Friday, 19 June 2015

Fossils on the small screen at Dinosaur Encounter, SeaCity.

As part of the exhibition at SeaCity I was commissioned to create videos to accompany two of the exhibits, the Sandown Academy crocodile which was worked on by Michela Johnson and the nodosaurid which is being worked on by myself and Sarah Strachan. These videos are intended as interpretive aids to help visits understand the fossils and hopefully allow people to see how the bones fit together and give an idea of what the animals looked like in real life.

Still from the croc video showing bone outline highlighted to
aid interpretation of the specimen.


The croc skull itself is still encased in the block of matrix it was found in. This means that from the outside only cross sections of bone can be seen and these can be difficult to interpret to the untrained eye (and often to the trained eye too). The skull has been scanned using the University of Southampton’s CT scanner and 3D data had been extracted. The croc skull video features footage of this CT data and concentrates on how this technique allows us obtain detailed data without even prepping the fossil. In fact, as CT resolution improves over the years it’s entirely possible we won’t need to prep some specimens that might prove difficult to reveal for any number of reasons including matrix that is too hard or too soft. The great thing about the CT data is it translates readily into visuals and thus lends itself to motion graphics; we can highlight certain elements and add labels to aid understanding. 


The crocodile video next to the specimen as part of the display.
Image: Liz Martin.

The Polacanthus video is more focussed on the bones themselves. As I’m working on this specimen for my PhD I already had enough data to attempt a reconstruction for the video, which is played on a screen situated above the display case containing the dinosaur. It has to be stressed this reconstruction was the first I have done of the dinosaur, and was produced primarily for the video and not publication. For the sequences showing the bones of the specimen I used the actual photogrammetry data and this also enabled me to make relatively accurate inferences about the length and height of the animal. I based the missing elements of the skeletal reconstruction on Polacanthus foxii and other nodosaurids. The final muscle and life reconstructions were far more speculative but give a relatively good idea of how the animal looked in life. The neutral pose was chosen deliberately to keep the orientation of the bones as easy to see on screen as possible; unfortunately time did not permit a more dynamic reconstruction, but watch this space . . . 

First reconstruction of the nodosaur currently being studied at
University of Southampton. Video still.

Monday, 15 June 2015

Encountering dinosaurs at SeaCity Museum

As is fitting following the arrival of the summer blockbuster Jurassic World, dinosaurs are coming to the south of England this summer with a major exhibition at SeaCity museum in Southampton along with events at other venues in the region (website here), and I was fortunate enough to have been involved in this exciting project.

All it needs is a real dinosaur . . .
the exhibition space at SeaCity with the build in progress.
The work of palaeontologists, all postgrad students and Research Associates from the University of Southampton, is well represented with several of the members of the Southampton Vertebrate Palaeontology Groups’ work featuring in the exhibition. This is a great opportunity to see the research happening at the university and the specimens we are working with, as  the subjects of our research will be on display too.

I’m pleased to say the nodosaurid will be prominently featured and this is a good chance to see this superb specimen, along with a crocodile skull and other material from Britain currently under study at the university. Also featured are a cast of the skeleton of the ornithopod dinosaur Maiasaura and skull casts of Tyrannosaurus rex and Triceratops; these are impressive exhibits and along with an animatronic tyrannosaur and baryonychid provide a real sense of drama, but it’s always the bones that are the highlights for me.

Doing the dinosaur jigsaw.
I was responsible for laying out the dinosaur in its display case and producing two of the videos that serve as interpretive aids to the public: one for the nodosaur, one for the crocodile. After a couple of trips out to Ikea to get decent packing boxes (mmm . . . meatballs) and ordering in a jumbo roll of bubble wrap I got down to the task of carefully stowing the specimen in boxes for the trip to SeaCity. A few days later we arrived at the exhibition hall and started the job of laying out the dinosaur in it’s impressive 3m x 2m display case. As part of the video I had already planned the layout so this saved time, but of course there were issues . . .

Firstly, although I’d recorded the majority of the specimen for my PhD there were significant parts missing and I didn’t have time to record all of these so this will have to wait until the exhibition closes at the end of September. This meant I was unfamiliar with some elements and needed to be sure I was putting them in the correct place, not too hard a task. Secondly, the fragmentary nature of the some of the skeleton, especially the limbs meant that when laid out they looked a little lost and out of context. Rather than place these bones where I thought they might have gone in life I grouped them; a bit of artistic licence to enable easier interpretation of the skeleton as otherwise odd bits would be scattered around the appendicular skeleton and osteoderms and look lost.

The nodosaur final layout.
The final layout certainly looks the part. I had to curl the tail to fit the skeleton in and compress certain parts of the skeleton that are either missing or held at other institutions. Most of the sacral shield is missing because although it was recovered it remains in hundreds of pieces a little smaller than roman tesserae; however some is still present and is viewable on the upper surface of the ilium, although this needs prepping out as it is partially covered with matrix from the plant debris bed it was excavated from. This is an impressive skeleton and gives a real idea of the size of this dinosaur plus its spectacular armour.

The accompanying video gives an aid to interpretation and also shows a tentative 3D reconstruction of both the skeleton and life appearance of the dinosaur. This will be the subject of my next post, so stay tuned.


Wednesday, 27 May 2015

SVPCA 2015 Second circular

The second circular for the SVPCA is now available, and can be downloaded as a pdf from here or viewed on the SVPCA website here.


Abstract deadline is 24th July, so now’s the time to start thinking about talks and posters. I hope to see you there!

Tuesday, 3 March 2015

SVPCA 2015 First Circular



This year the SVPCA is being hosted at the National Oceanography Centre, Southampton (NOCS) by the Ocean and Earth Science school. It's worth making a note in your dairy of the dates as there are field trips to the Jurassic Coast (in association with Flugsaurier which is being held at Portsmouth this year) and a post-meeting trip, location to be confirmed. The Jurassic Coast trip is being held in association with the Flugsaurier 2015 meeting being hosted at Portsmouth immediately before the SVPCA (see here: http://www.flugsaurier2015.com).

The circular is available for download here, and the SVPCA website is here.

Monday, 24 November 2014

Tracking Dinosaurs on the Isle of Wight: Paper and SVP 2014 poster

I thought I'd upload an image of the poster I presented at the SVP 2014 in Berlin earlier this month.  The poster features some of the research discussed in a paper that was part of the special edition of The Biological Journal of the Linnean Society that was inspired by the successful Celebrating Dinosaur Island: Jehol-Wealden meeting held last year at the National Oceanography Centre, Southampton (see my write-up here). This paper, entitled Tracking Dinosaurs on the Isle of Wight: a review of tracks, sites, and current research (Pond et al, 2014) is a review of dinosaur ichnology on the Isle of Wight and looks at both tracks and sites. It came as a shock to realise many of these sites had never  been written up and although they had been mentioned in a couple of book chapters Martill and Naish 2001 and Batten 2011) they had been pretty much ignored.

Also discussed in the paper was the presence of the thyreophoran ichnotaxa Tetrapodosaurus and Deltapodus, the latter having been assigned in a poster by Belvedere et al (2012) and which is interpreted as a having been made by a stegosaur. As Tetrapodosaurus is considered as having been made by an ankylosaurian track maker it seems possible there was more going on with thyreophorans in the Wessex Sub-Basin than was previously thought . . .

This paper was very much a team effort and big thanks to my co-authors Neffra Matthews, Brent Breithaupt, Martin Lockley and Jeremy Lockwood. I co-authored a couple of other papers with Martin, Jeremy and Lida Xing and all can be had from the link to the BJLS above (Unfortunately the papers are behind a paywall but if you want a copy of any of them then drop me a line and I'll send one on).


References:
Batten DJ, ed. 2011. English Wealden fossils. London: Palaeontological Association.

Belvedere M, Pond S, Simpson M, Downes D, Dyke G. 2012. Variety and interpretation of dinosaur tracks from the Isle of Wight (Lower Cretaceous, Southern UK). In: Royo-Torres R, Gasc F, Alcal L, eds. 10th Annual Meeting of the European Association of Vertebrate Palaeontologists, ¡Fundamental! 20: 1–290.

Martill D, Naish D. 2001. Dinosaur trace fossils: footprints, coprolites and gastroliths. In: Martill D, Naish D, eds. Dinosaurs of the Isle of Wight. London: Field Guide to Fossils No. 10: Palaeontological Association, 310–323.

Pond S, Lockley MG, Lockwood JAF, Breithaupt B, Matthews N. 2014. Tracking dinosaurs on the Isle of Wight: a review of tracks, sites, and current research. Biological Journal of the Linnean Society 113: 737–757.



Friday, 29 August 2014

For palaeontologists and public, the future is 3D.

Indet. ornithopod caudal vertebra recorded using photogrammetry.
480,342 polygons, with and without texture.

Here’s a prediction: 3D meshes of dinosaur bones and ichnites will become the main method of interaction with specimens for many palaeontologists within a decade. While not a panacea for all the issues that access to specimens raises for workers, this trend might go some way to mitigating some of the more persistent problems associated with the process. This prediction might come across as either a little obvious or a rather hubristic depending on your current engagement with virtual specimens and either view might be correct, but here’s why I think it will happen.

As the technology for recording, creating, distributing and working with 3D models becomes ever more widely used it’s becoming apparent that the usefulness of 3D specimen data is far more than originally envisaged. The advent of 3D printing and the ubiquity of 3D content on the internet means that meshes provide robust, testable data that is can used in a variety of ways. Biomechanics, finite element analysis and morphometrics are already well-established uses for 3D data as are comparative and descriptive purposes, reconstruction and illustration. By returning data to the physical world by 3D printing, specimens can be shared without ever having to leave the collections they are accessioned to. It’s now possible to carry and entire dinosaur skeleton on an iPad, each bone viewable at any time. Physical interaction with specimens is at the core of what we do as palaeontologists and from the field to the lab we need to be able to work on actual fossils, and this will never change. However, this might not be the most pragmatic way for us to get to all the specimens we need and 3D meshes will provide a way of accessing specimens in the future. 

Many ichnologists already do this and for them this is a no-brainer. Like many fossils, ichnites are often vulnerable to destruction and degradation, from collectors and erosion to specimens that need to remain in situ and are rightly afforded special protection so everyone can enjoy them. These can now be taken back to the lab (or pub) in as 3D data for study, recorded for research and posterity, a 3D snapshot in time. We can record how these resources change over the years, refer back to them countless times, and share them with each other easily.

For open access advocates, the rising popularity of 3D data for research should be a big deal. In an ideal world all described and figured specimens would be freely available for download at any time, by anybody. The ability to do this might have consequences for all palaeontologists, and the institutions specimens are housed in. One issue that continues to vex palaeontologists is the thorny issue of access to specimens in private and public collections. Whilst the argument that having first-hand access to a specimen is always best is irrefutable, practicalities dictate that it’s not always possible. 

Vitally, free open-access to specimens for everyone (not just scientists) might have many more benefits. The commercial trade in fossils is a subject of huge concern to any palaeontologist. With the insidious tendrils of the free market feeling their way towards more and more specimens it is a real and present danger more that more data will be lost forever; the self-regulation of markets is a myth. However, if palaeontologists can gain access to private collections or collections about to be dumped on the market by institutions (as San Deigo Museum nearly did with their Sternberg collection) all is not lost. We can now record specimens held in these collections and archive the data in a way we’ve never been able to before; there’s a tremendous amount of data out there that never gets studied. Using high-quality 3D data will remove the need for direct access the fossils to a certain degree and allow specimens otherwise unavailable to science to be worked on. We all know of specimens that are languishing in collections and might disappear at any time, lost forever and never published up. By depositing 3D data in an open access repository there will be easily obtained testable data available for research. 

This democratisation of data might have an important side effect if we could print off any fossil we wanted to. Fancy a .25 scale Tyrannosaurus rex skull on your mantlepiece? No problem, a specialist fabricators could print one off for a fraction of the price of the original. The kids want an ankylosaur spike for a school project? Download and print one off at the local high street print shop (or at home when the hardware becomes more affordable). This might be of help in pulling the rug from under a commercial fossil market that routinely prices important specimens out of the price range of virtually all public institutions; when they go, so so might the data they represent.

How could all this new data be curated? Firstly, there is now a real and present need for a cohesive set of standards to ensure the future viability of digital collections; file formats have a habit of becoming obsolete as technology races forward. Secondly, a single file format needs to be established as the standard for archiving and accessioning digital specimens. My own preference would be for Alias Wavefront’s .obj file standard for several reasons: it’s read by virtually every 3D program available, is robust, it can retain texture information in a separate jpeg file and includes the UV information relating to the texture. 

Finally, an open-access online repository to hold this data, an idea that has been wafting around for a while (see this post by Peter Falkingham for example, on establishing a database of neoichnological digital specimes). This is the biggie, and the establishment of such a resource would raise some quite contentious issues. Uploading a mesh of a dinosaur footprint spotted on a beach or of a certain outcrop is one thing, but what would be the consequences of uploading the entire holotype of a dinosaur? Museum curators might get the howling fantods at the thought of their exclusive specimens being available for free online, potentially depriving them of revenue generated from visitors to their collections. After all, this data would be freely available and if someone had the urge to print an entire skeleton out and start their own museum they would be able to, without paying a penny. Would some sort of commercial licensing be necessary? Would institutions and individuals be able to veto the inclusion of specimens they hold in such a repository? Questions, questions . . .

At the end of the day, specimens held by public institutions are owned by the public and free, unfettered access to them by anyone is the ideal scenario. Of course it’s less than ideal to allow anyone in to have a gander at your one-of-a-kind ultra-delicate fossil, but by making an accurate 3D mesh of that fossil available for all then you won’t need to; just download and print one off! For scientists and the public alike, there’s great potential in this technology if only we can all agree at the outset of how we can curate and manage it.

Not a palaeontologist? Well, you could always share heritage items such as this 3D mesh of a
2.5m recumbent stone from Arbor Low stone circle in the White Peak of Derbyshire, UK.
Send it to anyone with an internet connection. You can't do that with the real thing.


Postscript: After I wrote this Peter Falkingham posted over at his blog on the same subject, albeit from a slightly different viewpoint. I highly recommend reading it if you're interested in the digitisation of palaeontological specimens: http://pfalkingham.wordpress.com/2014/08/28/not-just-pretty-pictures/

Monday, 18 August 2014

Mr. Lee's dermal plates: the first Polacanthus?

The illustration from Lee's report of 1843 of a single osteoderm and surrounding ossicles.

The first sign that there was an armoured dinosaur present in the rocks of Wealden Sub-Basin of the Isle of Wight was when one John Edward Lee reported the existence of three fossils from the Hastings Beds of Sandown on the Isle of Wight way back in 1843. However, the Hastings Beds don’t outcrop on the island, so if they didn’t actually come from there where did they come from? Lee describes these fossils as ‘dermal plates’, and goes on to describe them at length in his paper. Only one is illustrated however, and this and the second plate were sent to Mr. Sowerby (presumably this is James De Calre Sowerby, a mineralogist and illustrator who co-founded the Royal Botanical Society and Gardens) in a hackney carriage along with drawings of the fossils destined for publication in the Annal of Natural History. The third was in poor condition and not deemed worthy of illustration and is still held in the Natural History Museum, London (BMNH R643) according to Pereda-Suberbiola. The surviving illustration clearly shows a single large osteoderm surrounded by smaller ossicles, themselves set amongst more ossicles. This certainly looks like a section of Polacanthus sacral shield, but is it?

The holotype of Polacanthus was found by the remarkable Rev. Fox of Brixton (now Brighstone) on the Isle of Wight around 1865. Fox had found the shield intact but it crumbled as he excavated the specimen, and when J.W. Hulke finally got around to describing the fossil in 1881 the shield was still in numerous small bits. Five years passed and Hulke revisited Fox’s Polacanthus, the shield of which had been reconstructed piece-by-piece by the remarkable efforts of a Mr. Hall and Mr. Barlow. This revealed the ornamented upper surface of the shield which Hulke describes in some detail, including the arrangement of larger keeled osteoderms amongst smaller ossicles, very similar to Lee’s specimen. Polacanthus is not the only nodosaurid (if Polacanthus is actually a nodosaurid, but that’s another story) with a sacral shield, and a comparison via the literature with sister taxa such as Mymroopelta and Gastiona reveal their sacral shields were similarly ornamented (see illustration below).

A selection of osteoderms and ossicle arrangements from various nodosaurids.
Lee's specimen is top right, the others are redrawn from various papers.

It’s likely that Lee’s specimens were the first remains of a Polacanthus sacral shield ever reported. As was mentioned earlier, the fossils probably didn’t come from the Hastings Beds as they aren’t present on the Isle of Wight; Pereda-Suberbiola suggests these remains are from the Wessex Formation at Brook Bay (Pereda-Suberbiola, 1994), although a part of the Wessex Formation is exposed in the cliff at Sandown and he doesn’t give his reasons for favouring this location. As for the fossils themselves, Lee was an astute observer and commented on the histology of the osteoderms, recognising the fibrous nature of the bones. He compared them with the scales of extant iguanas and crocodilians, and despite the fragmentary nature of the material found no reason to connect them with lizards or crocodiles.

The two ‘plates’ and drawings never made it to Sowerby. They were sent in a hackney carriage but never arrived and so joined the list of other dinosaur specimens lost to science. Had they had done, it’s entirely plausible that Polacanthus would have been named twenty years before it actually was.


References:

Hulke, J.W. 1881. Polacanthus foxii, a large undescribed dinosaur from the Wealden Formation in the Isle of Wight. Philosophical Transactions of the Royal Society of London, Vol. 172; 653-662.

Hulke, J. W. 1887. Supplemental note on Polacanthus foxii, describing the dorsal shield and some parts of the endoskeleton, imperfectly known in 1881. Philosophical Transactions of the Royal Society of London, Vol. 178: 169-72.

Lee, J.E. 1843. Notice of Saurian Dermal Plates from the Wealden of the Isle of Wight. Annals of Natural History. London. 11: 5-7.

Pereda-Suberbiola, X. 1994. Polacanthus (Ornithischia: Ankylosauria), a transatlantic armoured dinosaur from the Early Cretaceous of Europe and North America. Palaeontographica, Abteilung A, 232: 133–159.