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.

Monday, 3 March 2014

Seeing the Wessex Formation afresh.


The week before last saw my first trip into the field as part of my PhD, down to the Isle of Wight where I have been so many times before as a tourist, amateur collector and research associate. My main focus on this trip was to meet local collectors to assess what might available for study, and also to spend some time at the National Oceanography Centre Southampton (NOCS) to give a workshop, talk with my supervisor and make sure I have what I need to get on with my research. It was a busy week, and also an eventful one as my wife and I crossed the Solent in a force 10 gale and spent one night lying awake listening to a huge Atlantic storm make landfall at the cliffs 500 yards away.

Beach conditions were variable; on one hand there was a lot of sand on the beach and there wasn't much to be seen, although I did pick up a couple of bits of rolled bone and a baryonychid tooth from the shingle. I visited a couple of locations looking for dinosaur footcasts and discovered one or two examples in locations that have not been recorded in any detail, the best of which I photographed and is shown below. The highlight of time spent on the field was the Wessex Formation itself, as the storms had washed many cliff sections clean of the slumps and mud runoffs that normally obscure the stratigraphy and with these gone it was possible to inspect clean sections along the coast, enabling one to see the complex bedding before the cliffs are covered again in the coming weeks.

Here's a couple of pictures from the trip:

A clean section of the Wessex Formation, normally hidden under slumps and mudflows.

You wait for one, then three come along at once. Three tridactyl footprints in a single block,
all orientated in the same direction and all different sizes.

Wednesday, 15 January 2014

Following the paper trail (starting the literature review)



It's a funny thing, life. At any one moment everything can change and your outlook is altered and new horizons open up as old vistas fade into the distance. On day 14 of being a doctoral candidate I feel this process as it is happening and a new reality hoves into view; the life of the palaeontologist and already it's quite obvious my routine outside of my day job is changing rapidly. After detailed discussions with both of my supervisors I am now constructing a framework for my research, and considering some of the practicalities of the process of actually doing a PhD.

First amongst these is the literature review. I have already been collecting the relevant literature around my key research subject, the nodosaurid Polacanthus foxii. Recent years have shown an increased amount of interest around Early Cretaceous ankylosaurs and this work will provide the structure in which my own research will sit. There's lots to do, and plenty of specimens to see in the UK alone so I'm looking forward to getting into the various collections to examine their fossils. I'm also hoping to look at all Early Cretaceous thyreophorans to compare material, and there are constant rumours of finds by collectors that might warrant further investigation.

Of course planning a literature review is a project in itself and there is plenty to consider when setting out on such a large undertaking. Aside from the process of selecting, reading and annotating the core literature there are also the practical matters of organising and structuring this library, with directory structures, naming conventions and the effective and efficient filing of notes and references to deal with. Here I can fall back on my own commercial experience as a motion graphics artist and animator as many of the projects I work on have large amounts of assets in the form of scripts, visual and written reference material as well as often very large amounts of data (sometimes 100s of gigabytes) and files generated during the production of a complex animation, and I have developed a system and directory structure that I can adapt for my research.

Then there is the subject of annotating the papers themselves. Should I pile them all on my iPad and use an app such as iAnnotate? Should I write in a book or use and index card system and type up onto the computer? Which is the best for data integrity and security? If the electricity goes off, could I still work? How do I keep my bibliography up to date and accurate?

There's plenty to be going at, and there's not a moment to loose in implementing a system so I'd better crack on. I'm sure any procedure I put in place for conducting my literature view might change over time, so I want to keep it as flexible as possible without sacrificing efficiency and most importantly, a method of keeping accurate notes and refs making papers quick and easy to locate.


So off we go . . .