Wednesday, 20 December 2017

Caution: Animals may bite

So the past 6 months have been absolutely manic as many people may have known. For those of you who don't know the reason, it was possibly the worst kept secrets at the vet college. Crocodiles, Nile crocodiles. We had been working with a group of them trying to understand their locomotion across a range of behaviours (see the project website here). What this actually means is we had been trying to get crocodiles to walk, run, turn and jump in a runway or a treadmill (all work fully approved of by both the RVC in-house ethics board, and the UK Home Office). During these activities we were looking at the crocodiles' movements, and to get the best insights we used a combination of light videos, X-rays (to look at how the bones move during locomotion), force plates (to measure the forces exerted by the crocodiles on the ground as they move) and EMG (electromyography - measures muscle activity by measuring their electrical activity).

And when I am talking about working with crocodiles, everyone instantly thinks of the famously enormous ones in the Masai Mara taking on wildebeest. It leads to an abundance of concern (the health and safety people had a field day), which is obviously healthy to have around animals that have dozens of teeth and eat meat. Let me allay fears now, or reduce how impressed you are about my awesomeness as the new Crocodile Dundee, these crocodiles were all small (all less than 2m and 7.5kg, with most less than 4kg). Why would we pick small ones? Besides the health and safety, and the difficulty in working and housing large crocodiles, small crocodiles actually exhibit a wide range of locomotor behaviours, including low walking/belly sliding, high walks, trotting/galloping, jumping, and climbing (ours regularly were found in the foliage added to their enclosures). As crocodiles get bigger, they are unable to perform some of the higher energy behaviours due to their increased weight .
One of the crocodiles looking out of the straight runway through an acrylic end
Crocodile showing off a high walk. Force plates just visible below the crocodile's neck, and the two X-ray systems receiving drums visible in the background.

Our work with them has now ended, and in the end we have something like 150 hours of working with the crocodiles and have collected some incredible data. There will be many months of analysing it, writing papers, and then combining the data into digital models of an "average" crocodile.

X-ray picture of a crocodile skull
However, it was not all smooth sailing. Working with animals is incredibly difficult (see post on felid field work), let alone mostly aquatic animals who tend to enjoy dominance in their environments. This means motivating them to walk (or run) on demand can be difficult. Or often, impossible. As such, we often had hours of crocodiles being nothing more than angry lumps refusing to do anything. This leads to great videos of stationary crocodiles, and increasingly delirious conversations between the people present.

For our data collection we also needed to move the crocodiles regularly from their enclosures to the research area, which undoubtedly meant lots of handling crocodiles. We were trained by crocodile experts in how to handle crocodiles safely (more for our safety than the crocs I think). Inevitably, I was the one who got it wrong one day trying to tape the jaws of our smallest crocodile shut (in the oral history of this story, she was far bigger, and I may have been doing some heroic act to save some small child). The tape slipped and the croc did what crocs do, and bit the nearest thing. Just this time it happened to be my finger. 
All taped up, finger still attached. The healed picture is even more disappointing so wasn't worth showing
No major damage (think cat bite), just a few punctures and a nice cut across the top of my finger which will leave a memorable scar. I had to go to the hospital to get it cleaned up and get my antibiotics. Funnily they had run out of tetanus jabs (in a walk in centre for minor injuries no less), and it has led to health and safety having to write a bunch of new forms (oops).

I have to say this was one of the more interesting and most frustrating parts of my career. However, the work continues on new things! Keep an eye out on the blog for future updates on our research, and crocodile updates.

A year to never repeat

For long term readers of my blog (thanks and apologies to you all at the same time), you know that I seldom talk about personal feelings linked to work, besides a post on the stress of finding jobs. And stress linked to the job is what I am going to talk about in this post. Academia has a mental health crisis that often goes undiscussed and overlooked (a study on it here). This post won't be me preaching how to manage it (read on and you'll see why). It is a discussion about why I am ready for my year to be over.

Work has been crazy. There is no better way to say it. I have enjoyed academia, particularly the flexible working hours and doing what I love. However, the part of the project I have been doing has meant that the hours are less flexible and have been long for months on end. Added to that is a lack of holidays. I haven't really been able to take a break of anything more than a 3 day weekend since February because doing so means stuff doesn't get done, and major deadlines are approaching. Add to that additional academic things like completing papers and work from previous projects, and the never ending search for a permanent position (I got awfully close to one) has meant that I am drained.

And it is noticeable. Not as much at work, where I hope the quality of my work hasn't decreased, but I have grumbled a lot about needing a break. I am still getting things done on the long hours, but I have not had a functional personal life since the end of July. I remember having a conversation with my boss early this year where I discussed trying to get a better work life balance (I was pretty exhausted by work at the end of last year too). Clearly I failed, and I am aware of what it has done to me. To friends and family who I have not seen much of I am sorry, but I am overwhelmed. When I get home after a day of work (or across weekends), I just want to be alone and shut down/relax. Chances are I am already feeling like awful and feeling like I am letting you down further that I really really don't want to be going out (I don't like people seeing me down, and it takes a lot of effort to hide). Relaxing doesn't come easily and I often have a drink to take the edge off. Sometimes it is many. This is particularly true after some of the things I have done at work which haven't been the most pleasant. I don't sleep properly anymore, the joyous combination of crappy sleep at night and just exhaustion/naps on the weekend. The lowest I got was the two nights in a row I actually cried myself to sleep (thankfully only those two).

I am not calling out for help and I think I am getting through the lowest bit, particularly now the workload lightens into the Christmas break. I got all of my side of things caught up and completed last week and I will get the better part of 10 days off with only some work to get done. I also hope people do not judge me for it (writing this has been hard and a worry that publishing it will affect my career). I am merely hoping to bring awareness and general conversation as no-one knows quite how low I have been. I have always encouraged friends with their issues to talk to others and I have not practised what I preached and have been the stereotypical academic suffering mental health issues.

In the New Year, I already have things I am looking forward to such as 2 trips away early in the year (ok, both work related, but a conference and a dig are different and far more enjoyable than the current workload). I will also be making sure that I actually get home at a reasonable hour and get out and do more things (even if it's exercise which has mostly been dropped, and is usually the first thing that goes when it gets busy). A request for anyone who reads this though, please don't look at me or treat me particularly differently. If you see me working long hours many days in a row again and drifting away, just encourage me to join in things (preferably ones that aren't always drinking), and accept (without kicking up a fuss) that sometimes I do just want to go home and do nothing.

I will be back blogging normally in the New Year (probably about the conference), and work will resume. Hopefully you all will have stuck around!

Monday, 14 August 2017

Alternative fieldwork

The summer is here, and it's field season for all palaeontologists (and field scientists) in the Northern Hemisphere. My Facebook and Twitter have been inundated with photos (including articulated dinosaurs, ankylosaur skulls, tyrannosaur teeth, etc etc.). Check the Twitter tag #fieldwork for an idea for some of the things. Sadly I don't have any field plans and am busy with my mysterious experimental work for the rest of the year. However, I was craving my fieldwork fix so organised a trip down to the Jurassic Coast with a few friends from RVC and UCL to go find some fossils.

If you've missed my previous posts, I have a soft spot for the Jurassic Coast. This stretch of coastline spans 95 miles of Dorset and Devon and ranges in age from the Triassic to the Cretaceous (185 million years). It was made famous by Mary Anning finding large numbers of fossils near her home in Lyme Regis, and is today a World Heritage Site. It was also on the coast at Charmouth where I first went fossil hunting when I was a young kid.

Our car consisted of 5 enthusiasts with backpacks, a couple of rock hammers, and a chisel. None of the usual pick-up trucks filled with pick axes, shovels, plaster, tents etc. We even failed to bring the usual supply of beers (although that was rectified from the field site). A 3 hour drive turned into 4 after a decision to drive by Stonehenge (where traffic was awful), but we eventually made the beach at Charmouth in the rain.

This section of coast is famous for it's ammonites and marine reptiles, although many other things are found here including belemnites, crinoids, starfish, fish, sea urchins, and occasionally dinosaur bits. We parked in the Charmouth car park and worked towards Lyme Regis, focussing on the area around Black Venn. Although not as impressive as it used to be, the slide still gets eroded daily and fossils continually wash out. Highlight was finding my first ichthyosaur vertebra (at a massive 1cm), although found some lovely pyrite (fool's gold) ammonites too.

We repeated this on Saturday, when the weather was far nicer, with another ichthyosaur vertebra being found and lots more ammonites across the group. Sunday we decided to mix it up, and walked to Lyme Regis overland (tide was in) so everyone could see the famous little town and pay respects to Mary Anning at her grave.
Mary Anning and her brother share a grave site. Easily identified in the cemetery as it has a fossil alter at the bottom that we duly added to.
We also had a quick walk around the town, one of the fossil shops (a trend seems to be increasingly less of the local stuff, and far more imported fossils), before lunch on the sea wall before heading down onto the beach and walking back towards Charmouth. The offerings to Mary Anning seemed to have helped as two nice ichthyosaur vertebrae were found in quick succession as we walked along the beach admiring all the ammonites in the rocks (and failing to extract many from the rock falls). As we got back to the Charmouth side, we passed a group of people going for the first time with a guided walk from the heritage centre at Charmouth. The group of 30 or so people (mostly kids) had found a bunch of fossils, and one lady found a pair of articulated ichthyosaur vertebrae.

Then we bundled back into the car and drove down to Lulworth Cove, where faulting and folding have created this beautiful natural cove as the softer chalks inland get eroded.

Bright sunshine over Lulworth Cove. Portland just visible off in the distance on the left of the sun.
After that it was a long old drive back up to London and getting some sleep before work began again in earnest in the office on Monday. I did find some time to take some photos of all the fossils I collected on the weekend:
The random little collection. Everything from millimetre sized ammonites/gastropods to bits of bones. There could have been hundreds of more pieces but I leave many bits on the beach now (particularly the belemnites), and try to give away a good number of finds to kids who are struggling to find their own so they aren't paying for them at the shops.
Piece of pyrite ammonite shell showing off sutures
A small pyrite ammonite showing more sutures.
Nicest two ammonites.
Nothing spectacular as far as science is concerned, but always love finding fossils, and some of them are gorgeous (if I do say so myself). I never tire of finding pyrite ammonites, although it can be tedious finding them when the beaches are so heavily picked across the summer. If you want to find your own, go search! I can offer my limited advice on where to find these sort of things (get in touch), but am still needing to go with some of the local pros to see what they do.

Sunday, 9 July 2017

A day in the life of a palaeontologist

I regularly get asked what I do on a day to day basis, and the honest answer is there is no standard day. So I came up with a lot of things that I reasonably could be be doing on any given day (minus paperwork).

If I was to average all of my days from the beginning of my PhD to now, the majority of days would be sat in front of a computer doing CT scan segmentation. I love (and hate) CT scan segmentation. It's basically high tech colouring in, and who doesn't love that (although I admit some geographers I've teased for their degrees being sponsored by Crayola now get the last laugh).
Fig. 1 from Cuff et al., 2017. See last post for all the details.
Whilst it may not sound particularly fun, and it is incredibly time consuming where the bones are hidden amongst the rock, it is often the first time a lot of the material has ever been seen by anyone and those digital bones can be used for so many more things, like reconstructing skeletons, estimating body masses etc.
Fig. 2 from Cuff et al., 2017. Skeletal reconstruction showing the original bones from Panthera atrox.
But what about those days I escape the computer and get to do other things? It really varies a lot. Most recently there has been nearly all of my time out of the office as we are preparing a new experimental setup in the lab for XROMM (X-ray Reconstruction Of Moving Motion). We will have some animals moving through two X-ray beams to be able to look at their bone movement in real time, and because we have two aligned sources, we are able to get 3D models (see the website by the brilliant people at Brown University which explains it all in greater detail if you are interested). As such we are building runways, aligning and testing settings of the X-rays, and spending far too many hours in X-ray protective lead vests in a surprisingly warm English summer:
Rocking the lead protective gear, with the X-ray setups to the left of the figure with a "bent" runway between them. Also a dog treadmill at the right which we will be using too.
However, due to the fact the experimental stuff is all in the early stages I won't be saying more about it now, but I promise you there will be a lot of posts on it when it is all done. Suffice it to say we've just gotten some preliminary data and it looks incredible! I've also done experimental work on skulls for my PhD using strain gauges which was a whole different set of issues. Linked to this sort of work is a lot of coding too, but my coding is generally rubbish compared to people who spend a lot of time on it, so I won't linger.

Besides that I've also spent a lot of time learning anatomy and carrying out dissections (please note, all of the animals have been humanely euthanised, and were not put down just for the research). This is perhaps the area that has changed the least since Richard Owen's times (1800s) when comparisons with modern animals helped him to realise that fossils of dinosaurs belonged to a completely different and now extinct (ignore birds) group. Whilst for some it seems incredibly disgusting, there is something indescribably fascinating about actually getting to see how the inside of animals works:
Tiger dissection at the early stages of identifying the muscles.
It would appear that a lot of people agree, as we ran a public dissection of a cheetah after hours in the vet college last year and we got hundreds of people attending over the sessions (more photos here).
The cheetah dissection being carried out for the audience, showing off various bits of the anatomy of the animal.
Which brings us nicely to something I spent a lot of time doing during my PhD, and still am actively involved in, which is outreach. Teaching the public (of all ages) about science is incredibly fun and rewarding. During my PhD, I taught over 1000 kids in various small classes in and around Bristol about the Bristol dinosaur (Thecodontosaurus) as well as interacting with thousands of people at various science festivals and events.
The junior school children are often the most easily enthused about dinosaurs. Who doesn't love dinosaurs when they are young? Why do so many grow out of it?
Since then I've co-curated museum exhibits, done talks, and recently have been back in schools as part of the DawnDinos project where we've been working through science and art to teach about evolution (see updates here).

We also do a lot of travels for work as conferences take us all over the world. Since my PhD I have been to Las Vegas NV, San Francisco CA, Barcelona, Raleigh NC, Berlin, Los Angeles CA, Dallas TX. Whilst conferences are a lot of work (attending talks, meeting people, presenting your research), there is always at least some time to go have an explore of the cities.

However, the things I enjoy as part of my job above all else are the days in the field. Working with animals is great, although cats are particularly hard work and scared(y).
Setting up forceplates, whilst being closely watched by a tiger.
Nothing compares, for me, to fossil hunting though. Those special few weeks a year (in a very good year) where I get to leave a lot of my usual work behind and just enjoy being in the wilderness, and finding some new fossils. It's a lot of hard work, but I'd do it a lot more if I got the chance to.
Last day of a long season in Dinosaur Provincial Park, we dug up a turtle and then hiked it back a few kilometres. The long sleeves was a mistake for this bit...
So those are the things I do as part of my job. I will also note my list above will be very different to other palaeontologists who have different interests, e.g. people who work on reconstructing phylogenies (family trees) will not do most of what I do and vice versa. I am lucky in that my job is so varied and I love it (or I most certainly wouldn't be doing it). I wonder how many people can say they look forward to going to work more often than not?

Wednesday, 24 May 2017

Reconstructing a fossil lion

I'm overdue for a post but am back with the best reason, a new paper is out! And for the first time in a while it is freely available as it is published in the open access journal Palaeontologia Electronica:

Cuff et al., 2017. Reconstruction of the musculoskeletal system in an extinct lion. Palaeontologia Electronica 20.2.23A: 1-25.

As my last paper post was also on Panthera atrox (or at least its brain) hopefully everyone already knows what I am talking about. If not, P. atrox is an extinct lion from North America. The species evolved from a "cave" lion (P. spalaea) population from Eurasia that crossed the Bering Sea around 340,000 years ago. These lion populations in turn split from the lineage that gives rise to the modern lions about 1.89 million years ago (Barnett et al., 2016).

However, despite this paper being about this cool fossil lion as the specimen of choice, it is more about the methods we are using to help reconstruct extinct animals. When we have only the bones, how do we estimate their masses?

Traditionally we estimate body masses of animals from their bones based on scaling equations (be it lengths, widths, circumferences etc.). Generally, the long/big bones of the limbs are useful as they tend to scale in a predictable manner with increases in body sizes. In mammals, skulls are also pretty good for this too. As such we can estimate masses of similar animals if we know the lengths of these bones. There is also a more modern method for estimating body masses called convex hulling. This method works by wrapping individual bones or regions (where you connect all the edges of each bone so no bone is left uncovered, basically imagine cling film/saran wrap), adding the volumes together and multiplying the volumes by a calculated density. This method has proved to be surprisingly robust, but is sensitive to the density used (much like the bone scaling is sensitive to which bone/metric). Additionally, whilst great for calculating a decent total mass, it will be highly inaccurate if you are trying to get accurate segment masses as it ignores all the soft tissues (e.g. the muscles which are large proportion of the mass of the limbs). So is there a way to estimate those bits more accurately?

So let us get back to our lion. La Brea Tar Pits is the source of "Fluffy" as our lion is affectionately known. Fluffy is the most complete specimen known to date, so we got all of the bones CT scanned. I then segmented the CT scans to have a lot of digital bones. I imported them into Meshmixer (although any software that you can manipulate 3D models would work) and aligned them into a natural pose. However, even the most complete P. atrox individual was not complete (or at least not completely scanned) and the Fluffy reconstruction was lacking the ribs, tail, hands and feet. These missing bits were replaced with equivalents from Asian lion (P. leo persica) that I scaled to match the expected size (based on scaling equations of head and femoral length). This gave us a skeleton:

Fig 2 from Cuff et al., 2017. Skeletal reconstruction showing the original bones from Panthera atrox and those which have been copied from other vertebrae (red), or from P. leo persica (blue). 1, lateral; 2, dorsal; 3, anterior views. Scale bar is 50 cm.
We had a predicted mass from the bones (195-219kg) and wanted to see what convex hull results would produce:
Fig 4. from Cuff et al., 2017. Convex hull model from the reconstructed Panthera atrox skeleton shown in Figure 2. 1, left lateral view; 2, dorsal view. Scale bar is 50 cm.
The volume reconstruction from the convex hull gave mass estimates of 180-219kg satisfyingly close to that predicted from the bones alone, but perhaps not unsurprising  as we scaled some important regions from the Asian lion to match the mass generated from the bones (it is a little circular). However, as discussed before you can see how small the limbs look, particularly the upper region compared to what an expected healthy animal would look like.

This is where we did something clever. Previous work we have done on how muscles scale in living cat species (see papers 1 and 2, or blog) gives us scaling equations for expected lengths and masses. The Asian lion which we borrowed the various missing skeletal elements from again came in useful. The CT scans of that specimen showed the muscles even without special staining so I was able to segment them out individually.

Fig. 1 from Cuff et al., 2017. CT scan slice showing an approximately mediolateral view (i.e., longitudinal section) of an Asian lion’s forelimb. 1, Dark grey is adipose and connective tissues, lighter grey is muscles, white is bone. Bottom right corner white is a density calibration phantom (1.69 g cm-3; “cortical bone”). 2, Segmentation of the lion forelimb with select muscles highlighted. Abbreviations: FCU - flexor carpi ulnaris; DDF - deep digital flexors; ECR - m. extensor carpi radialis; Pro Quad - m. pronator quadratus; Abd1 - m. abductor digiti I.
I then scaled them to the predicted mass of  P. atrox (we were working with 207kg as an average from the bone measures):

Mass P. atrox = Mass P. leo x length scale factor x width scale factor 2

Not all of the muscles could be isolated from the CT scans (particularly the vertebral ones) and neither could most of the tendons of the hands and feet, in both cases due to a lack of contrast on the CT scans. The tendons were reconstructed by creating a tube of material off of the muscle and extending it to the insertion point whilst maintaining the volume to match the predicted mass as best as possible. The result:
Fig. 3 from Cuff et al., 2017. Muscled reconstruction of Panthera atrox showing the major muscle groups in lateral view. Abbreviations: FCU - m. flexor carpi ulnaris; ECU - m. extensor carpi ulnaris; ECR - m. extensor carpi radialis; EDL - m. extensor digitorum longus. Scale bar is 50 cm.
If you overlay the muscled reconstruction on the convex hull you can see the differences, with muscles visible wherever they extend beyond the convex hull:

Fig. 5a from Cuff et al., 2017. Reconstructed muscles overlaid on the convex hull of just the bones. Any muscles that are visible extend beyond the range of the convex hull, thereby demonstrating the underestimation of size by convex hulls based solely on bone
These massive differences between the segmental masses are not a huge deal for overall mass calculations as the densities of the hulls have correction factors built in, but if we wanted to do more complex modelling this matters a lot (e.g. musculoskeletal modelling). Thus we needed to see if we could create an accurate segmental mass calculation.

We compared the mass estimates for models of the bones, muscles and bones, and convex hulls over the bones, and convex hulls over the muscles on an Asian lion to see which produced the most realistic results. (Un?)surprsingly, convex hull muscle models produce results that are really close to those for the actual lion data (whether that is segmental masses, moments of inertia and segmental centres of mass (See tables 4-6 in the paper)). This gave us confidence in the results for the P. atrox reconstruction and segmental masses which we will be using (hopefully) one day for some musculoskeletal models. The overall body centre of mass doesn't move much, but this is likely due to the fact that the body hull grossly overestimates actual mass as it does not deal with air spaces or soft tissues.
Fig. 5b from Cuff et al., 2017. Reconstructions showing the posteroventral movement of the centre of mass (COM) between the bone convex hull and the muscled convex hull models of Panthera atrox. Scale bar is 50 cm.
It's a cool method that works, and the results can be achieved using only freely available software (although in our paper we used a licensed segmentation software). It does have the important caveat that the muscle scaling is easily doable as the species in question falls within the phylogenetic bracket of those we have worked on. For species that fall outside of that range (e.g. Smilodon, the other large La Brea felid, which is far more distantly related) this scaling pattern is likely to be more uncertain, although a similar method would probably still produce reasonable results.

Tuesday, 28 March 2017

Collecting fossils: Free for all or just the pros?

This is obviously an opinion piece and my feelings on it make no difference to the legality of collecting fossils in various places. If you are in doubt about what you can and cannot collect, please do check the local laws or speak to a palaeontologist in your closest museum about it.

Quite simply, I probably would not be a palaeontologist if I had not been able to collect fossils when I was a child. I found my first fossils on the Jurassic Coast in the UK (aged about 4 or 5) where anybody can collect fossils from the foreshore (there are laws about certain sites and hammering into cliffs/rocks is not allowed nor is it safe). In a very Victorian way, I loved collecting things growing up. I had rocks/minerals, coins, stamps but most prized were my fossils (yes, I am a nerd). Over the years and various travels around the world I collected fossils and back home they reminded me of travels as well. It must be said that none of my collection are rare or important. It is made up of mostly ammonites, belemnites, crinoids, some plant fossils, some trilobites and some shark teeth.

Me, somewhat embarrassingly, way back in my youth about to go diving in the Cooper River for fossil shark teeth.
The haul on my first trip covering teeth, vertebrae, tusks, whale ear bones etc. All eroded out of the sediment by the river, and have lost their geological provenance. 
Pretty much the same things you find in the fossil starter boxes you get for children, except in my case I had found most of them. The exceptions are the various fossil fish from the Green River formation of the USA, and some of my first Megalodon teeth that I had were bought in fossil shops and off of eBay. Both the collecting, trading and the buying are things that are worth discussing as both are subject to various laws (and again please check your local legislation if you are not sure, and I do not claim to be a lawyer or know all of the current laws).

In general, collecting on private land is not possible unless you have permission from the land owners. There may be an added layer of complication in some places that fossils count as minerals, so you need mineral rights to collect, so you can purchase the rights to that without owning the rest of the land. If for some reason the owner of the land denies you access to the land you may end up unable to access your rights resulting in a legal battle.

Out in the public realm, I will refer a lot to places I have been to or have knowledge of. One of them is the Jurassic Coast, made famous by Mary Anning who was collecting fossils there back in the 1800s. The Jurassic Coast (and the UK public land in general) deals with fossil collecting by allowing everyone to collect, but this is because the rate of erosion is so high that if fossils are not collected they are rapidly lost to the sea forever. It should be said that because of this there are a great number of professional collectors who collect, prepare, and sell the fossils for money. There remains an unwritten rule that the fossils of particular importance are offered to back to public collections (e.g. the Weymouth Bay pliosaur and the David Sole specimens of Scelidosaurus).

The Weymouth Bay pliosaur. Figure from Foffa et al., 2014 Functional anatomy and feeding biomechanics of a giant Upper Jurassic pliosaur (Reptilia: Sauroptergyia) from Weymouth Bay, Dorset, UK. Journal of Anatomy 225, 209-219.
Inevitably some fossils will end up being sold to private collections and/or leave the country which is where the issues come from, particularly if they are important for science (discussed below). In the USA you are (or at least of my last checking) able to collect invertebrate fossils on most public land, but any vertebrate material requires a licence to collect it; a famous example is "Big Al" a very complete Allosaurus which was found just on public land (the crew had thought they were on private land they were allowed to collect on). In Canada, the rules vary from province to province with Alberta having the strictest in that you can only surface collect (no digging) in crown lands that are not provincial/national parks or protected areas (no collecting there), and even then all fossils are still owned by the state and cannot leave the province without permission from the the government.

I personally think everyone should be allowed to collect (with some clear caveats below). It is particularly important in this day and age where we are struggling with the rise of anti-intellectualism, an increasing lack of enthusiasm for the outdoors, and a surprising lack of awareness of palaeontology (despite the Jurassic Park effects). Fossils make a lot more sense when in context and you can see how the layers exist and how different fossils appear in each layer, with fossils that increasingly resemble modern forms as you get closer and closer to the surface. You also get to wander around lots of great places from beaches, to hills, and badlands as well as seeing all manner of nature and wildlife. Additionally, like the Jurassic Coast and many badlands of North America, fossils on the surface have a lifespan of anywhere from hours to a couple of years. If people aren't actively searching and collecting many things may simple erode away and will never be found (or found in a state useless to science).

Some small pieces of well preserved, but exploded, dinosaur bone. We know there was probably a complete dinosaur bone here once, but beyond that these bone fragements are seldom of use.
I will put this with a big caveat though (I appreciate this is where a lot of palaeontologists will have been previously been screaming loudly at me). Sometimes very important fossils will end up in hands of people who don't know how important they are, fossils may be poorly prepared and end up damaged, fossils lose their geological context and perhaps most importantly someone may surface collect something small which was part of a far bigger thing that is just underground and we may never find the rest because of it.

What do I suggest we should do? Well, anyone with no formal training in fossil hunting wanting to go find fossils (anywhere they are allowed to) should first find someone with experience. There are an abundance of sources for amateurs (e.g. UKFossils) where you can get locale information, fossils you are looking for etc. etc.. I would suggest that people look for local clubs or sites. On the Jurassic Coast at Charmouth there are daily guided trips to the beach from the Heritage Centre with people who know what they are looking for who help. At a bare minimum, everyone should get into the habit of carrying a GPS, camera (or camera phone), and some collection bags/containers and some paper for notes. When a fossil is found, GPS the site, write down a detailed note (date, time, GPS coordinates) and put it near the fossil (assuming the fossil isn't enormous) and take a photo. If the site is going to be tricky to refind (even with GPS coordinates), take some photos of surrounding features that help triangulate the location later. Then collect the fossil and put it in a specimen holder/container. If you don't have a field book keeping track of your finds, do so when you get home. These methods are almost exactly the same as what palaeontologists do. I tend to have a GPS on my phone and screen shot the location, take a photo of the fossil with a scale and then collect it (if it is worth collecting whilst prospecting). That way I have all of the data to hand for recording later. If you have an unusual/rare fossil find, ideally leave it in situ (unless a real risk it might be destroyed before coming back, and only collect within the law) and take lots of photos and GPS locations, to show an expert in a museum. If you have collected a fossil of importance, it is far easier for you and a professional to relocate the site if there is something more exciting to be found in future. Do remember that the many new species are found by amateurs, and it is only with their help that these fossils come to light!

Argentina, Brazil, China, Germany, Mongolia and I'm sure many more have severe limitation on export of fossils, and Germany's new laws (from what I understand) limit the value of fossils you can own as a private collector. The Society of Vertebrate Palaeontology, of which I am a member, does not condone the commercial sale or trading of vertebrate fossils unless it keep them within or brings them into public domain (see their ethics statement here). Therefore my youthful buying as part of my collection would have brought me directly into violation of one of the societies of which I am a member. I must say I haven't purchased any vertebrate fossils in the last decade or so, and many of the fossils I have collected have been distributed to young friends and family who are interested in fossils.

The fossil trade does raise interesting issues though, and something that is increasingly worth talking about. There are well documented cases of famous celebrities owning a dinosaur (or part thereof) such as Nicholas Cage owning a Tarbosaurus bataar skull that he voluntarily returned to Mongolia having been informed of its illegality. It is not uncommon to see famous auction houses offering up fossils (of all types, not just vertebrates), and even the largest T. rex ever found, SUE, was purchased by the Field Museum in Chicago (with the support of various individuals and companies including Walt Disney and McDonalds) for $7.6 million from an auction and remains the most ever spent on a dinosaur. Sophie the Stegosaurus at the Natural History Museum, London was purchased from a private dealer too. The commercial industry responsible for the trade of fossils has led to massive issues with poaching of fossils (e.g. Mongolia, although it is working hard with authorities across the globe to get its fossils back), and even fake fossils (e.g. Morocco). More importantly many of these fossils will be sold to private collectors at a vastly inflated price and will never be studied by scientists and their information lost to the public. In private conversations with many people who carry out field work, they have suggested that for the price paid for various fossils (e.g. the €177k spent on a Triceratops skull earlier this year) could fund the finding of far more specimens that would end up in public collections (with field seasons costing anywhere $10k-100k a year depending on exotic locales and size of crews) as evidenced by the Museum of the Rockies vast collection of not just Triceratops (I believe they have about 100 now), but many dinosaurs including about half of the known T. rex specimens.

What should we do? I have no good answer here. The trade of fossils has always existed, from the snakestones of Dorset (carved ammonites that look like snakes which were sold to Christian pilgrims near Whitby) to the famous Mary Anning selling fossils on the Jurassic Coast to generate a living (and likely give rise to the She Sells Sea Shells tongue twister) to eBay (only picked because it is the place I purchased fossils from many years ago).
Ammonites carved to look like snakes from the Whitby Museum website.
Commercial traders are responsible for discovering and bringing many fossils into the public light, but regularly the commercial industry is responsible for crimes (particularly the export/trade in illegal fossils, poaching of fossils or destruction of specimens to get the claws and teeth which are smaller, more collectable and far easier to trade). With the rise of GPS location tracking, and a drive to more open publication practices, fossils (and their locales) that were once safely out of the eye of commercial traders (or even opportunistic locals) are no longer safe.

Buying fossils only fuels the trade, and as such the commercial trade of fossils should be approached with caution if you are a private collector, and only for bringing fossils into the public holdings if you are an academic (see SVP ethics above). I searched eBay (UK) for fossils tonight in the collectables<rocks/fossils/minerals<fossils section and found 38,098 items for sale (as of 23:30BST, 27/03/2017). The most expensive is a Triceratops skull (£660,501.98 + £40,000 postage), with 3 items over £100,000 and the first 200 all over £1600. That is just eBay UK and gives you an idea for the magnitude of the fossil trade. It is a great resource for people looking to add to their collection, but really do consider if the item is worth that much (and fakes aren't uncommon on eBay) or if you would do better to go and spend your money finding something yourself (e.g. £100 for a nice ammonite would allow you to go from London to the Jurassic Coast and stay overnight, giving you at least 2 days of collecting time and who knows what you might find). If you are a millionaire reading this and looking to get a dinosaur/other large fossil for your own collection (unlikely, I appreciate), really consider why you want it and whether would it be better to sponsor some digs, have your name permanently attached to those specimens (and regularly new species are named after people/companies who fund the expeditions), and those specimens to appear to the wider public as a whole.

This has been a long discussion on my points of view on the issues of finding and trading fossils. I will say I love my fossil collection, but I do cherish those that I found above those I have bought or been given (which will have been purchased somewhere). With time, experiences finding fossils, and my career in palaeontology it has become easy for me to turn away from the purchase of fossils. I would hope that people considering buying fossils might go out and search for their own (please do get in touch if you are struggling to find contacts in your area and I will happily help to the best of my abilities to help get you in touch with someone). If anything happens to me, I hope my collection would be donated to a university or museum that might be able to use them to educate the public rather than be sold off (not that it is worth much anyway). If you have anything to add please do comment and let me know if you agree/disagree with what I have said. I would love to hear from people around the world, particularly those in locations where fossil collecting is illegal to see how it affected your enthusiasm about palaeontology.

Wednesday, 18 January 2017

The brains of cats

So 2017 begins on a high for publishing with another paper hot off the presses and long overdue:

Cuff AR, Stockey C, Goswami A, 2017. Endocranial morphology of the extinct North American lion (Panthera atrox). Brain, Behavior and Evolution. DOI: 10.1159/000454705.

To quickly catch everyone up, P. atrox is an extinct lion from North America (as the paper title suggests). The species evolved from a "cave" lion (P. spalaea) population from Eurasia that crossed the Bering Sea around 340,000 years ago. These lion populations in turn split from the lineage that gives rise to the modern lions 1.89 million years ago (Barnett et al., 2016).

Phylogeny of the lion species
A quick note, endocasts are the natural cast (the infilling) of the endocranium (the braincase). In mammals the brain almost entirely fills the cavity so brain and endocast are almost identical (which is why brain swelling is such a major health issues). Birds are similar with their brains filling most of their endocast, but most non-avian dinosaurs and crocodiles have large sinuses that take up large volumes of the endocranium. Prior to our study the only data for P. atrox was from casts of skulls, (where they infilled brain cases with material to produce a cast) carried out in 1932 (Merriam and Stock, 1932). The new study adds some more details to those casts, as well as some additional information on the inner ear (red in the figure below).

From Cuff et al., 2017. Fig. 1. Endocranial reconstruction of P. atrox in left lateral ( a ), right lateral ( b ), dorsal ( c ), and ventral ( d ) views. Anterior is toward the left in a, c, and d and toward the right in b . The endocast is rendered in blue, the inner ear in red, and the cranial nerves in yellow. CN II, optic nerve; CN V 1–3, trigeminal nerve (ophthalmic, maxillary, and mandibular branches); CN VII, facial nerve; CN VIII, vestibulocochlear nerve; CN IX, glossopharyngeal nerve; CN X, vagus nerve; CN XII, hypoglossal nerve; hy, hypophysis/pituitary; ob, olfactory bulb; ocx, olfactory cortex; pf, paraflocculus; v, vermis. Scale bar = 20 mm. The endocranial orientation in a and b is linked to the likely “alert” head posture
We also compared the morphology of the extinct North American lion to modern Asian/Asiatic lions (below).
From Cuff et al., 2017.Figure 2. Endocranial reconstruction of P. leo persica in A, left lateral; B, right lateral; C, dorsal; and D, ventral views. Anterior is toward the left in A, C, D and toward the right in B. The endocast is rendered in blue, the inner ear in red, and the cranial nerves in yellow.; CN II optic nerve; CN V1-3, trigeminal nerve (ophthalmic, maxillary and mandibular branches); CN VII facial nerve; CN VIII vestibulocochlear nerve; CN IX, glossopharyngeal nerve; CN X, vagus nerve; CN XII, hypoglossal nerve; hy, hypophysis/pituitary; ob, olfactory bulb; ocx, olfactory cortex; pf, paraflocculus; v, vermis. Scale bar = 20 mm. Endocranial orientation in A and B linked to the likely “alert” head posture. 
Overall the endocasts look fairly similar, but something that you might have noticed is how much more elongate the P. atrox brain looks relative to the modern lion (P. leo). There are some previously published 2D models of some extinct taxa (Radinsky, 1975), with the oldest species showing this similar "elongate" morphology. However, the morphology seen in P. leo where the forebrain sits further back on the hindbrain is more "folded" and was also seen in some of the extinct species (particularly the sabre-tooth cats). So we needed a way to quantify the elongate/folded brain morphology (linked to cephalic flexure), which ended up being a simple ratio of length of hindbrain not covered relative to total brain length (P. atrox and P. leo shown below):

Long line is total length, short line is "exposed" hindbrain not covered by the forebrain.
We however lacked information for many of the extant species on whether the elongate or folded brains were more common and if there were any patterns. Therefore we got hold of a bunch of CT scans from colleagues (Z.J. Tseng, C.Grohé, and J.J. Flynn), and Christopher Stockey (a summer student joined us from Imperial). Chris segmented endocasts from a wide range of extant taxa (see below).
From Cuff et al., 2017. Figure 3. Brain anatomy through Felidae. Proailurus, Pseudaelurus, Dinobastis and Smilodon are all modified from Radinsky[1975]. Phylogeny modified from Piras et al.[2013], total length 27Ma. All scale bars = 2cm.
The results are shown in the table below, with the species with the most elongate brain morphologies with the highest proportion "exposed". P. atrox has 18.6% exposed, whilst P. leo is only 5.9% exposed (actually the lowest we measured). Typically, as with all biology, there is a spectrum rather than a hard and fast rule about the elongation of the brain of felids. Just within the pantherines (Panthera spp. - the big cats) there is a large range in the level of folding. Most of the other living species of cats are fairly consistent in their levels elongation.

Cerebrum and cerebellum length
“Exposed” cerebellum length
Proportion “exposed”
Dinobastis sp.*
Smilodon fatalis*
Neofelis nebulosi
Panthera tigris
Panthera pardus
Panthera atrox
Panthera leo
Pardofelis marmorata
Carcal aurata
Leopardus wiedii
Lynx rufus
Acinonyx jubatus
Puma concolor
Prionailurus viverrina
Felis silvestris

What does this mean? Honestly I don't know. It's a weird quirk of felid morphology that deserves further study, so there is a project if anyone wants to collaborate.

Beyond the crazy brain shapes, what about their sizes? We measured the volume of the endocasts and multiplied it by standard brain tissue density (somewhere between 1.027 g/cm3 [Schröder, 1968] and 1.100 g/cm3 [Barber et al., 1970]). This was this compared to the body size to get a relative brain size.

From Cuff et al., 2017. Figure 4. Regression of log maximum brain mass against log body mass (both in kilograms) for Felidae.
Most cats are fairly similar in relative brain size, with P. atrox slightly above that expected for its body mass. In addition, the absolute brain size (both of this endocast and some of the other P. atrox measured in 1932) is higher than any other felid species measured to date. But what does that mean for the intelligence? Actually in cats there doesn't appear to be an obvious correlation between brain size and sociality with similarly "brainy" cats being capable of both solo living and group living so we cannot say if P. atrox lived in prides like its modern relatives.

Barber TEDW, Brockway JA, Higgins LS (1970): The density of tissues in and about the. Acta Neurol Scand 46: 85–92.

Barnett R, Shapiro B, Barnes I, Ho SY, Burger J, Yamaguchi N, et al. (2009): Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Mol Ecol Apr;18:1668–1677.

Merriam JC, Stock C (1932): The Felidæ of Rancho La Brea. Washington, Carnegie Institute of Washington.

Radinsky L (1975): Evolution of the felid brain. Brain Behav Evol 11:214–254.

Schröder R (1968): Über das spezifische Gewicht des Hirngewebes in der Nachbarschaft von Tumoren. Aus dem Max-Planck-Institut fur Hirnforschung, Abteilung fur Tumor forschung und expirementelle Pathologie, und der Neurochirurgischen Universitiitsklinik, Koln.