Wednesday, 30 December 2015

My year in review

So it is that time of year, where everyone is putting up their exciting top finds and top science stories, and thought that I could do the same for my academic year. I won't over big it up, as the review won't be too exciting, but a fun way for me to link together my blog posts and papers, and put things into perspective of where I'm heading for 2016.

As it turns out 2015 was the first calendar year of my postdoc (although Feb 2014-Feb 2015 was the first full year). The year started off really well in India, where we were in the field on the 1st of January (we had been there for a few days by this point).

The artistic New Years messages in front of many houses in Tamil Nadu
After another 10 or so days in the field, we'd found bits of dinosaurs, sharks, ichthyosaurs, ammonites, sea urchins, belemnites, turtles, and fish. A good field season if you asked me.

When back from the holidays I got the stark reminder of how difficult it is balancing work and social life as an academic. Something I remain very envious of all of my friends who have successfully managed it. I instead buried myself in work and very rapidly had my first manuscript of my postdoc submitted and in review on felid body mass evolution. Before Easter had rolled around I was also at a very advanced stage of revision with a paper on ornithomimosaur cranial reconstructions, and had submitted a long running paper on finite element validation in an ostrich cranium. I had also helped put together a small display in the UCL Grant Museum for their Strange Creatures exhibit showing how palaeontologists and biomechanists work together to understand what dinosaurs looked like, and how they moved.

I was also lucky enough to be involved in some field work with felids at Colchester Zoo, where we had a forceplate in enclosures with their tigers and cheetah. This was part of a BSc project looking at forces exerted by cat species on the ground at various speeds, and how limb posture changes with gaits in different sized felids. As this is ongoing research that we are hoping to add to I will save that for another time. It was lots of fun but worrying when my supervisor scampers away when she first saw the tiger behind me without saying a word...

The shock moment when a tiger says hello!
June was a great month for my publications, as both the cat body mass paper and ornithomimosaur crania papers were accepted. We finished up all the dissections from the various cat species by the end of June, having had a bit of a delay with missing data and vertebral column issues whilst figuring out the best way to analyse all of the data in regressions. Thankfully we fixed those issues and those manuscripts were getting written.

Tiger dissection. If you want to see the photogrammetry click here.
In July, John went to Los Angeles and we acquired some stunning scans of two extinct felids fom the La Brea Tar Pits: Panthera atrox (North American lion); and Smilodon fatalis (the commonly known, although equally misnamed, sabre tooth tiger).

In August/September I was off on field work again, this time in Argentina. It was an amazing place, with lots of fossil finds ranging from dinosaurs, to mammals, fish, frogs, crocs(?).

The rock formations were spectacular, even if you aren't a trained geologist or palaeontologist
I spent the end of the summer reconstructing the P. atrox skeleton, resulting in the most complete reconstruction of a single individual of the species (the rest, as with S. fatalis, are composites of several individuals).

Panthera atrox skull
The resulting skeleton allowed estitmates for the body mass, and using the scaling equations for the muscles (how muscles scale with body mass) for all extant felids I was able to reconstruct the muscles for P. atrox. A sneaky side project meant that I also extracted the endocast for the specimen, allowing the first digital brain, and endosseous reconstruction.

In October my ostrich validation paper came out meeting my minimum estimate for number of publciations for the year (was hoping 3-5 based on ongoing projects at the start of the year). The joyous SVP was also upon us again for the year. Dallas was a good conference, and I presented the dissection data, as well as the reconstructions to a good reception as my first invited poster.

November rolled around and the forelimb and hindlimb muscle papers were submitted, and work began on attempting to validate loading cat bones by loading them and measuring the strain patterns. Unfortunately, this would be an ongoing problem through December when I finally gave up with it. Our rig is just too unstable for small scale things.

December led to the submission of the P. atrox brain paper, the submission of a big grant, and also a fun interview with a crew as part of a new ITV and PBS documentary called Story of Cats. Apparently I am now considered a domestic cat expert (or at least the easiest one to get at short notice), which is flattering but always thought it would be dinosaurs first! Continuing the outreach, I was also invited to give a public talk as part of the Animal Showoff (Science Showoff spinoff) at the Grant Museum, which was a load of fun. I also finally got to get on to the Smilodon reconstructions, so that has been a fun holiday project. Paper-wise, the hindlimb paper came back out of review with relatively minor corrections, as did a collaboration on vertebral column morphology in cats. More excitingly, and in a beautiful wrapping up of 2015, a collaboration on a fish fossil from India was accepted for publication. It is my first fossil find that is being published on, and have already written the blog for that whenever it comes out fully.

So 2015 is pretty much done and dusted, what's lined up for 2016?
1) Building on the 3 papers this year, I'm hoping there will be 4-5 first author papers (3 are already in review/revision, 2 in prep), and equal numbers of co-authored ones (1 accepted, 1 with minor corrections already, 2 to be submitted).
2) More zoo visits for experiments in Jan/Feb which will hopefully lead to a fun blog post with pics and videos.
3) Off to Argentina in March for some more fieldwork in different areas that will hopefully yield more fossils, and maybe something new to add to my Indian find?
4) The rest of the year will be getting the FE validation done (we've got leads to possibly use another setup), and then hopefully computer modelling of the musculoskeletal models.
5) September brings about the biggest and scariest (potentially) change of the year, as I will be out of my current contract. The big grant that I am named on, and a job application will be out, but due to the joys of academia, I may still be stuck and searching for the next big research project. If you do know of any, please let me know!

Thanks for reading the blog, and hope everyone had a good 2015, and has a great 2016!

Sunday, 25 October 2015

Finite element analyis: the importance of being valid

On the back of finally getting another paper out:

it required another blog post. I won't over blog it as it is open access and apparently far clearer than some of my other papers to my parents (my metric for how overly complicated I've made things). This one is about the importance of validating finite element analyses (see FEA for "dummies"), but will also touch on the joys of trying to publish negative results (i.e. when experiments don't match computer models). A quick background for those who don't want to read the previous post, finite element analysis (FEA) is a method for analysis how complex structures deform under loads, by simplifying them to a series of finite interconnected units (be it bricks, tetrahedra or any triangles: the elements) that have been given material properties appropriate for the structure (e.g. if it is a steel beam, the elements are given steel structural properties). It is known the method works incredibly well on man-made objects, and it is indeed the engineering tool used for everything from designing cars (and crashing them virtually) or planes, to bridges and buildings. Basically anything that an engineer might build, there is probably a finite element model out there somewhere.You may see where I am going with this then, the method works with varying degrees of success on biological structures for replicating strain magnitudes and orientations. Most recent work on mammals (monkeys, pigs) and reptiles (particularly alligators) manages to get very close replication of strain patterns across the models, but to date few studies have looked at birds. Birds are important as they have very mobile skulls (they have loads of extra little joints in the skull compared to most mammal and reptile skulls) are in a palaeontological context are important as the nearest living relatives to dinosaurs (being descended from them). Many studies have looked at how dinosaur skulls perform under feeding loads, but what does that really mean if we don't know how accurate models are on even their living relatives?

So building on the previous limited work that has looked at ostrich mandibles (Rayfield 2011), and finch beaks (Soons et al., 2012a,b,c), and in preparation for trying to understand ornithomimosaur (ostrich mimic dinosaurs) skull function, I started looking at validating an ostrich cranium (n.b. skull is cranium plus the jaws). We had some frozen ostrich skulls from an ostrich farm in the UK, and I used several in the course of the project, first as a practice dissection, then as a practice experiment, then one for the actual experiment/validation, and one more for material property testing. The one used for the validation was sent frozen to Hull/York Medical school for CT scanning prior to any work so we had a full digital copy, and could use it for making the computer models.

Labelled ostrich crania, showing the ‘average’ ten month old ostrich crania. From Cuff, 2014.

Myological reconstructions of an ostrich skull. A) M. depressor mandibulae, B) M. adductor mandibulae externus, C) M. adductor mandibulae posterior, D) M. pseodtemporalis profundus, E) M. pseudotemporalis superficialis, F) M. pterygoideus. From Cuff, 2014.
From the initial work, it was decided that the M. pseudotemporalis superficialis (See D in the above figure) was the best load to use. I dissected the muscles of the experimental specimen. From the dissection I was able to measure muscle mass, fibre lengths and angles and using these metrics you can estimate the force a muscle can produce. I actually measured higher potential force production by the muscle than we used, but this was to keep well within safety factor of the experimental set-up and the cranium whilst producing visible bending in the cranium. For the experiment, Jen Bright (now Sheffield) and I first had to apply a way of loading the cranium that would replicate a muscle. Previous work has either used the original muscle, or screwed some metal attachment to the skull. We tried something somewhere in between by screwing an artificial tendon (made of layers of fibreglass, resin and a carbon fibre loop) instead that would allow a flexible load application (a design that Colin Palmer, an engineer and now a part-time PhD at Bristol).

From Cuff et al., 2015. Artificial tendon. (A) Schematic of the artificial tendon construction showing the carbon fibre loop sandwiched between layers of fibreglass. (B) The artificial tendon screwed into place on the M. pseudotemporalis superficialis. Screws highlighted in black circles.
Once the tendon was attached, 13 strain gauges were applied to the dissected ostrich cranium, and cranium was then placed on the rig. For anyone who follows the field, they may have noticed this is the same one as seen in some of Jen Bright's earlier work on pigs (hence the affectionate name "pig rig", which now is the "ostretch")

From Cuff et al., 2015. Ex-vivo experimental set up. (A) Experimental testing of ostrich with gauges attached, under loading of the artificial tendons. (B) Schematic of experimental rig showing load and constraints.
From there we applied the loads, and using the gauges measured the strains. Unfortunately, and for reasons we do not know, gauge 6 was not functional during the experiment. Then came the fun computer model which was, to the best of our abilities, as identical to the experimental set-up. This involved first isolating the bone of the cranium (two types, the surface cortical bone, and the deeper honeycomb-esque trabecular bone), the beak, and sutures.

From Cuff et al., 2015. Digital reconstruction of the ostrich skull. Red triangles represent the constraints, black arrows show orientation and location of loads, red rectangles are membrane elements that mirror the strain gauges. Gauge 6 was non-functional so was not included in the model, but its location is marked. The blue lines are sutures, and the yellow material is the keratinous rhamphotheca. The trabecular bone is not visible. Gauges labelled with an asterisk (*) are sites where nanoindentation was performed. Direction from grid one is labelled as the white arrow from which strain orientation were measured.
And what the skull more or less looks like under loading to give an idea of the areas where strains will be highest (NB this is only to give an example, and is a skull, with only cortical bone, no beaks, and loaded with muscles).

From Cuff 2014. Ostrich cortical bone, and muscle model showing strain patterns.
As you can see from the two images showing the ostrich models, missing gauge 6 is a shame as it is in one of the high strain areas. It becomes important, when considering strain magnitudes (effectively change in shape, i.e. deformation) which don't particularly match:

From Cuff et al., 2015. Maximum and minimum principal strains for both ex-vivo experiments, and finite element models in microstrain. (A) Maximum, and (B) minimum principal strain for models with material properties from the literature; (C) Maximum, and (D) minimum principal strain for models with posthoc material properties; (E) Maximum, and (F) minimum principal strain for models with material properties from nanoindentation. Material properties for each model are listed in Table 1. Note that both experimental trials are shown.
This is particularly true for absolute magnitudes of maximum principal strain where gauge 7 far exceeds anything we could reasonably produce, but from here you can see the recurring theme for the other metrics we measured. Strain magnitudes, ratios (maximum: |minimum|) and strain orientations are similar in magnitudes in certain places, but don't match as well as we would expect in others. Generally the patterns are correct (where there are high or low strains), but that is the best we could achieve no matter what material properties we used (and included some novel ostrich property measurements).

These results are particularly interesting as similar methods have worked on mammals and alligators producing models that closely match those of the experiments. As for why the results are so far off in our models is unknown, and something that needs further investigating. It may come down to how we modelled the materials of the cranium, because joints in the skull are far more difficult to model than we have, because our new tendons were worse than before, or a myriad of other factors that I've not discussed here or in the paper. However, the data in the paper are all interesting and this is the first full attempted cranium validation of a bird ever. As a spin off issue from the paper, it showed me how difficult it is to publish negative results. Negative results are where the results of a study show no match between models and the experiments or in the case of medical science, where the medicine are no better than a placebo. However, these results are really poorly represented in publishing as they don't make sexy stories. This leads to the potential for replication of experiments that don't work repeatedly through time:

My paper went through a round of major corrections at one of the "traditional" journals, before being rejected when we put in more data showing the fact the model doesn't match. As such we sent it to PeerJ (a new open access more welcoming to all result types) who sent it through a round of major revisions, before accepting it. Most of the biggest problems stem from reviewers believing our results are wrong through some fault in the methodology and telling us to do more experiments (I accept some of the corrections were things that we needed to clarify, or tidy, or explain further). 1) This is problematic as the specimen quickly dries out during testing so would require a complete redoing of the entire thing which took me almost a year and 2) this perpetuates the not publishing negative results trend. If the method doesn't work, why shouldn't we tell people this doesn't work and not to try it again, or to come up with modifications that might improve it? I believe if our results had been very close with no issues it would have been published rapidly in the "traditional" journal and not taken 2.5 years. It is something I would love to test, but the ethics of sending papers out to review that are the same methods, but differing results is a bit dubious and would require some thoughts. If anyone has any idea or willingness to get involved on this, please let me know.

Cuff AR, 2014. Functional mechanics of ornithomimosaurs. Thesis. University of Bristol.
Rayfield EJ. 2011. Strain in the ostrich mandible during simulated pecking and validation of specimen-specific finite element models. Journal of Anatomy 218:47-58.
Soons J, Herrel A, Aerts P, Dirckx J. 2012a. Determination and validation of the elastic moduli of small and complex biological samples: bone and keratin in bird beaks. Journal of the Royal Society Interface 9:1381-1388.
Soons J, Herrel A, Genbrugge A, Adriaens D, Aerts P, Dirkx J. 2012b. Multi-layered bird beaks: a finite-element approach towards the role of keratin in stress dissipation. Journal of the Royal Society Interface 9:1787-1796.
Soons J, Lava P, Debruyne D, Dirckx J. 2012c. Full-field optical deformation measurement in biomechanics: digital speckle pattern interferometry and 3D digital image correlation applied to bird beaks. Journal of Mechanical Behavior Biomedical Materials 14:186-191.

Wednesday, 30 September 2015

Argentinian Fieldwork

So a few weeks after getting back from Argentina, and catching up on lots of work (including SVP preparation), I finally am getting around to writing about what we got up to out there.

Anjali Goswami, my UCL supervisor, has spent a long time searching for new field sites to add to the India fieldsite she has been working on for the last decade (or more). As such she has been looking for locations in Gondwana (the old southern continental land mass of Antarctica, South America, Australia, Africa and India), particularly sites that have never been searched for microfossils. Microfossils are the little fossils that are often overlooked when people are hunting for dinosaurs, but can be anything from dinosaurs teeth, down to any microscopic remains. Anjali however, is interested in the mammals, particularly with work from Thomas Halliday who finished his PhD at UCL (and continues as a postdoc) on Palaeocene mammals, suggesting that the placental mammals (what we are, compared to marsupials - e.g. kangaroos, and montoremes e.g. platypuses) originated just before the K-Pg mass extinction (the one that killed all the non-avian dinosaurs). As such the time just before and after the mass extinction are incredibly important in understanding mammalian evolution. Argentina is a well known locale for its dinosaurs. Patagonia in the south, is home to loads of different dinosaurs from large theropods, to some of the largest sauropods that ever lived. However, in the north of Argentina there are also dinosaurs, and some of the beds extend into neighbouring countries as well as covering the really important K-Pg boundary (although damned if we saw it). Enough of my rambling prelude though...

So we flew into Salta in NW Argentina, Anjali, Thomas and myself where we met our Argentinian collaborators, Agustín Scanferla and his friend and technician Javier Guillermo Ochoa. After a night in Salta acclimatising to the altitude (with the help of some wine and empanadas), we drove up to Parque Nacional Los Cordones (The National Park of the Cactuses/Cacti) where we would be based.

Wiggly road from the "lowlands" into the mountains.
The drive up was a long winding road, ascending from 2000m up to 3500m (see above). I sometimes have issues with being stuck in a car for long period of times, and with the altitude must say I was feeling a bit rough. It was on this drive I tried coca leaves for the first time. I know what you are thinking, yes it is what cocaine is made from, but chewing the leaves is a traditional remedy for altitude sickness. They taste just like tea (or at least to my uncultured non-tea drinking taste buds) and actually made me feel sicker, so I disposed of mine pretty promptly. Finally we stopped ascending and got to the national park, where you drive into it along the line of an old Incan road (now under tarmac).

The Incas could build straight roads!
The Argentinians have been very successful at developing little stopping points in the area that allow tourists to have a wander around and read some of the old myths about cactuses the Incans had (something to do with protecting a young eloping couple from angry parents).

Whilst Anjali isn't exactly tall, the cactus sure is!
Having had a quick drive down the road past where we were staying, we drove back as the sun was setting and the moon rising. It was also the first time we got to see the reason this area was a desert. Every night the clouds roll in but get stuck (more or less) at the edge of the basin creating the appearance of a wall of clouds.

Moon rise, sunset, and a wall of clouds arriving.
The accommodation was pretty basic, but can't complain too much as it had walls, hot water/shower and central heating. And occasionally electricity/wifi although that was all dependent on a very temperamental generator. I am thankful for it as we did see temperatures dropping below freezing most nights even if it was in the 20+C region most days.

The least flattering picture of Thomas I took in the field, but shows our adobe brick home, with a mud roof covered by tin held down by big stones.
Our first day out in the field we headed to a site previously described to us by a field geologist up the side of a mountain. Most of the morning was spent climbing up and down finding very little (we were one peak adrift of the site as we prospected). My best find until getting to the actual location was a stromatolite - layers of mud held in place by algal mats that build up over time.

Stromatolite in section. The layers showing how they build up are clear.
It is worth pointing out that the region is truly gorgeous in terms of scenery, with the rock layers fluctuating in colours from whites, to reds, to greys and purples. Truly an amazing place.

The vertical rock beds, showing the different colour layers. Somewhere over there is fossils.
We spent the early afternoon at the site and found many fossils, but were unable to extract much due to the hardness of the rock (and not wanting to climb a generator 1.5km horizontally before 1km vertically). As such we collected some scree from the exposure to test how it will prepare under acid digestion.
From left to right Agustín, Javier, Anjali, Thomas. Up the hill (mountain) on day one.
The next day we did a major prospect and found nothing. This was to set the trend for the trip as we alternated days of no fossils and fossils for most of the first week. Just the occasional trace fossils. The Palaeocene seemed strangely devoid of macro fossils, but this is likely due to the environment of the basin which was forming as the Andes started to rise. It wasn't until the 3rd day we came across fossils in a location we didn't know about with Thomas finding a mammal tooth, and me being competitive climbed up a silly slope in the area and found a vertebrae and some other small bone of a mammal whilst the rest had taken a break. There were also a few teeth in amongst some of the small conglomerates (old river channels with rocks/pebbles instead of just sand).

Mammal vertebra in-situ
Over the duration of the trip it would become a recurring theme that it felt like the landscape didn't want you there. Many of the locations were giant sandstones with no fossils, and were covered in bucket loads of cactuses and thorny bushes. If you weren't careful you could easily sit on them as some cactuses were tiny (as Thomas and I can attest).
Spines, spines, and red rocks
If that wasn't bad enough, we realised we were in cougar/mountain lion territory with sittings of footprints, followed by Javier finding a panther hairball (as indicated by the size of it). Whilst in another place, location way up a mountain, I came across a lovely little cave filled with bones (I assume guanaco), so promptly made a hasty retreat from the area.

Puma hairball
Puma cave
I am going to blame that and the crazy amount of time climbing up and down mountains (and so watching your footing rather than looking for rocks) for our lack of finds as much as the locations. This can be attested to by poor Thomas who, whilst following Agustín up a hill (who successfully, and unintentionally, destroyed all the footholds by climbing up) slid down about 5m of hill before he managed to stop himself falling much further.

However, after much failing in one region to find anything, we spent some time in the Cretaceous where I found my first bits of Argentinian dinosaur bones. The first bits were scrappy, but due to the same bed being exposed for some way, I found much more as I followed it along, including a small vertebra.
My first Argentinian bits of dinosaur bone.
On the walk back to the car that day, I was trying to find my way to a GPS point on the top of the hill and apparently forgot that we were in the southern hemisphere so went the wrong way. In my typical lucky/persistent way I happen to stumble across a bunch of bones eroding out of a single location including some unusual shaped ones. Probably bits of girdle from a sauropod, but unfortunately they weren't very extensive, and the bits of rib and long bone were no better. However it was a start!

Chunk of dinosaur bone
The next day we were in a new location, once again expecting no fossils, as we were still alternating days on and off for fossils and we'd found dinosaurs the day before. After an adventurous drive we stopped at the intersection of hills and badlands. Thomas and I went up one hill, Anjali another, and Agustín and Javier into the badlands. Having climbed one hill, Thomas and I were on our way back when I spotted an eroded slab with a fossil on it. We believe it's a tooth, but still none the wiser until it gets prepped.

View from the top of the hill. Note the clouds rolling in.
However, whilst smacking more rocks to see what else we could find we heard Agustín and Javier shout in excitement. They said they'd found a skull. After some discussion, we believe it is indeed a skull, but heaven knows what. It is only the back of the skull if it is, and with the bone almost matching the colour of the rock extracting it was difficult for Javier. We spent another day and a bit there, searching the badlands and finding no more, but up on the hill some more fish bits, including a bit of skull (and maybe a mammal tooth...), as well as finding lots of locations for future exploration. We built/rebuilt the road so we could drive in and get the specimen out. It also turns out that it hand't rained in over a year, but between our 2 days of visiting the location, it did rain!

My nerdy photo of a fossil fish scale, with lichen growing on it, taken with an iPhone through a hand lens.
The final day in the area, we returned to the area where I'd found dinosaur bones to do a thorough exploration. Everyone found some more small bits of dinosaurs, but typically I waited until the last hour as we were returning to the car to stumble across a large bonebed full bones of all sizes (although to be determined if they are just bits of big dinosaur bones or actually small bones), plus a few teeth. There is even an almost complete dinosaur rib that dives into the hill, but that was left there for now. Almost certainly part of a sauropod, but we did find a theropod tooth.

That evening, after a bit of a rush due to my find, we left our field station, and headed down to the south to a town called Cafayate (although one of the things I learnt is that Argentinians, at least those from Buenos Aires, pronounce the y like a sh sound) where we stayed in a hotel for the night. We then headed to a previously published ancient lake full of fish and frogs. So we sat and split lots of slabs of rock. We found a few partial frogs, before Thomas found something that might be the biggest tadpoles at the site. Whilst packing up were were working to sort the good from bad (ie the keepers vs those we were leaving), and there was a nice pelvis on one rock I was keen to extract. I hit the rock and one of the layers popped apart, exposing a beautiful frog fossil, preserved down to the individual bones in the phalanges in the hand and foot. It was probably the find I loved most, despite always loving dinosaurs more than amphibians,

The fossil frog, part and counter part. The left specimen has the head facing down. Big man thumbs for scale?
Myself looking very proud of my frog
With that being the last find of the trip, that rounds up our reconnaissance of the area having found some new areas with fossils, seen lots of new areas to recon, and set the ground work for what will be a hopefully incredibly productive location for Anjali and her field crews for many more years (and grant money is already being applied for so there can be a return).

If you are still reading, I did a things I've learnt from the field in my last blog on the matter, which I will add some new things to here:

  1. Altitude is hard. Don't get tired because getting your breath back is far harder than taking it easier the whole time.
  2. Coca leaves taste like tea. Basically you chew leaves, get a buzz, don't feel altitude, and in my case feel sick. Everyone has a different experience though.
  3. Walking sticks can be useful. Everyone else used them and raved about them. I however, did not, and this links to point 4.
  4. Walking sticks have downsides... Climbing steep slopes with them becomes a pain unless you are Agustín and climb like a mountain goat. How I envy him. I am very much a scrambler requiring 2 hands as well to climb things.
  5. Pumas are everywhere but remain hidden. Same goes for snakes.
  6. People look ridiculous wrapping fossils whilst wearing gloves.
  7. Argentina does good steak, wine and cheese (as if people didn't already know).
  8. Despite this I still lose weight in the field even after getting fit for the altitude first,
  9. The scenery in Argentina is the most spectacular anywhere I've ever been. I'd go back just for that!
  10. I remain lucky (or have some crazy 6th sense) at finding fossils. Long may it last as it means I get taken to go hunting for more!

Saturday, 4 July 2015

Big cat: small cat

So it’s been a while since my last post, but this one comes as an exciting advancement in my scientific career (and a day late for my birthday). My first postdoc paper was accepted and has now been published:

Cuff et al., 2015.Big cat, small cat: Reconstructing body size evolution in living and extinct Felidae. Journal of Evolutionary Biology. doi: 10.1111/jeb.12671.

This post isn’t to say how amazing the work is, more a way of me distilling and simplifying the information so that my family, non-scientific (or at least phylogenetics based) friends and interested others may be able to understand what I have published on (see last post). If you are interested in a copy and do not have access to it online (we unfortunately could not justify the £2000 for open access), and can't wait a year, please do email me and I can get you a copy.

The postdoctorate I am working on is part of a larger project trying to understand how all living cat (felid) species vary particularly with respect to their muscles, bones and scaling with body size. In modern species this size range is from 1ish kilos in the black-footed cat and rusty spotted cat, to 3-4kgs in domestic cats, to the largest male lions and tigers pushing 300kgs.

Body mass ranges of living felids.
If we look back in time there were even bigger cat species, with some of the sabre toothed cats (belonging to the Machiarodontidae) and largest cave lions pushing 4-500kgs. Despite work being done on other groups’ evolutionary history (e.g. dogs – Valkenburgh et al., 2004) no-one had yet looked at it in felids, and this is where this paper comes in.

Body mass range of living and extinct felids.
So the first step in trying to understand the evolution of body mass in the felids, is getting a family tree (phylogeny) of all living and extinct species. There are some great phylogenies of modern taxa (e.g. Johnson et al., 2006), but the problem with these trees based on genetic material is that very few contain fossil taxa (there are some exceptions including cave lions and the American lion, for which some DNA has been preserved. The challenge then became tracking down an extensive phylogeny for both modern and extinct taxa. The best available at present is that from Piras et al., (2013) which has a very thorough sampling of modern and fossil taxa. From this phylogeny it should be stated here that we used a variety of permutations that affect particularly the fossil ages: first occurrence (when the first fossil appeared, or at least the oldest estimate for the fossil is), mid (midpoint between first and last), last occurrence (when the species died out or oldest estimate for a fossil), as well as looking at only the modern clade of felids (both including and excluding fossil taxa).I will caveat here that a few modern species have moved relations compared to the genetic information (particularly those of the Panthera genus – lions, tigers leopards etc.). There are also some newer fossils belonging to the Panthera genus that were not included (e.g. P. blythaea: Tseng et al., 2014). However, I am hopeful that even when a new, bigger Felidae phylogeny is made, the results will hold true. We’ve also included all of our materials and methods in the supplementary information so it should be easy enough to replicate.

The next step was finding a database of felid body masses. For most of the living taxa there is a lot of data known on the body masses (or at least a range for male and female). These were used to calculate an average for each species (nearly all of my data came from a coauthor’s previous paper – Randau et al., 2013). For the remaining species where the data wasn’t readily available, estimates for body mass were taken from their describing papers, or from an average calculated from skull length (condylobasalar length – from snout to vertebral attachment) using an equation calculated from living species.

Now we have the data for family tree, and for each of their masses. The next step was to remove all of the species from the tree for which we didn’t have body masses. When this tree pruning was done, the next step was to assess the amount of phylogenetic signal in the data - the amount the shape of the tree, and the position of the species on the tree affect the data. In simplest terms, you’d expect the most closely related species to have masses more similar to each other than species that are less closely related. In our data it turns out there is a lot of phylogenetic signal allowing us to carry out the next tests, testing mode of evolution that family was undergoing. When I say mode of evolution, I really mean the way body mass evolves. Initially we tested for Brownian motion, white, trend, OU and early burst.

Brownian motion is a random walk pattern. Imagine flipping a coin, heads you increase in body mass, tails you decrease. Over time you could have all heads, all tails, but more likely a relatively even mix of both the longer the length of time studied. A white model has no change at all through the tree. A trend model is best described as a Brownian motion pattern where there is a directional pattern (e.g. selection that meant only heads were flipped if going back to our coin analogy). There are some famous models e.g. Cope’s “rule” which suggests there is an increase in body mass through lineages in time (not going to discuss the joys of Cope’s rule here as that would be as long as this post is too). OU (Orstein-Uhlenbeck) models are similar to trend models initially, so there is a selection pressure encouraging animals to evolve in a particular direction (e.g. all heads), however once they reach an optimal position they stay there (i.e. there is stabilising pressure so that masses stop increasing or decreasing from the optimum). This is often best described in an adaptive landscape (I am changing analogies here), where fitness of an animal is described as a hill (or island depending on preference), if you are at the bottom, you want to get to the top where you are more optimally adapted for the environment. But once at the top (or above sea level), it’s disadvantageous for the species to leave this hilltop/island, so they stay there. Early burst is the final model, where there is a rapid evolutionary pulse near the origin of the group where all major morphospaces (hills/islands) are occupied, with then some further expanding (into the small islands) of the range across the rest of the group’s history. The Cambrian explosion often is cited as a good example of this.

The test for which model all of these is best is called the Akaikes information criterion (AIC). A more recent version corrects for finite sample sizes (as we do not have infinite numbers of samples) and is perhaps understandably known as the corrected Akaikes information criterion (AICc). This method compares the probability that a model fits the data and then gives a likelihood of any model being best (normally displayed as a percentage as in our results). From this there was the suggestion that an OU model best described the data for the first occurrence phylogeny, and Brownian models best explained the mid-, last and modern occurrences. However, with the AICc we could only test single OU optimum models, and this is where SURFACE and bayou come in. Both of these packages are plug-ins for R (which is rapidly becoming the go-to stats program online) independently developed and tested. Both of these packages allow for testing of multiple OU optima (e.g. a big size and small size) and whether there is convergence between them.

Using these programs, SURFACE recovered 2 optima for modern felids, with the Panthera lineages and Puma evolving to convergent large body masses, and the rest of the felids staying at smaller sizes. bayou did not recover any pattern different to that of Brownian motion. The first occurrence data was probably the most entertaining as far as things I’ve ever written into results with SURFACE finding a range of optima, including two ridiculous ones: a large body mass (near the size of Juipiter); and a small body mass (close to carbon atom size). These are obviously not real optima, although they are entertaining to consider, and the crazy scale is most likely associated with: 1) the optima being evolved towards have not been reached; 2) the strength of the selection across the tree (i.e. how quickly things walk or run up their hills) varies across the tree. Because bayou runs many simulations (I ran 1,000,000 per model) multiple selection strengths could be tested, and the results found again two optima, a small one and a larger one. The mean and last occurrence data, both found two convergent optima supporting a large and small body masses in SURFACE, but this is only also recovered for the last occurrence data in bayou.

From Cuff et al., 2015. Phylogeny of all extant and extinct felid taxa using last occurrence dates (modified from Piras et al., 2013) showing the results from ‘SURFACE’ and ‘bayou’. (a) ‘SURFACE’ and ‘bayou’ phylogenies with shifts shown. ‘SURFACE’ shifts shown on the branches (red and blue), whereas ‘bayou’ rates are shown on the nodes with the colours representing increases and decreases, and the size of the circles showing the probability. (b) Phenogram showing distribution of taxa body masses against their phylogeny for posterior probabilities >0.2 (Table S4). Convergence shows the puma/cheetah lineage mostly being in the large body mass optima, whereas the clouded leopard species converge into the small body mass optima.
What does this all mean? Well there is some data for Smilodon from the La Brea tar pits suggesting they do attain larger body masses through evolutionary time. So despite using average masses (which would hide this signal), there is reason to believe that the last occurrence results are most realistic and best match what we see in the modern world. If this is the case, felids evolve two body mass optima, with large body forms and small body forms. The exact value for these optima varies depending on the method used, but generally they are divided somewhere around 5kg and >25kg ranges. The upper body mass limit fits with previous biomechanical and ecological data showing that large felids (>25kgs) have to take prey as large or larger than themselves in general to maintain their energy levels, whilst smaller species tend to take small prey. From this it may also be able to extend our understanding to some of the extinct species and what their ecologies were. Our results differed from what has been found in canids (dogs, foxes, wolves etc.) where there seems to be a trend towards continued larger body sizes (i.e. Cope’s rule), except in the foxes which show smaller sizes (Van Valkenburgh et al., 2004; Finarelli, 2007). It should still be mentioned that despite canids evolving increases in body size, the largest (at 70kgs in wolves), do not match even the largest living felids, let alone the incredible size (500kg) found in some of the extinct species.

Cuff et al., 2015.Big cat, small cat: Reconstructing body size evolution in living and extinct Felidae. Journal of Evolutionary Biology. doi: 10.1111/jeb.12671.

Finarelli, J.A. & Goswami, A., 2013. Potential pitfalls of reconstructing deep time evolutionary history with only extant data, a case study using the canidae (Mammalia, Carnivora). Evolution 67, 3678-3685. doi:10.1111/evo.12222

Johnson, W.E., Eizirik, E., Pecon-Slatter, J., Murphy, W.J., Antunes, A., Teeling E., et al., 2006. The late Miocene radiation of modern Felidae: a genetic assessment. Science 311:73-77

Piras, P., Maiorino, L., Teresi, L., Meloro, C., Lucci, F., Kotsakis, T., et al., 2013. Bite of the cats: Relationships between functional integration and mechanical performance as revealed by mandible geometry. Syst. Biol. 62: 879-900

Randau, M., Carbone, C. & Turvey, S.T. 2013. Canine evolution in sabretoothed carnivores: natural selection or sexual selection? PLoS ONE 8: e72868

Tseng, Z.J., Wang, X., Slater, G.J., Takeuchi, G.T., Li, Q. & Liu, J. et al. 2014. Himalayan fossils of the oldest known pantherine establish ancient origin of big cats. P Roy Soc B-Biol Sci 281 (1774): 20132686.

Van Valkenburgh, B., Wang, X. & Damuth, J. 2004. Cope’s Rule, hypercarnivory and extinction in North American canids. Science 306: 101-104.

Tuesday, 12 May 2015

The importance of outreach in palaeontology

Over the years, many great scientists could be accused (often fairly) of being very snobbish when it comes to engaging with the public. There are many scientists who often say it isn't their job to, but I'm here to suggest it should be (with a specific focus on palaeo matters).

This actually breaks down into two main sections and I will address them in turn:

General education - This one I feel like is probably the most important, particularly in this day and age with the increase in rise of fundamentalism and decreased scientific literacy in the general public. Specifically for palaeontology is the rise of creationism (or its pseudoscientific equivalent, intelligent design - ID). If anyone reading my blog isn't aware of this I would be surprised, but there are increasingly large numbers of people who have literal interpretations of the Bible (they aren't the only religion but the one that is most pervasive and actively trying to undermine evolution in many countries). Effectively the belief is that the Earth was formed in 4004BC based on work by the Archbishop James Ussher in 1650 who counted the ages of everyone in the Bible (start with Adam and Eve and figure out who begat whom etc.). This would make the Earth 6019 years old, although some have a "loose" interpretation of this and allow up to 10000 years to be safe. Whilst many people who have a level of scientific literacy say why should we care about the tiny religious group, the are not a tiny group any more...

In the USA there is the Creation Museum (there was an interesting debate between Bill Nye and the head of Answers in Genesis), the Discovery Institute (am organisation devoted to publishing peer reviewed papers about the "science" supporting the Biblical account), and the countless public school boards that are trying to ban evolution or at least force the teaching of creationism or ID alongside as viable options. Thankfully for science the USA has the separation of church and state laws, and several famous trials have quashed the teaching of first creationism and then ID. This separation of church and state does not exist in the UK (mainly because the Church of England is intricately linked to the state), and there is no regulation of what gets taught in private schools. There are ever increasing numbers of creationists out there, and a surprising example is my alma mater in Bristol there is even a professor (in engineering) who is a creationist. This was brought up in one of our first biology lectures, and is particularly surprising for a university that hosts one of the largest palaeontology departments in the world. It's not just individuals though, just outside of Bristol is the creationist zoo called Noah's Ark Zoo Farm. I am reliably informed (I refused to go on principle) that the signs there talk about the days animals are created in Genesis, and it is overtly as well as covertly teaching creation stories (although the website suggests there is a more complex story, please go have a read if you are interested). What I want to be explicitly clear about here though, isn't that teaching creationism or ID should not be allowed, but it should be clear that they are religious studies with no scientific backing and therefore kept out of the science classrooms.

The other major controversy sweeping the countries of the world that has as much to do about a distrust of scientists as much as a failure to properly educate people is man-made (anthropomorphic) global warming/climate change. The scientific community is more or less unanimous in the cause, humans burning fossil fuels, and the effects (although the magnitudes of the changes in the future are less certain and associated with unknowns in our climate models). The data is pretty clear as the recordings from Hawaii show CO2 increasing every year. The means that we have experienced a crazy number of years of warm temperatures over the long term averages, with 2014 the hottest on record, and 2001-2010 the warmest decade on record. According to reports (which I have not independently verified), February 1985 was the last month that had equal or below average temperatures - before I was even born! The Earth has never been below the long term averages in my life time, and equally an entire generation of people.

Global surface temperatures for the land and ocean. NB the last combine Land and Ocean at average is 1985 (land only is in the 90s)
Whilst there are variations in temperatures found throughout geological time (not just the ice ages - we are still technically in one as we have ice on the poles), associated with Milankovitch Cycles (tip of the planet on its axis, distance from the sun, and variation in rotational axis) and major climactic events (volcanism, large impacts, catastrophic degassing of deep ocean reservoirs etc.) the current trend is far beyond anything ever seen and far beyond anything that can be explained by those alone. There was a talk at UCL about ongoing research suggesting that humans have been messing with the climate long before fossil fuel burning due to us changing land use, particularly cutting down forests and planting crops giving reason to suggest we are in a new age for the Earth, the Anthropocene. Whether this is prehistoric as the UCL talk suggested, in 1610 or 1964 (as the Nature paper link suggests) will be debated, but undoubtedly humans are leaving a clear mark on the planet that will be recorded in the rock record. The data is clear, but there is still much debate within countries with politicians showing a lack of enthusiasm to address the problem due to a distrust in the data, and the costs of fixing OUR (humankind's) problem. A good example was the "Climategate" scandal where some researchers had their computers hacked and there were communications about how to manipulate the data for display purposes. 8 separate investigations were carried out and cleared the researchers of any wrongdoing, but called on them to do more to regain public. Another is where politicians (the USA Republicans are particularly good at it), hold up their hands and say that they aren't scientists so how should they know whether global warming is real (whilst ignoring the research from their scientists/governmental research e.g. NASA).

It is very much in the scientific community's best interest to engage the general public, whether in schools or helping teachers and politicians understand the work in an open and transparent way. This is particularly vital for people with their own work, and that is where I next focus.

Explaining your research - It is incredibly important for researchers to be able to explain the value of their own research to not just the general public, but also people from different scientific backgrounds. From my limited publication record, my family (of various backgrounds) are happy if they can understand 1 word in every 4 or 5 of my papers. As such they do not understand most of what I do. Obviously explaining your work to friends and family isn't the main reason for doing it, but underlines the issues that people outside our specific fields face. Probably the most important reason is being able to distil your research down into something that everyone can understand so that the funding bodies, which are made up of people from all scientific areas, can interpret your work and decide if you deserve more money! But being able to explain you research is also vital for press releases and for general communications to make sure that your research is correctly presented.


Schools programs - When it comes to palaeo it is incredibly easy to get young kids enthused and thinking about it. Pretty much all young children love dinosaurs (it's how I got into palaeontology aged 4 or 5), so utilising that love is easy. University of Bristol was incredibly good at doing outreach into schools as part of the Bristol Dinosaur Project. In the duration of the funding of the project (which was almost 3 years), the project reached 10000+ kids in schools around Bristol. These weren't large groups, these were standard classroom sizes (20-25 kids at most), which were taught by 2 people from the university. The standard exercise involved seeing what dinosaurs they could name, which countries they thought dinosaurs were found in and showing maps of dinosaur finds including Antarctica and thinking about how climates changed, how big dinosaurs got, what do they reckon dinosaurs closest living relatives were, how fossils form, and how we can tell what dinosaurs ate. From there the talk then focussed on the Bristol Dinosaur (a prosauropod from Bristol cave deposits), and we had a lifesize jigsaw puzzle for them to put together, and to look at its proportions (long tail, small head) and what that might mean for its lifestyle, then let them try to match replica bones to the skeleton, then we put a photo of a tooth up and asked what they thought it might have eaten. After all of this talking we got out a bunch of fossils that were borrowed/donated from the uni and city museum collections and let the kids touch and think what these fossils might be. Some were more obvious (ammonites), whilst bits like the ball (from the ball and socket joint) of a mastodon femur let them think. Then we showed them pictures of the reconstructions of what the animals looked like before letting them asking any questions they may have had.

Talking about the fossils the kids had on their desk. Specifically horsetails

Obviously this is not the only method, and every year at SVP there are increasingly more demonstrations of outreach in schools and how various universities are approaching the issue.

Science festivals/fairs - Again I base a lot of what I say here based on my experience with the Bristol Dinosaur Project. Every year there is a large science festival in Bristol known as the Festival of Nature. There are 2 days of only school children visits (Thursday and Friday) then Saturday and Sunday were open to the general public. Our activities varied from year to year, but always involved a couple of sandboxes filled with dinosaur bones that had magnets in them. The children then tried to match the bones to a magnetic skeleton outline on a board.

Helping the kids dig up dinosaur bones at the Bristol Festival of Nature

In addition we had a selection of the fossils from the school sessions, sometimes they got a chance to make plaster or paris casts of trilobites or claws to take home, and sometimes we had some of the microfossils from the dinosaur locales for people to look at under miscroscopes. With these sessions you may or may not actually get to teach as much as you might in school sessions, but the goal was still to get the kids (and parents) thinking about fossils and things that they look like that are alive today. The Festival of Nature had up to 30,000 visitors across the days so gives a chance to get to people from a much larger spectrum. I was involved in other festivals in Bristol and Bath, but there are other large ones in the UK such as Cheltenham. One of the most interesting moments we had was when a creationist woman brought her child who came and spent ages with us and we talked dinosaurs and science to him, whilst she refused to enter the tent we were based in. The plus side of festival is they do draw so many people, young and old, and there are often lots of good exhibits that you can link up with to help bring big picture ideas together, like dating archaeological things, fossils and the age of the universe and how they all relate.

Museums - Museums are already large outreach centres as well as repositories for collections and research. Most in the UK are actively involved in projects not just within their normal daytime hours. Bristol City Museum hosted a few late nights where they opened the doors for talks and displays from the university to showcase their collaborations. The Natural History and Science Museums both do massive late night showcases where they have drinks and talks as well. Due to their large numbers of guests already they are ideal locations to showcase work, or even help design information panels for the displays - I am collaborating with Anjali Goswami on a piece on how we know what dinosaurs looked like that's going in the UCL Grant Museum for part of their Strange Creatures Exhibit. Just last week (7th May) I was involved in a Show'n'tell session at the Grant Museum discussing my PhD research on dinosaurs to members of the general public.

3D printed skull of Ornithomimus used to show my PhD work.

Public speaking events - These are often the best way to display your research to the public as you can focus what you are trying to say for your specific audience. Whether this is for a specific group (e.g. meetings for local geological societies), or a general open day thing to showcase some work in coordination with other activities. There are also other less traditional ways from radio podcasts (see for a good listen), to comedy nights (like the Infinite Monkey Cage do with comedians and Brian Cox for physics) which all allow different ways to engage your audience with information.

Media - Whether newspapers, television or radio the media will probably always be the biggest outlet for research to the public. Whether this is people actively involved in documentaries, being interviewed, or providing the press releases, all of these have a large impact on how people view research. The media are often incredibly important for young researchers to get their work noticed, normally in the form of press releases and follow up interviews. Within palaeontology we often like to think we have made it (I have yet to), when the Daily Mail publish some highly erroneous article on the newest fossil creature discovered that we have been involved in. Whether it was the fish that supposedly was the ancestor of whales, or the anomalocarid that was. To give them a bit of credit I have gone back through their science articles and the articles are far tidier and less ridiculous than on first press release, but the http link continues to say the original writing. The comments sections are normally even funnier/scarier depending on your point of view. To that end it is imperative that we as scientists clearly explain our work to everyone so that their can be no mistakes or misquoting/misrepresenting of the science.

Social Media - Much like blogs they allow interaction readily with the public. Twitter and Facebook are probably the most common, and quick searches of some of the famous scientists in any scientific field and you will see how they interact with short "wordbites" of information and science. Normally its them teaching the world or sharing information, but occasionally you will see personal interaction on a one to one level over certain things. Neil Degrasse Tyson would be a good port of call for people searching. However, much like the mass media some of this needs to be approached with caution. Even IFLS (I ****ing Love Science) which does a world of good for publishing science to the wider public is known to have issues with it's reporting, so much like with the media it is important to make sure there cannot be any misrepresentation, accidental or otherwise.

Blogs - I started my blog as an outreach to discuss my work and experiences particularly for friends and family who haven't got a damn clue what I do as all they hear is nerdy things from me and effectively jibberish in my papers as they aren't scientists. But it also has a secondary effect of giving me practice distilling down my work to make sure I fully understand the concepts I am talking about. Einstein is reported to have explained his theory of gravity being deformations in space time to a child by explaining it as a blind ant walking over a curved branch and never being able to see what he could. He also enjoyed the concept of racing light waves and looking at a clock if you raced away at the speed of light and how it would appear stationary to the observer moving away, but not to any other people (theory of relativity). Blogs are a great way to involve the general public in your work on your grounds, and combined with other social media, allow people a chance to engage directly wit you.

Undoubtedly there will be many more ways people can and do regularly engage the public in science. There are also probably limits to how far we should go to engage the public (see this interesting article from John Hutchinson) particularly when it comes to incomplete or ongoing research. We must as scientists endeavour to make our work not just some unattainable work in a journal, but something that the wider public can understand.

Saturday, 7 March 2015

Virtual methods in palaeontology

So this post is a much delayed one (I'd like to blame work, but it's been more slacking on my behalf). I taught a couple of geology MSc students a few weeks back about some of the virtual/digital methods used in palaeontology, which focussed on the ones I have some experience with. Inevitably this means I will have missed some and for that I will have to return in later blogs! Any program names used here are only because I have experience, and is not to say they are the only, let alone best for the methods. I would encourage people to try out as many as they can to find out what is best for them and for pretty much every product that involves a license, there are free equivalents.

Laser Scanning/Photogrammetry

Laser scanning - As the name suggests the laser scanner uses a laser to scan the surface of an object. It works by shining a laser that reflects off of the surface and is picked up by a receiver. In the case of most palaeotological applications the scanners are based on triangulation - the receiver has a central location where reflected light hits for a known distance. Deviations from this location are caused by the object being scanned being closer or further away. For each scan a point is produced that get coalesced into a cloud that define the object. Some modern scanners also incorporate cameras that take photos of the object being scanned and overlay the photographs onto the cloud to create the entire surface/texture. Scanners are used particularly for objects where they cannot be CT scanned due to size, and only the external shape is required (as the scanner captures no internal structure) and where high detail (on the micron scale) is required. However, laser scanning can be quite time consuming and as it is based on line of site, often struggles around many complex structures e.g. the struts in skulls, which result in gaps in the model emerging unless additional scans are carried out for these areas.

Laser scanning a sauropod vertebra
Photogrammetry - Much like laser scanning, this method works by creating a surface of the object. However, unlike laser scanning, requires no exceptional equipment and is based only on photographs. Indeed these photographs don't even have to be digital for this method to work. A series of photographs is taken of the object, roughly equally spaced (in terms of degrees if imaging the entirety of an object) all the way around the object. This is then repeated at different angles (normally higher or lower angled than the first photo series) as many times as wanted. These photographs are put into a computer program which identifies perspective and relative landmarks (sometimes automatically, sometimes requiring user input depending on the program) and using this creates a point cloud as in laser scanning. This point cloud can have the textures of the photos overlain to create the object digitally. A good example is the Stegosaurus specimen at the NHM in London which was reconstructed digitally for some of the research using photogrammetry. A major proponent of this method is Peter Falkingham (with whom I had the privilege to share an office for almost a year) as it allows for quick and easy reconstructions of trackways and give detail far beyond what traditional ichnotaxonomists do with standard line drawings. I would recommend anyone wanting to know more about the method to read his 2012 paper about it which also provides access to some of the free software. You can even try out 123D Catch (one of the programs I have used on my computer) on your iPhone! As with laser scanning there is problems with line of site, but this can be rectified by just taking some more photos from different angles. The number of photos taken, the regularity and evenness of spacing, and the number of separate planes/angles will improve quality of the final reconstruction. I've had models work with 20-50 photos, whilst others have failed at over 100. It depends on the complexity of the structure and what you are trying to do. Experimentation is free though and is reliant only on computer power! This method has become one of the preferred ways for digitising specimens in museum due to its low cost.

Photogrammetry of an Asian elephant from Falkingham, 2012.

Scanning and image segmentation

Scanning - Fossil scanning has been used for a long time originally as just x-ray imaging, but increasingly CT and synchotron scanning. CT and synchotron scanning involves usually radial scanning of a specimen producing (post-processing) a series of 3D x-ray scans. The biggest difference between the two methods is the energy and size of the machines. CT scanners vary from desktop size to large walk in units, but even the biggest do not compare to synchotrons. Synchotrons are particle accelerators, that specifically spin electrons around a ring at near light speed. In doing so the electrons give off x-rays, which are focussed down beam lines. Specific beam lines are set up for studying fossils (and to my knowledge 3 synchotrons in Europe currently are used study fossils - Swiss Light Source, European Synchotron Radiation Facility and Diamond Light Source).

Swiss Light Source synchotron - the giant ring at the front, but all the other buildings are associated
The choice of method is determined by size of the specimen (synchotrons don't work well with specimens beyond a few cm, unless you take many scans and merge them all together), the resolution required (a medical CT scanner will provide a lower scan quality than a microCT, which in turn is lower resolution than a synchotron), the cost and availability (synchotron time is often free and funded by research but is highly competitive, whilst access to CT scanners can run into the £100s/hr but is often easier to get time on). Beyond this there are other factors that need to be considered including length of time required to make sure good CTs are taken with no artefacts or beam hardening effects (often associated with a lack of x-rays penetrating the specimen due to the x-rays having too low energy or not enough time to allow sufficient numbers to get through). When it comes to fossils there is often a bit of trial and error involved in this process and linked to what is seen post processing and during segmentation

Piece of pliosaur jaw in Southampton CT scanner. Went on to be published in Foffa et al. 2014 (x2) with which I was involved.
Segmentation - After the resulting CT scans a process called segmentation is carried out. This is where the object of interest is isolated from the CT scans. I've endured both Avizo and Mimics with various degrees of swearing and relearning techniques as I flip between the two. They both have advantages and disadvantages depending on what you are trying to do, but I won't discuss further here (feel free to get in touch/leave a comment). The complexity of this varies from simple and often can be carried out in an automated way for single bones, to a highly intensive process that often involves many hours of someone (I have been this person many times) manually isolating the required item from the scan, be it a bone, endocast or internal anatomy.
CT scan demonstrating the god awfulness of fossils in matrix. Blue is toothy bits (mostly), although there is lots of noise in the image, whilst the red area is my deselecting pixels.

The complexity of the process is often determined by the preparation of the fossil (more matrix makes segmentation more tricky), the x-ray density of the fossil compared to the matrix (e.g. where bone is more x-ray opaque than the matrix there is clearer delineation between the two), the type of matrix (iron or pyrite rich matrix, for example, tends to make it tricky for good CTs to be made), how well scanned the item was/number of artefacts.

Using these digital preparations is becoming more common to guide the actual preparation of fossils in large museums where CT scanner access is now easy. Another thing the virtual reconstructions allow is retrodeformation (basically the undoing of damage suffered whilst the specimen is fossilised). Stephan Lautenschlager has been incredibly good at it, and I have a paper in review at the minute discussing my experience so stay tuned!

The resulting reconstructions can then be used for publication, or exported in various formats (commonly .stl or .ply) to create 3D pdfs, create 3D printouts or use in functional analyses. There are some good .stl repositories for fossils e.g. that allow of exchange and sharing of models.

Printing/3D PDFs

3D printing - 3D printing has been on the rise with the printer costs becoming far cheaper. These printers work by melting a layer of plastic or resin (SLA and ABS are the most common) and extruding this onto the print surface (not dissimilarly to standard printing). What varies however is the fact that these layers of plastic are then built up on top of each other layer by layer until the final structure is built. Nowadays a decent 3D printer with a 20x10x10 print area costs around £1000, with the cost falling year on year, and the print material is about £50 for a roll of about 1kg. However, with this decrease in cost, has come an increase in print size areas, speed, accuracy, and nowadays you can print in multiple materials at the same time (e.g. a dissolving print material to create supports that when the printout is immersed in water dissolves, leaving only the wanted 3D structure, or even some rigid and some flexible components). With 3D printing special consideration has to be given into the design of the structure as often supports need to be added (most printer programs do this automatically) to ensure that overhanging bits are printed correctly. These can be easily broken off at the end but can affect the surface quality where they attached. This is all well and good, but I hear you asking what's the point beside creating lots of pretty printouts? Well the printouts are awesome, but there are both research and outreach components to it. In terms of research, 3D printing allows for a quick and easy way of enlarging otherwise microscopic fossils into a size that can be handled and manipulated easily. In addition you can quickly send files to collaborators in other parts of the world and they can print out their own copy of the specimen in question rather than risking damaging or destroying it in transport (particularly if it is fragile). They may also be useful for recreating original specimens if it is lost, but scans exist  and when no other method (traditional casting and moulding) will work. In terms of outreach, they are incredibly useful to take these replicas to show people what you work on in terms of fossils or research that again otherwise runs the risk of being damaged whilst on show.

Let's be honest this is cool, and you kind of want one.

3D pdfs - This is much like 3D printouts, except in its digital format that opens with most Adobe Readers. 3D pdfs allow for users to gain access to reconstructions, and in the highest quality ones can allow users to interact by removing components (often things like soft tissues from around skulls). Again these have the ability to be rapidly sent to collaborators worldwide, but they also allow for more detailed figures within publications to allow for better understanding of features that are being described. If you are unsure of what I mean, please do go check out the Witmer Lab's work as they are one of the main users for both scientific and outreach purposes.

Functional analyses

Beam theory - This method works on the principle of bending beams. If you assume a beam is held at one end (a cantilever beam) and a force is applied to the other it will produce tension on one side and compression on the other. Due to this, there must be a region somewhere that undergoes neither compression or tension, the neutral axis. How the material is distributed away from this determines how resistant to bending an object will be:

Shamelessly taken from my own paper on spinosaurs:  (A) When a load is applied to a beam with one fixed end (a cantilever beam), the effect of the beam is a deflection in the direction of the force. This results in the most extreme tension on one side of the beam, and the most extreme tension on the opposite side. In the middle, there is a point where there is no tension or compression, called the neutral axis. B) Two circular cross sections of equal cortical area (black). Beam theory states the solid tube (hollow circle) will have higher resistance to bending and torsion than the solid circle due to the material being distributed further from any neutral axis. DOI10.1371/journal.pone.0065295.g004
For this method to work best cross sections are needed, and these are best acquired from CT scans, although other methods work. There are many papers out there on the method (it was my first paper), but this method is falling out of favour with more complex models like FEA. It does however maintain use as a predictor of relative resistance to bending and torsion of objects and allows for gross comparisons across taxa.

FEA - See the earlier blog post I did for lots of details.

Musculoskeletal modelling - This method is one that is increasingly popular for understanding the influences on muscles and bones, and how they interact in posture and locomotion. I am still a newbie at this and am learning the method now. However, it is already extensively used within palaeontology to answer questions such as how fast could T. rex run? Effectively the structure in study (let's work with limbs here because that's easiest), is modelled. The limb then has muscles attached as informed by either muscle scarring locations or by using extant phylogenetic bracketing (finding the closest relatives and using them to help inform us of extinct life). The model can then be tweaked with muscle parameters - mass/force production/relative contribution of tendons etc etc. (again inferred from modern relatives), and then the computer can work out ideal postures, how fast the limb (and animal) can move, how big muscles need to be to move at certain speeds, what order muscles are likely to activate in to allow biologically reasonable movements.

T. rex model with all of the muscles attached to the limb and pelvis, from Hutchinson et al., 2005
Convex hulls/Body mass estimates - I will not attempt to explain this method in much detail, beyond saying that the method takes the original skeleton (or limb or whatever biological structure) and attempts to wrap surfaces over it which may infer the extent of the soft-tissues overlaying the structure. I direct all interested parties to Pete's blog which has links to papers describing the method, and walks you through how to do it yourself.

Stegosaurus convex hulls. From Brassey et al., 2015

So that wraps (pun definitely intended) up some of the methods we use and why we use them when it comes to palaeontology on computers. Most of these methods are less than 20 years old. Just imagine where we will be in the next 20!