Vulnerability, Strength and Success

I’ve been doing a series of career guidance sessions with my research team, and this past week we talked about how to structure a successful career path as a scientist. As part of that, I gave my thoughts on how to maximize chances of that “success” (traditional definition; getting a decent permanent job as a researcher, and doing a good job at it); without knowingly being a jerk or insincere. This process led me to re-inspect my own career for insights — not that I’ve been on perfect behaviour, but I do routinely reflect on choices I make.

I asked myself, “What does success mean to me?” to see what my answer was today. That led to me writing up this story of my career path, as an example of the twists and turns that can happen in the life of a scientist. I originally intended to share this story just with my team, but then I decided to turn into a full-on blog post, in my ongoing personal quest to open up and share my thoughts and experiences with others. For those who have read my advice to PhD students, there are some commonalities, but plenty of this is new.

Where my last post was partly about publicly exposing vulnerabilities in other scientists, this one is about privately finding one’s own vulnerabilities along with the strengths, and sharing them publicly. The story is about me, but the key points are more about how “success” can evolve in science (N=1 plus anecdotal observations of others).


Growing Up in Grad School

As an undergraduate student, I was clueless about my career until I applied to graduate school a second time. The first time I tried applying, I didn’t even know how to really go about it, or what I wanted to do beyond some sort of biology. Yet to my credit I was curious, creative, a swift learner with a great memory for science, and broadly educated in biology and other fields (thanks, parents and past teachers!). I read and watched “Jurassic Park” and lots of Stephen Jay Gould and Darwin or palaeontology books, and I just tried to actively learn all I could, reading compulsively. I even resolved to quit non-science reading for a few years, and stuck to that. I realized that a research career combining evolution and biomechanics was of interest to me, involving vertebrates and maybe fossils.

I got into grad school in 1995 and had a great project to study how dinosaurs moved, but I felt inadequate compared to my peers. So I dedicated myself even harder to reading and learning. I didn’t pass my first orals (qualifying exam; appraisal/defense) but that helped me to refocus even more resolutely on deep learning, especially to fill gaps in my knowledge of biomechanics methods that I’d later use. During this time I also learned website design and HTML code (mid-90s; early WWW!), working with several others on Berkeley’s UCMP website in my free time. I intensively networked with colleagues via email lists (the long-lived Dinosaur listproc) and at a lot of conferences, trying to figure out how science worked and how to go about my project. That was a powerful initial formative period.

It was a gruelling struggle and I’d had serious health problems (a narrow escape from cancer) around the same time, too. I frequently, throughout the 1990’s, doubted if I could make it in the field. I looked around me and could not see how I could become successful in what I wanted to do (marry biomechanics and evolutionary biology in stronger ways). I was so scared, so uncertain of my own work, that I didn’t know what to do—I had a project but had no clue how to really implement it. So two years passed in semi-paralysis, with little concrete science to show for it, and I gave a lot of *bad* internal seminars in Berkeley’s Friday biomechanics group. However, those bad seminars helped me to become a better speaker. I had a terrible fear of public speaking; on top of having little data, this experience was brutal for me. But I used it as practice, bent to the task of bettering myself.

A change in my career trajectory happened as my research slowly took root. I wrote some book chapters for a dinosaur encyclopedia in 1997, a simple paper describing a little dinosaur in 1998, then another paper on taxonomy published in 1999. [For those wanting to find out what any of these papers I mention are, they are on my Publications page, often with pdfs] These papers at least showed I could finish a research task; when I was younger I’d had some bad habits of not finishing work I started.

I visited a lot of museums and hung out with people there, socializing while learning about diverse fossils and their evolutionary anatomy, implementing what I’d learned from my own dissections and literature studies of living animals. This led to a poster (actually two big posters stacked atop each other; plotting the evolution of the reptilian pelvis and muscles) at a palaeontology meeting (SVP). This poster turned a few heads and I suppose convinced some that I knew something about bone and soft tissue anatomy.

Then in 1998, I did a 4-month visiting scholarship at Brown University with Steve Gatesy that had a big impact on my career: Steve helped me consolidate ideas about how anatomy related to function in dinosaurs, and how to interpret data from living animals (I did my first gait experiments, with guineafowl, which went sort of OK), and I loved Brown University’s EEB department environment. For once, I felt like a grown-up, as people started to listen to what I had to say. In retrospect, I was still just a kid in many other ways. I didn’t really achieve a lot of what Steve asked me to do; I was unfocused, but changing steadily.

In 1999, I gave a talk at SVP that was well received, based on that research with Gatesy, and then I gave it again at SICB. I had a few prominent scientists encouraging me to apply for faculty jobs (e.g., Beth Brainerd was very supportive)– this gave me a new charge of excitement and confidence. I finally began to feel like a real expert in my little area of science. That talk became our 2000 “Abductors, adductors…” paper in Paleobiology, which I still love for its integrative nature and broad, bold (but incompletely answered) questions. Yet when a respected professor at Berkeley told me before my University of Chicago faculty job interview “You act like a deer in the headlights too often,” I knew I had a long journey of self-improvement left. And a lot of that improvement just came with time– and plenty of mistakes.

Momentum continued to build for my career in 2000 as I took my anatomical work into more biomechanical directions and passed my orals. I gave an SVP Romer Prize (best student talk) presentation on my new T. rex biomechanical modelling work, and I won! I felt truly appreciated, not just as an expert but as an emerging young leader in my research area. I’ll never forget the standing ovation at the award announcement in Mexico City—seeing people I saw as famous and amazing get up and cheer for me was such a rush! Then I published two lengthy anatomical papers in Zool J Linn Soc in 2001, which still are my most cited works — even more than some of my subsequent Nature papers.


Evolution: Postdoc to Faculty

Also in 2001, I was awarded a NSF postdoc at Stanford to do exactly what I’d long wanted to do: build detailed biomechanical models of dinosaurs, using the anatomical work I’d done before. That was it: I saw evidence that I had “made it”. But that took about six years; toward the end of my PhD; to truly feel this way most of the time, and in some ways this feeling led to youthful overconfidence and brashness that I had to later try to shed. I feel fortunate that the rest of my career went more smoothly. I doubt I could have endured another six years of struggling as I did during my PhD. But it wasn’t easy, either. During my postdoc I had to force my brain to think like a mechanical engineer’s and that was a difficult mental struggle.

The year 2002 became a wild ride for me.

First, my T. rex “not a fast runner” paper got published in Nature, and I was thrown into the limelight of the news media for two weeks or so. Luckily I was ready for the onslaught — one of my mentors, Bob Full, warned me, “This will be huge. Prepare!” I handled it well and I learned a lot about science communication in the process.

Shortly after that publication, just before my wedding’s bachelor party, I developed terrible leg blood clots and had to cancel my party—but I recovered in time for the wedding, which was a fantastic event on a California clifftop. I enjoyed a good life and seemed healthy again. I kept working hard, I got my second paper accepted at Nature on bouncy-running elephants, and then…

Then I had a stroke, just before that Nature paper got published.

Everything came crashing to a halt and I had to think about what it all meant—these were gigantic life-and-death questions to face at age 31! Luckily, I recovered without much deficit at all, and I regained my momentum with renewed stubborn dedication and grit, although my recover took many months, and took its toll on my psyche. I’ve told this story before in this post about my brain.

I started seeing therapists to talk about my struggles, which was a mixed blessing: I became more aware of my personality flaws, but also more aware of how many of those flaws wouldn’t change. I’m still not sure if that was a good thing but it taught me a lot of humility, which I still revisit today. I also learned to find humour and wonder in the dark times, which colours even this blog.

In winter of 2003 I went to a biomechanics symposium in Calgary, invited by British colleague Alan Wilson. Later that spring, Alan encouraged me to apply for an RVC faculty job (“you’ll at least get an interview and a free trip to London”), which I said no to (vet school and England move didn’t seem right to me), but later changed my mind after thinking it over.

I got the RVC job offer the day before my actual job talk (luckily colleague David Polly warned me that things like this happened fast in the UK, unlike the months of negotiation in the USA!). I made the move in November 2003 and the rest was hard work, despite plenty of mistakes and lessons learned, that paid off a lot career-wise. If I hadn’t taken that job I’d have been unemployed, and I had postdoc fellowships and faculty job applications that got rejected in 2002-2003, so I was no stranger to rejection. It all could have gone so differently…

But it wasn’t a smooth odyssey either—there were family and financial struggles, and I was thousands of miles away while my mother succumbed to Alzheimer’s and my father swiftly fell victim to cancer, and I never was 100% healthy and strong after my troubles in 2002. Even in the late 2000’s, I felt inadequate and once confided to a colleague something like “I still feel like a postdoc here. I’m a faculty member and I don’t feel like I’ve succeeded.”

Since then, I’ve achieved some security that has at last washed that feeling away. That was a gradual process,  but I think the key moment I realized that “I’ll be OK now”  was in 2010 when I got the call, while on holiday in Wales (at the time touring Caernarfon Castle), informing me that my promotion to full Professor was being approved. It was an anticlimactic moment because that promotion process took 1 year, but it still felt great. It felt like success. I’ll never earn the “best scientist ever” award, so I am content. I don’t feel I have something big left to prove to myself in my career, so I can focus on other things now. It “only” took 15 or so years…


Ten Lessons Learned

When I look back on this experience and try to glean general lessons, my thoughts are:

1)     Socializing matters so much for a scientific career. “Networking” isn’t a smarmy or supercilious approach, either; in fact, that insincerity can backfire and really hurt one’s reputation. I made a lot of friends early on — some of my best friends today are scientist colleagues. Many of these have turned into collaborators. Making friends in science is a win-win situation. Interacting with fellow scientists is one of the things I have always enjoyed most about science. Never has it been clearer to me how important the human element of science is. Diplomacy is a skill I never expected to use much in science, but I learned it through a lot of experience, and now I treasure it.

2)     Developing a thicker skin is essential, but being vulnerable helps, too. Acting impervious just makes you seem inhuman and isolates you. Struggling is natural and helped me endure the tough times that came along with the good times, often in sharp transition. Science is freaking hard as a career. Even with all the hard work, nothing is guaranteed. Whether you’re weathering peer review critiques, politics, or health or other “life problems”, you need strength, whether it comes from inside you or from those around you. Embrace that you won’t be perfect but strive to do your best despite that. Regret failures briefly (be real with yourself), learn from them and then move on.

3)     Reading the literature can be extremely valuable. So many of my ideas came from obsessive reading in diverse fields, and tying together diverse ideas or finding overlooked/unsolved questions and new ways to investigate them. I can’t understand why some scientists intentionally don’t try to read the literature (and encourage their students to follow this practice!), even though it is inevitable to fall behind the literature; you will always miss relevant stuff. I think it can only help to try to keep up that scholarly habit, and it is our debt to past scientists as well as our expectation of future ones—otherwise why publish?

4)     I wish I learned even more skills when I was younger. It is so hard to find time and energy now to learn new approaches. This inevitably leads to a researcher becoming steadily less of a master of research methods and data to more of a manager of research. So I am thankful for having the wisdom accumulated via trial and error experiences to keep me relevant and useful to my awesome team. That sharing of wisdom and experience is becoming more and more enjoyable to me now.

5)     Did I “succeed” via hard work or coincidence? Well, both—and more! I wouldn’t have gotten here without the hard work, but I look back and I see a lot of chance events that seemed innocent at the time, but some turned out to be deeply formative. Some decisions I made look good in retrospect, but they could have turned out badly, and I made some bad decisions, too; those are easy to overlook given that the net result has been progress. Nothing came easily, overall. And I had a lot of help from mentors, too; Kevin Padian and Scott Delp in particular. Even today, I would not say that my career is easy, by any stretch. I still can find it very draining, but it’s so fun, too!

6)     Take care of yourself. I’ve learned the hard way that the saying “At least you have your health” is profoundly wise. I try to find plenty of time now to stop, breathe and observe my life, reflecting on the adventures I’ve had so far. The feelings evoked by this are rich and complex.

7)     If I could go back, I’d change a lot of decisions I made. We all would. But I’m glad I’ve lived the life I’ve lived so far. At last, after almost 20 years of a career in science, I feel mostly comfortable in my own skin, more able to act rather than be frozen in the headlights of adversity. I know who I am and what I cannot be, and things I need to work on about myself. In some ways I feel more free than I’ve felt since childhood, because the success (as I’ve defined it in my life) has given me that freedom to try new things and take new risks, and I feel fortunate for that. I think I finally understand the phrase “academic freedom” and why it (and tenure) are so valuable in science today, because I have a good amount of academic freedom. I still try to fight my own limits and push myself to improve my world—the freedom I have allows this.

8)     When I revisit the question of “what does success mean to me?” today I find that the answer is to be able to laugh, half-darkly, at myself—at my faults, my strengths, and the profound and the idiotic experiences of my life. I’ve found ways to both take my life seriously and to laugh at myself adrift in it. To see these crisply and then to embrace the whole as “this is me, I can deal with that” brings me a fresh and satisfying feeling.

9)     Share your struggles —  and successes — with those you trust. It helps. But even just a few years ago, the thought of sharing my career’s story online would have scared me.

10)     As scientists we hope for success in our careers to give us some immortality of sorts. What immortality we win is but echoes of our real lives and selves. So I seek to inject some laughter into those echoes while revelling in the amazing moments that make up almost every day. I think it’s funny that I became a scientist and it worked out OK, and I’m grateful to the many that helped; no scientist succeeds on their own.

A major aspect of a traditional career in science is to test the hypothesis that you can succeed in a career as a scientist, which is a voyage of self-discovery, uncovering personal vulnerabilities and strengths. I feel that I am transitioning into whatever the next part of my science career will be; in part, to play a psychopomp role for others taking that voyage.

That’s my story so far. Thanks for sticking with it until the end. Please share your thoughts below.

This post is solely my opinion; not reflecting any views of my coauthors, my university, etc, and was written in my free time at home. I am just putting my current thoughts in writing, with the hope of stimulating some discussion. My post is based on some ruminations I’ve had over recent years, in which I’ve seen a lot of change happening in how science’s self-correcting process works, and the levels of openness in science, which are trends that seem likely to only get more intense.

That’s what this post ponders- where are we headed and what does it mean for scientists and science? Please stay to the end. It’s a long read, but I hope it is worth it. I raise some points at the end that I feel strongly about, and many people (not just scientists) might also agree with or be stimulated to think about more.

I’ve always tried to be proactive about correcting my (“my” including coauthors where relevant) papers, whether it was a publisher error I spotted or my/our own; I’ve done at least 5 such published corrections. Some of my later papers have “corrected” (by modifying and improving the methods and data) my older ones, to the degree that the older ones are almost obsolete. A key example is my 2002 Nature paper on “Tyrannosaurus rex was not a fast runner“- a well-cited paper that I am still proud of. I’ve published (with coauthors aplenty) about 10 papers since then that explore various strongly related themes, the accuracy of assumptions and estimates involved, and new ways to approach the 2002 paper’s main question. The message of that paper remains largely the same after all those studies, but the data have changed to the extent that it would no longer be viable to use them. Not that this paper was wrong; it’s just we found better ways to do the science in the 12 years since we wrote it.

I think that is the way that most of science works; we add new increments to old ones, and sooner or later the old ones become more historical milestones for the evolution of ideas than methods and data that we rely on anymore. And I think that is just fine. I cannot imagine it being any other way.

If you paid close attention over the past five months, you may have noticed a kerfuffle (to put it mildly) raised by former Microsoft guru/patent afficionado/chef/paleontologist Nathan Myhrvold over published estimates of dinosaur growth rates since the early 2000’s. The paper coincided with some emails to authors of papers in question, and some press attention, especially in the New York Times and the Economist. I’m not going to dwell on the details of what was right or wrong about this process, especially the scientific nuances behind the argument of Myhrvold vs. papers in question. What happened happened. And similar things are likely to happen again to others, if the current climate in science is any clue. More about that later.

But one outcome of this kerfuffle was that my coauthors and I went through (very willingly; indeed, by my own instigation) some formal procedures at our universities for examining allegations of flaws in publications. And now, as a result of those procedures, we issued a correction to this paper:

Hutchinson, J.R., Bates, K.T., Molnar, J., Allen, V., Makovicky, P.J. 2011. A computational analysis of limb and body dimensions in Tyrannosaurus rex with implications for locomotion, ontogeny, and growth. PLoS One 6(10): e26037. doi: 10.1371/journal.pone.0026037  (see explanatory webpage at: http://www.rvc.ac.uk/SML/Projects/3DTrexGrowth.cfm)

The paper correction is here: http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0097055. Our investigations found that the growth rate estimates for Tyrannosaurus were not good enough to base any firm conclusions are, so we retracted all aspects of growth rates from that paper. The majority of the paper, about estimating body mass and segment dimensions (masses, centres of mass, inertia) and muscle sizes as well as their changes through growth and implications for locomotor ontogeny, still stands; it was not in question.

For those (most of you!) who have never gone through such a formal university procedure checking a paper, my description of it is that it is a big freakin’ deal! Outside experts may be called in to check the allegations and paper, you have to share all your data with them and go through the paper in great detail, retracing your steps, and this takes weeks or months. Those experts may need to get paid for their time. It is embarassing even if you didn’t make any errors yourself and even if you come out squeaky clean. And it takes a huge amount of your time and energy! My experience started on 16 December, reached a peak right around Xmas eve (yep…), and finally we submitted our correction to PLoS and got editorial approval on 20 March. So it involved three months of part-time but gruelling dissection of the science, and long discussions of how to best correct the problems. Many cooks! I have to admit that personally I found the process very stressful and draining.

Next time you wonder why science can be so slow at self-correction, this is the reason. The formal processes and busy people involved mean it MUST be slow– by the increasingly speedy standards of  modern e-science, anyway. Much as doing science can be slow and cautious, re-checking it will be. Should be?

My message from that experience is to get out in front of problems like this, as an author. Don’t wait for someone else to point it out. If you find mistakes, correct them ASAP. Especially if they (1) involve inaccurate data in the paper (in text, figures, tables, whatever), (2) would lead others to be unable to reproduce your work in any way, even if they had all your original methods and data, or (3) alter your conclusions. It is far less excruciating to do it this way then to have someone else force you to do it, which will almost inevitably involve more formality, deeper probing, exhaustion and embarassment. And there is really no excuse that you don’t have time to do it. Especially if a formal process starts. I can’t even talk about another situation I’ve observed, which is ongoing after ~3 years and is MUCH worse, but I’ve learned more strongly than ever that you must demonstrate you are serious and proactive about correcting your work.

I’ve watched other scientists from diverse fields experience similar things– I’m far from alone. Skim Retraction Watch and you’ll get the picture. What I observe both excites me and frightens me. I have a few thoughts.

1) The drive to correct past science is a very good development and it’s what science is meant to be about. This is the most important thing!

2) The digital era, especially trends for open access and open data for papers, makes corrections much easier to discover and do. That is essentially good, and important, and it is changing everything about how we do science. Just watch… “we live in interesting times” encapsulates the many layers of feelings one should react with if you are an active researcher. I would not dare to guess what science will be like in 20 years, presumably when I’ll be near my retirement and looking back on it all!

3) The challenge comes in once humans get involved. We could all agree on the same lofty principles of science and digital data but even then, as complex human beings, we will have a wide spectrum of views on how to handle cases in general, or specific cases.

This leads to a corollary question– what are scientists? And that question is at the heart of almost everything controversial about scientific peer review, publishing and post-publication review/correction today, in my opinion. To answer this, we need to answer at least two sub-questions:

1–Are we mere cogs in something greater, meant to hunker down and work for the greater glory of the machine of science?

(Should scientists be another kind of public servant? Ascetic monks?)

2–Are we people meant to enjoy and live our own lives, making our own choices and value judgements even if they end up being not truly optimal for the greater glory of science?

(Why do we endure ~5-10 years of training, increasingly poor job prospects/security, dwindling research funds, mounting burdens of expectations [e.g., administrative work, extra teaching loads, all leading to reduced freedoms] and exponentially growing bureaucracies? How does our experience as scientists give meaning to our own lives, as recompense?)

The answer is, to some degree, yes to both of the main questions above, but how we reconcile these two answers is where the real action is. And this brew is made all the spicier by the addition of another global trend in academia: the corporatization of universities (“the business model”) and the concomitant, increasing concern of universities about public image/PR and marketing values. I will not go any further with that; I am just putting it out there; it exists.

The answer any person gives will determine how they handle a specific situation in science. You’ve reminded your colleague about possible errors in their work and they haven’t corrected it. Do you tell their university/boss or do you blog and tweet about it, to raise pressure and awareness and force their hand? Or do you continue the conversation and try to resolve it privately at any cost? Is your motive truly the greater glory of science, or are you a competitive (or worse yet, vindictive or bitter) person trying to climb up in the world by dragging others down? How should mentors counsel early career researchers to handle situations like this? Does/should any scientist truly act alone in such a regard? There may be no easy, or even mutually exclusive, answers to these questions.

We’re all in an increasingly complex new world of science. Change is coming, and what that change will be like or when, no one truly knows. But ponder this:

Open data, open science, open review and post-publication review, in regards to correcting/retracting past publications: how far down the rabbit hole do we go?

The dinosaur growth rates paper kerfuffle concerned numerous papers that date back to earlier days of science, when traditions and expectations differed from today’s. Do we judge all past work by today’s standards, and enforce corrections on past work regardless of the standards of its time? If we answer some degree of “yes” to this, we’re in trouble. We approach a reductio ad absurdum: we might logic ourselves into a corner where that great machine of science is directed to churn up great scientific works of their time. Should Darwin’s or Einstein’s errors be corrected or retracted by a formal process like those we use today? Who would do such an insane thing? No one (I hope), but my point is this: there is a risk that is carried in the vigorous winds of the rush to make science look, or act, perfect, that we dispose of the neonate in conjunction with the abstergent solution.

OK I used 1 image...

There is always another way. Science’s incremental, self-correcting process can be carried out quite effectively by publishing new papers that correct and improve on old ones, rather than dismantling the older papers themselves. I’m not arguing for getting rid of retractions and corrections. But, where simple corrections don’t suffice, and where there is no evidence of misconduct or other terrible aspects of humanity’s role in science, perhaps publishing a new paper is a better way than demolishing the old. Perhaps it should be the preferred or default approach. I hope that this is the direction that the Myhrvold kerfuffle leans more toward, because the issues at stake are so many, so academic in nature, and so complex (little black/white and right/wrong) that openly addressing them in substantial papers by many researchers seems the best way forward. That’s all I’ll say about that.

I still feel we did the right thing with our T. rex growth paper’s correction. There is plenty of scope for researchers to re-investigate the growth question in later papers.  But I can imagine situations in which we hastily tear down our or others’ hard work in order to show how serious we are about science’s great machine, brandishing lofty ideals with zeal– and leaving unfairly maligned scientists as casualties in our wake. I am reminded of outbursts over extreme implementations of security procedures at airports in the USA, which were labelled “security theatre” for their extreme cost, showiness and inconvenience, with negligible evidence of security improvements.

The last thing we want in science is an analogous monstrosity that we might call “scientific theatre.” We need corrective procedures for and by scientists, that serve both science and scientists best. Everyone needs to be a part of this, and we can all probably do better, but how we do it… that is an interesting adventure we are on. I am not wise enough to say how it should happen, beyond what I’ve written here. But…

A symptom of scientific theatre might be a tendency to rely on public shaming of scientists as punishment for their wrongs, or as encouragement for them to come clean. I know why it’s done. Maybe it’s the easy way out; point at someone, yell at them in a passionate tone backed up with those lofty ideals, and the mob mentality will back you up, and they will be duly shamed. You can probably think of good examples. If you’re on social media you probably see a lot of it. There are naughty scientists out there, much as there are naughty humans of any career, and their exploits make a good story for us to gawk at, and often after a good dose of shaming they seem to go away.

But Jon Ronson‘s ponderings of the phenomenon of public shaming got me thinking (e.g., from this WTF podcast episode; go to about 1 hr 9 min): does public shaming belong in science? As Ronson said, targets of severe public shaming have described it as “the worst pain ever”, and sometimes “there’s no recourse” for them. Is this the best way to live together in this world? Is it really worth it, for scientists to do to others or to risk having done to them? What actually are its costs? We all do it in our lives sometimes, but it deserves introspection. I think there are lessons from the dinosaur growth rates kerfuffle to be learned about public shaming, and this is emblematic of problems that science needs to work out for how it does its own policing. I think this is a very, very important issue for us all to consider, in the global-audience age of the internet as well as in context of the intense pressures on scientists today. I have no easy answers. I am as lost as anyone.

What do you think?


EDIT: I am reminded by comments below that 2 other blog posts helped inspire/coagulate my thoughts via the alchemy of my brain, so here they are:

http://dynamicecology.wordpress.com/2014/02/24/post-publication-review-signs-of-the-times/ Which considers the early days of the Myhrvold kerfuffle.

http://blogs.discovermagazine.com/neuroskeptic/2014/01/27/post-publication-cyber-bullying/ Which considers how professional and personal selves may get wounded in scientific exchanges.

Short and sweet post here; it’s sunny outside and I want to be there BBQing!

I had a buried folder of CT files labelled as a species of fish, but on digging them out and segmenting them I realize it is not what I expected (inner fish or not!), as you will see.

Stomach-Churning Rating: 2/10; simple CT scan of a body.

Mystery Anatomy 2014same rules as before; remember that the scoreboard has been reset.

Identify the animal in the CT scout/pilot image below, as specifically as you can. But… (READ THE SENTENCE BELOW FIRST BEFORE ANSWERING!)

Today’s special rule: Summertime is coming and that means superhero films! Your answer must be in the form of a dialogue between a superhero(ine) and a supervillain(ess)! 

Difficulty: Even I am not 100% sure what this is but I have a decent idea. Not super hard, but not a super good segmentation.

Pow! Bam! Biff! Go forth and conquer! Then invite the Human Torch to your BBQ.


It’s World Penguin Day! Watch your back though… these penguins aren’t as nice as they seem. But they need us to be nice to them!

Hahaha?Whether you watch a classic GIF like the one above, or a kid-friendly TV/film documentary, you might get the impression that penguins lead carefree, or at least silly or slapstick, lives– happy feet and all that. It works for Hollywood: a Charlie Chaplin comedy relief role to play.  And that’s the vision of penguins I grew up with: they were living cartoons to me.

But what’s the reality? Plenty of documentaries, most notably to my mind the recent Attenborough’s “Frozen Earth” episodes or “March of the Penguins” film, have dealt with the darker side to these two-toned, tuxedo-toting antipodeans. And anyone who has experienced penguins in the wild has probably seen those not-so-light facets of penguinity firsthand. On realiizing just how compulsively horny young “hooligan cock” male penguins were, Natural History Museum ornithologist Douglas Russell wrote: ““just the frozen head of the penguin, with self-adhesive white O’s for eye rings, propped upright on wire with a large rock for a body, was sufficient stimulus for males to copulate and deposit sperm on the rock.”

Stomach-Churning Rating: 5/10; some tears may be shed over cute baby penguins and you might choke if you’re a rhea trying to swallow one, but the anatomy shown is mostly skeletal or dessicated. No penguin juices. Except those just mentioned above.

I’m quick to admit, I didn’t know much about penguins until recently. I couldn’t name many species or say much about their behaviour, anatomy or evolutionary history. When I was a graduate student at Berkeley, I was enthused by a now-classic, elegantly simple study (published in 2000) that fellow PhD student Tim Griffin and biomechanist Dr. Rodger Kram conducted on penguin waddling. They found that the waddling gait of penguins isn’t mechanically disadvantageous, as it appears, but rather is a way that they conserve energy while walking. It’s the short legs, instead, that make their gait metabolically expensive, because shorter legs mean that more frequent, costly steps need to be taken, incurring high costs due to rapid firing of leg muscles to support the body. My vicarious enjoyment of Griffin’s & Kram’s research began my scientific introduction to penguins. Fast forward to 2014: I get a crash course in penguinology.

Punta Tombo (4)

Mostly-fledged Magellanic penguin

That’s what this post is about, and how it brought me in touch with The Existentialist Penguin– the haggard, storm-tossed, predator-harried, starved and bullied wanderer of wastelands.

My personal introduction to penguins over the past year has been initiated by a collaboration with PhD student James Proffitt and long-time colleague Dr. Julia Clarke, both at the University of Texas in Austin. They kindly invited me to collaborate on applying modern biomechanics to the surprisingly excellent fossil record of penguins (Sphenisciformes), among other extant water birds. Before diving into it all, I happened to go to Argentina.

Punta Tombo (2)

Penguin tries to keep cool in the shade, opening its mouth to shed heat in the autumn sun.

Just before I travelled to Patagonia on unrelated business (to study sauropodomorph dinosaurs!), I did a little googling and came across Punta Tombo reserve, near the city of Trelew that I was visiting (more about that in a future post!). It’s where some 1+ million Magellanic penguins (Spheniscus magellanicus) gather every southern summer to breed and fledge before making a long ~5 month swim up to Brazil. I asked my host, Dr. Alejandro Otero, if we might take a day off to visit this spot, where guanacos, rheas and other wildlife were also said to be common, and he basically said “Hell yes!” as he’d never been there. My Flickr photostream gives a big set of my favourite photos from that trip, but here are some others below, to show some of my experiences. We rented a car and took a lovely 90-minute drive south across the Patagonian plains, observing wildlife like tinamous (yes! So exciting for me) as we went. You could get within 1.5m of the penguins according to park rules, and the penguins were very permissive of that!

This jaunty chap was staying put in his burrow while people walked by. We came closer and he kept rotating his head around, staring at us. I first took it as cute juvenile behaviour, but on later observations of penguins realized it was a threat- "My beak is sharp! Stay back, bro, or I'll glock ya!"

This jaunty chap was staying put in his burrow while people walked by. We came closer and he kept rotating his head around, staring at us. I first took it as cute juvenile behaviour, but on later observations of penguins realized it was a threat- “My beak is sharp! Stay back, bro, or I’ll glock ya!”

The video below shows a penguin encounter that left me with no doubts that these animals don’t mess around. The smaller penguin escaped, losing its cool burrow and some of its tough hide, too. Indeed, penguins can be remarkable assholes to each other.

With battles like this erupting all around us, where the penguins struggled to find shade in the desert-like inland parts of the park, often hundreds of meters away from the cool ocean, it came as no surprise to find casualties. The juveniles (and some remaining adults; most having left by now while the ~1 year-old juveniles fledge) not only battled, but also fasted, and roasted in the heat as they shed their insulatory fluff for waterproofed streamlining. This poor little flat Spheniscus had been trodden a bit past streamlined:Punta Tombo (3)

Near the end of our visit, just after I saw an informative sign about the lesser rhea or “choique” (Pterocnemia/Rhea pennata), we managed to get very close to a rhea and follow it for a while, as penguins stood around in apparent disinterest. I’ll never forget that meeting: two flightless birds, yet adapted to such different lifestyles and habitats. The penguins were in the rhea’s domain; a hot, wind-blown, scree-scoured scrubland on the edge of the fertile ocean.rhea-penguin

The choique soon found a dry old hatchling penguin carcass, no meatier than the surrounding thickets, and tried to swallow it. The loss of teeth by its distant ornithurine ancestors proved to be a bad move, because it struggled to get the jerky-like mass through its beak:

That Punta Tombo visit was an experience I’ll never forget. I returned to the UK, abuzz with excitement about penguins. I “got” them now, I felt, at least in a very unscientific, anthropomorphic way. It took the face-to-beak experience to drive that home, more than any emotive film treatment could. Whether enduring Antarctic wintery blasts or unforgivingly hot and dry, burrow-speckled coastal badlands, penguins are buggers with true grit. Survivors, as their >60 million year fossil record attests to. On my return, I delved through my photos of museum specimens to get a better appreciation for penguin anatomy, preparing to also get familiar with that fossil record; all as part of that ongoing work with Proffitt and Clarke. Here’s some of that anatomy:

My first encounter with a penguin in the wild is probably this specimen washed up on a beach in Uruguay. I'm going with the tentative ID of a juvenile penguin skeleton; probably Magellanic.

My first encounter with a penguin in the wild (but not a live one) is probably this specimen washed up on a beach in Uruguay. I’m going with the tentative ID of a juvenile penguin skeleton (short foot; flat wing bones); probably Magellanic. The bevy of vertebrate morphologists investigating dead penguins on this beach during our conference in 2010 will not soon be forgotten!

Magellanic penguin skeleton, "flying" through the Punta Tombo visitor centre.

Magellanic penguin skeleton, “flying” through the Punta Tombo visitor centre.

University Museum of Zoology Cambridge skeleton of one of the "great penguin" (do not confuse with the great pumpkin!) species; either King (patagonicus) or Emperor (forsteri).

University Museum of Zoology Cambridge skeleton of a “great penguin” (do not confuse with the great pumpkin!) species of Aptenodytes; either King (patagonicus) or Emperor (forsteri). Characteristic features, in addition to the robust, dense skeleton, include the short neck, flattened but robust wings and scapulae, robust furcula (wishbone), stubby legs (with a big blocky patella) and thin but longish tail (supposedly used to balance with while walking/standing).

I’ll visit some more penguin anatomy in coming images- those photos are just teasers. And they set the stage for me to go back to my one-stop-shopping for awesome ornithological specimens, the Natural History Museum at Tring (images below presented with kind permission from the Natural History Museum, London; but I took the photos), to pick up an assortment of 11 frozen penguins from helpful curator Hein van Grouw! Such as this “gagged” King penguin:
NHMUK penguin

And this handsome Emperor penguin, going through the Equine Imaging Centre’s CT scanner as I do my usual routine of (1) get cool critters, (2) barrage them with radiation to peek inside:penguin CT (3)

CT scanner monitors as I scan a penguin; mid-torso x-ray slice shown on the right.

CT scanner monitors as I scan a penguin; mid-torso x-ray slice shown on the right.

Awwwwww... baby Gentoo penguin (Pygoscelis papua). Unhappy feet, I'm afraid.

Awwwwww… baby Gentoo penguin (Pygoscelis papua— EDIT: Probably Aptenodytes; see comments below). Unhappy feet, I’m afraid… Happy CT scanning, however– specimens like this are NOT easy to come by in these northern nether regions!

Because I love the CT scan images of these penguins so much (their skeletons are awesome and bizarre!), I’ll share the pilot scans of the best ones now:

Calling all penguin experts! What's up with this? Is that really how much gastrolith volume a penguin carries, or did a museum curator stick rocks up its bum? Seems very caudal in position. I'm fascinated.

Calling all penguin experts! What’s up with this? Is that really how much gastrolith (stomach stone; near bottom of image) volume a penguin carries (answer after some literature reading: maybe yes!), or did a museum curator stick rocks up its bum? It seems very caudal in position, and this is consistent with other animals I’ve seen (some below). A paper on this phenomenon and potential role in ballast is here. Another here.

Side view.

Side view. Nice view of the head at least.

The fluffy baby shown in the photo above. Nice pose, and lots of anatomy shown. And check it out- gastroliths?!? In such a young animal-- is it even feeding yet?

Young juvenile. Nice pose, and lots of anatomy is shown. And check it out- gastroliths?!? In such a young animal– is it even feeding yet? (presumably straight after hatching) And they are relatively big pebbles, too! If I noticed this 5 years ago, it would have been a nice paper to report- first recognition of gastroliths in penguin chicks seems to have been then. Indeed, that study observed some chicks intentionally swallowing stones.

Another youngun.

Another youngun; the fluffy one from the photo above. More rocks up its wazoo.

Three wee little chicks.

Three wee little chicks, all with stomach stones.

CT reconstruction of adult skeleton. This specimen was gutted and flattened, so the gastroliths are few and scattered. Check out the long tail:

From recent skeletons to fossil ones, penguins have wacky anatomy; they break most of the “rules” of being a proper bird, putting other oddballs like rheas to shame. I can’t ably review the many penguin species we know of, but the ancient Palaeocene penguin Waimanu features prominently in recent scientific discussions of penguin evolution, such as the superb research and blog of Dan Ksepka  as well as many workers in the southern hemisphere. I haven’t had a chance to inspect that creature’s bones, but while in Trelew, Argentina, I was very pleased to run into some excellent specimens of a later animal:

Part of the rather nice skeleton of Palaeospheniscus patagonicus, an Oligocene/Miocene largish penguin; from the MFN collections in Trelew, Argentina and collected nearby.

Part of the nice skeleton of Palaeospheniscus patagonicus, an Oligocene/Miocene largish penguin; from the MEF collections in Trelew, Argentina and collected nearby. The genus has been known since Ameghino’s description in 1891, and is closely related to living penguins, especially Aptenodytes. It was not a large penguin, but at about 5kg body mass was no slouch as birds go (roughly similar in size to a Magellanic penguin). I also got to see  Madrynornis mirandus, a Miocene form.

For me, the diagnostic trait of a penguin skeleton: the very short, tobust tarsometatarsus. From Palaeospheniscus, as above.

For me, the diagnostic trait of a penguin skeleton: the very short, tobust tarsometatarsus. From Palaeospheniscus, as above. The great palaeontologist GG Simpson wrote of it: “Despite the innumerable variations in details, the tarsometatarsi, on which all species but P. robustus are based, are quite stereotyped in general structure and leave little doubt that the forms placed here by Ameghino do all belong to a natural group.” A ratio of length to proximal width of >2 is typical of most penguins.  Synapomorphy FTW!

From beach skeletons, to mass suffering of landbound birds, to 3D imaging and fossil skeletons, I’ve had quite the immersion in penguinness lately. And through that experience, I’ve been drawn closer to penguins in more ways than one. I’ve been impressed by their adaptability and durability. In some ways, penguins’ adaptations to harsh freezing winters in wastelands also aid them to survive harsh baking summers in dry badlands.

Yes, those badlands are still coastal, and penguins can still drink the saltwater and excrete salt via their supraorbital glands, but those penguins in Punta Tombo were not having a keg party. They were clearly enduring some serious discomfort, and not all making it through the ordeal. I watched silently along with other penguins as one penguin lay prone in an awkward pose on a bleached-white stretch of hardpan soil, while one flipper meekly raised, then flopped down. It was not long for this world, and there was a host of large scavengers around ready to make the most of that, while penguin-eating giant petrels (a sister group to penguins) wheeled overhead.


Waddlers of the wastes

While penguins still spend most of their lives at sea, they retain a sometimes astonishing array of behaviours they use on land: burrowing, hopping/jumping, costly short-legged (but efficiently waddling) walking, and perhaps more that we haven’t yet discovered! Their unique anatomy reflects a compromise between all these factors, and we’re fortunate to have knowledge of their fossil record that shows a lot of detail on how they evolved it all. While penguins are a highly aquatic species, they show how aquatic and terrestrial adaptations can coexist in harmony; it’s not just a black-or-white issue. But with climate change in progress, the ~18 species of penguins have some rapidly altering challenges to adapt to, or go the way of Waimanu. This is a critical Kierkegaardian moment for The Existentialist Penguin.

I raise a glass in toast to that versatile, resilient, gravel-gizzarded Existentialist Penguin! May it persevere all the troubles our ever-changing world throws at it, as it has done since the Palaeocene. And may we draw inspiration from its tenacity, to face our own troubles, together on this crazy spinning globe!


by animalloz, on deviantart

This post was just published yesterday in a shorter, edited form in The Conversation UK, with the addition of some of my latest thoughts and the application of the editor’s keen scalpel. Check that out, but check this out too if you really like the topic and want the raw original version! I’ve changed some images, just for fun. The text here is about 2/3 longer.

Recently, the anatomy of animals comes up a lot, at least implicitly, in science news stories or internet blogs. Anatomy, if you look for it, is everywhere in organismal and evolutionary biology. The study of anatomy has undergone a renaissance lately, in a dynamic phase energized by new technologies that enable new discoveries and spark renewed interest. It is the zombie science, risen from what some had assumed was its eternal grave!

Stomach-Churning Rating: 4/10; there’s a dead elephant but no gore.

My own team has re-discovered how elephants have a false “sixth toe” that has been a mystery since it was first mentioned in 1710, and we’ve illuminated how that odd bit of bone evolved in the elephant lineage. This “sixth toe” is a modified sesamoid kind of bone; a small, tendon-anchoring lever. Typical mammals just have a little nubbin of sesamoid bone around their ankles and wrists that is easily overlooked by anatomists, but evolution sometimes co-opts as raw material to turn into false fingers or toes. In several groups of mammals, these sesamoids lost their role as a tendon’s lever and gained a new function, more like that of a finger, by becoming drastically enlarged and elongated during evolution. Giant pandas use similar structures to grasp bamboo, and moles use them to dig. We’ve shown that elephants evolved these giant toe-like structures as they became larger and more terrestrial, starting to stand up on tip-toe, supported by “high-heels” made of fat. Those fatty heels benefit from a stiff, toe-like structure that helps control and support them, while the fatty pads spread out elephants’ ponderous weight.

Crocodile lung anatomy and air flow, by Emma Schachner.

Crocodile lung anatomy and air flow, by Emma Schachner.

I’ve also helped colleagues at the University of Utah (Drs. Emma Schachner and Colleen Farmer) reveal, to much astonishment, that crocodiles have remarkably “bird-like” lungs in which air flows in a one-way loop rather than tidally back and forth as in mammalian lungs. They originally discovered this by questioning what the real anatomy of crocodile lungs was like- was it just a simple sac-like structure, perhaps more like the fractal pattern in mammalian lungs, and how did it work? This question bears directly on how birds evolved their remarkable system of lungs and air sacs that in many ways move air around more effectively than mammalian lungs do. Crocodile lungs indicate that “avian” hallmarks of lung form and function, including one-way air flow, were already present in the distant ancestors of dinosaurs; these traits were thus inherited by birds and crocodiles. Those same colleagues have gone on to show that this feature also exists in monitor lizards, raising the question (almost unthinkable 10-20 years ago) of whether those bird-like lungs are actually a very ancient and common feature for land animals.

Speaking of monitor lizards, anatomy has revealed how they (and some other lizards) all have venom glands that make their bites even nastier, and these organs probably were inherited by snakes. For decades, scientists had thought that some monitor lizards, especially the huge Komodo dragons, drooled bacteria-laden saliva that killed their victims with septic shock. Detailed anatomical and molecular investigations showed instead that modified salivary glands produced highly effective venom, and in many species of lizards, not just the big Komodos. So the victims of numerous toothy lizard species die not only from vicious wounds, but also from worsened bleeding and other circulatory problems promoted by the venomous saliva. And furthermore, this would mean that venom did not evolve separately in the two known venomous lizards (Gila monster and beaded lizard) and snakes, but was inherited from their common ancestor and became more enhanced in those more venomous species—an inference that general lizard anatomy supports, but which came as a big surprise when revealed by Bryan Fry and colleagues in 2005.

There’s so much more. Anatomy has recently uncovered how lunge-feeding whales have a special sense organ in their chin that helps them detect how expansive their gape is, aiding them to engulf vast amounts of food. Scientists have discovered tiny gears in the legs of leafhoppers that help them make astounding and precise leaps. Who knew that crocodilians have tiny sense organs in the outer skin of their jaws (and other parts of their bodies) that help them detect vibrations in the water, probably aiding in communication and feeding? Science knows, thanks to anatomy.

Just two decades or so ago, when I was starting my PhD studies at the University of California in Berkeley, there was talk about the death of anatomy as a research subject; both among scientists and the general public. What happened? Why did anatomy “die” and what has resuscitated it?


TH Huxley, anatomist extraordinaire

TH Huxley, anatomist extraordinaire, caricatured in a lecture about “bones and stones, and such-like things” (source)

Anatomy’s Legacy

In the 16th through 19th centuries, the field of gross anatomy as applied to humans or other organisms was one of the premier sciences. Doctor-anatomist Jean Francois Fernel, who invented the word “physiology”, wrote in 1542 that (translation) “Anatomy is to physiology as geography is to history; it describes the theatre of events.” This theatric analogy justified the study of anatomy for many early scientists, some of whom also sought to understand it to bring them closer to understanding the nature of God. Anatomy gained impetus, even catapulting scientists like Thomas Henry Huxley (“Darwin’s bulldog”) into celebrity status, from the realisation that organisms had a common evolutionary history and thus their anatomy did too. Thus comparative anatomy became a central focus of evolutionary biology.

But then something happened to anatomical research that can be hard to put a finger on. Gradually, anatomy became a field that was scoffed at as outmoded, irrelevant, or just “solved”; nothing important being left to discover. As a graduate student in the 1990s, I remember encountering this attitude. This apparent eclipse of anatomy accelerated with the ascent of genetics, with anatomy reaching its nadir in the 1950s-1970s as techniques to study molecular and cellular biology (especially DNA) flourished.

One could argue that molecular and cellular biology are anatomy to some degree, especially for single-celled organisms and viruses. Yet today anatomy at the whole organ, organism or lineage level revels in a renaissance that deserves inspection and reflection on its own terms.


Anatomy’s Rise

Surely, we now know the anatomy of humans and some other species quite well, but even with these species scientists continue to learn new things and rediscover old aspects of anatomy that laid forgotten in classic studies. For example, last year Belgian scientists re-discovered the anterolateral ligament of the human knee, overlooked since 1879. They described it, and its importance for how our knees function, in novel detail, and a lot of media attention was drawn to this realisation that there are some things we still don’t understand about our own bodies.

A huge part of this resurgence of anatomical science is technology, especially imaging techniques- we are no longer simply limited to the dissecting knife and light microscope as tools, but armed with digital technology such as 3-D computer graphics, computed tomography (series of x-rays) and other imaging modalities. Do you have a spare particle accelerator? Well then you can do amazing synchrotron imaging studies of micro-anatomy, even in fairly large specimens. Last year, my co-worker Stephanie Pierce and colleagues (including myself) used this synchrotron approach to substantially rewrite our understanding of how the backbone evolved in early land animals (tetrapods). We found that the four individual bones that made up the vertebrae of Devonian tetrapods (such as the iconic Ichthyostega) had been misunderstood by the previous 100+ years of anatomical research. Parts that were thought to lie at the front of the vertebra actually lay at the rear, and vice versa. We also discovered that, hidden inside the ribcage of one gorgeous specimen of Ichthyostega, there was the first evidence of a sternum, or breastbone; a structure that would have been important for supporting the chest of the first land vertebrates when they ventured out of water.

Recently, anatomists have become very excited by the realization that a standard tissue staining solution, “Lugol’s” or potassium iodide iodine, can be used to reveal soft tissue details in CT scans. Prior to this recognition, CT scans were mainly used in anatomical research to study bone morphology, because the density contrast within calcified tissues and between them and soft tissues gives clearer images. To study soft tissue anatomy, you typically needed an MRI scanner, which is less commonly accessible, often slower and more expensive, and sometimes lower resolution than a CT scanner. But now we can turn our CT scanners into soft tissue scanners by soaking our specimens in this contrast solution, allowing highly detailed studies of muscles and bones, completely intact and in 3D. Colleagues at Bristol just published a gorgeous study of the head of a common buzzard, sharing 3D pdf files of the gross anatomy of this raptorial bird and promoting a new way to study and illustrate anatomy via digital dissections- you can view their beautiful results here. Or below (by Stephan Lautenschlager et al.)!


These examples show how anatomy has been transformed as a field because we now can peer inside the bodies of organisms in unprecedented detail, sharing and preserve those data in high-resolution digital formats. We can do this without the concern that a unique new species from Brazilian rainforests or exciting fossil discovery from the Cambrian period would be destroyed if we probed certain questions about its anatomy that are not visible from the outside– a perspective in which science had often remained trapped for centuries. These tools became rapidly more diverse and accessible from the 1990s onward, so as a young scientist I got to see some of the “before” and “after” influences on anatomical research—these have been very exciting times!

When I started my PhD in 1995, it was an amazing luxury to first get a digital camera to use to take photographs for research, and then a small laser scanner for making 3D digital models of fossils, with intermittent access to a CT scanner in 2001 and now full-time access to one since 2003. These stepwise improvements in technology have totally transformed the way I study anatomy. In the 1990s, you dissected a specimen and it was reduced to little scraps; at best you might have some decent two-dimensional photographs of the dissection and some beetle-cleaned bones as a museum specimen. Now, we CT or MRI scan specimens as routine practice, preserving many mega- or gigabytes of data on its internal and external, three-dimensional anatomy in lush detail, before scalpel ever touches skin. Computational power, too, has grown to the point where incredibly detailed 3D digital models produced from imaging real specimens can be manipulated with ease, so science can better address what anatomy means for animal physiology, behaviour, biomechanics and evolution. We’re at the point now where anatomical research seems no longer impeded by technology– the kinds of questions we can ask are more limited by access to good anatomical data (such as rare specimens) than by the ways we acquire and use those data.

My experience mirrors my colleagues’. Larry Witmer at Ohio University in the USA, past president of the International Society for Vertebrate Morphologists, has gone from dissecting bird heads in the 1990s to becoming a master of digital head anatomy, having collected 3D digital scans of hundreds of specimens, fossil and otherwise. His team has used these data to great success, for example revealing how dinosaurs’ fleshy nostrils were located in the front of their snouts (not high up on the skull, as some anatomists had speculated based on external bony anatomy alone). They have also contributed new, gorgeous data on the 3D anatomy of living animals such as opossums, ostriches, iguanas and us, freely available on their “Visible Interactive Animal” anatomy website. Witmer comments on the changes of anatomical techniques and practice: “For extinct animals like dinosaurs, these approaches are finally putting the exploration of the evolution of function and behavior on a sound scientific footing.

I write an anatomy-based blog called “What’s in John’s Freezer?” (haha, so meta!), in which I recount the studies of animal form and function that my research team and others conduct, often using valuable specimens stored in our lab’s many freezers. I started this blog almost two years ago because I noticed a keen interest, or even hunger for, stories about anatomy amongst the general public; and yet few blogs explicitly were about anatomy for its own sake. This interest became very clear to me when I was a consultant for the BAFTA award-winning documentary series “Inside Nature’s Giants” in 2009, and I was noticing more documentaries and other programmes presenting anatomy in explicit detail that would have been considered too risky 10 years earlier. So not only is anatomy a vigorous, rigorous science today, but people want to hear about it. Just in recent weeks, the UK has had “Dissected” as two 1-hour documentaries and “Secrets of Bones” as back-to-back six 30-minute episodes, all very explicitly about anatomy, and on PRIME TIME television! And PBS in the USA has had “Your Inner Fish,” chock full of anatomy. I. Love. This.

Before the scalpel: the elephant from Inside Nature's Giants

Before the scalpel: the elephant from Inside Nature’s Giants

There are many ways to hear about anatomy on the internet these days, reinforcing the notion that it enjoys strong public engagement. Anatomical illustrators play a vital role now much as they did in the dawn of anatomical sciences– conveying anatomy clearly requires good artistic sensibilities, so it is foolish to undervalue these skills. The internet age has made disseminating such imagery routine and high-resolution, but we can all be better about giving due credit (and payment) to artists who create the images that make our work so much more accessible. Social media groups on the internet have sprung up to celebrate new discoveries- watch the Facebook or Twitter feeds of “I F@*%$ing Love Science” or “The Featured Creature,” to name but two popular venues, and you’ll see a lot of fascinating comparative animal anatomy there, even if the word “anatomy” isn’t necessarily used. I’d be remiss not to cite Emily Graslie’s popular, unflinchingly fun social media-based explorations of gooey animal anatomy in “The Brain Scoop”. I’d like to celebrate that these three highly successful disseminators of (at least partly) anatomical outreach are all run by women—anatomical science can (and should!) defy the hackneyed stereotype that only boys like messy stuff like dissections. There are many more such examples. Anatomy is for everyone! It is easy to relate to, because we all live in fleshy anatomical bodies that rouse our curiosity from an early age, and everywhere in nature there are surprising parallels with — as well as bizarre differences from — our anatomical body-plans.


Anatomy’s Relevance

What good is anatomical knowledge? A great example comes from gecko toes, but I could pick many others. Millions of fine filaments, modified toe scales called setae, use micro-molecular forces called van der Waals interactions to help geckos cling to seemingly un-clingable surfaces like smooth glass. Gecko setae have been studied in such detail that we can now create their anatomy in sufficient detail to make revolutionary super-adhesives, such as the product “Geckskin”, 16 square inches of which can currently suspend 700 pounds aloft. This is perhaps the most famous example from recent applications of anatomy, but Robert Full’s Poly-Pedal laboratory at Berkeley, among many other research groups excelling at bio-inspired innovation in robotics and other fields of engineering and design, regularly spins off new ideas from the principle that “diversity enables discovery”, as applied to the sundry forms and functions found in organisms. By studying the humble cockroach, they have created new ways of building legged robots that can scour earthquake wreckage for survivors or explore faraway planets. By asking “how does a lizard use its big tail during leaping?” they have discovered principles that they then use to construct robots that can jump over or between obstacles. Much of this research relates to how anatomical traits determine the behaviours that a whole, living, dynamic organism is capable of performing.

Whereas when I was a graduate student, anatomists and molecular biologists butted heads more often than was healthy for either of them, competing for importance (and funding!), today the scene is changing. With the rise of “evo devo”, evolutionary developmental biology, and the ubiquity of genomic data as well as epigenetic perspectives, scientists want to explain “the phenotype”—what the genome helps to produce via seemingly endless developmental and genetic mechanisms. Phenotypes often are simply anatomy, and so anatomists now have new relevance, often collaborating with those skilled in molecular techniques or other methods such as computational biology. One example of a hot topic in this field is, “how do turtles build their shells and how did that shell evolve?” To resolve this still controversial issue, we need to know what a shell is made of, what features in fossils could have been precursors to a modern shell, how turtles are related to other living and extinct animals, how a living turtle makes its shell, and how the molecular signals involved are composed and used in animals that have or lack shells. The first three questions require a lot of anatomical data, and the others involve their fair share, too.

Questions like these draw scientists from disparate disciplines closer together, and thanks to that proximity we’re inching closer to an answer to this longstanding question in evolutionary biology and anatomy, illustrated above in the video.  As a consequence, the lines between anatomists and molecular/cellular biologists increasingly are becoming blurred, and that synthesis of people, techniques and perspectives seems to be a healthy (and inevitable?) trend for science. But there’s still a long way to go in finding a happy marriage between anatomists and the molecular/cellular biologists whose work eclipsed theirs in past decades. Old controversies like “should we use molecules or morphology to figure out how animals are related to each other?” are slowly dying out, as the answer becomes evident to be “Yes. Both.” (especially when fossils can be included!) Such dwindling controversies contribute to the healing of disciplinary rifts and the unruffling of parochial feathers.

Yet many anatomists would point to lingering obstacles that give them concern for their future; funding is but one of them (few would argue that gross anatomical research is as well off in provision of funding as genetics is, for example). There are clear mismatches between the hefty importance, vitality, popularity and rigour of anatomical science and its perception or its role in academia.

Romane 1892, covering Haeckel's classic, early evo-devo work (probably partly faked, but still hugely influential)

Romane 1892, covering Haeckel’s classic, early evo-devo work (probably partly faked, but still hugely influential) (source)


Anatomy’s Future

One worry the trend that anatomy as a scientific discipline is clearly flourishing in research while it dwindles in teaching. Fewer and fewer universities seem to be teaching the basics of comparative anatomy that were a mainstay of biology programmes a century ago. Yet anatomy is everywhere now in biology, and in the public eye. It inspires us with its beauty and wonder—when you marvel at the glory of beholding a newly discovered species, you are captivated by its phenotypic pulchritude. Anatomy is still the theatre in which function and physiology are enacted, and the physical encapsulation of the phenotype that evolution moulds through interactions with the environment. But there is cause for concern that biology students are not learning much about that theatre, or that medical schools increasingly seem to eschew hands-on anatomical dissection in favour of digital learning. Would you want a doctor to treat you if they mainly knew human anatomy from a CGI version on an LCD screen in medical school, and hence were less aware of all the complexity and variation that a real body can house?

Anatomy has an identity problem, too, stemming from decades of (Western?) cultural attitudes (e.g. the “dead science” meme) and from its own success—by being so integral to so many aspects of biology, anatomy seems to have integrated itself toward academic oblivion, feeding the perception of its own obsolescence.  I myself struggled with what label to apply to myself as an early career researcher- I was afraid that calling myself an “anatomist” would render me quaint or unambitious in the eyes of faculty job interview panels, and I know that many of my peers felt the same. I resolved that inner crisis years ago and came to love identifying myself at least partly as an anatomist. I settled on the label “evolutionary biomechanist” as the best term for my speciality. In order to reconstruct evolution or how animals work (biomechanics), we first often need to describe key aspects of anatomy, and we still discover new, awesome things about anatomy in the process. I still openly cheer on anatomy as a discipline because its importance is so fundamental to what I do, and I am far from alone in that attitude. Other colleagues that do anatomical research use other labels for themselves like “biomechanist”, “physiologist,” or “palaeontologist”, because those words better capture the wide range of research and teaching that they do, but I bet also because some of them likely still fear the perceived stigma of the word “anatomy” among judgemental scientists, or even the public. At the same time, many of us get hired at medical, veterinary or biology schools/departments because we can teach anatomy-based courses, so there is still hope.

Few would now agree with Honoré de Balzac’s 19th century opinion that “No man should marry until he has studied anatomy and dissected at least one woman”, but we should hearken back to what classical scientists knew well: it is to the benefit of science, humanity and the world to treasure the anatomy that is all around us. We inherit that treasure through teaching; to abscond this duty is to abandon this trove. With millions of species around today and countless more in the past, there should always be a wealth of anatomy for everyone to learn from, teach about, and rejoice.

X-ray technology has revolutionized anatomical studies; what's next? Ponder that as this ostrich wing x-ray waves goodbye.

X-ray technology has revolutionized anatomical studies; what’s next? Ponder that as this ostrich wing x-ray waves goodbye.

Like this post? You might also find my Slideshare talk on the popularity of anatomy interesting- see my old post here for info!

Fat Cat

I’ve described our “Walking the Cat Back” Leverhulme Trust-funded project with Dr. Anjali Goswami and colleagues before, but today we really got stuck into it. We’re dissecting a 46kg male Snow Leopard (Panthera uncia) as the first “data point” (actually several hundred data points, but anyway, first individual) in our study of how limb and back muscles change with size in felids. No April Fools’ pranks here; real science-as-it-happens.

Stomach-Churning Rating: 7/10 for skinned leopard and globs of fat. Much worse in person, hence the downgrading from what could be a higher score. Don’t click the photos to emkitten them if you don’t want to see the details.

This leopard is the same one that Veterinary Forensics blogged about. It died in a UK cat conservation/recovery centre. Today is simply a short post, but it is the first in what will surely be a continued series of posts on felid postcranial anatomy and musculoskeletal biomechanics by our felid research team, with bits of natural history and evolution thrown in when we can manage. As befits one of my curt “Anatomy Vignette” posts, pictures will tell the story.

Skinned and mostly de-fatted snow leopard, with fat piled up on the lower left hand corner near the hind feet. Here we are identifying and then removing and measuring the individual muscles. Project postdoc Andrew Cuff is hard at work on the forelimb while I'm mucking around with the hindlimb.

Skinned and mostly de-fatted snow leopard, with fat piled up on the lower left hand corner near the hind feet. Here we are identifying and then removing and measuring the individual muscles. Project postdoc Andrew Cuff is hard at work on the forelimb while I’m mucking around with the hindlimb. The fat here is about 3kg subcutaneous fat, so around 6.5% of body mass. And as the cat has been around for a while, that fat has gone a bit rancid and that is not nice. Not nice at all, no… Usually smells do not bother me, but this took some adjustment. Fortunately, the muscles are still OK, and work is coming along well.

UCL PhD student Marcela Randau,, carving up our cat's limb muscles. As usual in comparative biomechanics, we measure the "architecture"- parameters of the muscle that relate in a somewhat straightforward fashion to function.

UCL PhD student Marcela Randau, carving up our cat’s limb muscles. As usual in comparative biomechanics, we measure the “architecture”- parameters of the muscle that relate in a somewhat straightforward fashion to function. This muscular architecture includes things like muscle mass, the lengths of the fibers (fascicles) that make up the muscles, and the angle of the fascicles to the muscle’s line of action. These parameters correlate reasonably well with the force and power that the muscle can develop, and its working range of length change. Other posts here have discussed this more, but by measuring the architecture of many muscles in many felids of different sizes, we can determine how felids large and small adapt their anatomy to support their bodies and move their limbs. This will help to solve some lingering mysteries about the odd ways that cats move and how their movement changes with body size.

This research is being driven forward mainly by Andrew and Marcela, shown above, so I wanted to introduce them and our odoriferous fat cat. Upcoming dissections: 1-2 more snow leopards, tiger, various lions, ocelot, black-footed cat, leopard, and a bunch of moggies, and whatever else comes our way. All were EU zoo/park mortalities (there are a LOT of big cats out there!).

EDIT: Had to add a photo of the CLAWS! Whoa dude.


Hey I almost forgot, it’s the blog’s second anniversary! What the hell happened this year?

Stomach-Churning Rating: there’s an 8/10 photo of ostrich guts here; otherwise 2/10ish.

I bring you tidings from the past and future!

I bring you tidings from the past and future!

This was the Year of the Rant, and I enjoyed ranting to you on this blog. Sometimes you ranted with me, and that was even better. It kicked off with that cat documentary that spurned me in a feline dismissive fashion, then I lit off on documentaries in general and how they should give more back to scientists (what a discussion in the comments!!!!). Ooooh that felt good. And helped me sort out my thoughts about the topic. And after then, I got paid more often and still did a lot of documentaries– if you haven’t been watching Secrets of Bones on BBC4, you should be weeping bitter, bitter dregs (and be scrambling to get access). Catch me tomorrow (Tues) night with some of our emus! They paid me reasonably and in return I worked hard for them; before, during, and after filming, and I think we all felt good about it. Or I did anyway. The show is excellent, so I feel even better!

Sneak peek from BBC4's Secrets of Bones episode 3... recognize anyone?

Sneak peek from BBC4’s Secrets of Bones episode 3… recognize anyone? (from their website)

But no ranting palaeo-related blog would be complete without a good T. rex rant, and I did that this year. Took a big dump on the scavenger-predator non-troversy. That went over so well, Slate picked it up- I never had expected that to happen! I also appreciated how many colleagues joined in to condemn the senseless perpetuation of this dead issue by the media and a few scientists.

There were also some posts on more introspective things, like the feeling of being lost that pervades both visiting a strange foreign city and doing science. And like how science needs both the qualities of a Mr Spock and a Captain Kirk. Those were fun experiments in combining  a personal, internal experience with a broader message.

Darwin greets Chinese visitor Microraptor in my office.

Darwin greets Chinese visitor Microraptor in my office.

When I asked for suggestions last year, you wanted more coverage of other people’s stuff, and so I did that to a degree, reviewing the All Yesterdays and Unfeathered Bird books. And then I fell off that wagon, which I may come back to. But along the way I realized I don’t enjoy writing about papers that other people have already published because, generally, I then lack the personal experience of doing the science and showing it in progress, which is what this blog tends to be about and what excites me on a personal, visceral level. Once the paper is out, I feel like the cat is out of the bag and it’s not as fun to talk about unless it’s totally mind-blowingly (A) cool or (B) idiotic. Anyway, I might do a solicited post if someone gets me excited about a paper before it comes out, or who knows, I may change my mind.

Entirely unfeathered Indian peafowl in matching views.

Entirely unfeathered Indian peafowl in matching views, with Unfeathered Bird’s author-illustrator.

I also posted on a fabulous blog that more people need to hit, because you may be surprised just how fascinating it is- Veterinary Forensics. I get the feeling often, both on my blog and from scientific colleagues, that veterinary anatomy/pathology issues are seen as “lesser science” than basic, even descriptive anatomy. Somehow, insanely weird diseases or pathologies don’t excite people as much as insanely weird “normal” anatomies. I know there are exceptions to that generalization, but I think it’s a common (mis)perception people have, and part of it is likely because those fields (veterinary medicine and zoology, for example) are historically separate, and people tend to see anatomy and pathology as separate things- as opposed to points along a continuum. Since coming to the RVC, I have come from that kind of a misperception to one in which pathology enormously enriches my understanding of form, function and evolution. I also love the “applications of basic science to helping animals live better lives” angle. We should all be trying to do that as scientists, but from time to time I notice that it isn’t taken seriously (I even get reviewers’ comments bluntly stating that it’s none of our business as basic scientists, or for anatomy/experimental biology journals to mention!). Whoops better stop there or I’ll be writing a new ranty post!

Can't get enough of this -xray GIF, so here it is again.

Can’t get enough of this x-ray GIF, so here it is again.

Darwin Day got into some of the vet-y issues regarding feet, in a post on hooves and then another on pigs’ feet.

Toward the end of the year I got some guest posts going, by two main people from my team: Sophie Regnault on rhino feet, and Julia Molnar on crocodile spines. I liked those posts a lot, and so did you, it seems, so there will be more of those coming in year 3. Quite a few are planned already.

One of my favourite papers I’ve ever done came out this year, by Vivian Allen et al. on dinosaur body shape/postural evolution, and that went nicely as a blog post with tons of extra context and stuff. Digital 3D dinos, what’s not to love?

I was on sabbatical for much of the year, so I was posting a lot about patellae (kneecaps) and how fun they are to study, which led to posts about basal bird skeletons and more, like Darwin’s chickens and a joke about cake that only I seemed to find funny, and ending with a grand summary of avian kneecaps. I also reported on some new (post-sabbatical) research, still ongoing, with Dr. Stephanie Pierce and Dr. Maedeh Borhani at the RVC, on how salamanders walk. During Freezermas, I plugged our new comparative cat project.

The mesenteries are so gorgeous!!!!!!

The mesenteries are so gorgeous!!!!!!

Speaking of Freezermas: It happened, it was terrifying, and we’ve all grown from the experience of surviving it. I had a blast dissecting that ostrich, and the x-ray pics were a hit with everyone, too!

Then there was random “freezer love” and assorted posts to give insight into the daily life of a freezer manager, such as doing an inventory and reflections on childhood. I snuck in a tour of Dublin museums and the amazing Crocodiles of the World near Oxford. I meant to do more of those “anatomy road trip posts” and still aim to.

And we ended the year by ending the ongoing drama of the Mystery Anatomy competition, starting off a new year with a new scoreboard. We got more poetic and lyrical in 2013 with the answers to those mysteries, and that will continue (groans from those who are poetically challenged).

Elephant skull mystery x-ray

Elephant skull mystery x-ray

Some brief numbers: view-wise the blog has been pretty close to last year; about 87,000 views in the past 12 months for a total of almost 200,000, wow! This year, Twitter just barely edged out Facebook for bringing people to the blog (3,134 vs 3,022 clicks) but then geenstijl.nl bizarrely brought 2,732! There was no big Reddit or other social media site moment this year, but various sites and links continued to bring in a steady flow of visitors to add to the Google-search-firehose’s. Thanks to folks who linked here!!!

What google searches brought people here the most often? The top 3 are the most interesting; the fifth one just makes me laugh because I’ve never discussed Deepstaria enigmatica anatomy here, but will continue to promote people finding the site by searching for it, if only to annoy cnidariologists:

rhino 83
giraffe 76
camel anatomy 62
what’s in john’s freezer 60
deepstaria enigmatica 56

I’m a little surprised “elephant” and “dinosaur” don’t bring as many searches here, but there are probably more sites about those animals and hence I get fewer of the hits. Looking forward to more hits on “ostrich anatomy”…

My two top rants were the top posts this year, and that’s no surprise given the comments and other attention they got. Thanks for helping by participating! Those were nice group-rants. Healthy and vigorous. Shockingly, a poetry round of mystery anatomy came in 3rd! People just liked the chickens + bones + poetry. Those, and some hits from year 1, broke the 1000-views marks.

Americans came here in a 3:1 ratio to Brits, which means that Brits punched above their weight per capita (~5:1 ratio)! Canadians, you tried, too. Here, have some back bacon of dubious provenance. :) Saint Kitts and Nevis with 670 views, wow! Very unexpected- you beat Italy and many others!

Most importantly, the blog has been about sharing my passion for anatomy (as preserved via freezers). I shared a conference talk about this subject here, using the blog as a prime example, to a warm reception. I want to try experimenting in new ways to use the blog to share things this year. I think you will like what I (we!) have lined up. Thanks for showing up and staying with me!


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