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 . . .

Wednesday, 1 January 2014

Vertebrate Palaeontology Ph.D, Day One.


The Polacanthus model at Dinosaur Isle, Sandown, Isle of Wight.



Happy new year!

Today is the first day of my Ph.D, and I'm pretty excited (as you might have gathered from my previous posts and tweets). I always find new year to be a time of optimism and anticipation, with the festivities of Christmas and New Year's Eve behind us* and the opportunity to get stuck into work without interruption ahead. Of course, the fact I'm now studying part-time with Ocean and Earth Science, National Oceanography Centre Southampton is an added thrill, and the fact my research will be on dinosaurs makes it about as good as I could ever have hoped for.

So what am I actually working on? This extract from my project proposal will answer that question:

Digital reconstruction of dinosaur movement and soft tissues informed by morphology and biomechanics.

The ornithischian dinosaurs within clade Nodosauridae have been known from the fossil record since the dawn of modern palaeontology, and their presence on the Isle of Wight was confirmed by the discovery of a partial specimen by the Reverend William Fox of Brixton (now Brighstone) in 1865 (Blows, 1996). However, despite a number of partially complete specimens, the biomechanics and functional morphology of these obligate quadrupeds has not been subject to the same degree of study as other dinosaurian taxa. Two notable exceptions are a finite element analysis of ankylosaur tail club impacts (Arbour and Snively, 2009) and a more general functional investigation of ornithischian limb morphology (Maidment et al, 2012). The reconstruction of nodosaurid and more derived ankylosaurian morphology, and locomotion, however, remains to be achieved in enough detail to interpret the lifestyle, and palaeoecologyof these extinct animals. Doing this, within a rigorous comparative and statistical framework, is the aim of this PhD project.

So big spiky thyreophorans will be at the core of this project. In addition, I will be drawing heavily on my experience as a 3D artist and animator to create accurate reconstructions of how these dinosaurs moved. I have a huge amount to learn, and recognise that I will need to address some gaps in my knowledge quickly, but then I'm I'm studying for that very reason.

So I've stepped onto the path, and now to see where it takes me. I really can't wait to find out.

Best wishes to everyone for 2014, and I hope perhaps I'll see you at a meeting or on a field trip at some point in the year.


*Not to moan or owt, but some of us spent the festive period ill. Cough.

References:

Arbour, V. M., & Snively, E. (2009). Finite element analyses of ankylosaurid dinosaur tail club impacts. Anatomical record (Hoboken, N.J.: 2007), 292(9), 1412–26. doi:10.1002/ar.20987

Blows, W.T., 1996. A new species of Polacanthus (Ornithischia; Ankylosauria) from the Lower Cretaceous of Sussex, England. Geological Magazine, 133 (<5), 1996, pp. 671-682.

Maidment, S.C.R. et al., 2012. Limb-Bone Scaling Indicates Diverse Stance and Gait in Quadrupedal Ornithischian Dinosaurs A. A. Farke, ed. PLoS ONE, 7(5), p.e36904. Available at: http://dx.plos.org/10.1371/journal.pone.0036904 [Accessed May 27, 2012].

Wednesday, 4 December 2013

PhD preparations in full swing

A way too spiky Polacanthus, with no sacral shield to boot.
I mean, we've known the dinosaur had one since 1881. Get a grip!

With less than a month to go before I start my Phd in earnest I am organising myself for the coming years of research. I already have a reasonable system of filing and directory structure that I've adapted from the methods I use in my day job as a motion graphics designer and 3D animator. I am used to handling large amounts of data (projects can run into hundreds of gigs for a large animation) and lots of footage is generated which means I need to keep track of exactly which versions I'm working on at any one point, and this has the potential to become very confusing if not careful. As I will be working on 3D data this system can be readily adapted to research, and I can use a similar system for writing and research.

Being self-funded also presents many challenges and I will have to choose activities such as visits to collections and meetings very carefully, and plan well ahead. Funding is going to be tight, and I could have called this blog 'Doing a PhD on a shoestring' as every penny will have to be watched and accounted for. This is not as bad as it sounds, as funding for the first couple of years is in place much of the software I use to earn a living shall be used in the course of research. The real issue will be affording hardware, and for the time being Im going to have to make do with what Ive got.

Part-time study needs to be reconciled with the day job and by necessity will be subordinate to paying work. I have no grants and no sponsorship and so need to keep working; l will be looking into both of these funding resources though, although part of me feels perhaps grants would be better off going to young researchers. I don't have the luxury of a permanent office in my institution and I will be studying from home most of the time although Im set up for this already (my institution, the University of Southampton is actually 200 miles away from where I live).

Even though I am working and studying at the same time I can turn this to my advantage. I will be creating a crossover between work and research which means I shall use the skills developed in either, in both. As much if my day job involves scientific visualisation I will be able to communicate more clearly with my customers as a consequence of being immersed in scientific method. Clients will appreciate having an artist that is also a scientist working for them, helping them to communicate.

Conversely, the years I have spent working in the cut and thrust of the commercial world should hold me in good stead when doing research. The work ethic is a given; I routinely work on high-pressure projects with tight deadlines and for very long hours in extensive stretches, so the volume of work isn't intimidating (yet). More important are the skills I have acquired using complex software for scientific visualisation and animation, and these will be put to good use and expanded upon in my research. Also, I will be looking at how some of the methodologies of the commercial world might be used in science outreach, for instance when assessing how the best delivery systems for 3D meshes and other data, including the re-use of data and assets generated during research and making the presentation of this data engaging whilst retaining scientific integrity. These will be part of the palaeontology outreach solutions I will be working on.

Another step closer to the mountain.

Thursday, 7 November 2013

PaleoIllustrata is dead. Long live PaleoIllustrata!



Palaeontologists spend a lot of time looking at rocks and fossils that have endured for eons and now provide us with a glimpse back into the past of our planet and its inhabitants, a journey into the vastness of deep time. Studying these specimens you get a real idea of the transience and impermanence of our world, a realisation that everything we see about us is in a state of constant flux; from the weathering of the sediments containing the fossils we study, the appearance and extinction of species, the uplift of mountain ranges and the constant drift of tectonic plates across the surface of the planet. Always in motion is the earth.

This sense of transience also applies to our everyday lives and the last year has, for me been a case in point. When I started PaleoIllustrata I intended it to be a portal for palaeoart on the internet, my own work and other oddments that caught my eye. However, as I became more involved in research at the National Oceanography Centre Southampton (NOCS), University of Southampton then I started posting more about events such as the SVP, SVPCA and Jehol meetings, my own research and things palaeontological in general, and less of the art. As it happens, palaeoart is well-served online by sites such as the excellent Love in theTime of Chasmosaurs and picfest Paleoillustration (to name but two) and so my contribution was, with hindsight, superfluous. PaleoIllustrata wasn't realising it's potential, and that's because I was not focussed enough and needed to alter the way I was approaching research. As it happens, a solution presented itself at just the right moment.

Just under a year ago it was suggested I might consider applying for a part-time, self-funded PhD at NOCS. I had never considered studying at this level before so took my time and sought advice off trusted colleagues and friends before looking for a suitable project. There were some issues with the practicalities of how this course of action might work. Firstly, it had to accommodate my job, as I am self-employed and the need to work is paramount and comes before everything (including sleep). Secondly, any degree I did would have to draw on my quarter-century as a commercial artist, animator and designer, especially as regards to my 3D work; in fact I wanted the exchange to be two-way, as a fair few my clients are scientific communicators and they will benefit from skills learned in the course of my research.

More importantly, was I capable of doing a PhD? I have learnt a lot since I started more structured research at NOCS, have attended and presented at meetings so was out of the blocks so to speak, but this was a major step and I spent a lot of time reflecting on and considering if I had the intellectual capacity, discipline and thoroughness to be a successful postgrad student. In some respects, I still don't know whether I do have these qualities or not, and time will tell. However, nearly a decade of being a sole trader has taught me much about my ability to draw on my own resources and tough out the hard times, so I was less worried by my work ethic.

Once it was established that I could make a part-time PhD work for me, I set out to find a project. I made many calls and spent many hours in conversation with friends who are established palaeontologists and patiently talked over the various research ideas I had. I spent time at meetings talking it over with colleagues who were generous with their advice and offered their opinions. I am so very grateful for this help which was massively important. I owe some beers.

I had my interview in September and accepted an offer a couple of weeks ago, and I start on the 1st January, with Dr. Gareth Dyke as my supervisor. I'll still be living up north at the edge of the Peak District and doing the day job (which I love and involves scientific visualisation, 3D and motion graphics and graphic design) so will be studying from a distance. However, my second supervisor is in Manchester and we're frequently on the south coast anyway. In fact, despite being raised a Brummie I was actually born in Winchester, so it feels right to be at Southampton.

Obviously, this means I am going to be pretty busy, and I can't see me continuing to post to PaleoIllustrata as I have been doing, so I am sorry to say the blog in its old form has passed. Gone. It has ceased to be. It is an ex-blog.

However . . . as outreach is a major part of my research proposal I need an online presence to document my research and my journey as a Phd student in his late forties. A blog would be ideal! So the next post will be on the new-look PaleoIllustrata, relaunched as one of the methods I will use to disseminate my research and write about the whole process of studying for a doctorate for someone like me, coming from a non-academic background. I'll still be posting about meetings and field trips as previously, but with a bigger dose of science and research. I will feature my artwork here too, as before but the focus has changed; indeed there is now a real focus to my research.

So what am I going to be working on? I'll expand on that in future post(s), but mainly on the Early Cretaceous nodosaurid Polacanthus, including biomechanics and soft tissue reconstruction.

A new journey, a new stage in my life. As a palaeontologist. Here goes! 

Thursday, 26 September 2013

Celebrating Dinosaur Isle: Jehol-Wealden International Conference. 2013

Last week saw the first ever ‘Celebrating Dinosaur Isle: Jehol-Wealden International Conference’ at the National Oceanography Centre (NOCs), Southampton, UK and hosted by the University of Southampton Ocean and Earth Sciences and the Confucius Institute. There were around 90 delegates for the talks and 40 for the field trip, including palaeontologists from all over the UK, Europe, China and the USA. As a venue NOCs is hard to beat as the building sits on the dock front and from the cafe are excellent views down Southampton Water, across the Solent to the Isle of Wight in the distance and has superb facilities. A room was dedicated to displays and vendors and next door was the lecture theatre, with lunch and refreshments served on the wide landing right outside the two, the proximity of which was useful as it maximised the time spent with other delegates. 

The exhibit room at the conference.


As the title suggests, the whole meeting concentrated on the Early Cretaceous of the Jehol of China and the Wealden of Europe.  The day kicked off with an introduction by conference organiser Gareth Dyke of the University of Southampton, followed by a brief welcome by Mark Cranshaw of the Confucius Institute. The first talk was John Radley on the Geological Conservation Review and featured the work of Percival Allen on the Wealden climate, work that is still relevant today. In an entertaining talk Hugh Torrens than discussed the ‘first dinosaur’ as recognised by Richard Owen and discovered on the Isle of Wight. In the next room was the specimen itself, kindly lent by the National History Museum, and naturally it attracted a lot of attention. Jeff Liston then talked about the legalities of fossil collecting in China, where there are strict rules about moving fossils across even provincial boundaries. Pascal Godefroit was unable to attend but Mark Witton finished the first session with a typically excellent talk on Jurassic pterosaurs and their importance in understanding the evolution of Early Cretaceous forms.

After coffee Paul Barrett delivered a comprehensive and well-illustrated review of dinosaurs from the Jehol Biota. He was followed by Darren Naish who has been working on the Eotyrannus monograph and whose description of the specimen was very thorough, providing lots of information along with great images of the fossil. Dave Martill discussed the dentition of the pterosaurs Istiodactylus and Longchengpterus, again with excellent hi-res photos of the specimens which looked spectacular on NOCs’ excellent projector system. Unfortunately M. Matsukawa was also unable to attend the meeting but Martin Lockley delivered his talk in his place, no easy task considering the complexity of recreating ancient food webs and trophic cascades.

Lunch gave everyone a chance to really study the exhibits in the room next door to the lecture theatre. Apart from the thrill of seeing the ‘first dinosaur’ there were parts of a Polacanthus on display, with a very impressive ilium and sections of the sacral shield, as well as various vertebrae and parts of the pectoral girdle and limbs. A team from Dinosaur Isle had various specimens on show, including a complete Iguanodon mandible and some large Baryonyx teeth. The model of Microraptor featured in Dyle et al’s Nature paper was present along its balsa wood counterpart, more on that later. The chaps from Lyme Regis had fetched over a selection of fossils for sale and The Bristol Dinosaur Project also had a display on their local dinosaur, Thecodontosaurus antiquus.

The first of the afternoon sessions started with Zihui Zhang from Beijing discussing an enantiornithine bird skull and its implication for other enantiornithines. A small enantiornithine was also the subject of Dongyu Hu’s (Shenyang) talk, and he was followed by Colin Palmer who gave an excellent talk on the work that went into the Microraptor paper mentioned earlier. Colin’s talk finished with video of the balsa model  of Microraptor being flown, and demonstrating the flightpath predicted by computer simulations was pretty accurate. Next up was Mike Howgate, who was expounding his view that Microraptor was in fact a ‘archaeopterygid’ bird and Eoraptor was a possible bird ancestor. Mark Young then talked about the “Shanklin Shocker”, a large metriorhynchid with teeth similar to may extant fish species such as piraƱa in that when the jaw is closed they give a shearing motion, very effective for tearing lumps of flesh off prey. The images of the damage a cookie-cutter shark can do to a human leg could put a person off paddling for life.

The final session started with my own review of dinosaur ichnology on the Isle of Wight, and this was followed by Martin Lockley (who needs no introduction to vertebrate ichnologists) who showed some of the work being done in China at the moment, including some of the quite astonishing museums being built to house collections and cover track sites, including one shaped like a huge tridactyl print. Steve Sweetmen then talked about his fascinating work on Wealden microvertebrate assemblages, and also showed a spectacular print from Cowlease Chine, in-situ in the cliff, made in mudstone and infilled with sandstone. Pam Gill closed the session with a comprehensive review of Wealden-Jehol mammals.

The evening was spent in the Red Lion in Southampton, a 12th century pub where delegates were entertained by Luke Muscutt and friends. Luke is a PhD student at the university and a brilliant musician. Needless to say, a good time was had by all and much discussion was had, including an impromptu ichthyosaur mini-conference in the back room.

Walking through the upper Wessex and Vectis formations, first stop on the field trip.
Next morning the field trip started out from the Red Jet terminal in Southampton and were soon heading across the Solent to East Cowes on the Isle of Wight, where everyone boarded a bus and headed to Sandown, home of Dinosaur Isle. The first stop was the beach at Yaverland, where under the guidance of expert Trevor Price delegates inspected the uppermost section of the Wessex Fm and the whole of the Vectis Fm, both of which are exposed in this small but very productive stretch of coast. The beach conditions meant the footprint layers were covered by sand, but everyone could search for fossils in the shingle and along the cliffs. Next up the trip visited the Wessex-Vectis junction and then spent some time examining the section, including the footprint-bearing beds of the Shepherd’s Chine Member, eventually making its way towards to Lower Greensand and its beautifully preserved shelly fossils. I’m pleased to say dinosaur bone was found!

Heading towards Hanover Point.

After an introduction by Jeremy Lockwood a superb lunch was had at Dinosaur Isle, where the lab was open and local collectors were present with their finds and palaeontologist Steve Hutt was present to discuss the collection. This included new Iguanodon material from Nick Chase (who donates to the museum), a piece of thyreophoran armour and some quite incredible Baryonyx material representing at least two animals; let us hope these important specimens not lost to science.

The multicoloured sands of Alum Bay. My Nan had a small glass tube of these on her
sideboard, but this was the first time I'd seen them first hand.

Next on the itinerary was a visit to Hanover Point and Brook Bay on the west coast of the island, led by Steve Hutt, Penny Newbery and Trevor Price. There delegates inspected the dinosaur footcasts that litter the beach on this part of the coast and which were particularly abundant given the time year (I’m pleased to say) and spent time prospecting in the shingle for fossils. More bone was found. Following pickup by the bus, everyone was taken to the Needles Park where many brave souls rode the chair lift to the beach to look at the famous Alum coloured sands, and upon re-ascent were treated to a fine buffet and drinks. We took the Red Jet back to Southampton around 9.15pm and the conference ended.

The chairlift down to the beach at Alum Bay. Gulp.
This meeting was a resounding success. The talks were all fascinating (I’m excluding mine here, others can be the judge of that), the venue and organisation spot on, as was the field trip. It was great to see so many Early Cretaceous workers in one space, and personally I’m hoping a lot will come out of the discussions had during the coffee breaks, in the pub and on the field trip. Having so many experts on the field trip was a real treat, and I personally learnt much for their generous and patient instruction despite having spent many years visiting some of these sites. Thanks are due to Gareth Dyke for organising the conference and Jessica Lawrence who assisted, as well as Dinosaur Isle and The Needles Park for their hospitality.

I am sure I join many others in hoping this conference will be repeated in years to come.