Underwhelming fish fossil of the year

The title is a bold claim, particularly for so early in the year. This fossil is obviously not a big flashy dinosaur, it is two tiny bits of tooth plates from a Cretaceous fish. However, it has special meaning for me for two reasons. Firstly, I am on a quest to publish on all groups of vertebrates (not actively pursuing but it would be nice to do) and this will cross of teleosts (the bony rayed fishes - most of the things you count as fish today) along with dinosaurs, marine reptiles, and mammals (these groupings may also get more specific as I get further along too). Secondly, and more exciting for me, is these fossils are the first I've found myself that have been published:
http://onlinelibrary.wiley.com/doi/10.1002/spp2.1040/full (if you want a .pdf email me)

A bit of background, the fossil is from the Kallamedu formation of SE India. The area has been published on a fair bit as it is one of the largest Cretaceous exposures of fossil bearing strata in India. That being said it is still remarkably poorly represented in publishing when compared to the North and Central regions known for the intertrappean layers where small pockets of material lay between the massive Deccan trap eruptions layers. These areas are interesting for the sheer size of the erupted material as it covers an area the size of Texas twice over, and to a depth of up to 2km in places. The eruption has also been implicated by some for climactic events that led to the demise of the dinosaurs (either with or because of the meteor that hit Mexico).

I digress again, back to the site in the Kallamedu. The fossils found in the formation are typical of Gondwanan locales of similar late Cretaceous age, with teeth of crocodilians, abelisaurid and troodontids dinosaurs, bones of titanosaur sauropods, bothremydid turtles, and fish scales. The sediment is a mix of clays and sandstones and has been interpreted as a fluvial/deltaic region with occasional marine influence. Thus it may not come as a surprise you find fish teeth in it, however the type of teeth is what makes them interesting.

After much ado:

From Halliday et al., 2016 - Photographs in lateral, occlusal, and apical views of specimens DGUF/145 (left) and DGUF/146 (right). Scale bar = 1cm.

So there you have it, two tiny pieces of tooth plates, both barely more than a centimetre in size. They aren't just any standard tooth plate, they are what are called pharyngeal toothplates. In fish that feed on shells and hard objects, they develop what is functionally a second set of jaws in their throats designed to crush. It is these teeth that help determine which group they belong too. The size and apparent replacement pattern meant we took it a step further and CT scanned these specimens.

From Halliday et al., 2016 - CT scans of DGUF/145 (A) and DGUF/146 (B) in lateral (1), occlusal (2), and apical (3) views. The bony matrix has been digitally removed to illustrate the stacking of the teeth. Convex teeth are organized in vertical stacks; each stack is arranged in a row offset from adjacent rows. The apical surface of the teeth shows no foramen housing a pulp cavity, as is also true for NHM-UK 38814.

From the CT scans we can see the teeth are small, rounded on the occlusal (top) surface, covex on the apical (bottom) side, and arranged in nice linear columns. All of these are important for not just figuring out the group of fish that they belong to (Phyllodontidae), but also narrow it down to probably Egertonia sp.. It's tough to be more specific as we lack any more material from the fish, although there are living relatives (bonefish and ladyfish) which give us an insight into probably biology (shell and crustacean crushing, shallow salt water fish), and they have similar teeth although they are stacked alternatively.

The most interesting thing to derive from two otherwise minute underwhelming fossils is that the fish is otherwise unknown from India in the Cretaceous. The taxa has only ever been found once before in the Cretaceous, although indeterminate fossils belonging to the family have been found across Eurasia from this time. The only other definitive occurrence is from Madagascar showing the close links these two regions maintained in terms of what animals were there despite the fact that Madagascar and India were joined until about 85 million years ago (about 20 million years earlier than these fossils). Keep an eye out for another paper by Halliday et al., that is following hot on the heels of this one (mainly as it was reliant on this publishing before it could be) addressing the faunal similarities between these areas.

Anyway, that's all from me on my underwhelming fish fossil. I thought I could give you a lovingly crafted drawing of what part the fossils come from on a fish (see the entertaining blog from which this one post derives inspiration https://blogs.ucl.ac.uk/museums/tag/underwhelming-fossil-fish-of-the-month/), but could not do it justice. So instead here is a picture of a black drum showing off its crazy throat teeth that do look superficially similarly (but I can tell you they are very different indeed):

A black drum (Pogonias cromis) showing off its smiles, inside and out. From http://img.photobucket.com/albums/v464/Vetcraft/drumJune52008008_zps2af54b6d.jpg

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!

Finite element analyis: the importance of being valid

On the back of finally getting another paper out:

Cuff AR, Bright JA, Rayfield EJ. (2015) Validation experiments on finite element models of an ostrich (Struthio camelus) cranium.PeerJ 3:e1294 https://dx.doi.org/10.7717/peerj.1294

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:

From: http://theupturnedmicroscope.com/comic/negative-data/

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.

References
Cuff AR, 2014. Functional mechanics of ornithomimosaurs. Thesis. University of Bristol.

Cuff AR, Bright JA, Rayfield EJ. (2015) Validation experiments on finite element models of an ostrich (Struthio camelus) cranium. PeerJ 3:e1294 https://dx.doi.org/10.7717/peerj.1294

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.