had its two-year rough patch, this blog has been quieter and less interactive than it used to be, but that is the nature of things and maybe part of a broader trend in blogs, too. My creative juices in terms of social media just haven’t been at their ~2011-2014 levels but much is out of my control, and I am hopeful that time will reverse that trend. Enough about all this. I want to talk about science for the rest of this post.

My team, and collaborators as well, have published six recent studies that are very relevant to this blog’s theme- how about we run through them quickly? OK then.

  1. Panagiotopoulou, O., Pataky, T.C., Day, M., Hensman, M.C., Hensman, S., Hutchinson, J.R., Clemente, C.J. 2016. Foot pressure distributions during walking in African elephants (Loxodonta africana). Royal Society Open Science 3: 160203.

Our Australian collaborators got five African elephants together in Limpopo, South Africa and walked them over pressure-measuring mats, mimicking our 2012 study of Asian elephants. While sample sizes were too limited to say much statistically, in qualitatively descriptive terms we didn’t find striking differences between the two species’ foot pressure patterns. I particularly like how the centre of pressure of each foot (i.e. abstracting all regional pressures down to one mean point over time) followed essentially the same pattern in our African and Asian elephants, with a variable heelstrike concentration that then moved forward throughout the step, and finally moved toward the outer (3rd-5th; especially 3rd) toes as the foot pushed off the ground, as below.

African elephant foot COP traces vs. time in red; Asian elephant in orange. Left and right forefeet above; hindfeet below.

African elephant foot COP traces vs. time in red; Asian elephant in orange-yellow. Left and right forefeet above; hindfeet below.

Gradually, this work is moving the field toward better ability to use similar techniques to compare elephant foot mechanics among species, individuals, or over time– especially with the potential of using this method (popular in human clinical gait labs) to monitor foot (and broader musculoskeletal) health in elephants. I am hopeful that a difference can be made, and the basic science we’ve done to date will be a foundation for that.

  1. Panagiotopoulou, O., Rankin, J.W., Gatesy, S.M., Hutchinson, J.R. 2016. A preliminary case study of the effect of shoe-wearing on the biomechanics of a horse’s foot. PeerJ 4: e2164.

Finally, about six years after we collected some very challenging experimental data in our lab, we’ve published our first study on them. It’s a methodological study of one horse, not something one can hang any hats on statistically, but we threw the “kitchen sink” of biomechanics at that horse (harmlessly!) by combining standard in vivo forceplate analysis with “XROMM” (scientific rotoscopy with biplanar fluoroscopy or “x-ray video”) to conduct dynamic analysis of forefoot joint motions and forces (with and without horseshoes on the horse), and then to use these data as input values for finite element analysis (FEA) of estimated skeletal stresses and strains. This method sets the stage for some even more ambitious comparative studies that we’re finishing up now. And it is not in short supply of cool biomechanical, anatomical images so here ya go:

fig5-vonmises

Above: The toe bones (phalanges) of our horse’s forefoot in dorsal (cranial/front) view, from our FEA results, with hot colours showing higher relative stresses- in this case, hinting (but not demonstrating statistically) that wearing horseshoes might increase stresses in some regions on the feet. But more convincingly, showing that we have a scientific workflow set up to do these kinds of biomechanical calculations from experiments to computer models and simulations, which was not trivial.

And a cool XROMM video of our horse’s foot motions:

  1. Bates, K.T., Mannion, P.D., Falkingham, P.L., Brusatte, S.L., Hutchinson, J.R., Otero, A., Sellers, W.I., Sullivan, C., Stevens, K.A., Allen, V. 2016. Temporal and phylogenetic evolution of the sauropod dinosaur body plan. Royal Society Open Science 3: 150636.

I had the good fortune of joining a big international team of sauropod experts to look at how the shapes and sizes of body segments in sauropods evolved and how those influenced the position of the body’s centre of mass, similar to what we did earlier with theropod dinosaurs. My role was minor but I enjoyed the study (despite a rough ride with some early reviews) and the final product is one cool paper in my opinion. Here’s an example:

fig6a-bates-sauropod-com-evol

The (embiggenable-by-clicking) plot shows that early dinosaurs shifted their centre of mass (COM) backwards (maybe related to becoming bipedal?) and then sauropods shifted the COM forwards again (i.e. toward their forelimbs and heads) throughout much of their evolution. This was related to quadrupedalism and giant size as well as to evolving a longer neck; which makes sense (and I’m glad the data broadly supported it). But it is also a reminder that not all sauropods moved in the same ways- the change of COM would have required changes in how they moved. There was also plenty of methodological nuance here to cover all the uncertainties but for that, see the 17 page paper and 86 pages of supplementary material…

  1. Randau, M., Goswami, A., Hutchinson, J.R., Cuff, A.R., Pierce, S.E. 2016. Cryptic complexity in felid vertebral evolution: shape differentiation and allometry of the axial skeleton. Zoological Journal of the Linnean Society 178:183-202.

Back in 2011, Stephanie Pierce, Jenny Clack and I tried some simple linear morphometrics (shape analysis) to see how pinniped (seal, walrus, etc) mammals changed their vertebral morphology with size and regionally across their backbones. Now in this new study, with “Team Cat” assembled, PhD student Marcela Randau collected her own big dataset for felid (cat) backbones and applied some even fancier techniques to see how cat spines change their shape and size. We found that overall the vertebrae tended to get relatively more robust in larger cats, helping to resist gravity and other forces, and that cats with different ecologies across the arboreal-to-terrestrial spectrum also changed their (lumbar) vertebral shape differently. Now Marcela’s work is diving even deeper into these issues; stay tuned…

fig2-randau-measurements

Example measurements taken on felid vertebrae, from the neck (A-F) to the lumbar region (G-J), using a cheetah skeleton.

  1. Charles, J.P., Cappellari, O., Spence, A.J., Hutchinson, J.R., Wells, D.J. 2016. Musculoskeletal geometry, muscle architecture and functional specialisations of the mouse hindlimb. PLOS One 11(4): e0147669.

RVC PhD student James Charles measured the heck out of some normal mice, dissecting their hindlimb muscle anatomy, and using microCT scans produced some gorgeous images of that anatomy too. In the process, he also quantified how each muscle is differently specialized for the ability to produce large forces, rapid contractions or fine control. Those data were essential for the next study, where we got more computational!

mouse-mimics

  1. Charles, J.P., Cappellari, O., Spence, A.J., Wells, D.J., Hutchinson, J.R. 2016. Muscle moment arms and sensitivity analysis of a mouse hindlimb musculoskeletal model. Journal of Anatomy 229:514–535.

James wrangled together a lovely musculoskeletal model of our representative mouse subject’s hindlimb in the SIMM software that my team uses for these kinds of biomechanical analyses. As we normally do as a first step, we used the model to estimate things that are hard to measure directly, such as the leverages (moment arms) of each individual muscle and how those change with limb posture (which can produce variable gearing of muscles around joints). James has his PhD viva (defense) next week so good luck James!

mouse-simm

The horse and mouse papers are exemplars of what my team now does routinely. For about 15 years now, I’ve been building my team toward doing these kinds of fusion of data from anatomy, experimental biomechanics, musculoskeletal and other models, and simulation (i.e. estimating unmeasurable parameters by telling a model to execute a behaviour with a given set of criteria to try to perform well). Big thanks go to collaborator Jeff Rankin for helping us move that along lately. Our ostrich study from earlier this year shows the best example we’ve done yet with this, but there’s plenty more to come.

I am incredibly excited that, now that my team has the tools and expertise built up to do what I’ve long wanted to do, we can finally deliver the goods on the aspirations I had back when I was a postdoc, and which we have put enormous effort into pushing forward since then. In addition to new analyses of horses and mice and other animals, we’ll be trying to push the envelope more with how well we can apply similar methods to extinct animals, which brings new challenges– and evolutionary questions that get me very, very fired up.

Here we are, then; time has brought some changes to my life and work and it will continue to as we pass this juncture. I suspect I’ll look back on 2016 and see it as transformative, but it hasn’t been an easy year either, to say the least. “Draining” is the word that leaps to mind right now—but also “Focused” applies, because I had to try to be that, and sometimes succeeded. I’ve certainly benefited a lot at work from having some talented staff, students and other collaborators cranking out cool papers with me.

I still have time to do other things, too. Once in a while, a cool critter manifests in The Freezers. Check out a hippo foot from a CT scan! It’s not my best scan ever (noisy data) but it shows the anatomy fairly well, and some odd pathologies such as tiny floating lumps of mineralized soft tissue here and there. Lots to puzzle over.

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I still have my original photocopy, from my grad school days circa 1996, of the 1983 Ted Garland classic paper “The relation between maximal running speed and body mass in terrestrial mammals”, festooned with my comments and highlighter pen marks and other scribblings. That paper remains the backbone of many research questions I am interested in today, and I often think about its underlying concepts. Here’s the key scatterplot from that paper, which I could almost replot by hand from memory, it is so full of implications (and can be clicked to embiggen it, perhaps even speedily depending on your internet connection):

Garland 1983- max speed

Stomach-Churning Rating: 1/10; data and their ramifications; offal-free.

The major points (IMO there are less exciting ones about which theoretical scaling model the data best fit) of the paper are: (1) the fastest-running mammals are neither the smallest nor largest, but those around ~100 kg body mass; (2) if you fit a linear equation to the data (see above; hashed line), it seems like speed increases with body mass linearly (with no limit to that increase, within the body mass range of the data), but if you analyze individual groups of mammals they either don’t change speed significantly with size or they get slower– refer back to point #1 and the polynomial regression that is shown in the figure above (curved line). That’s the biological-question-driven science at the core of the paper (with some methods-y questions at their foundation; e.g. should we use a linear or polynomial regression to fit the data? The latter fits best, and gives a different answer from the former, so it matters.).

But what also fascinates me is the question of data. As the author, who taught me Evolution as an undergrad at U Wisconsin (this had a big impact on me), fully admits in the paper, the ~3-page table of data “necessarily sacrifices some accuracy for completeness”. This paper is about a big question, how mammal speed changes with size, and so its big question explicitly allows for some slop in the data (I will return to this issue of slop later). But given that very few of the data points have very accurate measurements for speed, or for body mass for that matter, how much can we trust an x-y plot of those data, no matter what method is used? Oh there is so much opportunity here for geeky pedantry and niggling scrutiny of data points, true, but hold on…

Plenty of follow-up papers have mused over that latter question, and spin-off ones. Here are some of their plots, re-analyzing the same or very similar data in different contexts. A look at how these papers examine these data and related questions/methods leads into some avenues of science that fascinate me:

Garland 1988- max perf

Garland and Baudinette (link to pdf here) checked whether placental (i.e. most; including us) mammals could run/hop faster than marsupial (pouched; e.g. kangaroos) mammals. Their results said “not really”, as the plot intimates. Scatter in the data, especially between 0.01-10 kg, confounds the issue- there’s a lot of specialization going on (notably, animals that are very slow for their size, e.g. sloths). But marsupials are not, as had been suggested before, inferior to placentals in some basic way such as running ability.

GarlandJanis1993-Fig5

Above, Garland and Janis 1993 (link to pdf here) examined how the ratio of metatarsal (“sole bones” of the lower end of the leg/foot) vs. femur (thigh bone) length relate to speed, with evolutionary relationships taken into account. The methods (“independent contrasts” and its conceptual kin; I won’t delve into that morass more here!) did not exist for looking at phylogeny’s effects on the results in Garland’s 1983 paper. Yet “cursoriality” (relative elongation of the lower limb) had been thought to relate to running speed for over 80 years at that time, so that was what they tested: how much does limb-elongation correlate in a positive way with maximal running speed? They found that the answer was “sort of”, but that other things like home range size, energetics, ecology, etc. might explain as much/more, so caveat emptor. And by looking at the plot above, it’s evident that there’s a lot of specialization (scatter, along the x and/or y axes– check out the giraffe/Giraffa and cheetah/Acinonyx outliers, for example). While ungulates seemed to have a better relationship of speed and limb dimensions, their predatory carnivoran relatives did not.Christiansen 2002- max speed

Christiansen was one of two studies in 2002 that looked back on those Garland 1983 data in a new way, and like the 1993 study with Janis considered these data in light of limb lengths too.  The plot above delved into how running speed changes with lengths of forelimb bones, again finding appreciable curvilinearity (indirectly supporting the non-linear scaling idea– even at large sizes, relatively longer-legged mammals aren’t faster). The plot on the right side (b) measured the relative length of the olecranon process; the “funny bone” that acts as a lever for support of the elbow joint against gravity. Again, even mammals that have stouter elbow-supporting processes aren’t faster; there’s a “happy medium” of elbow-osity for optimizing running speed (and huge scatter in the data!). Ultimately, this analysis concluded that it wasn’t speed that animal anatomy seemed to be optimizing overall, especially as size increased, but rather energetic cost, although there was a lot of variation in the data and accounting for phylogeny only muddled things up more (as it tends to do).

diaz2002

Iriarte-Diaz was the other 2002 study to tackle the speed-vs-size issue. It focused primarily on whether mammal speeds showed “differential” (i.e. non-linear) scaling with size, as per the polynomial regression in Garland’s 1983 study. It showed that smaller mammals seemed to either get slightly slower with increasing size or else not change maximal speed (depending on detailed methods/data stuff that don’t matter here), whereas bigger mammals exhibited very strong declines of speed with size past a threshold (optimal) body mass.

So, repeated analyses of Garland’s 1983 data (and modifications of those data) at least uphold the fundamental conclusion that big land mammals cannot move quickly, in an absolute sense (meters/sec or kph or mph) — and much more so in a relative sense (e.g. body lengths/second or other normalized metrics). We might then ask why, and my research scrutinizes this issue in terms of the fundamental mechanisms of movement biomechanics and anatomy that might help to explain why, but for brevity I won’t go there in this post. I want to wander elsewhere.

I want to wander back to those data used in the above (and other) studies. All of the studies discuss the quality of the data and bemoan the lack of quality. I’d agree with them that it’s hard to imagine most of the data being consistently off in a biased way that would fundamentally alter their conclusions. But I still worry. We should worry about the data points for the extreme animals- the fastest, slowest, largest and smallest. We should worry about subjectively removing “outliers” such as hippos or cheetahs, as they do change some of the results.

I worry about elephants, for example: my work has shown that they can “run” about 7 meters/second or ~25 kph; not the 35 kph used as data for African elephants (from speedometer-y anecdotal estimates)– ~1.4 times the speed we’ve been able to measure for both species. See this old “blog post” (sort of) for more information on the tortuous history of characterizing elephant speeds and gaits. And are a white rhino and hippo able to run at this same 25 kph speed as the original data in the 1983 study state, or faster/slower? No one has really nicely measured this so we can’t be sure, but I can imagine it being off by a similar 40% or so. On the other hand, if the bigger animals in the dataset are slower than the original data, that actually strengthens the conclusion that bigger animals are slower, so who cares that much, in the grand scheme of things?

We could worry about plenty of other maximal speed data points, and the “average” adult body masses assumed (although I doubt those would change the results as much as the speed errors). Maybe another question is, in doing such broad-scale analyses should we only include data points that have maximal precision (e.g. elephants, horses, cheetahs, greyhounds, humans and a few others)? We’d maybe be able to do a study of 20 or so species. I doubt it would show much that is different if we did, although I expect that sample size and noise would begin to dampen out the signal. See below.

However, a double standard begins to become evident here. In modern biomechanics (and probably the rest of biology/science), there’s a strong emphasis on data quality and technologically precise measurement. Garland’s 1983 study might be hard to get past peer review today (or maybe not). We agonize over single-species studies trying hard to measure animals’ maximal speeds (a very hard thing to be sure of in terms of motivation, but not intractable unless one takes an almost antiscientific/overly cynical view that animals could always be holding back some critical reserve unless they run for their lives– is that reserve 1%, 10% or 100%? Probably closer to the middle, in good studies). We measure multiple animals and many trials, in field and/or lab conditions, with documented video footage at high resolution and frame rate, with GPS tracking or other tools to maximize precision. We take pride in these high standards today. That’s what makes scientists wriggle uncomfortably when we look back at the data in those older maximal speed papers and ponder how few data points are verified, documented, precise and essentially trustworthy.

So should broad studies be working by the same standards as narrow studies? (I’m far, far, far from the first scientist to think about this but it’s interesting for me at least to think about it in this case and others) There is potential tension here between empiricists who want precise data and theoreticians who want to tackle those Big Questions, and that’s a pattern one can see throughout much of science. I sit on the fence myself, doing both approaches. I can think of plenty of similar examples, in “big data” palaeobiology, morphometrics, genomics, physics and so on. Some of those fields have nice databases with quality control over the data; they’ve maybe solved this problem to a large degree. This tiny area of mammalian maximal speeds hasn’t solved it, but how urgent is the need to?

On the flip side, even if the data points have some error of 10-20% or even 40% that error will probably be largely random, not biased toward assuming that bigger or smaller animals are slower than they truly are, or medium-sized animals faster. We still have the reliable cheetah data point (and racehorses, and greyhounds) showing >100 kph (and 70 kph) speeds for ~100 (and ~40, 400ish) kg animals, so there is evidence for a peak of maximal speed (the cheetah outlier, and one might also throw in pronghorn antelope or others that are pretty damn fast but not yet well measured) at medium body size. I expect there would be incremental overall progress if we did improve the data quality, and that would still be nice (comforting!) but it would be a tough, tough slog. Indeed, my team is doing its share of that, already tackling the data point for giraffes this year (stay tuned!). The potential gains are still there, especially for understanding the unique biology of individual species– that noise in the data (or specialization, if you prefer) is interesting!!! We need that kind of work, partly because the big questions, sexy as they are, still depend on having data quality as a foundation, and old questions still need revisiting from time to time as data quality is improved by those in the trenches of gathering it.

My team’s journal club has gone over the Garland paper lately and we’re hitting the others later this summer, but I wanted to throw these thoughts out there on this blog now to see if they generated any fun discussion, or they might introduce others to the science of maximal speeds and what we do/don’t know. One thing we don’t know much about is what kinds of patterns non-mammalian groups exhibit today. Chris Clemente did some great work on this with lizards, finding a pattern similar to the mammal one. I’ve struggled in my work to move toward trying to address similar questions for extinct groups, but there the data quality presents a challenge I find exciting rather than depressing, although I still have to shrug when I see limb lengths or proportions being used as a proxy for speed. We can do better.

So I’d love to hear your thoughts on any of the points here. Maybe some of the old-timers have stories from ye olden days when Garland’s work was originally published; I’d love to hear those, or other points/questions/favourite papers.

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I was inspired this week, after a stimulating conference, to put into writing what my team stands for. What do we have in common with other scientists, or what makes us different, or what should we all be doing together beyond the actual science itself? I’ve written advice for my team before, but not something like this, and with new staff/students coming soon, I want something ready for them to see what we’re about, and what we need to become more of, too. Not a rant, but a calm codification of our core beliefs. I presented this to my team later in the week for edits and ideas, and felt that it’s now ready for sharing. There’s no reason to keep it private; I personally like what’s here at the moment, and response from my team was positive, too. I am sure opinions will vary, and it’s my team to lead so I might not agree with some, but the fact that I’m posting this means that I expect it’s quite likely that this “mission statement” will improve if commenters pipe up.

No images this time, except for Jerry above. I want the emphasis to be on the thoughts.

Stomach-Churning Rating: wot? No, not that kind of post.

Here we outline my team’s fundamental principles and ethos for our scientific activities, beyond the rules of the RVC and other institutions (e.g. funders) that we adhere to, and basic common sense or morality, or elaborating on and emphasizing those in relation to our work. This is a document that will evolve as we learn from our experiences. We welcome input and discussion. It applies to all of Team Hutch’s staff and students (and Prof. John Hutchinson [JRH], too). The intent is positive: to remind us of our overarching scientific standards, to foster lively debate and to educate ourselves by challenging us to think about what we stand for. The motivation is to communicate the team’s ethos, benefiting from past lessons. The application is flexible, to accommodate the fact that everyone is different, although some of our ethos must be rigid.

While we are unified by research interests, we respect and value other aspects of science including teaching and administrative work. We consider science communication and public engagement to be part of research, too. Our focus is on the evolution of locomotor biomechanics in organisms and, to maintain a strength in this focus, we try to remain within it. However, “side projects” are enthusiastically supported as long as the main research foci of projects (including past work) remain the top priorities and on target.

We aim to conduct high quality research (and other scientific efforts), where possible setting and following gold standards, and acting in a professional leadership role. We are willing to slow our research progress in order to improve the quality of the work, although we also recognize that science is an imperfect human venture. “Minimal publishable units” are not a goal of our research but we fully recognize that early career scientists need to publish in order to move on in many careers.

We are scholars- we care deeply about communicating with each other, our colleagues, and the past and future of science via the literature. We try to keep up with progress in our fields. This is normal practice but we try to do even better than normal. We aim to publish all research we do; otherwise it is wasted effort.

We also treasure openness in science, from publishing our work in open access formats where feasible, to externally sharing open data and methods with the broader community and public, as quickly and comprehensively as possible.

Regular communication within the team and with collaborators is immensely valuable and so we respond promptly to it (sensibly—working or communicating out of normal working hours is not expected!). We participate in regular lab meetings as part of the team culture and communication. In socializing within and outside the team, we respect others, attempting to avoid offense caused by demeaning or other behaviour. Our team members should not be condescended to in discussions or otherwise made to feel stupid- speaking out should be cultivated, not repressed with aggression or egotism.

Quality of writing (and other communication such as oral presentations) in science is something that we aim to maximize, improving our own writing skills and products by pushing ourselves to learn to be better and by constructive critiques of others’ writing.

Ethical practice in all of our work is immensely valued. This includes diversity of people and skills, which broaden our perspectives and help us to transcend disciplinary boundaries that might otherwise blind us to broader insights. We are a team- we support each other in our work and careers, trying to eschew internal competition or territoriality. Mutual benefits from teamwork need to be raised above selfish individualism; focusing on one person’s need for career boosts may reduce others’ prospects.

One of the most treasured ethical principles that we cleave to is integrity. Among the worst scientific crimes that can be committed are fraud, intellectual property theft and plagiarism—no goal justifies those actions. We seek to be our own toughest critics, within reason, to minimize errors or worse outcomes in our science. We promptly correct our published research if we find errors needing amendment.

Ethical sourcing of and handling of data or specimens is important to us. Whether it is favouring publically accessible as opposed to privately held fossil (or other) specimens or cadaveric material that was obtained via traceable sources that maintain legal or optimal standards of animal welfare, we target the “high road” in obtaining material for study. If we conduct in vivo animal research we attempt to transcend the standards of the “three R’s” and set a high example, maximizing animal welfare and benefits from that research—as we are at a veterinary university, we involve vets and other health and welfare specialists in transferring knowledge from our work to improving the lives of animals.

We try to be inclusive in coauthorship of publications (following RVC rules) but especially do not tolerate “honorary coauthors” who contribute little or nothing to research. We value idea production, data collection and provision, analysis, writing and revision as ingredients that earn coauthorship.

[these next two paragraphs still feel too formal/negative to me, but they highlight something important that I’ve learned about; to a degree there must be hierarchy, and I’m the only one that will be in Team Hutch for as long as it lasts, so I have to be the enforcer of its long-term rules. It’s the aspect of this job that I probably enjoy least, but it looms there whether I like it or not.]

As per RVC intellectual property (IP) rules (as well as rules of funders etc.), all IP generated while working at the RVC remains its IP, managed by JRH. Such IP can and should be used by those generating it, and others that would benefit (including those who have since left the lab) but to ensure proper conduct, JRH must approve usage.

JRH is the leader of the team and as manager has final say in decisions, but encourages negotiation and reasonable disagreement to seek mutually acceptable solutions. JRH makes mistakes too and welcomes them being pointed out. JRH seeks to help his team succeed in whatever career goals they have and for long after they depart Team Hutch, but expects solid effort at work in return, and dedication to the principles outlined here.

We are human. We want fun, enjoyable lives including at work, and this pursuit of fun colours all that we do, because science is fun and so are scientists. We want that fun to radiate upon the world and echo through time.

=====

That’s as it stands right now. What do you think? I am certain that I have left things out, but it’s a start.

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I’m now asked all the time how I’m holding up in light of recent changes in my life, and I have a hard time answering that question, as I am still not sure – except that I am still here, more or less. Over the past year I’ve grown to embrace the notion, reinforced very strongly by my own frequent experiences, that I am disabled (in the medical/legal sense). I’ve had a harder time embracing the idea that I am now part of a minority group (I have strongly accepted that I am a senior, white, male scientist in the upper-middle class; which conflicts with “minority” in every way). Categorization aside, one conclusion I’ve been grappling with is the strong sense that I have been diminished. I can’t think as clearly, my memories are fading and my body is increasingly decrepit in physical and physiological ways that are becoming obvious to me. And yet I struggle to explain these feelings to people. So here I am, writing a blog post that is partly about what it’s like to feel that my personal “glory days” as a human scientist have passed. It’s not very uplifting stuff although there is a surprise of sorts at the end.

Stomach-Churning Rating: 1/10; a medical imaging scan of my disintegrating body, and a cartoon of surgery.

Before I go into my sob story, I should reinforce that there’s not just doom and gloom here. There is a heady, very complex mix of feelings. I’ve still got a great family (save the demise of all of my close relatives from my parental generation and before) and friends. Much of the time I’m still able to smile and have some fun. I’m not a Syrian refugee clinging to life in a tent while the world turns its back on me, or an Indonesian orangutan aloft in a tree watching the forest burn around it while the palm oil plantations spring up in the distance. All is relative. I know my life best and that’s what I blog about, so here is that infinitesimal perspective on life.

At work, I am buoyed by a fantastic team of scientists; some of the best I’ve ever worked with. They churn away at the science while I try to lead them. We’re doing some very hard science lately; some of the most challenging work I’ve been involved in. And my declined health hasn’t helped me to lead them, so sometimes they’ve had to rely on each other for spans of time. It’s not the best analogy but I often feel like we are in the open sea and I am swimming in front of our boat full of precious science, navigating while I barely keep my head above water and they struggle with the oars and their own exhaustion. In real life, it’s seeing their smiling faces and the wonderful science they show me on a regular basis that helps me keep afloat, personally.

Indeed, one take-home message of this post is that, while feel myself diminish, struggling with normal ageing and major new health problems, I see those I mentor grow and I get a vicarious thrill and pride from it. This is something that I know many research scientists experience to varying degrees, and often in conjunction with the too-often-metaphorized(?) experience of parenting and having the joy of seeing one’s offspring mature while one feels old age encroaching. As many research managers witness, I see my team’s collective research expand and build new levels of coolness in our little domain, I get wiser by reflecting on the successes and failures, and one could say I enjoy some credit from my team’s work by navigating our general course of research while they do the daily technical work and I help mentor them through their careers.

But first, a content cat.

But first, a content cat.

At the same time, as my collaborations and range of projects broaden, following my increasingly integrative interests, I see my relative expertise decreasing. It seems a long way now from my postdoc years, just over a decade ago, when I could run most or all of the software and hardware I needed to do the science. I am increasingly uncomfortable with that. However, I still learn new skills and knowledge so I am far from static as a scientist, and I am pushing myself more and more to learn more, wrestling with my age/health-imposed difficulties in learning. Furthermore, as a human being I feel far more aware of the world and the broader issues at stake than ever before (thanks in part to social media, I should add; but also thanks to my curiosity about life beyond my research). Improving my mind is still a goal of mine. The “diminishing” label I apply here is not that fair perhaps, but it’s how I feel about myself and I am sure there is some truth to it. It is the foe I grapple with.

So I get bemused reactions when I’m asked how it’s going and I respond, somewhat glumly, that I’m “hanging in there”. Many know I’m having health problems and tell me they are inspired by how I’ve held up and how well my (team’s) research and science communication and other work seems to be going, from the outside. Indeed, we’re cranking out more papers and surprising amounts of funding (see below) than ever before, so on paper it does look very good. It helps a little to hear those comments of how impressed some friends and colleagues are, but I don’t feel very impressed with myself. I feel lucky to have a great team of scientists and to have a great job in an insanely good laboratory environment, because otherwise things would be very different for me. I’m starkly aware of my privilege and feel vastly fortunate for having it.

My personal experience in work/life doesn’t reflect the joy of “success” that might seem to spring forth from my CV or the image that the outside world might get of me. I’m seesawing back and forth between those intermittent joys (and other happiness that comes from life away from work!) and a sense of hopelessness. I see the grim state of humanity and the broader world, and I look within and see my own decrepitude advancing, and I feel sad. It’s not a clinically manic-depressive seesaw but I can see some similarities when I apply my scientific detachment skills and look at myself from a quasi-objective perspective. I’m not the naïve, “everything is excellent” optimistic grad student I was—I just see flickers of that person these days. Sometimes I like to see him.

Much of the torques applied to the seesaw come from my oscillating health status- I alternate between good and bad days, with hints of a broader weekly rhythm that my physicians and I are still trying to grasp. Those oscillations determine everything for me: I can be bursting with energy and make strong inroads on my “to do” list, or I can be utterly drained and unable to do much more than stare vacantly or maybe fire off some emails to make incremental progress on work. I tend to be lingering somewhere in the middle, with far less vitality on average than I had two or so years ago. I look back on those past years and feel like I am looking up at the peak of my life and career. Time will tell if that’s “true” in some way or not.

Regardless, over the past 18 months there have been huge “valleys” from when I end up in hospital after major epileptic attacks, with a couple of weeks of recovery afterwards. Overall, my capacity to do what I used to be able to do has been halved. At best, I feel like I can operate at maybe 90% of my peak capacity and that never lasts long. Some of this is the inevitable decline that comes with entering one’s mid-forties, but some is a new step-change that has hit me over the past 18+ months since I became an epileptic suffering from tonic-clonic (“grand mal”) seizures every 2-3 months. Why is this suddenly happening and why haven’t the doctors resolved it yet? Well, the short answers are that my brain had damage (I told that story here) that can lead to epilepsy later in life, and that medicine still isn’t perfect. Epilepsy that cannot be entirely suppressed by existing medication is still common. We’re still experimenting with medications for me but it’s too soon to tell if we’ve found a solution, and we might never.

I heard some wise words a while ago that “we’re more content to blame ourselves than to accept that some things are beyond our control” and I’ve taken that to heart. Life is scary and short and it’s true that a lot is out of our control, especially the end of life. In reflection, I’ve been tempted to look back on choices I made in life and try to blame myself for what damage that has wrought on me (or others), but in terms of health I question that assumption. I may just be the victim of bad luck (genes, etc), but some people find bad luck too hard to accept, implying an indifferent universe rather than free will leading to misfortune/fortune. I’m not out of hope but I’ve accepted that the current state of my life might be just how it will be, and that’s been a hard lesson, but one I’ve learned again and again with my many chronic health problems over 20+ years. I don’t blame myself (much) for all that. More than ever, I appreciate the other wise words that “everyone is fighting a struggle you know nothing about”. I might look to an external observer like I’m kicking ass, but I feel anything but that kind of triumphant, fist-pumping jubilation.

I feel lucky to still be here, and eager to keep it that way, but I am so, so tired. Intellectually, physically, emotionally, it’s like a vampire has been paying me regular visits. And so I have to sigh, more than I used to, when confronted with bullshit like excessive paperwork or petty politics or something else I wish I didn’t have to endure, deeply feeling life slipping past as I do endure it, but that’s life for you. And at work, as a senior research manager, that’s often my job to endure it, in ways I’d never experienced as a junior researcher. I just have to cope with being pummelled by waves of difficulties and not grow weaker if I can avoid it. Coupled with life’s other burdens, the diminishing scientist faces a different beast of challenges and can often feel very alone. It’s a strange new place I’ve found myself in, far more complex than the worries I had as a postdoc, with harder choices to make and vast grey areas to traverse.

Nonetheless, as welfare science likes to term it, it’s entirely “a life worth living”. I have to pick my battles more than I used to, and I’ve had to learn to take more time to get exercise, rest, and avoid the stresses (or even unpleasant people) that can cause my health to take rapid downward spirals. I’m more fragile in many ways, such as having to stop doing karate because my shoulders have weakened. Here’s some interesting anatomy for you from a recent MRI scan of my right shoulder:

My left shoulder in top cross-sectional view, with the missing parts of my humeral head crudely outlined in red. There's more amiss here, too.

My left shoulder in top cross-sectional view, with the missing parts of my humeral head crudely outlined in red. There’s more amiss here, too.

My seizures cause my shoulder flexors to spasm, raising my arms up and crushing my humerus against my glenoid cavity of my scapula and causing occasional dislocations that abrade the humerus against the rim of the glenoid. The result, after numerous seizures, has been the wearing away of the articular cartilage of my shoulder and then the crumbling of the bony head of my humerus. Thus, once my NHS surgeon is ready to in coming months, I am due to have my coracoid process of my scapula cut off and moved, with its attached muscles and ligaments, to be screwed into the front of my glenoid cavity, bracing my humeral head more tightly against the glenoid and thereby resisting future dislocations. Luckily that operation can be done with several small incisions and endoscopy; invasive as the surgery is; thus recovery time won’t be so long.

Latarjet surgery (view of right shoulder joint [glenoid] from front): coracoid process moved posteroventrally. More details (w/videos) here.

Latarjet surgery (view of right shoulder joint [glenoid] from front): coracoid process moved posteroventrally. More details (w/videos) here.

It amuses me that all of this intense surgery looming on the horizon doesn’t worry me. I just want it done. I’ve been through a comparable surgery with my left shoulder, involving screwing my greater tuberosity back onto my humerus, so I know what recovery is like, and now that shoulder is doing fine. All that aside, my physical integrity has declined and I feel it every day. I may never return to my karate classes and earn that black belt I was seeking as a life-goal, but time will tell. I am trying to do what I can to remain as strong as I can for as long as I can.

A year from now all of my major funding and most or all of my research team were due to finish or be finishing. Over the past year, I was thinking forward to this eventuality and truly looking forward to having a smaller, quieter team, with less pressures on me. Many of those pressures are self-imposed because I am still ambitious and love doing science. I can still feel that youthful passion welling up inside me sometimes, so strong that I imagine it to be a tidal wave that could consume the world. It fuels my drive to try to do more, better science, but is dampened now by the problems I’ve lamented above, but it’s still there. So that passion and drive led me to, on a whim, resubmit an EU grant that was rejected a couple of years ago. I didn’t take it super seriously and so writing the grant didn’t stress me out. But a week after submitting it, I was back in hospital anyway, in bad shape. Over the following nine months, I grew to hope that the grant wasn’t awarded and expected that it wouldn’t (given <20% funding rate especially as a young Advanced Investigator in that ERC funding programme; https://goo.gl/Ps0Rhd if you want to know what that means). A big part of me still wanted to have that smaller team and less (or no) funding. I’d even contemplated leaving academia. I dream sometimes of retiring early to a quiet life with my family or wandering off into some jungle for a foolish adventure, but neither is realistic.

Yet a few weeks ago, the email from the EU came with an answer. I got the grant: 2.5 million Euros for 5 years of research on dinosaur evolution and biomechanics. More about that later. The funding details are still in negotiation but I now am on course to be advertising (in ~August) 4 new jobs to work with me for up to 5 years on this project, beginning in October. My reaction has puzzled those colleagues I’ve told about the grant, although I have kept that news quiet (until now) while I finish the paperwork for the grant award. I feel mixed about getting a large grant at this time in my life. It’s a helluva lot of work and five years seems a very, very long time to me, and to focus on one major theme—and to study dinosaurs.

I had also looked forward to moving away from dinosaur research—but, like Al says in the video above, their siren call can drag us back to the Mesozoic era with questions that entice us and with spectacular fossils that are a riot of fun to study. In this case, we’re going to be looking back on the “locomotor superiority” hypothesis that has been bounced around for >40 years as a possible explanation for why dinosaurs flourished whereas other archosaurs (except crocodylomorphs) didn’t, and how much bipedality relates to that, in terms of various behaviours and motions. Can these questions even be answered? We shall see.

Yes, boo hoo! Poor me, getting a coveted grant and all that! I am not surprised if that is hard for others to understand, and I still am figuring out how I feel about it all. Professionally, this is a wonderful thing; no question. Personally, it’s pressure I didn’t need to put my disabled, diminished self through. Irony and conundrum aside, I want to do it and I should try. Regardless, off I go, with a new-team-to-come and my research focus dominated by one main project, the largest grant I’ve ever managed (by a long shot!). It’s interesting times for me ahead. Life has come full circle, returning me back to science-ing the dinosaurs/archosaurs I’d focused on in my PhD work. But I am not the same person, and so it will be a very different experience. Somehow I have to balance this challenging project with the struggles in my life in general, and that will test me in diverse ways. I’m sure there will be many surprises in my work and personal life during the next five years, and I’ll be sharing them here on this blog when I can.

I’ve tried to express my own journey through the big ups and downs I’ve seen over two years. Maybe it will help others who are quietly, or noisily, struggling. I’m curious to hear from others that have experienced feelings of themselves declining as their careers/lives (in science/elsewhere) move along in some direction.

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Goodbye Pedro (?/?/2014-23/4/2016). We had too little time together. What we shared was so lovely. Parting has been terrible sorrow.

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