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A very short post here to plug BBC Radio 4’s excellent second series of “Just So Science”. These are 15 minute stories involving a reading of parts of Rudyard Kipling’s great British/natural history stories, and then examining how the science of today informs us about the real lives of animals, without resorting to just-so stories a la Kipling (co-opted as a term in evolutionary biology, too!). I was featured last year on rhinos.

I’m featured this year on kangaroos (now available online) and elephants (also available online now). I just listened to the kangaroo episode and it was good fun. I’ve studied the biomechanics of kangaroos a bit, in as-yet unpublished work featured here in a BBC News story (video from that work is below), and we’ve done other work on their bone morphology and how it relates to body size that is sure to come out in not too long.

Don’t blink! Or, for your enjoyment, a looping GIF:

kangaroo hop

My freezers feature heavily in one bit, in which you can hear me vent my frustrations about an unlabelled bag and stacks of specimens– where is the wallaby? And what’s that crinkling noise?

Best beloved, it is the sound of science. Just so. Enjoy!

Welcome back to my two-part British Museum series; I covered crocodiles before. Here, I celebrate the less common creatures depicted in human art, design and culture. And we begin back in Egypt, with a bit of crocodile to provide a nice segue:

With the head and torso of a hippo, the legs of a lion and the tail of a crocodile, the Egyptian goddess Taweret just rocks. More info here- https://www.britishmuseum.org/explore/highlights/highlight_objects/aes/b/breccia_statue_of_taweret.aspx

With the head and torso of a hippo, the legs of a lion and the tail of a crocodile (not easily visible here), the Egyptian goddess Taweret just rocks. More info here.

Anatomy in art is best when the anatomy is actually used as a substrate for art, as in this later piece from Egypt, and another piece that follows it:

Scapula (shoulder blade) from an ox, from Roman Egypt. Click to embovine for closer examination and explantion.

Scapula (shoulder blade) from an ox, with Roman enscriptions. Click to embovine for closer examination and explanation.

~8000 BC red deer antler headdress from England (click to enstaggen for closer examination and text details).

~8000 BC red deer antler headdress from England (click to enstaggen for closer examination and text details in upper left). Picturing an Ice Age shaman wearing this gives me a sense of awe.

Human anatomy in our artwork, to my mind, reaches its pinnacle in Aztec religious masks like this, which was too cool to omit:

Use of a human skull to make a stunning mask decorated with obsidian, representing Tezcatlipoca, the Smoking Mirror and master of creation/destruction; slayer of Quetzalcoatl. Badass dial turned to 11!

Use of a human skull to make a stunning mask decorated with obsidian, representing Tezcatlipoca, the Smoking Mirror and master of creation/destruction; slayer of Quetzalcoatl. Badass dial turned to 11! He is also sometimes represented as a jaguar.

Continuing the mask theme, the following masks show off sawfish, sharks and other species from the region:

Awesome diversity of ceremonial fish masks from Africa.

Awesome diversity of ceremonial fish masks from Africa.

Lions find their way into plenty of artwork such as European royal heraldry. Yet the huge depictions of an Assyrian lion hunt in the British Museum are not only anatomically impressive but also evocative of a time long past, when Asian lions ranged far across human territories. In viewers today, however, they may inspire more sympathy for the fleeing lions than awe for the lordly charioteers, horsemen and archers that pursue them.

Assyrian lion hunt Royal Lion Hunt

I finish with some statues and other depictions of animals that are more globally uncommon than lions:

You don't see tapirs much in art but here seems to be one, as a bronze statuette from ~400s AD in China.

You don’t see tapirs much in art but here seems to be one, as a bronze statuette from ~400s AD in China.

Statue of the Indian elephant diety Ganesha from ~750 AD. As the placard explains, Ganesha got his elephant's head when Shiva freaked out and cut off the human one, then promised to make amends by substituting the head of the next animal he saw.

I love Indian artwork for its plethora of proboscideans. Here, a statue of the Indian elephant diety Ganesha from ~750 AD, engaged in a dance. As the placard explains, Ganesha got his elephant’s head when Shiva freaked out and cut off the human one, then promised to make amends by substituting the head of the next animal he saw.

North Chinese (~11-12th century) ceramic plate depicting a funky, vaguely humanoid dancing bear tied to a pole.

More dancing! North Chinese (~11-12th century) ceramic plate depicting a funky, vaguely humanoid dancing bear tied to a pole. The anatomical exaggerations here make the piece more memorable and vaguely demonic, but not so much as the next item.

The dance is over, thanks to ass demons. That’s right, ass demons. Many Burmese were surely frightened or inspired by these terracota warriors from 1400s AD. These warriors represented king Mara’s forces that attempted to disrupt the Buddha’s meditation. As ass demons would tend to do. (I hate it when that happens)

I hope you enjoyed this brisk dance through atypical animals and their anatomy in artwork! Coming next, a look at one of the greatest anatomists ever.

I visited the British Museum a while ago with my daughter and was struck by some of the animal imagery in the loot on display– particularly, as an archosaurophile, the crocodiles (Crocodylia, crocodylians, etc.; no alligatoroids to show in this post). So I decided to go back and photograph some of them for a blog post about the more obscure and rare animals that sometimes appear in human art and design.

It’s easy to think of horses, lions, dogs, eagles and other familiar, domestic or prized beasts in human decorations. Yet what roles do less common animals play? This post is the first of two on the unsung beasties of human artwork, as represented in the British Museum.

Stomach-Churning Rating: 1/10. Tame art and a dried crocodile skin.

Wherever humans and crocodiles coexist, the primeval appearance and dangerous potential of crocodiles are sure to impress themselves upon our psyche. Hence they will manifest themselves in art. This should especially apply in the early days of a civilization, before we extirpate local crocodiles or exclude them to the hinterlands, or in cases in which crocodylians become revered and protected.

Much of Western culture lacks such an emphasis, because it developed in more temperate climes where crocodiles were long since absent. It’s fun to think about what our culture would be like if it had developed with crocodiles as a prominent aspect, as in Egypt, which is the natural place to begin our tour, featuring mummies of course!

All images can be clicked to emcroccen them.

Small Nile crocodile mummy from >30 B.C, El Hiba, Egypt

Small Nile crocodile mummy from >30 B.C, El Hiba, Egypt

Second small Nile crocodile mummy from >30 B.C, El Hiba, Egypt

Second small Nile crocodile mummy from >30 B.C, El Hiba, Egypt

Those mummies remind me of a recent scientific study that used such mummies to reveal the history of the “cryptic” species Crocodylus suchus, a close relative of the Nile croc C. niloticus, and one that seems to be more threatened.

We proceed on our tour with a box showing an example of shabti, or doll-like funeral offerings of “enchanted” mummified figurines:

This shabti box was for a noble daughter, Neskshons, in Thebes, from around 650 B.C.

This shabti box was for a noble daughter, Neskshons, in Thebes, from around 650 B.C.

A crocodile deity receives the shabti from the departed soul, accompanied by  serpent god as well as a more human, ankh-bearing divinity.

A crocodile deity receives the shabti from the departed soul, accompanied by serpent god as well as a more human, ankh-bearing divinity.

Next, some amazingly preserved papyrus scrolls:

This papyrus is from around 900 B.C., with short blurbs about the woman Tentosorkon, part of a new style of funeral provisions in the 22nd Dynasty of Egypt.

This papyrus is from around 900 B.C., with short blurbs about the woman Tentosorkon, part of a new style of funeral provisions in the 22nd Dynasty of Egypt.

Crocodile featured in the story of Tentosorkon.

Crocodile featured in the story of Tentosorkon. What’s it doing? Why is a feathered snake-thing touching its butt? I wish I knew.

The "Litany of Ra", from around 1000 B.C., which is a style like that of the previous 22nd Dynasty papyrus and would have decorated a tomb's wall, dedicated to the lady Mutemwia. Ra, the sun god, is shown in his different manifestations, including a crocodile form, called Sobek-ra: http://www.princeton.edu/~achaney/tmve/wiki100k/docs/Sobek.html

The “Litany of Ra”, from around 1000 B.C., which is a style like that of the previous 22nd Dynasty papyrus and would have decorated a tomb’s wall, dedicated to the lady Mutemwia. Ra, the sun god, is shown in his different manifestations, including a crocodile form, called Sobek-ra (AKA Sebek); a protector and comforter of the dead:

egypt croc 1But crocodiles also feature prominently in other cultures around the world– I was hoping to find some in Thai, South American, or other cultures’ art (especially east/western Africa). However, the museum didn’t exhibit any I could find. I did find these, though, starting with this fantastic Roman armour with a great backstory (and hard to take photos of; argh!):

croc armour caption croc armour 1 croc armour 2 croc armour 3

Roman soldiers in a Sobek cult, running around Egypt while wearing badass armour and getting into all kinds of Bronze Age trouble: I DEMAND TO SEE A SWORD-AND-SANDALS MOVIE FEATURING THIS!

I searched for this next one but did not see it:

A crocodile mask from Mabuiag island near Australia- for some cool details, see this page where the image comes from (I didn’t get to see the original).

There were more tenuous links to crocodiles– surely some dragon images throughout the world relate at least partly to crocodiles, such as this one which seems very crocodylian to me:

A water spirit figure called a belum, from Sarawak, Malaysia, 18/1900s. Belief among  the Melanau people  was that these dragons would wrap their tails around someone's body to protect or drown them. Possibly inspired by saltwater or Phillipine crocs that they lived near.

A water spirit figure called a belum, from Sarawak, Malaysia, 18/1900s. Belief among the Melanau people was that these dragons would wrap their tails around someone’s body to protect or drown them. Possibly inspired by saltwater or Phillipine crocs that they lived near.

And that’s it- all I managed to find, but not a bad haul from this huge museum.  I looked for the Aztec croc-god Cipactli to no avail. If you have £850 to spare you might like to walk away with this one from the museum. I gladly accept donations of such things to my, err, research.

That’s just one museum’s view of crocodylians’ role in our culture. What crocodile imagery from human art around the world do you fancy?

 

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.

penguin-waddle

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!

Cheers!

by animalloz, on deviantart

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