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.

Wednesday, 23 July 2014

Exoneoichnology and photogrammetry: traces on Mars

If by some chance the human race manages to survive itself and thrive in the far future, it's likely we will one day explore the other planets in our solar system and perhaps beyond. Future exopalaeontologists and exoichnologists will have exciting jobs, looking for traces of past life on other planets. But could they actually recognise them in the field?

Neoichnology is the study and recording of modern traces to assist us in our understanding of the traces left by past life, and is an important part of an ichnologists work. The current standout work on neoichnology is Tony Martin's excellent Life Traces of the Georgia Coast, a book that is packed with insights into the process of trace making by the denizens of the barrier islands off the coast of the southern USA (Tony's excellent blog is here). For an example of neoichnological data gathering using photogrammetry see this previous post.

One technology that is very well suited to palaeontology and ichnology work in particular is photogrammetry. I've posted before on the subject and there is a discussion and primer here and here. One of the huge advantages of photogrammetry is you don't actually have to visit a site personally to obtain accurate data. For palaeontologists unable to get into the field this means we can still work on data collected by colleagues and, er, robots.

Robots? As it turns out, yes. Currently Mars has two operational NASA rovers on it. Curiosity and Opportunity are robot geologists that are roaming the surface of the red planet, sending back lots of high-quality data and changing our view of Mars on what seems like a daily basis. NASA are superb access advocates, and every image from these two intrepid machines is posted on their respective websites for us to use; Curiosity's are here.

Five images taken by Curiosity on sol 629 and used for photogrammetrical reconstruction.


I wondered if was possible to generate a 3D mesh from images the rovers had sent back. As it would be useful to record an actual trace I decided to find some suitable images from the hand lens imager. This natty bit of kit is basically the rover's equivalent of the hand lens we all know and love so well. It has a 4cm camera and can resolve features as small as 12.5 micrometers. Sol 629 had what I was looking for, a sequence of images that looked like they might work so I loaded them into Photoscan. The images show a hole drilled by the rover in a martial rock to extract a sample for the onboard sample analysis instruments, plus three smaller marks caused by a laser that is part of the kit that analyses the chemical composition of rock.



In all I used five images from the Sol 629 sequence (3715, 3717, 3719, 3721, 3723). Photoscan was able to produce a high-quality mesh of the hole, the surrounding debris rim and a part of the rock itself. The hole measures 1.63cm across. The illustration above shows the textured mesh, a plain mesh and a mesh coloured according to elevation. The movie below shows a 360 of the mesh.

video


So what was learnt? Well, we can use as few as five images to generate an accurate mesh. There are some issues around the lip of the hole where the software hasn't recognised the hole itself. The surrounding debris and rock is clearly represented with few artefacts; a perfectly useable mesh.

So we now have a 3D record of one trace on another planet. Exoneoichnology is born, although hardly a new science as humans and their robotic proxies have been leaving marks on other rocky planetary bodies since Luna 2 impacted on the lunar surface in 1959, and Curiosity's wheels are designed to leave the letters 'JPL' in morse code in the Martian dust. We'll have to wait for exoichnology, but hopefully not too long.

What has this got to do with dinosaurs? This exercise is further confirmation that we can use photographic data taken for another purpose to generate robust 3D data for research. Falkingham et al (2014) have successfully done this with the Paluxy River tracks and it is anticipated the technique could be used in the future for this sort of data analysis. Furthermore, if we can't get into the field and our colleagues can then some simple instruction on the picture-taking technique will mean we can have workers gathering 3D data anywhere a palaeontologist (or robot) is present. The possibilities are endless.

Reference:

Falkingham PL, Bates KT, Farlow JO (2014) Historical Photogrammetry: Bird's Paluxy River Dinosaur Chase Sequence Digitally Reconstructed as It Was prior to Excavation 70 Years Ago. PLoS ONE 9(4): e93247. doi:10.1371/journal.pone.0093247

*I wondered about the term for the study of traces and came to the conclusion it could be 'astroichnology' or 'exoichnology', as both 'astro' and 'exo' are used as prefixes for 'geology' when studying the rocks of other planets. Exoichnology sounds cooler, so that's what I chose.

Thursday, 12 June 2014

Ph.D update: On being a testudine, not a lagomorph.

How does a being a part-time PhD researcher actually work in daily life? This is a question I gave some considerable thought to before I started my doctorate in January, as I wanted to be sure I could make the commitment to research whilst working in a job that often means long hours for weeks at a time. Now the reality is becoming apparent and the past six weeks have gone some way to answering this question more fully than previously, as the practicalities of keeping research momentum when the day job gets busy have had to be addressed (see my work here).

As I've mentioned on this blog previously one of my specialities is creating 3D animations of drug mechanisms of action; these tend to be commissioned during the middlelater stages of a drug's development to show the target audience how the drug works at a molecular level. This involves modelling lots of proteins, cells, viri, bacteria, DNA, RNA etc, often referring to published data of the structures themselves for accuracy. The animations are mainly educational in nature (being targeted at consultants and doctors) and are based on some quite remarkable cutting edge science and I love working on them. They are also extremely labour intensive and time-consuming.

So recently I've been in full animation production mode and research has had to be put on the back-burner. Well, almost. Gaps in the production process (which occur for any number of reasons i.e. awaiting assets, team and client review, rendering) for the MOA are little windows of opportunity to keep things moving, even in a small way. I had photographed most of the vertebral column and some dermal armour elements of the Polacanthus specimen I'm working on for processing into 3D data. If a machine is not rendering a sequence of animation, it can be crunching through these data and making lovely 3D models of dinosaur bones. Despite being a basic set up, the results so far have been encouraging; I'm getting good quality, detailed meshes of the specimen.

My photogrammetry setup. A tad bottom end to be sure, but it's delivering good results.
Periods of reduced work activity also give me time to get on with other small but essential tasks such as reading and annotating papers, reviews, planning next steps and keeping up with developments in the field. I use this time to get to grips with new subjects such as looking at methods of statistical analysis, bones need measuring and drawing, meetings have to be booked, talks prepared amongst the myriad of other tasks that need attending to keep the whole process moving forward.

video
Animation showing the mesh obtained from the photogrammetry setup shown above.


All this can be done without the slightest disruption to my work as an artist and graphic designer. Although there are periods where I work long hours for many consecutive days (running into weeks on large projects) and can't get any research done at all generally I can take tortoise-like, small steps towards the mountain on a daily basis.


It's a marathon and not a sprint for sure.

Thursday, 22 May 2014

Triceratops 3D model: finished!


Click to see the critter bigger.

I've finally finished (abandoned - as the man says artists never 'finish' a work) the Triceratops sculpt that has been part of a glacially-paced occasional series that has seen the model evolve from a simple cube to the finished thing. I've now added a texture to the mesh and have decided to leave it there.

This has been a valuable learning experience and help from Scott Hartman and comments from both Scott and Jaime Headden have been most welcome. I'm looking forward to working on many more of these.

From a technical point of view, I've been able to learn zBrush, and can't sing it's praises highly enough. A truly incredible programme that will have a permanent place in my PhD workflow. There's much I would do differently; my UV's are so messed up and I need to address that from the start of the sculpt and the whole model needs re-topologising. I'm not concerned about completing these for this model, the next project is already up and running.

That project is of course my PhD and the Triceratops project has provided a solid foundation for the soft tissue reconstruction of Polacanthus. I'm processing the 3D data for the bones at present, and this process will take a while. What's really important is that as a proof of concept exercise modelling Triceratops means I know I can move ahead with the science and get a better understanding of how that and the modelling process can work together.

Lots to think about!

Sunday, 13 April 2014

PhD report: the first three months.

Whoooosh! There goes March and nearly half of April. Blimey.

It has been over three months since I started my part-time PhD and since then I have spent most of my time completing my first paper and organising how I am going to approach my research. I’ve now sorted easy access to the Polacanthus specimen I am working on, and have started testing the methods I will be using to record the specimen in the hope this will make the early stages of research as problem-free as I can.

As for my lit review, I decided I was unhappy with the idea of building and annotated bibliography soley on the computer, so I am using a hybrid system. This means printing out the paper and taking notes on index cards that I will then type up into a word file. I’m trying to use Endnote but it seems so time-consuming and I need to spend more time with the user manual. It remains to be seen if I will use it in the long run. How practical this system is remains to be seen, although it is flexible enough to be changed if needed.

I will be starting the 3D work shortly, but have made no real inroads into learning Maya. As I already use a 3D package this is not a priority and can be addressed over time and will not affect my research; I can take my time with this. There are plenty of new technologies to explore for both doing research and methods of outreach and this will be (another) ongoing branch of my PhD research.

Did I say branch? Perhaps thread might be a better word, as the deeper I get into the work the more threads seem to appear, forming a web-like pattern of possible research routes and links. This is both exciting and daunting, as it would be all too easy to end up clambering around this web without direction and I want to avoid being ensnared by the Shelob of distraction.

Lots to do!


The web of research.