SciComm Sunday: Hammerhead shark swimming kinematics

SciComm Sunday: Hammerhead shark swimming kinematics

Welcome to a new series we’re starting here on the blog! The aim is to have a new entry in this series every fortnight, but more often if circumstances are permitting. We’re going to be exploring together a new paper from the previous two weeks that has taken my interest – this could be because it’s groundbreaking new work, highly relevant to my current reading or, as in this week’s case, is just really damn cool. The aim is to communicate awesome science in such a way that it’s accessible to all, but in a more detailed way than seen in popular media.

First things first, today’s paper can be found here. All  research articles published in the Journal of Experimental Biology are open access six months after publication – so be sure to check back then if you want to read the full article and don’t have access currently.

Let’s get stuck in! The authors make observations that hammerhead sharks show a variety of cross species morphological (shape) changes, though this hasn’t been extensively looked at previously. It stands to reason that these changes in shape may have an impact on how the sharks swim, following the classic moniker “form ever follows function”. The phrase was actually coined in the 18th Century by American architect Louis Sullivan and used to describe a variety of natural instances of form-function associations such as a “branching oak” and “toiling work-horse”. It has since been considered integral to functional morphology in both living and fossil creatures.

The two species investigated are the scalloped hammerhead (Sphyrna lewini) and the bonnethead (Sphyrna tiburo). It’s clearly from the images below that these two species have very different morphology of the T-bar at the head of the animal, which is called the cephalofoil – cephalo meaning head. Previous studies have shown an inverse relationship between cephalofoil pectoral fin area, such as one increases the other decreases. The authors decided to investigate how body shape and cephalofoil area contribute to the swimming style of the sharks.

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Four of each species, for a total of eight sharks, were captured and filmed in large swimming pools using a GoPro video camera situated above the water. From these videos, several points across the animal (seen below) were tracked through steady swimming and the areas of the cephalofoil and pectoral fins were calculated. Any lengths were calculated using Total Body Length (TL) to standardise for body size. One specimen of each species was CT scanned so that the 3D shape of the body could be better analysed (see this post for more on CT scanning and how it works!). Parameters such as swimming speed, tail beat frequency and amplitude were measured and analysed.

Points tracked through video data

So what were the findings? Firstly, the relationship between cephalofoil and pectoral fin area proportions was recovered as in the historic studies. This is always reassuring to see, since peer-reviewed science should always be sound and reproducible. Secondly, the two sharks were found to have different body shapes in the anterior region of the post-cranial body, so the equivalent of the “torso” region in humans. The scalloped hammerheads measured in this study had a more laterally compressed “torso”, so had relatively taller and thin bodies compared to the dorso-ventrally (top-bottom) compressed “torsos” of the bonnethead sharks. Interestingly, standardised velocity and tail beat amplitude didn’t differ significantly between the two species, suggesting each is performing at relatively the same rate. Further analysis showed that the tail segment had the greatest flexion amplitude, as would be expected of tail based propulsion.

Tl;dr: bonnethead and scalloped hammerheads differ greatly in their morphology, particularly in the anterior region of the body. Differences are observed in the morphology of the cepahlofoil (spade-like in bonnetheads vs straight T-bar in scalloped hammerheads) and the anterior body shape (flatter bonnetheads vs taller scalloped hammerheads). Despite these morphological changes, no relative differences are seen in swim speed or undulation frequency, but do differ in undulation amplitude.

This was a fantastic, well-constructed study to read about some really cool animals. It also alludes to there being a “standard” relative speed for shark swimming, similar to how tetrapods move at similar relative speeds (Froude numbers).


Any thoughts on the format for these posts would be appreciate. We can make them snappier, maybe even a bit more visual if I dedicate some more time to developing my own graphics aside from those in the papers.


MicroCT and visualisation

Fancied getting my current plans out somewhere other than my notebook, hopefully sharing some useful resources I’ve been working with and keeping this blog up to date with my activities.

At the end of this month I’m going to be scanning some lizard specimens from the Cambridge Zoology Museum and the Natural History Museum assuming all arrangements go to plan.

I’ll be using micro computer topography, which essentially fires thousands of high intensity X-rays through the specimen, taking many thin slice pictures, which can then be stitched together to make a single 3D representation of the specimen. You can see individual slices in the top left and bottom left and right tiles below, with the overall model shown top right!

Working view of 3DSlicer, showing a scan of the Dwarf crocodile, Osteolaemus tetraspis. White areas indicate high density (bone/metal) and green areas show where I’ve highlighted particular bone, in this case in the limbs.

After a little bit of computer wizardry within a free program called 3DSlicer, you can generate fantastic 3D visualisations of the scanned specimens. For an example of this, see the limbs of O. tetraspis below.

Limbs of Osteolaemus tetraspis, complete with some of my working measurements.

These images can be created by anyone at home using 3DSlicer, open-source crocodile CT scan data from CrocBase and a handy guide by paleontologist Peter Falkingham. I’m using them to build up a comparative database of limb bone morphology across a range of quadrupedal and bipedal species to investigate whether things such as limb length ratio can contribute to facultative bipedality (the ability to rise up on two legs from four and move around). Currently, I’m working through some data from CrocBase and Digimorph (both free resources) before collecting primary data at the end of the month.

Hopefully this has given you a little insight into what I’m currently working on. Watch this space for more details about how scanning goes (and hopefully some fancy pictures) next month.

Any scans of any species of lizard or bird are gratefully accepted should you have any available! Limbs are of particular importance. 

Cambridge PhD: a six month reflection

So, I’ve made it 6 months into my PhD at the University of Cambridge.


Today we’re going to reflect on what it’s like here, both in terms of my work and the general atmosphere of being in Cambridge. I realise when beginning my own PhD I hadn’t got the foggiest idea what to expect, so maybe this gives someone else insight into what your experience may be like. A lot of this is unstructured rambling, and is more life based then science-y.


Academic life


Going to start with how “work” is. I’m based in the Earth Science department here, which is largely a geology/climatology department, with a smattering of palaeontologists hidden in the woodwork. Of these, most study shelly fossils and early invertebrates, but there are a few vertebrate people, of which I’m one. Which is kind of a falsehood, since I won’t be doing any real paleo work for a year or so, so I’m still really a biologist in the earth science department.


To begin with, this was tough. Listening to conversations in the common room was alien and daunting. Having little to no geology knowledge, I’d be left wondering exactly what these different rocks even were, or why certain magmatic systems (that’s volcanos) are more interesting than others. As time has progressed, I’ve picked up enough to understand the projects of my peers, so the alienation is gone. Additionally, I realized that my lack of understanding but desire to learn was shared. A hard-core earth scientist (that’s a geology joke in case you missed it…) doesn’t necessarily understand the musculoskeletal system at first, but that doesn’t mean they’re uninterested. Everyone listens to and learns from each other, so the department is very inclusive and open, which is great.


I get a desk in a shared office, with internet access and IT support should it be needed. So work space is provided, then there are also college and university-shared working spaces should you fancy a change of scenery. I do this often, finding that it’s really draining to write at my office desk but far easier to analyse data there than anywhere else. So that is also great.


Sometimes it can be a little weird trying to understand how Cambridge works, which systems to follow for different things, but these become clear soon enough.


I also managed to secure space in a different department for dissection work when I start that this summer, which was an achievement since Cambridge departments can allegedly be notoriously uncooperative (though this was not my experience).


I spent a couple of weeks this term “demonstrating”, which is essentially supervising practical lab sessions for undergraduate students answering questions and the such. This was good fun, and something I’m looking forward to doing again next term and each year leading forward. Oh, and you get paid at a decent rate too which is nice.


College life


This will vary greatly based on your college, but I can attest to the Darwin experience.


People: Good. Everyone I’ve met here seems a genuinely nice person, and the few college friends I have are great to spend time with. My college social circle is perhaps smaller than many people due to the amount of time I spend in the department, but this doesn’t bother me, and in fact makes managing college friendships a little easier.


Accommodation: Decent – but doesn’t promote socialising itself. The kitchen area is standard student accommodation, but lacks a “social” are such as a common room. As such, it highly promotes going to the college bar, but I find this is often annoying since I tend to get home from work, chill for a while, eat dinner and then not particularly want to drag myself back out to go to college, even if it is just a couple minute walk. But, as I said, that’s a shortcoming of living offsite. Living in house may be very different, as the bar then serves as the onsite “common room” function. High speed internet is good and I’ve got around 3m of desk space to fill with tech which is much welcome. Oh, we got freezers recently, so I can batch cook a meal without eating the same food for 5 days straight, so life in halls has improved dramatically since October, and I’d definitely consider living in college accommodation again, should the opportunity arise.


Social: Great – provided you put yourself out there. Darwin is regarded to have one of the best college bars in town, the legendary DarBar, I don’t go as often as I’d like, but it’s something I constantly am trying to improve. Without being an extrovert it can be tough to meet people at first, but I’ve managed it so most people would be fine! Also, a double rum for £3.50 is not to be missed out on.


Other factors


You may have heard of PhD students, and Cambridge students generally, often having a tough time dealing with the mental pressures associated with studying here. It’s something I’m likely going to address in detail in the future, but worth touching on here for reasons of comprehension.


It’s stressful. Some days you feel like you get nothing done – that’s stressful. Some days you feel like you did a lot but it wasn’t enough – that’s stressful. Some days everything goes right and you’re happy with how things went – thankfully not stressful. The pressure is indeed high to get work done, but it is by no means (at my stage at least) and unmanageable workload. I tend to manage the stress by making sure I never work late and by eating copious amounts of chocolate digestives. It’s working so far.


In any event that the stress does get too high or you fall prey to other pressures, Cambridge has A TON of pastoral care, from college tutors and councillors to departmental help and even more. That’s something I haven’t heard of being available in such abundance at other institutions.


So there you have a snapshot of what my first six months have shown me. There’s more I could talk about, but I think this covers all the main points. Rereading my last post, I said I’d keep this blog updated more. That’s gone really well this past six months, maybe I’ll manage two posts by next October.

My first week at Cambridge

I’m writing this 12 hours through what I’m hoping is a 24 hour sickness bug. Such is the way of freshers at a new institution – only this fresher’s flu includes a stomach bug as well as the usual multitude of cold symptoms. Woo! There’s no science in here to read, just the ramblings about my life here in Cambridge so far.

But moving on. I’ve started at Darwin College, a postgraduate only part of the University of Cambridge. There seems to be high science and engineering demographic, with a few arts students thrown in too. It’s a good mix, a large difference from the RVC where everyone is following the same discipline. The people seem friendly, the city is busy but in a different way to London. My accommodation here is so-so, the room is a good size but the but the building is loud and all of the water delivery pipes seem to run just behind my bed. I’ll get used to it. There’s no freezer in the kitchen. That’s my largest issue, since I’m used to cooking meals large enough for six and freezing portions down. Again, I’ll get used to it.

Moving on again! The department I shall be studying in for the next few years is amazing. The Earth Science School here is so incredibly friendly, everyone looks out for each other and is willing to share words of advice. I’ve got a great bunch of people to share an office with. The department meets for tea/coffee and lunch as a mass collective throughout the day, offering regular work breaks and opportunities to discuss current studies with people of many disciplines. I’m the only new paleo PhD in the school, surrounded by climatologists and geologists, but that doesn’t seem to be a barrier to meeting people which is fantastic. I also bumped into an old school friend who’s just started a Masters in the department!

I’m so far loving the whole experience here. Early next week I’m meeting with my supervisor, David Norman, to discuss where to head with my studies. The meeting was supposed to happen today, but illness struck and hence, regrettably, it had to be postponed.

More science-y posts are to follow. Maintaining this blog more regularly is something I’m aiming for this year, so please watch out for that.

Thanks for reading.

Degree status: 100%

So the last few months have been somewhere between busy and very busy on the busy-ness scale. And today it officially finished.

The last few months involved writing my dissertation on my cat work along with exam revision and sitting. A chaotic end to my degree, requiring lots of time management and focus. It’s all been worth it though.

I’m thrilled to have been awarded a First Class Honours degree in Bioveterinary Science, and in doing so have confirmed my place as a fully funded PhD candidate at the University of Cambridge studying the evolution of bipedality in dinosaurs. This will incorporate a lot of my current (growing) functional morphology knowledge and biomechanics, and I’ll develop skills in paleoscience which I can’t wait for.

Hopefully I’ll be looking to get my cat work written up and published over the summer, so findings will be available there when that is done. I will say I was very pleased with how the work went, and cats are cool.


In light of my surprise degree classification I’m now going to celebrate and waste away the day.



PS: In future I hope this blog will be a bit more active, particularly once my PhD starts. I had wanted to investigate the effects Brexit may have on British Science, but that ship has sailed already, and isn’t such a hot topic anymore. Maybe next time I’ll be quicker to the party.

Recent goings on…

Quick update about how things have been going on over the last couple of months!

There’s been two trips to the Cat Survival Trust in Hertfordshire, a rehoming and breeding sanctuary for big and small cats. For a summary of how well data collection went there, see this article by Ed Yong in The Atlantic. It summarises some of the aims of my current research nicely, as well as painting me as a true cat whisperer (something I can’t seem to shake now).

More recently was an overnight stay near the Wildlife Heritage Foundation (find them here) to study their cats. This was a far more successful trip, and despite not having many photographs myself due to working the equipment, I can point you to Andrew Cuff’s post about our time away. In all, it was an incredible two days working up close with Cheetahs, a huge 200+kg African Lion, a feisty Fishing Cat (who was the star of the show) and more.

I’ve got plenty of data to analyse over the coming months, before writing up around May time for my dissertation!

In other news, I have an interview at the University of Cambridge next week for an awesome PhD programme studying the evolution of bipedality, so prep for that has been the past week or so’s bedtime reading. Here’s to a good interview, to say I’m nervous would be an understatement..!

Until next time, hopefully I’ll have some good news to share, and maybe some sneaky peeks at how the data is looking!

2016 has arrived

And with it comes another step on the adventure.

Data analysis for my third year project is well underway, with additional collection happening this month! This presents opportunities to get up close and personal with some awesome felid species across two feline sanctuaries in south westerly England.

Current data is looking great, hopefully we can get some more active cats this month to get some variation in the data set – cheetahs and tigers are fans of walking and not much else it seems.

The constant search for PhD studentships continues, fingers crossed January will bring some new projects that tweak my fancy, which will mean more applications to be made.

In the meantime, I’ve got another module starting this Monday, investigating different animal and cellular models that can be used for disease. A little outside my usual area of interest, but it seemed the most interesting option outside of the locomotion module.

I’ll end this short update here, there’s bound to be more #SICB2016 tweets to catch up on by now – so much cool science to read about!