tag:blogger.com,1999:blog-23461783456558677482024-03-13T15:43:28.113+00:00Paleo IllustrataStu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.comBlogger108125tag:blogger.com,1999:blog-2346178345655867748.post-84745455804237341822018-03-18T13:29:00.001+00:002018-05-22T07:39:22.481+01:00Final thoughts following my withdrawal from my PhD.<div style="font-family: Palatino; font-size: 13px; font-stretch: normal; line-height: normal; text-indent: 18px;">
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<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-LaTfRBOgv3c/Wq5wbPMgGeI/AAAAAAAADPY/AZFt5LebrsUlL3gncP55m983nmr-nTHqwCLcBGAs/s1600/stu_NHM_spet_2014.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="797" data-original-width="1123" height="283" src="https://1.bp.blogspot.com/-LaTfRBOgv3c/Wq5wbPMgGeI/AAAAAAAADPY/AZFt5LebrsUlL3gncP55m983nmr-nTHqwCLcBGAs/s400/stu_NHM_spet_2014.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Happy days: PhDing at the NHM with the holotype of <i>Polacanthus foxii</i>.</td></tr>
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We rightly hear a lot about early career researchers (ECRs) and the trials they face as they embark on their careers as scientists and academics, a daunting and challenging time in any scientist’s life. However, there is also a smaller group of people active in academia who are a bit longer in the tooth and might well have already had a career, or at least still be in the middle of one. These are the mature students, and I was one of them.<br />
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I came to academia late in life. I was in my early 40’s when I realised I wanted to become engaged in paleontological research in a more formal and structured manner than just picking bits of dinosaur bone off the beach on my frequent trips to the Isle of Wight (an activity I still enjoy). In 2010 I went on a week’s dig on the Hell Creek, followed a year later by the SVP at Las Vegas and from there became a research associate at the National Oceanography Centre Southampton (NOCS), part of the University of Southampton. I had tried to apply for an MRes course but it was suggested I didn’t have the qualifications. Actually, that’s correct. I have three ‘O’ levels, a general art and design certificate and a B/TEC in Graphic Design… and that’s the lot (I fluffed several ‘O’ levels because I was bad at exams and got in a panic; I’ve been an advocate of continuous assessment ever since). But I had relevant “life experience” after a long career in graphics. I was an active paleontological researcher and had presented my work and co-hosted workshops at international meetings etc<br />
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Growing up, university was never mentioned at school or home, except once when my physics teacher told me he’d buy me pint when I got my degree. University was not on the radar at all, it was an option so out of my reach that it was never discussed, ever. It never occurred to me I could go on to higher education. So I went to art school, got my graphic design qualification and that’s been my career for over 30 years, the last 14 of them running my own business.<br />
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When I was offered the opportunity to study for a self-funded, part-time vertebrate palaeontology PhD at NOCS, I was both surprised and excited. I went through the process of application, had my interview (toughest I’d ever done) and to my joy and amazement was accepted. I was very happy; here was a chance to make up for opportunities I didn’t have when younger. I was the first of my family to go to university.<br />
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Part of the reason I left salaried employment to run a business was that I wanted to study more, but the reality of being a sole trader made that difficult to achieve, and this became clear in the first couple of years. Structured courses were problematic as my day job comes first and I ended up missing exams etc to meet deadlines; weekends were spent working and lessons would be missed, and even part-time distance learning proved to much. Work comes first, end of. No work, no money.<br />
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The PhD was different. I could plan my research and even if I didn’t go near it for months could come back when things were quiet and resume without problem. Even on days I was stacked with work I could move my research on even if only incrementally. I’d send an email, download a paper, make a note of something, process data on an idle machine or any other of the myriad of activities a PhD student has do. It didn’t impact my work, but the tiny tasks returned tangible results, gave me a sense I was still progressing and during downtime I could make good headway. I enjoyed this period of my degree immensely. I was learning and becoming part of the wider community of palaeontologists who work on vertebrates. Even though I was 200 miles from the department I felt part of the Vertebrate Palaeontology (VP) group. The PhD began to feed back into my day job in ways I'd never anticipated, but were enormously beneficial.<br />
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Our VP group were a busy bunch. We hosted international vert palaeo meetings, we talked about our research, presented posters, taught and gave workshops and I co-supervised a brilliant MRes student. I was making good progress, my panel were happy and I was preparing to upgrade, and then my supervisor left, suddenly and without warning. Following this event issues with the specimen I was working on came to light (and was totally unaware of when I started), and over a period of several months my PhD imploded completely.</div>
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If this wasn’t bad enough, the university really didn’t care. Understandably and rightly it was the ECRs who needed to be supported most; their future careers depended on getting through the months that followed our supervisor’s departure. This was the priority, and I’m pleased to say they have all graduated. Liz Martin Silverstone, another member of the team, posted her thoughts on what could be learnt from her experience in this excellent blog post: https://gimpasaura.wordpress.com/2018/01/02/things-i-learned-during-my-phd-dos-and-donts-for-students-to-staff/<br />
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Things went from bad to worse. The senior staff simply did not seem to give a damn about my PhD. In my first call to one of them when I told her I had no undergrad or masters her exact words were; “How did you get in?”. It was suggested I could move to an MPhil instead as a consolation; my PhD was dead in the water, they had decided. The issues with the specimen meant that even this became impossible and the legal department pretty much stopped answering my emails. I became stressed, developed alopecia (my beard hair fell out in patches; it’s grown back now) and in the face of utter indifference from the senior staff I withdrew; I had no choice. My fees were returned but it was a financial disaster as I’d spent as much again on my doctorate, an investment with no return. As for the time invested… best not think about that.<br />
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I probably could have handled it better in some ways. I am very honest with my clients, and this sort of candour which is essential in business was not appreciated by the senior staff. I reply to emails, I keep people informed and if there is an issue I let them know at the earliest possible opportunity, however difficult this might be to inform them of. I didn’t know how an institution like a university works as I’d not experienced it before. I was angry and upset and this hinders communication (I still am, and having spoken to friends whose PhDs were also ended through no fault of their own it’s likely I will be for a long time).<br />
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It’s an oft-repeated myth that for those of us without a degree that life experience is taken into account when older students apply for higher degrees. True, I DID get accepted at NOCS on this basis (my day job meant there was some crossover in both the technology and ability to plan and execute large projects), but had the person I spoke to on the phone been in charge, I’m inclined to think I wouldn’t have. I’m now not sure I ever will again.</div>
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Universities have a duty of care to all their students, from ECRs building careers in a competitive and challenging environment to the late comers who want to try to realise some of their own potential that they weren't in a position to earlier in life. Older students can find universities intimidating places (EVERYONE is so much cleverer than you) and when things go wrong senior staff have to treat mature students as equals and with respect, not as some sort of irritating distraction. I was deadly serious about my PhD, but it turns out the senior staff at the school were not. All students, including the older ones, put their trust in senior staff and do not expect to be let down in such a manner, and in the case of the VP group we all were.<br />
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Positives? There are plenty. I learned a lot and loved being a VP PhD student. Most other palaeontologists have been fantastically supportive and understanding of the situation and I am looking forward to the future with an exciting project in the pipeline, working with people that I admire and can learn from and I look forward to contributing to the science. For a non-academic academic, I’m lucky to have such an opportunity. More on that later.<br />
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Had I failed at my PhD because I couldn’t complete for some reason of my own, such as being intellectually or academically incapable, financially compromised or whatever else that would have been one thing, but to fail because of the (in)actions and indifference of those who are in a position to ensure all students are helped through tough times? That should worry all of us.</div>
Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com2tag:blogger.com,1999:blog-2346178345655867748.post-49384827286275438872017-08-06T09:34:00.001+01:002017-08-06T09:34:35.858+01:00Back soon...<div class="separator" style="clear: both; text-align: center;">
<a href="https://3.bp.blogspot.com/-ZHXL1TB-Uu0/WYbUiUWjFNI/AAAAAAAABrA/jAacG0XDU40KdE7K8klbXUKcptCjCIRzQCLcBGAs/s1600/ankylosaurus_rawr.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1000" data-original-width="994" height="320" src="https://3.bp.blogspot.com/-ZHXL1TB-Uu0/WYbUiUWjFNI/AAAAAAAABrA/jAacG0XDU40KdE7K8klbXUKcptCjCIRzQCLcBGAs/s320/ankylosaurus_rawr.jpg" width="318" /></a></div>
<br />Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com2tag:blogger.com,1999:blog-2346178345655867748.post-6849305261125973112016-10-27T17:31:00.000+01:002016-10-27T17:31:01.334+01:00Utilising a commercial workflow when reconstructing dinosaur skeletons in 3D<div style="font-family: Palatino; font-size: 13px; line-height: normal; text-indent: 18px;">
Reconstructing fossils digitally has become a vital technique in palaeontology in recent years. The ability to reconstruct the entire skeletons of extinct taxa gives us the opportunity to look at aspects of an organism’s life that would prove difficult or impossible using physical models, for example in biomechanics and gait analysis.</div>
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<tr><td style="text-align: center;"><a href="https://4.bp.blogspot.com/-Mlr_rs62nrg/WBImzPNg6_I/AAAAAAAAA1M/sQdBYyFkPS8fFCo68aTZL2kzi6FIfmXYgCLcB/s1600/gorgosaurus_skel.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="143" src="https://4.bp.blogspot.com/-Mlr_rs62nrg/WBImzPNg6_I/AAAAAAAAA1M/sQdBYyFkPS8fFCo68aTZL2kzi6FIfmXYgCLcB/s400/gorgosaurus_skel.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Er, hi. The final, posed <i>Gorgosaurus</i> model, created in zBrush 4R7 and Cinema 4D R16.</td></tr>
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A recent paper by Stephan Lautenschlager (http://rsos.royalsocietypublishing.org/content/3/10/160342) on digital fossil restoration techniques provides a good overview of the methodology using tools available for digital palaeontology in most labs, including Avizo, Blender and Maya. I highly recommend this paper for anyone interested in the digital restoration of fossil specimens and the workflow involved, much contained in the paper being relevant to the digital reconstruction of specimens for research and outreach.</div>
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Last year I worked on a project with Dr. Willam Sellers of Animal Simulation Laboratory (<a href="http://www.animalsimulation.org/">http://www.animalsimulation.org</a>) at the University of Manchester which required the creation of six accurate and complete dinosaur skeletons (see my previous post on the project: http://paleoillustrata.blogspot.co.uk/2016/01/walking-and-making-dinosaur.html), and for this I used a workflow developed in my work creating scientific animations and illustrations for the MedComms industry, a workflow not dissimilar to many commercial studios where 3D assets of all description are produced. axon, the makers of one of the 3D modelling and animation applications I use, Cinema 4D R18, covered this project on their website: https://www.maxon.net/en/industries/visualization/article/everybody-walk-the-dinosaur/</div>
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<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-1ap7_PflE9w/WBImyy0yGBI/AAAAAAAAA1I/fFa32ejPZgQ6pj_yIq31AbUWE8mlsgvGgCEw/s1600/R175_pol_femur.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://1.bp.blogspot.com/-1ap7_PflE9w/WBImyy0yGBI/AAAAAAAAA1I/fFa32ejPZgQ6pj_yIq31AbUWE8mlsgvGgCEw/s400/R175_pol_femur.png" width="256" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">A specimen (NHM R175) recorded using photogrammetry<br />
and suitable for use as a basis for reconstruction of the bone.</td></tr>
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The reference used to create individual elements comes from a number of sources. Primary amongst these are meshes generated using with photogrammetry, Lidar or CT scanning. These data are often received as point clouds that require the generation of a mesh. These datasets can be pretty hefty (especially if they are of entire mounted skeletons or other large, complex subjects) so they require chopping down into manageable chunks prior to meshing to make processing more efficient, for example isolating part of a limb or the skull. I use MeshLab (http://meshlab.sourceforge.net) for this part of the processes, saving sections of the point cloud and meshing them individually. The meshes generated from this procedure are the basis for the reconstruction and these are imported as reference meshes into the main 3D package prior to starting modelling. The literature was consulted and where possible collections were visited and photographs taken to maximise the available reference for modelling. This is important because as there is a fair amount of morphological variation within a particular taxa and this needs to be taken into account when modelling the skeletons, and in fact the final models are composites and don’t represent a single specimen.</div>
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Like many studios I use more than one application to create my models of palaeontological specimens. As mentioned earlier, the main 3D application I use for both research and commercial work is Cinema 4D R18 by Maxon (<a href="https://www.maxon.net/">https://www.maxon.net</a>). Within C4D I block out the basic form of the model by generating primitives, extruding polygons and dragging edges and points into approximate position (see this post for how this works: <a href="http://paleoillustrata.blogspot.co.uk/2011/09/building-dinosaur-pulling-polygons-and.html">http://paleoillustrata.blogspot.co.uk/2011/09/building-dinosaur-pulling-polygons-and.html</a>). To make these models practical for biomechanical work and 3D printing, so they needed to have as few polygons as possible whilst retaining accuracy. By starting with very simple, blocky shapes it is far easier to keep control of the polygon count as you model and make sure the mesh density is as low as possible for the final model.</div>
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<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-SXs3Eztkfho/WBImyxwRD3I/AAAAAAAAA1E/oXh0db3LDcwEfTW5wfA3Ck3_iHSTpVEYQCEw/s1600/giraff_skulls.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://1.bp.blogspot.com/-SXs3Eztkfho/WBImyxwRD3I/AAAAAAAAA1E/oXh0db3LDcwEfTW5wfA3Ck3_iHSTpVEYQCEw/s400/giraff_skulls.png" width="280" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Low resolution, blocked-out skull ready for importing to zBrush for further sculpting (top),<br />
and the skull in the process of being modelled at a higher resolution.</td></tr>
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Once the basic shape is modelled in C4D, the meshes (both reference and model are imported into Pixologic zBrush 4R7 (<a href="http://pixologic.com/">http://pixologic.com</a>), a 3D modelling package that uses sculpting in clay as a metaphor for modelling 3D meshes. Why not continue modelling in Cinema 4D or anther package? Well, zBrush’s tools are intuitive, fast and easy to use (once you’re used to them) and well suited to creating organic shapes. As a modelling tool widely used in the gaming industry zBrush also offers excellent retopologising and mesh decimation tools, which means models can have a low mesh density whilst retaining detail; it produces very ‘clean’ meshes which are perfect for importing into a wide variety of other applications. Once the model is completed the final mesh is imported back into Cinema 4D for positioning and texturing (if required). I cannot recommend zBrush highly enough for organic modelling and anyone creating reconstructions in 3D should take a close look at this package.</div>
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<tr><td style="text-align: center;"><a href="https://4.bp.blogspot.com/-b7XqBl91V5I/WBImzb2XQGI/AAAAAAAAA1Q/rrSwKG1rcSop2oSjnLXEqkyGZWqEd-4xgCEw/s1600/gorgo_skull_zBrush.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="250" src="https://4.bp.blogspot.com/-b7XqBl91V5I/WBImzb2XQGI/AAAAAAAAA1Q/rrSwKG1rcSop2oSjnLXEqkyGZWqEd-4xgCEw/s400/gorgo_skull_zBrush.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The skull of <i>Gorgosaurus</i> during the modelling process, showing the layout within zBrush 4R7.</td></tr>
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Assembling a skeleton in Cinema 4D is a task made easier by some of the tools that are add-ons to the application and widely used by modellers and animators. Foremost amongst these is the Mograph module, which allows the cloning of a single element and the manipulation of these clones. This is tremendously useful when creating multiple copies of broadly similar elements such as vertebrae. For example, the tail several vertebrae from certain points along the sequence would be modelled and then those in between generated by cloning and these would then be adjusted individually to match the reference.</div>
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<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-JDxMwGNiaTc/WBImzfdnU5I/AAAAAAAAA1U/_i_iR36nX9g0iG2plC8LSArdjUr2R7HCACEw/s1600/trike_gaitsym.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="248" src="https://1.bp.blogspot.com/-JDxMwGNiaTc/WBImzfdnU5I/AAAAAAAAA1U/_i_iR36nX9g0iG2plC8LSArdjUr2R7HCACEw/s400/trike_gaitsym.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The <i>Triceratops</i> skeleton rigged and hot to trot in GaitSym.</td></tr>
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The final model can be exported out as any type of 3D file, with the most useful being .obj and .fbx at present, but anticipate this changing in the future and save in several formats as well as the proprietary format of the modelling applications.</div>
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<tr><td style="text-align: center;"><a href="https://4.bp.blogspot.com/-7GzG6UpWCl8/WBImy9hPDnI/AAAAAAAAA1A/nBeBKYYPkm83xdAg95BJrID1ynpWZ6HsACEw/s1600/giraffititan_skel.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="270" src="https://4.bp.blogspot.com/-7GzG6UpWCl8/WBImy9hPDnI/AAAAAAAAA1A/nBeBKYYPkm83xdAg95BJrID1ynpWZ6HsACEw/s400/giraffititan_skel.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The <i>Giraffititan</i> model, posed.</td></tr>
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The use of commercial tools such as zBrush is becoming more common for palaeontologists and palaeoartists, and by paying close attention to the structure of production pipelines and workflows of commercial digital studios is something we as palaeontologists should consider, as there is much to learn from their techniques and methods which we can incorporate into our own reconstruction and restoration arsenal of techniques for generating 3D meshes useful or wide variety of research pathways.</div>
Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com0tag:blogger.com,1999:blog-2346178345655867748.post-4750695739861184872016-05-03T13:12:00.000+01:002016-05-03T13:12:08.531+01:00Horshamosaurus: An enigmatic Wealden ankylosaur.<div style="font-family: Baskerville; font-size: 12px; line-height: normal; text-indent: 27px;">
<span style="font-kerning: none;">I recently visited the small but excellent museum in Horsham to take a look at one of the most enigmatic dinosaurs found in the Wealden, <i>Horshamosaurus</i>. Of the three species of Early Cretaceous ankylosaurs currently recognised in the English Wealden, <i>Horshamosaurus</i> is the least known. </span></div>
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<span style="font-kerning: none;">The specimen was discovered in a brickworks quarry near Rudgwick, Sussex in 1985, in the Barremian-aged rocks of the Wealden Sub-basin. Somewhat typically for Wealden dinosaur remains there is not much of it and whilst <i>Hylaeosaurus</i> and<i> Polacanthus foxii</i> are known from partial skeletons, the material representing <i>Horshamosaurus</i> is more fragmentary and consists of only a few elements which were found associated but disartuclated.</span></div>
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<tr><td class="tr-caption" style="text-align: center;">Dorsal vertebra of <i>Horshamosaurus</i>.<br />
A) dorsal B) ventral C) right lateral D) left lateral E) anterior F) posterior</td></tr>
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<span style="font-kerning: none;">The fossils were originally assigned by British ankylosaur expert Bill Blows to <i>Polacanthus rudgwickensis</i>, as it displays some affinities with <i>Polacanthus foxii, </i>the majority of which specimens come from the Wessex Formation but with one specimen having been found in the earlier Valanginian Fm near Bexhill, Surrey. <i>Horshamosaurus</i> shares several synampomorphies with <i>Polacanthus</i>: unfused caudal chevrons, astralagus fused to the tibia and similarities in the dermal armour, but the paucity of material associated with this specimen is problematic.</span></div>
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<span style="font-kerning: none;">There are some differences between the Rudgwick ankylosaur and <i>Polacanthus foxii</i> too. It's suggested that <i>Horshamosaurus</i> is significantly bigger than the <i>P. foxii </i>holotype, around 30%, but this estimate must be viewed with caution and requires further testing. It also displayed differences in vertebral morphology and the length of the tibia, plus the geological occurrence of the skeleton indicated it was not <i>P. foxii</i>.</span><span style="font-family: "times new roman"; line-height: normal;"> </span><span style="font-kerning: none;">In his recent book <b>Polacanthid Dinosaurs of Britain </b>(see my review <a href="http://paleoillustrata.blogspot.co.uk/2015/09/book-review-british-polacanthid.html" target="_blank">here</a>), Blows re-assigns <i>P. rudgwickensis</i> to <i>Horshamosaurus </i>and suggests it is perhaps a nodosaurid and not a polacanthid based on a reassessment of the character differences between it and <i>P. foxii</i>. Of course, the existence of a monophyletic ‘polacanthid’ clade is not settled.</span></div>
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<tr><td class="tr-caption" style="text-align: center;">Scacpulocoracoid of <i>Horshamosaurus</i>.<br />
A) dorsal B) ventral C) right lateral D) left lateral E) anterior F) posterior</td></tr>
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<span style="font-kerning: none;">The main parts of the specimen consist of one complete dorsal vertebra and one broken, a couple of partial caudals of which one is a left half only, some rib sections including the proximal part of a large dorsal rib, the distal end of the scapulocoracoid, two osteoderms, the distal end of left humerus and the proximal and distal sections of the right tibia; the tibia is broken into two parts and a section of unknown length is missing. The scapulocoracoid is distinctive but the pectoral girdle of <i>Polacanthus</i> is poorly known, with only the Bexhill specimen and a specimen in private hands having part of the scapular preserved, however this appears to be less robust than <i>Horshamosaurus</i>. The <i>Horshamosaurus</i> scapular and coracoid are fused, this condition is not known to be a characteristic of <i>Polacanthus</i> as the coracoids of all the other published specimens are missing..</span></div>
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<span style="font-kerning: none;">Of the two osteoderms preserved, one is a partial roof-like, thin-walled osteoderm, the other a large keeled osteoderm with a solid base. In his 1996 paper describing the specimen Blows suggests that the thin-walled osteoderm might be indicative of an ankylsoaurid affinity for this animal; there is some support for the taxonomic utility of ankylosaur osteoderms so this could be significant but as this is not a commonly seen morphology in Wealden ankylosaurs a larger sample size of these osteoderms is needed.</span><br />
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<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-bcDWE0_XnzE/VyXwrVOJRNI/AAAAAAAAAy0/2oDsjmoDHXIbD9elZlnY1Qi2UfzLC00qACKgB/s1600/horsham_display.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://1.bp.blogspot.com/-bcDWE0_XnzE/VyXwrVOJRNI/AAAAAAAAAy0/2oDsjmoDHXIbD9elZlnY1Qi2UfzLC00qACKgB/s400/horsham_display.jpg" width="395" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Horsham museums's dinosaur display cabinet, with <i>Horshamosaurus</i> on the white wall on the right.</td></tr>
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The reassignment of <i>Horshamosaurus</i> by Blows in his 2015 book is tentative and hopefully more remains of this enigmatic armoured dinosaur will be unearthed in due course, which will enable us to resolve it's taxonomy and shed more light on the relationships of Wealden ankylosaurs. In the meantime, if you're passing close to Horsham I can recommend dropping into the museum to see their vertebrate palaeontology collection which is small (one cabinet), but contains the world's only known <i>Horshamosaurus</i>.</div>
Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com0tag:blogger.com,1999:blog-2346178345655867748.post-31389722808673281442016-01-12T20:02:00.004+00:002016-01-25T08:12:02.723+00:00Walking (and making) the dinosaur<div class="separator" style="clear: both; text-align: center;">
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I was fortunate enough to work on a fascinating project last year led by Dr. Bill Sellers from the University of Manchester and which was published as a Peer-J preprint just before Christmas. The full preprint is available here: https://peerj.com/preprints/1584/</div>
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Dr. Sellers has been working on the biomechanics of dinosaurs and other tetrapods for several years and has developed an application called GaitSym that calculates walking or running gaits, testing walk cycles until the program finds the most efficient which can help form a hypothesis to be formed on how an animal might have moved around. GaitSym requires 3D skeletal data in the form of scans or models that are then rigged with muscles that allow the simulation to calculate the forward dynamics.</div>
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Dr Sellers then built a new version of GaitSym that allows people to control dinosaurs themselves. By replacing the algorithms that calculate forward dynamics with an external control system, in this case a Kinect for Xbox wired up to a Windows PC, a person standing a few feet away can control the rigged dinosaur on the screen, enabling it to walk, run or dance.<br />
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<tr><td class="tr-caption" style="text-align: center;">Triceratops skeleton rigged with virtual muscles in GaitSymKinect.<br />
Image courtesy of Dr. William Sellers.</td></tr>
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The software created by Dr. Sellers that allows people to control these dinosaur skeletons is called GaitSymKinect. The dinosaur skeletons are rigged as we think they would be in life and GaitSymKinect translates the movements of the user into movement for the dinosaurs, allowing a person to make <i>Tyrannosaurus rex </i>do the Charleston, or a <i>Triceratops</i> gallop. The system was tested last year at the Cheltenham Science Festival and is now freely available, along with the dinosaur skeletons to go with it, follow this link here: http://www.animalsimulation.org/files/84eab05587dbe0bdcd72eb098a692afe-7.html</div>
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My part was to create the dinosaur skeletons to be used in GaitSymKinect whilst also making them suitable for being made freely available for 3D printing and just about anything else a 3D mesh can be used for. The skeletons were created to be as accurate as possible whilst not representing an actual specimen; scans, photogrammetry and the literature were all sources referred to when creating the skeletons. They are not detailed down to the smallest foramen in order to keep the polygon count as low as possible but they are accurate and would be useful for adapting to specific specimens if required and were created in Maxon Cinema 4D R16 and zBrush 4R7.</div>
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Six complete skeletons were created: <i>Tyrannosaurus</i>, <i>Gorgosaurus</i>, <i>Triceratops</i>, <i>Edmontosaurus</i>, <i>Brachiosaurus</i> and <i>Edmontia</i>. The final skeletal models are ideal for biomechanical work, adding to artworks and of course 3D printing. All this and they are free, released under CC-BY The dinosaurs skeletons modelled are shown below. If you do use them for anything, it’d be great if you could show us what you’ve done with them.</div>
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<tr><td class="tr-caption" style="text-align: center;">The six dinosaur skeletons built as 3D meshes and available for free download.<br />
Clicking should embiggen.</td></tr>
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<b>References:</b></div>
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<span style="font-kerning: none; text-shadow: 0.0px 1.0px 0.0px rgba(255, 255, 255, 0);">Sellers WI, Pond SB. (2015) Kinect controlled dinosaur simulations for education and public outreach. <i>PeerJ PrePrints</i> 3:e1979 <a href="https://doi.org/10.7287/peerj.preprints.1584v1">https://doi.org/10.7287/peerj.preprints.1584v1</a></span></div>
Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com3tag:blogger.com,1999:blog-2346178345655867748.post-20948289512329489002015-09-23T15:45:00.004+01:002015-09-29T11:48:25.276+01:00Book review: British Polacanthid Dinosaurs by William T. Blows<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-GUkN5ddnN9I/VgOj1919r0I/AAAAAAAAAxg/xKeprTaf9m0/s1600/nodo_illustration_sm.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="200" src="http://3.bp.blogspot.com/-GUkN5ddnN9I/VgOj1919r0I/AAAAAAAAAxg/xKeprTaf9m0/s400/nodo_illustration_sm.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: Cochin; text-indent: 18px;">Tentative reconstruction of the ankylosaur currently under study at the University of Southampton.</span></td></tr>
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It would not be unreasonable to say that since their discovery in 1832 in a Sussex quarry, ankylosaurs have had a far more modest amount of attention directed at them than some of their more famous relatives. This may seem odd as the first to be discovered, <i>Hylaeosaurus</i>, was one of the three taxa that led Owen to erect the Dinosauria in 1842 and was the subject of one of Waterhouse Hawkins superb reconstructions at Crystal Palace. It seems that despite their spectacular array of spikes, clubs and shields they might forever be in the shadow of taxa considered more exciting by both palaentologists and the public alike, so a book dedicated to British ankylosaurs is a very welcome addition to the palaeontological literature.</div>
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William Blows has been working on British ankylosaurs for several decades and discovered and excavated one of the specimens discussed in this book (NHM R9293) and has published many papers on the subject in that time; he is probably the leading worker on British Wealden ankylosaurs. Siri Scientific Press, based in Manchester UK, are a prolific publisher of paleontological and natural history books and specialise in well-illustrated textbooks that often cover niche areas of interest, although they also publish more general volumes. One of their most recent publications was Dean Lomax and Nobumichi Tamura’s ‘Dinosaurs of Great Britain’, an exhaustive and lavishly illustrated review of British dinosaur specimens, some never figured before in the literature. </div>
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British Polacanthid Dinosaurs continues in the same vein, although obviously concentrating on a far smaller number of specimens. The book begins with a review of British ankylosaur research (fronted by the excellent Neave Parker reconstruction) which discusses systematics, polacanthid synapomorphies, stratigraphy and possible relationships with other taxa, principally those from North America. This is followed by a historical account of the discovery of <i>Hylaeosaurus</i> and the subsequent milestones in British ankylosaur research. This includes some gems like the tale of Mr Lee’s lost sacral shield specimens (which I discussed <a href="http://paleoillustrata.blogspot.co.uk/2014/08/mr-lees-osteoderms-and-taxi.html" target="_blank">here</a> last year) and contains some wonderful quotes from early dinosaur workers such as Hulke and Nopsca. This chapter is a good overview of the subject and a welcome addition to the literature, putting modern research into British ankylosaurs into context.</div>
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The main bulk of the book consists of descriptions of most of the currently known specimens, broken down into sections by skeletal element: skull and jaws, vertebrae and ribs, limbs etc and the descriptions of the specimens are clear and detailed. This part of the book contains many photographs and these images are of excellent quality, captioned with accession numbers and (with the odd exception) are accompanied by scale bars and are the real strength of this book for ankylosaur workers; these images are a valuable resource. Most of the known specimens are covered here, although some are being worked on and are not included (this does include the Soton specimen, although the parts of the specimen held at Dinosaur Isle are figured and described here). The remainder of the book is given over to a brief discussion of other polacanthids, especially the North American taxa and the re-assignment of <i>Polacanthus rudgwickensis</i> to the newly erected taxon <i>Horshamosaurus</i> which Blows now considers a nodosaurid and not a polcanthid.</div>
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But there are a couple of issues. Firstly, who is the book aimed at? At £59 plus postage this is an expensive volume and running at 220 pages not huge (although no-one can doubt the considerable work gone into creating it) and this would suggest it was aimed at academic and avocational palaeontologists rather than amateurs and curious layfolk. On the other hand, the tone of the book is not written in the scientific prose we expect from a paper or technical volume and the referencing is inconsistent. It contains some jargon but is more accessible than much of the scientific literature is, presumably for the benefit of the lay audience, but this gives the impression the book falls between two stools.</div>
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Secondly is the existence of the ‘Polacanthid’ clade. The author states his opinion on this subject right from the outset in the title of the book (as well as his distrust of modern phylogentics, stating: “It is possible too much faith is applied to cladograms”), and confirms his position in the text: Polacanthidae is a valid clade and most British ankylosaurs are polacanthids. A lay person coming to the subject via this book would be forgiven for thinking this issue is cut and dried, which it is not. There are conflicting hypothesis about whether Polacanthidae (a clade alongside Ankylosauridae and Nodosauridae) or Polacanthinae (a clade nested within either Ankylosauridae and Nodosauridae) represent a monophylectic clade. The author justifies his conclusion it is by citing support from Kirkland (1998), Carpenter (2001) and Burns and Currie (2014) as well as Martill and Naish (2001). Kirkland’s recovery of a polacanthine clade was based on morphological similarities between several taxa and supported by cladistic analysis, however Carpenter’s assignment of <i>Polacanthus</i> to polacanthidae was based on <i>a priori </i>sorting of the sampled taxa into the three clades which were then analysed. Martill and Naish (2001) adopt Kirkland’s suggestion of a polacanthid clade because of doubts about the evidence for polacathines as basal ankylosaurids rather then direct evidence to the contrary, whilst Barrett and Maidment (2010) adopt Thompson et al’s 2012 conclusion of these taxa as basal nodosaurids, however Arbour’s 2015 analysis of ankylosaurids recovers <i>Gastonia</i> as a basal ankylosaurid. There is much work to be done in untangling the relationships of basal ankylosaurs and at present the exact status of all British ankylosaurs are uncertain.</div>
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If you’re interested in ankylosaurs at all then it’s worth buying this book; if you're interested in or work with Early Cretaceous ankylosaurs it's essential. In years to come I can see this book being a very useful resource for workers and other interested parties alike; hopefully in future editions we will see more specimens are they come to light and are made available. It is a good review of the field as it stands from an author with decades of experience of studying British ankylosaurs and the images are superb, the specimen descriptions are detailed and the history of ankylosaur research is a great read.</div>
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If only it wasn’t so expensive.</div>
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Arbour, V. M., M. E. Burns, and P. J. Currie. 2011. A review of pelvic shield morphology in ankylosaurs (Dinosauria: Ornithischia). Journal of Paleontology 85:298–302.</div>
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Victoria M. Arbour & Philip J. Currie (2015): Systematics, phylogeny and palaeobiogeography of the ankylosaurid dinosaurs, Journal of Systematic Palaeontology, DOI: <span style="color: #0433ff;">10.1080/14772019.2015.1059985</span></div>
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Barrett, Paul M. and Maidment, Susannah C.R. 2011. Armoured Dinosaurs In: English Wealden fossils. Paleontological Association Field Guide to Fossils. Batten DJ, editor. 26: 391-406.<br />
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<span style="text-indent: 18px;">Blows, William Taylor. 2015. British Polacanthid Dinosaurs. Monograph Series Volume 7. Siri Scientific Press. Manchester, UK.</span></div>
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Michael E. Burns & Philip J. Currie (2014) External and internal structure of ankylosaur (Dinosauria, Ornithischia) osteoderms and their systematic relevance, Journal of Vertebrate Paleontology, 34:4, 835-851, DOI:<span style="color: #0433ff;">10.1080/02724634.2014.840309</span></div>
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Carpenter K (2001) Phylogenetic analysis of the Ankylosauria. In: Carpenter K, editor. The Armored Dinosaurs. Bloomington: Indiana University Press. pp 454–483.</div>
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Kirkland, J.I. 1998. A Polacanthine ankylosaur (Ornithischia: Dinosauria) fron the Early Cretaceous (Barremian) of eastern Utah. In Lucas, S.G., Kirkland J.I. and Estep, J.W. (eds), Lower and Middle Cretaceous Terrestrial Ecosystems. <i>New Mexico Museum of Natural History and Science Bulletin</i> 14: 271-281. </div>
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Martill D, Naish D. 2001. Armoured Dinosaurs: Thyreophorans. In: Martill D, Naish D, eds. Dinosaurs of the Isle of Wight. London: Field Guide to Fossils No. 10: Palaeontological Association, 310–323.</div>
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Richard S. Thompson, Jolyon C. Parish, Susannah C. R. Maidment & Paul M. Barrett (2012): Phylogeny of the ankylosaurian dinosaurs (Ornithischia: Thyreophora), Journal of Systematic Palaeontology, 10:2, 301-312</div>
Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com2tag:blogger.com,1999:blog-2346178345655867748.post-75924875629931500862015-09-06T14:13:00.000+01:002015-09-06T14:13:30.063+01:00SVPCA 2015<div style="font-family: Cochin; font-size: 14px; text-indent: 18px;">
This years SVPCA meeting was organised by Gareth Dyke and his team and was held at the National Oceanography Centre Southampton (NOCS), home of Ocean and Earth Science at the University of Southampton. Situated on the bustling docks and surrounded by hulking container ships and the floating tower blocks that modern ocean liners all seem to resemble these days, this excellent facility is home to vertebrate palaeontology research in Southampton, located as it is close to the Jurassic Coast and the Isle of Wight.</div>
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<tr><td class="tr-caption" style="font-size: 13px;">Talking ankylosaurs at SeaCity before the auction</td></tr>
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Following hard on the heels of the Flugsaurier meeting the previous week in Portsmouth and with the SPPC preparators meeting the day before, delegates convened on Tuesday 1st September to hear three days of talks, attend two poster sessions and various social events. This year there were around 160 delegates attending, from emeritus professors to young palaeontologists, undergrads, postgrads, professional and amateur workers alike and palaeoartists were well represented. The SVPCA is always a more relaxing meeting than the SVP, less daunting to those giving their first talks and people there are always constructive with their advice.</div>
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The talks were of a high quality and despite being restricted to 15 minute slots for both talk and questions didn’t seem rushed; the programme put together by Mark Young and Darren Naish contained a wide variety of talks that covered a satisfying wide variety of subjects. Even if a subject wasn’t particularly relevant to your own research chances are you left a session having learnt something or been found something to inspire new thinking in some way. There were no major technical glitches (although the movies didn’t work on my talk) and the sessions ran on time. There will be a special PeerJ volume based on papers arising from the meeting talks and posters, so if you did present it's time to get writing.</div>
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Conversations went on well into the night in the pubs near NOCS. The annual auction at SeaCity Museum raised a fantastic £1900 thanks to the sterling work of Jeff Liston as auctioneers as well as the SVPCA A Team of Jessica Lawrence Wujeck, Aubrey Roberts, James Hansford and Liz Martin-Silverstone. The conference dinner was held in a dockside Thai restaurant and was very enjoyable, although being the day before the field trip . . . </div>
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<tr><td class="tr-caption" style="font-size: 13px;">Delegates inspecting the Wessex Formation at Chilton Chine, Isle of Wight.</td></tr>
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The field trip was led by Steve Sweetman and visited Brighstone and Compton Bays where the group took a long walk down the beach to inspect the fossil-bearing strata of the Wessex Formation, some of the most productive dinosaur localities in Europe. Dinosaur bone, plant material and dinosaur footprints were found. Lunch was taken at The Wight Mouse Inn, a pub beloved of the many vertebrate palaeontologists who visit the island. The next stop was at Dinosaur Isle where delegates saw the museum and the team of Alex Peaker, Shaun Smith and Gary Blackwell retrieved specimens for closer inspection and photography.</div>
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Further reviews are here:</div>
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Liz Martin-Silverstone: <a href="http://gimpasaura.blogspot.co.uk/2015/09/flugsaurier-and-svpca.html">http://gimpasaura.blogspot.co.uk/2015/09/flugsaurier-and-svpca.html</a></div>
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Mike Taylor: <a href="http://svpow.com/2015/09/04/unhappy-thoughts-on-student-projects-at-svpca-2015/">http://svpow.com/2015/09/04/unhappy-thoughts-on-student-projects-at-svpca-2015/</a></div>
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Luis Rey: <a href="https://luisvrey.wordpress.com/2015/09/05/flugsaurier-and-svpca-2015-face-to-face-with-the-snake/">https://luisvrey.wordpress.com/2015/09/05/flugsaurier-and-svpca-2015-face-to-face-with-the-snake/</a></div>
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The next meeting will be hosted by Liverpool John Moores University, and I’m looking forward to it already. As one delegate said to me before leaving, “it’s been inspirational”. You can’t really ask for more than that can you?</div>
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Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com0tag:blogger.com,1999:blog-2346178345655867748.post-81125732952266574512015-08-22T12:41:00.000+01:002015-08-22T12:42:59.858+01:00SVPCA 2015 Abstracts volume<div class="separator" style="clear: both; text-align: center;">
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Although it's been while since my last blog post I have not been idle. Indeed along with the other members of the host committee I've been beavering away on various bits and bobs for this year's SVPCA meeting that is being hosted at the excellent National Oceanography Centre in Southampton.<br />
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The abstract volume is available for download from <a href="http://www.stupond.com/paleo/SVPCA2015_Abstracts.pdf" target="_blank">HERE</a>.<br />
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As you will see this meeting has an exciting range of talks as well as two poster sessions, an icebreaker at the SeaCity Museum (featuring the ankylosaur specimen we're working on), the auction, a field trip to the Isle of Wight and the conference dinner.<br />
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I hope to see you there!Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com0tag:blogger.com,1999:blog-2346178345655867748.post-36896087137941192522015-06-19T14:56:00.000+01:002015-06-19T14:57:11.556+01:00Fossils on the small screen at Dinosaur Encounter, SeaCity.<div style="font-family: Cochin; font-size: 14px; text-indent: 18px;">
As part of the exhibition at <a href="http://seacitymuseum.co.uk/" target="_blank">SeaCity</a> 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.</div>
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<tr><td class="tr-caption" style="text-align: center;">Still from the croc video showing bone outline highlighted to<br />
aid interpretation of the specimen.</td></tr>
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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. </div>
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<tr><td class="tr-caption" style="text-align: center;">The crocodile video next to the specimen as part of the display.<br />
Image: Liz Martin.</td></tr>
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The <i>Polacanthus</i> 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 <i>Polacanthus foxii </i>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 . . . </div>
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<tr><td class="tr-caption" style="text-align: center;">First reconstruction of the nodosaur currently being studied at<br />
University of Southampton. Video still.</td></tr>
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Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com2tag:blogger.com,1999:blog-2346178345655867748.post-55757407396599866562015-06-15T15:23:00.001+01:002015-06-15T15:26:28.312+01:00Encountering dinosaurs at SeaCity Museum<div style="text-indent: 18px;">
<span style="font-family: Times, Times New Roman, serif;"><span style="font-size: 14px;">As is fitting following the arrival of the summer blockbuster <a href="http://www.imdb.com/title/tt0369610/" target="_blank">Jurassic World,</a> 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 </span><a href="http://seacitymuseum.co.uk/" style="font-size: 14px;" target="_blank">here</a><span style="font-size: 14px;">), and I was fortunate enough to have been involved in this exciting project.</span></span></div>
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<tr><td class="tr-caption" style="text-align: center;">All it needs is a real dinosaur . . . <br />
the exhibition space at SeaCity with the build in progress.</td></tr>
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<span style="font-family: Times, 'Times New Roman', serif;">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.</span><span style="font-family: Times, Times New Roman, serif;"></span></div>
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<span style="font-family: Times, Times New Roman, serif;">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 <i>Maiasaura</i> and skull casts of <i>Tyrannosaurus rex</i> and <i>Triceratops</i>; 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.</span></div>
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<tr><td class="tr-caption" style="text-align: center;">Doing the dinosaur jigsaw.</td></tr>
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<span style="font-family: Times, 'Times New Roman', serif;">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 . . .</span></div>
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<span style="font-family: Times, Times New Roman, serif;">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.</span></div>
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<tr><td class="tr-caption" style="text-align: center;">The nodosaur final layout.</td></tr>
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<span style="font-family: Times, 'Times New Roman', serif;">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.</span><span style="font-family: Times, Times New Roman, serif;"></span></div>
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<span style="font-family: Times, 'Times New Roman', serif;">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.</span></div>
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Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com1tag:blogger.com,1999:blog-2346178345655867748.post-52239226194134363162015-05-27T11:45:00.001+01:002015-05-27T11:45:30.739+01:00SVPCA 2015 Second circular<div style="font-family: Cochin; font-size: 14px; text-indent: 18px;">
The second circular for the SVPCA is now available, and can be downloaded as a pdf from <a href="http://svpca.org/years/2015_southampton/second.circular.pdf" target="_blank">here</a> or viewed on the SVPCA website <a href="http://svpca.org/years/2015_southampton/second.circular.php" target="_blank">here</a>.</div>
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Abstract deadline is 24<span style="font-size: 9px;"><sup>th</sup></span> July, so now’s the time to start thinking about talks and posters. I hope to see you there!</div>
Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com1tag:blogger.com,1999:blog-2346178345655867748.post-74860443801820674122015-03-03T13:27:00.001+00:002015-03-03T13:27:23.115+00:00SVPCA 2015 First Circular<div class="separator" style="clear: both; text-align: center;">
<a href="http://1.bp.blogspot.com/-woDww05cKUI/VPWzxBuze_I/AAAAAAAAAuI/ddW3jIru8Dg/s1600/SVPCA_2015_logo.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://1.bp.blogspot.com/-woDww05cKUI/VPWzxBuze_I/AAAAAAAAAuI/ddW3jIru8Dg/s1600/SVPCA_2015_logo.jpg" height="400" width="145" /></a></div>
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This year the SVPCA is being hosted at the <a href="http://www.southampton.ac.uk/oes/index.page" target="_blank">National Oceanography Centre, Southampton (NOCS) by the Ocean and Earth Science school</a>. 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: <a href="http://www.flugsaurier2015.com/">http://www.flugsaurier2015.com</a>).<br />
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The circular is available for download <a href="http://www.stupond.com/paleo/SVPCA_circ_01.pdf" target="_blank">here</a>, and the SVPCA website is <a href="http://svpca.org/years/2015_southampton/index.php" target="_blank">here</a>.Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com1tag:blogger.com,1999:blog-2346178345655867748.post-9550698576194770882014-11-24T15:34:00.000+00:002014-11-24T15:34:01.529+00:00Tracking Dinosaurs on the Isle of Wight: Paper and SVP 2014 posterI 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 <a href="http://onlinelibrary.wiley.com/doi/10.1111/bij.2014.113.issue-3/issuetoc" target="_blank">The Biological Journal of the Linnean Society</a> 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 <a href="http://paleoillustrata.blogspot.co.uk/2013/09/celebrating-dinosaur-isle-jehol-wealden.html" target="_blank">here</a>). This paper, entitled <span style="font-size: 16px;">Tracking Dinosaurs on the Isle of Wight: a review of </span><span style="font-size: 16px;">tracks, sites, and current research (Pond <i>et al</i>, 2014)</span> 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.<br />
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Also discussed in the paper was the presence of the thyreophoran ichnotaxa <i>Tetrapodosaurus</i> and <i>Deltapodus</i>, the latter having been assigned in a poster by Belvedere <i>et al</i> (2012) and which is interpreted as a having been made by a stegosaur. As <i>Tetrapodosaurus</i> 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 . . .<br />
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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).<br />
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<span style="font-size: x-small;">References:</span></div>
<span style="font-size: x-small;"><b>Batten DJ, ed. 2011</b>. English Wealden fossils. London: <i>Palaeontological Association.</i></span><br />
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<span style="font-size: x-small;"><b>Belvedere M, Pond S, Simpson M, Downes D, Dyke G. 2012</b>. 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 <i>Annual Meeting of the European Association of Vertebrate Palaeontologists</i>, ¡Fundamental! 20: 1–290.</span><br />
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<span style="font-size: x-small;"><b>Martill D, Naish D. 2001</b>. 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: <i>Palaeontological Association</i>, 310–323.</span><br />
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<span style="font-size: x-small;"><b>Pond S, Lockley MG, Lockwood JAF, Breithaupt B, </b></span><span style="font-size: x-small;"><b>Matthews N. 2014</b>. Tracking dinosaurs on the Isle of </span><span style="font-size: x-small;">Wight: a review of tracks, sites, and current research. </span><span style="font-size: x-small;"><i>Biological Journal of the Linnean Society</i> 113: 737–757.</span><br />
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<br />Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com1tag:blogger.com,1999:blog-2346178345655867748.post-27414424741683565342014-08-29T11:45:00.002+01:002014-08-29T11:45:48.402+01:00For palaeontologists and public, the future is 3D.<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-5kOVIozbRPI/U_8umT_GR_I/AAAAAAAAAro/06ZUGhlcBSA/s1600/indet_ornitho_600.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://3.bp.blogspot.com/-5kOVIozbRPI/U_8umT_GR_I/AAAAAAAAAro/06ZUGhlcBSA/s1600/indet_ornitho_600.jpg" height="227" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Indet. ornithopod caudal vertebra recorded using photogrammetry.<br />
480,342 polygons, with and without texture.</td></tr>
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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.</div>
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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. </div>
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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.</div>
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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. </div>
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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 (<a href="http://www.utsandiego.com/news/2013/nov/18/natural-history-museum-backs-off-fossil-auction/" target="_blank">as San Deigo Museum nearly did with their Sternberg collection</a>) 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. </div>
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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.</div>
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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. </div>
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Finally, an open-access online repository to hold this data, an idea that has been wafting around for a while (<a href="http://pfalkingham.wordpress.com/2014/07/21/making-3d-dataphotographs-available-part-1-neoichnology/" target="_blank">see this post by Peter Falkingham for example</a>, 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 . . .</div>
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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.<br />
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<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-0uvZPRWRhyU/VABX1qaUoaI/AAAAAAAAAr4/SRPdXEdEf5k/s1600/arbor_low.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://4.bp.blogspot.com/-0uvZPRWRhyU/VABX1qaUoaI/AAAAAAAAAr4/SRPdXEdEf5k/s1600/arbor_low.jpg" height="251" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Not a palaeontologist? Well, you could always share heritage items such as this 3D mesh of a<br />2.5m recumbent stone from Arbor Low stone circle in the White Peak of Derbyshire, UK.<br />Send it to anyone with an internet connection. You can't do that with the real thing.</td></tr>
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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: <a href="http://pfalkingham.wordpress.com/2014/08/28/not-just-pretty-pictures/" target="_blank">http://pfalkingham.wordpress.com/2014/08/28/not-just-pretty-pictures/</a></div>
Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com0tag:blogger.com,1999:blog-2346178345655867748.post-49957639644548270062014-08-18T17:32:00.001+01:002014-08-18T17:37:49.548+01:00Mr. Lee's dermal plates: the first Polacanthus?<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-ZnmEp-GAjpc/U_Imxraf1UI/AAAAAAAAArU/Qv-X9zUjZos/s1600/lee_1843_fig.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://4.bp.blogspot.com/-ZnmEp-GAjpc/U_Imxraf1UI/AAAAAAAAArU/Qv-X9zUjZos/s1600/lee_1843_fig.jpg" height="340" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The illustration from Lee's report of 1843 of a single osteoderm and surrounding ossicles.</td></tr>
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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 <i>Polacanthus</i> sacral shield, but is it?</div>
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The holotype of <i>Polacanthus</i> 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 <i>Polacanthus</i>, 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. <i>Polacanthus</i> is not the only nodosaurid (if <i>Polacanthus</i> is actually a nodosaurid, but that’s another story) with a sacral shield, and a comparison via the literature with sister taxa such as <i>Mymroopelta</i> and <i>Gastiona</i> reveal their sacral shields were similarly ornamented (see illustration below).</div>
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<tr><td class="tr-caption" style="text-align: center;">A selection of osteoderms and ossicle arrangements from various nodosaurids.<br />
Lee's specimen is top right, the others are redrawn from various papers.</td></tr>
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It’s likely that Lee’s specimens were the first remains of a <i>Polacanthus</i> 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 <i>is</i> 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.</div>
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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 <i>Polacanthus</i> would have been named twenty years before it actually was.</div>
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<b>References:</b></div>
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Hulke, J.W. 1881. <i>Polacanthus foxii</i>, a large undescribed dinosaur from the Wealden Formation in the Isle of Wight. <i>Philosophical Transactions of the Royal Society of London,</i> Vol. 172; 653-662.</div>
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Hulke, J. W. 1887. Supplemental note on <i>Polacanthus foxii</i>, describing the dorsal shield and some parts of the endoskeleton, imperfectly known in 1881. <i>Philosophical Transactions of the Royal Society of London,</i> Vol. 178: 169-72.</div>
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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.</div>
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Pereda-Suberbiola, X. 1994. <i>Polacanthus</i> (Ornithischia: Ankylosauria), a transatlantic armoured dinosaur from the Early Cretaceous of Europe and North America. <i>Palaeontographica, Abteilung A</i>, 232: 133–159.</div>
Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com0tag:blogger.com,1999:blog-2346178345655867748.post-39210950732239417222014-07-23T15:38:00.001+01:002014-07-23T15:38:11.806+01:00Exoneoichnology and photogrammetry: traces on MarsIf 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?<br />
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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 <i>Life Traces of the Georgia Coast</i>, 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 <a href="http://www.georgialifetraces.com/" target="_blank">here</a>). For an example of neoichnological data gathering using photogrammetry see <a href="http://paleoillustrata.blogspot.co.uk/2012/05/neoichnology-bioturbation-around.html" target="_blank">this previous pos</a>t.<br />
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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 <a href="http://paleoillustrata.blogspot.co.uk/2013/05/a-photogrammetry-primer-for.html" target="_blank">here</a> and <a href="http://paleoillustrata.blogspot.co.uk/2013/04/the-photogrammetrical-palaeontologist.html" target="_blank">here</a>. 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.<br />
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Robots? As it turns out, yes. Currently Mars has two operational NASA rovers on it. <a href="http://mars.jpl.nasa.gov/msl/" target="_blank">Curiosity</a> and <a href="http://mars.jpl.nasa.gov/mer/home/" target="_blank">Opportunity</a> 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 <a href="http://mars.jpl.nasa.gov/msl/multimedia/raw/" target="_blank">here</a>.<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-zML1aGdr-HA/U8_C_qXfn6I/AAAAAAAAAq4/lfw63bM6pdg/s1600/sol629_strip.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://1.bp.blogspot.com/-zML1aGdr-HA/U8_C_qXfn6I/AAAAAAAAAq4/lfw63bM6pdg/s1600/sol629_strip.jpg" height="60" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Five images taken by Curiosity on sol 629 and used for photogrammetrical reconstruction.</td></tr>
</tbody></table>
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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.<br />
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<a href="http://4.bp.blogspot.com/-GWrjmOI9TO8/U8_DCePP2fI/AAAAAAAAArA/wOyq5jsKKts/s1600/sol_629_HLI_hole.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://4.bp.blogspot.com/-GWrjmOI9TO8/U8_DCePP2fI/AAAAAAAAArA/wOyq5jsKKts/s1600/sol_629_HLI_hole.jpg" height="311" width="400" /></a></div>
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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.<br />
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<iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dxZjXRYiARHD55w6-lPgC626PX0Da6-Z6UBSamynMV704Qgh1uX0K-zaIfQS8Pgswq8XTebuks1l9s3yfo9Gg' class='b-hbp-video b-uploaded' frameborder='0'></iframe></div>
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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.<br />
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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.<br />
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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.<br />
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Reference:<br />
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<span style="line-height: 18px;"><span style="font-family: Times, Times New Roman, serif;">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</span></span><br />
<br />
<span style="font-size: x-small;">*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.</span>Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com0tag:blogger.com,1999:blog-2346178345655867748.post-54350231046543893922014-06-12T20:09:00.003+01:002014-06-12T20:13:33.074+01:00Ph.D update: On being a testudine, not a lagomorph.<div class="Body">
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 <a href="http://www.stupond.com/" target="_blank">here</a>).<br />
<br /></div>
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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 middle<span style="font-family: "Arial Unicode MS"; mso-ascii-font-family: Helvetica;">–</span>later 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.<o:p></o:p></div>
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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 <i style="mso-bidi-font-style: normal;">Polacanthus</i>
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.<o:p></o:p></div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-WivOPOH-MFA/U5nRs7_BmZI/AAAAAAAAAqk/E34nwN7K1b8/s1600/pg_setup.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://2.bp.blogspot.com/-WivOPOH-MFA/U5nRs7_BmZI/AAAAAAAAAqk/E34nwN7K1b8/s1600/pg_setup.jpg" height="306" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">My photogrammetry setup. A tad bottom end to be sure, but it's delivering good results.</td></tr>
</tbody></table>
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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.<br />
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<span style="font-size: x-small;">Animation showing the mesh obtained from the photogrammetry setup shown above.</span></div>
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<o:p></o:p></div>
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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, <a href="https://www.youtube.com/watch?v=plWexCID-kA" target="_blank">small steps towards the mountain</a> on a daily
basis.<o:p></o:p></div>
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<div class="Body">
It's a marathon and not a sprint for sure.</div>
Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com0tag:blogger.com,1999:blog-2346178345655867748.post-84445294662229200942014-05-22T16:07:00.000+01:002014-05-22T16:12:37.887+01:00Triceratops 3D model: finished!<div class="separator" style="clear: both; text-align: center;">
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-VT9_hDnKiDA/U34SezbUTqI/AAAAAAAAAqU/Q7Ci-t2GEAQ/s1600/tri_post.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://4.bp.blogspot.com/-VT9_hDnKiDA/U34SezbUTqI/AAAAAAAAAqU/Q7Ci-t2GEAQ/s1600/tri_post.jpg" height="225" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Click to see the critter bigger.</td></tr>
</tbody></table>
<br />
I've finally finished (abandoned - as the man says artists never 'finish' a work) the <i>Triceratops</i> 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.<br />
<br />
This has been a valuable learning experience and help from <a href="http://www.skeletaldrawing.com/" target="_blank">Scott Hartman</a> and comments from both Scott and <a href="http://qilong.wordpress.com/" target="_blank">Jaime Headden</a> have been most welcome. I'm looking forward to working on many more of these.<br />
<br />
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.<br />
<br />
That project is of course my PhD and the <i>Triceratops</i> project has provided a solid foundation for the soft tissue reconstruction of <i>Polacanthus</i>. 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 <i>Triceratops</i> 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.<br />
<br />
Lots to think about!Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com0tag:blogger.com,1999:blog-2346178345655867748.post-60347784508006178342014-04-13T14:56:00.001+01:002014-04-13T14:56:54.495+01:00PhD report: the first three months.Whoooosh! There goes March and nearly half of April. Blimey.<br />
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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 <i style="mso-bidi-font-style: normal;">Polacanthus</i> 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.<o:p></o:p></div>
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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.<o:p></o:p></div>
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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.<br />
<br />
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.<br />
<br />
Lots to do!</div>
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<o:p></o:p></div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-zojwfN8Neas/U0bK_01X9dI/AAAAAAAAAp4/Om9kLCpjji8/s1600/web.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://1.bp.blogspot.com/-zojwfN8Neas/U0bK_01X9dI/AAAAAAAAAp4/Om9kLCpjji8/s1600/web.jpg" height="320" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The web of research.</td></tr>
</tbody></table>
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<br /></div>
Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com0tag:blogger.com,1999:blog-2346178345655867748.post-59864994055129656912014-03-03T22:20:00.002+00:002014-03-03T22:20:46.388+00:00Seeing the Wessex Formation afresh.
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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.<o:p></o:p></div>
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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.</div>
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Here's a couple of pictures from the trip:</div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-l0HyzKDjEv0/UxT7s9HbkxI/AAAAAAAAApo/U9Acr1WRgx0/s1600/grange_section.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://3.bp.blogspot.com/-l0HyzKDjEv0/UxT7s9HbkxI/AAAAAAAAApo/U9Acr1WRgx0/s1600/grange_section.jpg" height="640" width="424" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">A clean section of the Wessex Formation, normally hidden under slumps and mudflows.</td></tr>
</tbody></table>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-o_x9KglP2kQ/UxT7r2Wp1zI/AAAAAAAAApg/ojqAbHA8Z7I/s1600/sudmoor_3_print_block.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://2.bp.blogspot.com/-o_x9KglP2kQ/UxT7r2Wp1zI/AAAAAAAAApg/ojqAbHA8Z7I/s1600/sudmoor_3_print_block.jpg" height="293" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">You wait for one, then three come along at once. Three tridactyl footprints in a single block,<br />all orientated in the same direction and all different sizes.</td></tr>
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Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com0tag:blogger.com,1999:blog-2346178345655867748.post-68494769559711306212014-01-15T16:58:00.001+00:002014-01-15T16:59:58.114+00:00Following the paper trail (starting the literature review)<div class="separator" style="clear: both; text-align: center;">
<a href="http://3.bp.blogspot.com/-6Zj1pAjxfn8/Utayp13t-nI/AAAAAAAAApU/bPGRo1U6d0s/s1600/lit_rev_toon.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="http://3.bp.blogspot.com/-6Zj1pAjxfn8/Utayp13t-nI/AAAAAAAAApU/bPGRo1U6d0s/s320/lit_rev_toon.jpg" width="306" /></a></div>
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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. <o:p></o:p></div>
<div class="Body">
<br /></div>
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First amongst these is the literature review. I have already been
collecting the relevant literature around my key research subject, the
nodosaurid <i>Polacanthus foxii</i>. 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.<o:p></o:p></div>
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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.<o:p></o:p></div>
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<br /></div>
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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?<o:p></o:p></div>
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<br /></div>
<div class="Body">
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. <o:p></o:p></div>
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So off we go . . .Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com1tag:blogger.com,1999:blog-2346178345655867748.post-52243006925693007242014-01-01T18:00:00.000+00:002014-01-02T19:46:30.167+00:00Vertebrate Palaeontology Ph.D, Day One.<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-kAWVuQnUM6U/UsRWn9UZJfI/AAAAAAAAApE/vgCWK9nAjXo/s1600/di_pol.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="font-family: Arial, Helvetica, sans-serif;"><img border="0" height="233" src="http://1.bp.blogspot.com/-kAWVuQnUM6U/UsRWn9UZJfI/AAAAAAAAApE/vgCWK9nAjXo/s400/di_pol.jpg" width="400" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: Arial, Helvetica, sans-serif;">The <i>Polacanthus</i> model at Dinosaur Isle, Sandown, Isle of Wight.</span></td></tr>
</tbody></table>
<br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<span style="font-family: Arial, Helvetica, sans-serif;">Happy new year!</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<span style="font-family: Arial, Helvetica, sans-serif;">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 <a href="http://www.southampton.ac.uk/oes" target="_blank">Ocean and Earth Science, National Oceanography Centre Southampton</a> 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.</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<span style="font-family: Arial, Helvetica, sans-serif;">So what am I actually working on? This extract from my project proposal will answer that question:</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<div class="s2">
<span style="background-color: rgba(255, 255, 255, 0); color: #b6d7a8; font-family: Arial, Helvetica, sans-serif;"><b><span class="s5">D</span><span class="s5">igital reconstruction of dinosaur</span><span class="s5"> </span><span class="s5">movement and soft tissues informed by morphology and biomechanics</span></b><span class="s5">.</span></span></div>
<div class="s2">
<span style="color: #b6d7a8; font-family: Arial, Helvetica, sans-serif;"><br /></span></div>
<div class="s2">
<span style="background-color: rgba(255, 255, 255, 0); color: #b6d7a8; font-family: Arial, Helvetica, sans-serif;"><span class="s5">The ornithischian dinosaurs </span><span class="s5">within clade</span><span class="s5"> </span><span class="s5">N</span><span class="s5">odosaurid</span><span class="s5">ae</span><span class="s5"> 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). </span><span class="s5">However, despite a number of partially complete specimens, t</span><span class="s5">he </span><span class="s5">biomechanics and functional morphology of these </span><span class="s5">obligate quadrupeds ha</span><span class="s5">s</span><span class="s5"> not been subject to the same degree of study as other dinosaurian taxa</span><span class="s5">.</span><span class="s5"> </span><span class="s5">Two notable exceptions are a </span><span class="s5">finite element analysis of ankylosaur tail club impacts </span><span class="s5">(</span><span class="s5">Arbour and Snively</span><span class="s5">, 2009)</span><span class="s5"> and </span><span class="s5">a more general functional investigation of ornithischian limb morphology </span><span class="s5">(</span><span class="s5">Maidment </span><span class="s6" style="font-style: italic;">et al</span><span class="s5">, 2012)</span><span class="s5">. The reconstruction of nodosaurid and more derived ankylosaurian</span><span class="s5"> morphology, and locomotion, however,</span><span class="s5"> </span><span class="s5">remains to be achieved in enough detail to interpret the </span><span class="s5">lifestyle</span><span class="s5">,</span><span class="s5"> and palaeoecology</span><span class="s5">, </span><span class="s5">of these extinct animals</span><span class="s5">.</span><span class="s5"> Doing this, within a rigorous comparative and statistical framework, is the aim of this PhD project.</span></span></div>
<div class="s2">
<span style="background-color: rgba(255, 255, 255, 0);"><span class="s5" style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
<div class="s2">
<span style="font-family: Arial, Helvetica, sans-serif;">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.</span></div>
<div class="s2">
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></div>
<div class="s2">
<span style="font-family: Arial, Helvetica, sans-serif;">So I've stepped onto the path, and now to see where it takes me. I really can't wait to find out.</span></div>
<div class="s2">
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></div>
<div class="s2">
<span style="font-family: Arial, Helvetica, sans-serif;">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.</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<span style="font-family: Arial, Helvetica, sans-serif;">*Not to moan or owt, but some of us spent the festive period ill. Cough.</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<span style="font-family: Arial, Helvetica, sans-serif;">References:</span><br />
<span style="color: #eeeeee; font-family: Arial, Helvetica, sans-serif;"><br /></span>
<div class="MsoNormal">
<span style="color: #cccccc; font-family: Arial, Helvetica, sans-serif;"><span lang="EN-US"><span class="msoIns"><ins cite="mailto:Stuart%20Pond" datetime="2013-03-14T16:26">Arbour, V. M., & Snively, E. (2009). Finite
element analyses of ankylosaurid dinosaur tail club impacts. <i>Anatomical
record (Hoboken, N.J.</i></ins></span></span><span lang="EN-US"><span class="msoIns"><ins cite="mailto:Stuart%20Pond" datetime="2013-03-14T16:26"> </ins></span></span><i><span lang="EN-US"><span class="msoIns"><ins cite="mailto:Stuart%20Pond" datetime="2013-03-14T16:26">:
2007)</ins></span></span></i><span lang="EN-US"><span class="msoIns"><ins cite="mailto:Stuart%20Pond" datetime="2013-03-14T16:26">, <i>292</i>(9),
1412–26. doi:10.1002/ar.20987</ins></span></span><span lang="EN-US"><span class="msoIns"><ins cite="mailto:Stuart%20Pond" datetime="2013-03-14T16:26"> <o:p></o:p></ins></span></span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<em style="color: #cccccc; font-family: Arial, Helvetica, sans-serif;"><span lang="EN-US" style="font-style: normal;">Blows, W.T., 1996. A new species of </span><span lang="EN-US">Polacanthus</span></em><em style="color: #cccccc; font-family: Arial, Helvetica, sans-serif;"><span lang="EN-US" style="font-style: normal;">
(Ornithischia; Ankylosauria) from the Lower Cretaceous of Sussex, England. </span><span lang="EN-US">Geological Magazine</span></em><em style="color: #cccccc; font-family: Arial, Helvetica, sans-serif;"><span lang="EN-US" style="font-style: normal;">,
133 (<5), 1996, pp. 671-682.</span></em></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="color: #cccccc; font-family: Arial, Helvetica, sans-serif;">Maidment, S.C.R. et
al., 2012. Limb-Bone Scaling Indicates Diverse Stance and Gait in Quadrupedal
Ornithischian Dinosaurs A. A. Farke, ed. </span><i style="color: #cccccc; font-family: Arial, Helvetica, sans-serif;">PLoS ONE</i><span style="color: #cccccc; font-family: Arial, Helvetica, sans-serif;">, 7(5), p.e36904.
Available at: http://dx.plos.org/10.1371/journal.pone.0036904 [Accessed May 27,
2012].</span></div>
</div>
Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com3tag:blogger.com,1999:blog-2346178345655867748.post-59737661031290931642013-12-04T17:36:00.000+00:002013-12-04T17:36:49.235+00:00PhD preparations in full swing<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-iycNkI7U8Ac/Up9OxAHmktI/AAAAAAAAAoc/_T0VrgiUd0Y/s1600/spiky_polly.JPG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="281" src="http://1.bp.blogspot.com/-iycNkI7U8Ac/Up9OxAHmktI/AAAAAAAAAoc/_T0VrgiUd0Y/s400/spiky_polly.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">A way too spiky <i>Polacanthus</i>, with no sacral shield to boot.<br />
I mean, we've known the dinosaur had one since 1881. Get a grip!</td></tr>
</tbody></table>
<br /><div class="Body">
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.</div>
<div class="Body">
<o:p></o:p></div>
<div class="Body">
<br /></div>
<div class="Body">
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 I<span style="font-family: "Arial Unicode MS"; mso-ascii-font-family: Helvetica;">’</span>m going to have to make do with what I<span style="font-family: "Arial Unicode MS"; mso-ascii-font-family: Helvetica;">’</span>ve
got.<o:p></o:p></div>
<div class="Body">
<br /></div>
<div class="Body">
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 I<span style="font-family: "Arial Unicode MS"; mso-ascii-font-family: Helvetica;">’</span>m set up for this already (my institution, the University of
Southampton is actually 200 miles away from where I live).<o:p></o:p></div>
<div class="Body">
<br /></div>
<div class="Body">
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.<o:p></o:p></div>
<div class="Body">
<br /></div>
<div class="Body">
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.</div>
<div class="Body">
<br /></div>
<div class="Body">
<o:p>Another step closer to the mountain.</o:p></div>
Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com0tag:blogger.com,1999:blog-2346178345655867748.post-59758858670720099452013-11-07T15:57:00.003+00:002013-11-07T15:57:37.001+00:00PaleoIllustrata is dead. Long live PaleoIllustrata!<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://2.bp.blogspot.com/-EXRU2_W2FYg/Unuv1cVpJOI/AAAAAAAAAoI/aoi-HcpMRHc/s1600/polacanthus.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="362" src="http://2.bp.blogspot.com/-EXRU2_W2FYg/Unuv1cVpJOI/AAAAAAAAAoI/aoi-HcpMRHc/s400/polacanthus.jpg" width="400" /></a></div>
<div class="Body">
<br /></div>
<div class="Body">
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 it<span style="font-family: 'Arial Unicode MS';">’</span>s 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.</div>
<div class="Body">
<o:p></o:p></div>
<div class="Body">
<br /></div>
<div class="Body">
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 <a href="http://www.southampton.ac.uk/oes" target="_blank">National Oceanography Centre Southampton (NOCS)</a>, <a href="http://www.southampton.ac.uk/" target="_blank">University of Southampton</a> 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 <a href="http://chasmosaurs.blogspot.co.uk/" target="_blank">Love in theTime of Chasmosaurs</a> and picfest <a href="http://paleoillustration.tumblr.com/" target="_blank">Paleoillustration</a> (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.</div>
<div class="Body">
<o:p></o:p></div>
<div class="Body">
<br /></div>
<div class="Body">
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.</div>
<div class="Body">
<br /></div>
<div class="Body">
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.</div>
<div class="Body">
<br /></div>
<div class="Body">
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.</div>
<div class="Body">
<br /></div>
<div class="Body">
I had my interview in September and accepted
an offer a couple of weeks ago, and I start on the 1<sup>st</sup> 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.<o:p></o:p></div>
<div class="Body">
<br /></div>
<div class="Body">
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.</div>
<div class="Body">
<br /></div>
<div class="Body">
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.<o:p></o:p></div>
<div class="Body">
<br /></div>
<div class="Body">
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 <i>Polacanthus</i>, including biomechanics and soft tissue reconstruction.</div>
<div class="Body">
<br /></div>
<div class="Body">
A new journey, a new stage in my life. As a palaeontologist. Here goes! </div>
<!--EndFragment-->Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com3tag:blogger.com,1999:blog-2346178345655867748.post-34844152723164209202013-09-26T08:58:00.000+01:002013-12-04T17:37:50.218+00:00Celebrating Dinosaur Isle: Jehol-Wealden International Conference. 2013<div style="font-family: Cochin; font-size: 14px; text-indent: 18px;">
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. </div>
<div style="font-family: Cochin; font-size: 14px; min-height: 17px;">
<br /></div>
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<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-2owHbrLzdu8/UkMIpG2qjUI/AAAAAAAAAnk/RXT1myVYnsY/s1600/jehol_exhibits.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="http://4.bp.blogspot.com/-2owHbrLzdu8/UkMIpG2qjUI/AAAAAAAAAnk/RXT1myVYnsY/s400/jehol_exhibits.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The exhibit room at the conference.</td></tr>
</tbody></table>
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<br /></div>
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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.</div>
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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 <i>Eotyrannus</i> 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 <i>Istiodactylus</i> and <i>Longchengpterus</i>, 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.</div>
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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 <i>Polacanthus</i> 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 <i>Iguanodon</i> mandible and some large <i>Baryonyx</i> teeth. The model of <i>Microraptor</i> featured in Dyle <i>et al’s</i> 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, <span style="font-family: Verdana; font-size: 11px;"><i>Thecodontosaurus antiquus.</i></span></div>
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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 <i>Microraptor</i> paper mentioned earlier. Colin’s talk finished with video of the balsa model of <i>Microraptor</i> being flown, and demonstrating the flightpath predicted by computer simulations was pretty accurate. Next up was Mike Howgate, who was expounding his view that <i>Microraptor</i> was in fact a ‘archaeopterygid’ bird and <i>Eoraptor</i> 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 piraña 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.</div>
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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.</div>
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The evening was spent in the Red Lion in Southampton, a 12<span style="font-size: 9px;"><sup>th</sup></span> 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.</div>
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<tr><td><a href="http://2.bp.blogspot.com/-8lA5Mej_A9c/UkMIqUQgSiI/AAAAAAAAAn4/Tw40I_hKCZY/s1600/jehol_yaverland.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="color: black;"><img border="0" height="232" src="http://2.bp.blogspot.com/-8lA5Mej_A9c/UkMIqUQgSiI/AAAAAAAAAn4/Tw40I_hKCZY/s400/jehol_yaverland.jpg" width="400" /></span></a></td></tr>
<tr><td class="tr-caption" style="font-size: 13px;">Walking through the upper Wessex and Vectis formations, first stop on the field trip.</td></tr>
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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!</div>
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<tr><td><a href="http://3.bp.blogspot.com/-ebq9qNdpnKI/UkMIqUJ3xQI/AAAAAAAAAn0/HDBr_Kvs2pk/s1600/jehol_hanover_point.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="color: black;"><img border="0" height="197" src="http://3.bp.blogspot.com/-ebq9qNdpnKI/UkMIqUJ3xQI/AAAAAAAAAn0/HDBr_Kvs2pk/s400/jehol_hanover_point.jpg" width="400" /></span></a></td></tr>
<tr><td class="tr-caption" style="font-size: 13px;">Heading towards Hanover Point.</td></tr>
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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 <i>Iguanodon</i> material from Nick Chase (who donates to the museum), a piece of thyreophoran armour and some quite incredible <i>Baryonyx</i> material representing at least two animals; let us hope these important specimens not lost to science.</div>
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<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-if2RIUXBZQ8/UkMInM8DgsI/AAAAAAAAAnQ/VD2Raug9qEo/s1600/jehol_alum_bay.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="color: black;"><img border="0" height="252" src="http://1.bp.blogspot.com/-if2RIUXBZQ8/UkMInM8DgsI/AAAAAAAAAnQ/VD2Raug9qEo/s400/jehol_alum_bay.jpg" width="400" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The multicoloured sands of Alum Bay. My Nan had a small glass tube of these on her<br />
sideboard, but this was the first time I'd seen them first hand.</td></tr>
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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.</div>
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<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-qZXsSsMZNMc/UkMIoKeDbtI/AAAAAAAAAnc/wF-lJBXCJAc/s1600/jehol_chair_lift.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="color: black;"><img border="0" height="265" src="http://3.bp.blogspot.com/-qZXsSsMZNMc/UkMIoKeDbtI/AAAAAAAAAnc/wF-lJBXCJAc/s400/jehol_chair_lift.jpg" width="400" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The chairlift down to the beach at Alum Bay. Gulp.</td></tr>
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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.</div>
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I am sure I join many others in hoping this conference will be repeated in years to come.</div>
Stu Pondhttp://www.blogger.com/profile/03389601261560266346noreply@blogger.com2